Sultan Qaboos University College of Science Department of ... · Textbook: Biology. Neil A. Campbell and Jane B. Reece. (7th edition. ) 2005. Benjamin Cummings References (optional):

Sultan Qaboos University

College of Science

Department of Biology

Course outline for BIOL1003 Genetics In our Life

Description:

This course describes the major principles and the applications of genetics and biotechnology on

our life. The topics include various concepts in genetics and biotechnology with a brief emphasis

on the heritable human diseases and the ways to avoid them. The course focuses also on

application of biotechnology and their impacts on health, agricultural and environmental sectors.

Class discussions will be held to familiarize the students with importance of medical examination

before marriage and also the legal and ethical issues involved with the widespread application of

modern biotechnology.

Course credit: 2

Format: 1 lecture/week

E-mail: [email protected]

Prerequisite

Textbook: A booklet prepared by the Department of Biology, College of Science

Learning outcome: At the end of the course, students will be anticipated to understand the

scientific basis behind genetically inherited diseases and various fields of biotechnology.

ASSESSMENT : The course will be assessed A - F. The assessment will be as follows:

First exam 25%

Second exam 25%

Final exam 50%

COURSE SYLLABUS

1- Genetics and DNA.

2- What is the gene?

3- The concept of a mutation.

4- Biotechnology, definitions and applications.

5- Biotechnology and Health.

6- Traits and diseases inheritance in human.

7- Medical exam before marriage.

8- Genetic diseases in the Sultanate of Oman.

9- Genetically modified crops.

10- Human genome project.

11- Genetic finger print and ethical issues.

College of Science Department of Biology ___________________________________________________________________________ Course Code: 2101 Course Title: General Biology General Information Number of Credits: 4 Instructional Format: Lecture and Lab Contact Hours/Week: 2 (1.5 hr) Lectures + 1 (3 hrs) Laboratory / week Prerequisite: None Co-requisite: None Assessment: Test 1: 17.5%; Test 2: 17.5%; Lab quiz:5%; Lab test 1: 10%;

Lab test 2: 10%; Final: 40% Grading (A–F, Pass/Fail): A-F Textbook: Biology. Neil A. Campbell and Jane B. Reece. (7th edition).

2005. Benjamin Cummings References (optional):

1. Course Description This is the first of a two semester course in foundation biology. A basic introductory course in biology covering the view of science, chemical basis of life, cell biology, cell cycle and reproduction, cellular energetics, diversity of life including prokaryotes, protista and fungi and the biotechnological and environmental applications of microorganisms. This course also describes the present status and future opportunities in different fields of biotechnology in Oman. Laboratory work is designed to expose students to the practical aspects of these subjects. The details of the experiments are provided in the lab manual.

2. Course Objectives The purpose of this course is to give an overview of biological concepts and to understand the importance of biology in our lives. It also dealt about the applications of biology in the present and future. Students will use principles learned in the laboratory and apply them to everyday life. In order to do well in this course, it is imperative that students should keep up with reading the chapters and attending the lectures.

3. Learning Outcomes (a) Students will handle the microscope properly and measure the cell size

(b) They can identify the macromolecules present in the food materials (c) They can demonstrate the activity of enzyme

(d) Able to identify different stages of cell divisions

(e) They know how membranes are doing transport and how plasmolysis occurs

(f) Students understand the possible applications of biotechnology in Oman

4. Assessment

Assessment Criteria

Learning outcome:

Assessment criteria [For each learning outcome state the level of understanding a student needs to demonstrate to be able to achieve a specified grade.)]

A B C D F By the end of the course, students will be able to: (example) 1. Use and interpret the notion of joint and conditional distributions

Showing a clear mastery of the theory and application of joint and conditional distributions

Having a good grasp of the application and interpretation of results of joint and conditional distributions

A satisfactory grasp of the use and interpretation of the joint and conditional distributions.

Less than satisfactory ability to apply and interpret the joint and conditional distributions.

Demonstrating the inability of either use or to interpret correctly the results of joint and conditional distributions.

5. Course Structure The course is designed to be delivered in one semester of 15 weeks with 6 contact hours per week (3h practical and two (1.5h) theory. The course weight is 4 credit hours.

6. Topics [A breakdown of the syllabus into major components listed logically and by weekly coverage if need be. This should be detailed enough to enable another instructor to teach the course at the same level.] Unit

Topics Sections Lectures/Weeks

1 Unifying themes in Biology

1 Features common to all organisms 1.2 Unity, Diversity and Classification of Organisms 1.3 Domains Archaea and bacteria 1.4 Domain Eukarya 1.5 Biodiversity

6/1

2 Chemical Basis of life

2.1Chemical and Physical Properties of Water 2.2 Structure and function of macromolecules 2.3 Carbohydrates 2.4 Lipids 2.5 Protein structure and function 2.6 Nucleic acids 2.7 From gene to protein 2.8 Synthesis and processing of mRNA 2.9 Synthesis of proteins

11/2to4

2.10 Viruses

3. Cells, the basic units of life

3.1 How to study cells 3.2 Prokaryotic and eukaryotic cells 3.3 Cell organelles I 3.4 Cell organelles II 3.5 Cytoskeleton 3.6 Cell surfaces and junctions 3.7 Cell membranes and transport 3.8 Traffic across membranes

10/4to7

4 Cell cycle and reproduction

4.1 Cell cycle and mitosis 4.2 Regulation of cell cycle 4.3 Meiosis and sexual life cycle 4.4 Meiosis

5/8&9

5 The working cell and cellular energetics

5.1 Energy within the cell 5.2 Enzymes 5.3 Cellular respiration I 5.4 Cellular Respiration II 5.5 Photosynthesis

8/9&10

6 Biotechnology, Biodiversity and Environmental pollution

6.1 Biotechnology and recombinant DNA technology 6.2 Practical applications of DNA technology 6.3 DNA technology offers forensic, environmental and agricultural applications

5/10 to 15

7. Lab/tutorial content

Week Content 1 No Lab on week 1 2 Lab Safety consideration and laboratory rules 3 Using the transmission microscope under low, medium

power and high power. Focusing on coloured silk threads; comparing plant (Elodea) and human (squamous epithelia from cheeck) cells; measuring specimens and your drawings.

4 Using the transmission microscope under high powers. Using fixed Protista and live organisms in raw sewage

5 Using the transmission microscope under high powers. Using fixed fungi and green chees samples.

6 Using the transmission microscope under oil immersion. Gram stain technique and Bacteria in yoghurt.

7 Lab test 1

8 Identification of biological molecules (reactions). 9 Identification of biological molecules in foods. 10 Purification of the enzyme, amylase. 11 Membrane diffusion and transport correlate with intrusion of

sea and effect of brackish water on plants. 12 Mutation by ultraviolet radiation 13 Cell division: Mitosis and meiosis

DNA extraction 14 Lab test 2

BIOL 2102:

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BIOL 2102: Biology II

Course outline


1

Biology II


2



BIOL 2102: Biology II

Course Information

This is a 4 credit introductory course with 2 lectures of 80 minutes (equivalent to 3 normal lectures) and a 3-hour lab each week. This course covers plants and animals, with a focus on their biodiversity and an understanding of how they function. This involves understanding the relationship between body structures and their roles in physiological processes (their function), as well as understanding their ecology (adaptation for their habitat).

Evaluation

Two Theory Tests 35%

Final laboratory exam 15%

Practical quizzes and assessments 10%

Final examination 40% You are expected to attend all lectures and labs. Excessive absence from lecture or lab will be reported and you

can be barred from the final examination. Absence from any type of exam, quiz etc can not be made up, unless

you have a certified excuse.

Text Book

“Biology”, 7th

edition by Campbell and Reece.

Below is a reading guide listing the topics that will be discussed in your lectures. You are responsible for reading the text and understanding all figures, tables etc related to the reading assignments, even if they are not covered in the lectures.

Moodle There is a Moodle site, which you are expected to use. It includes videos, PowerPoints and other materials related to this course.

Course co-ordinator

Dr. Derek Roberts, room 2012 in new Biology building.

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Lectures Unit 1. Plant Diversity (3 lectures)

Evolution of Terrestrial plants: Charophycae algae → Mosses → Ferns → Conifers → Angiosperms Non-vascular plants: Mosses and Ferns: Characteristics and life cycles. Conifers: Seed evolution and advantages. Conifer characteristics and life cycles. Angiosperms: Functions of flowers and fruit; Angiosperm life cycle; Monocots and Dicots.

Unit 2. Plant Structure and function. (7 lectures) Roots, stems and leaves: Adaptations and functions. Plant tissues: Dermal, vascular and ground tissues. Meristems and growth: Primary and secondary growth. Vascular transport: Diffusion, bulk flow, root absorption, stem transport. Leaf stomata: Phloem transport of sugars. Plant nutrients; N2 availability; Mycorrhizae; unusual nutrition. Sexual reproduction; Flowers: Egg and pollen production, Pollination, seed development, fruits, seed germination.

Unit 3. Animal Diversity (9 lectures)

Introduction to the animals: Protostome evolutionary developments. Deuterostomes.

Sponges, Cnidaria, Flatworms: Turbellaria, flukes and tapeworms. Nematodes, Molluscs: snails, bivalves and Cephalopods. Annelida, Arthropods: primitive and advanced (insects).

Echinoderms.

Chordate characteristics: Tunicates, lancelets, Fish, Amphibia, Reptiles, Birds, and Mammals.

Unit 4. Animal Structure and Function (16 lectures)

Introduction: Body shape; Tissues + organs; metabolic rate and temperature control; Homeostasis.

Nutrition: Digestive systems; Human system and digestion; Effect of diet on digestion. Blood: Blood systems; Vertebrate circulations; heart and its control; Blood vessels and pressure; capillary functions; Blood cells and clotting.

Respiration: Skin, gills, trachea and lungs (frogs, humans and birds) and their ventilation; O2 + CO2 transport.

Osmoregulation: marine, freshwater and terrestrial. Excretion: Nephridia, malphigian tubules, kidneys.

Nervous systems: neurons and glial cells; resting, action potentials and impulse conduction; synapses; division of the nervous system. Endocrine: Pituitary, thyroids, pancreas (and diabetes), adrenal cortex and medulla.

Unit 5. Ecology of plants and animals. (7 lectures) Introduction: habitats and niches. Factors affecting species distribution: dispersal, behaviour, predation and pathogens. Factors affecting species abundance: - Introduction (patterns of dispersion, demographics, population growth). - Effects of climate, competition, territorial behaviour, diseases, predators, physiological stress. Community ecology: - Trophic levels and food webs. - Dominant and keystone species. - Biodiversity: effects of evapotranspiration, habitat stability, habitat size and distance between habitats. - Conservation of endangered species.

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Textbook Reading List for Lectures Unit 1: Plant diversity.

Chapter 29. Overview. Concept 29.1(pg 573-574): Concept 29.2; Derived Traits of Plants (pg.575), fig 29.5, Origin and Diversification, (pg 575, 578-579), fig 29.7: Concept 29.3 (pg.580-583); Concept 29.4; Ferns and other seedless Vascular Plants (pg 584-586), fig 29.12. Chapter 30. Overview. Concept 30.1 (pg.591-593): Concept 30.2(pg.593, 596-597): Concept 30.3. Characteristics of Angiosperms (pg.598-600), Angiosperm Diversity (pg.602-603); Evolutionary Links (pg 604); Concept 30.4 (pg.605-606).

Unit 2: Plant structure and Function.

Chapter 35. Overview. Concept 35.1 (pg.712-719): Concept 31.2 (pg720-721); Concept 35.3 (pg.721-724); Concept 35.4 (pg.725-728); Chapter 36. Overview. Concept 36.1, Selective permeability of Membranes (pg.738-739), fig 36.2,Three major compartments, fig 36.8, Functions of symplast and apoplast, Bulk flow (pg.743-744); Concept 36.2 (pg.744-746): Concept 36.3 (pg.746-749): Concept 36.4 (pg.749-751): Concept 36.5 (pg751-753). Chapter 37. Concept 37.1 (pg.756-757): Concept 37.3 (pg.763-764): Concept 37.4 (pg.764-8).

Chapter 38. Overview. Concept 38.1(pg771-776): Concept 38.2(pg 776-780): Concept 38.3 (pg.781).

Unit 3: Animal diversity.

Chapter 32. Overview. Concept 32.1 (pg.626-627); Concept 32.3 (pg630-633); Concept 32.4, Points of

Agreement (pg.633), fig 32.10. Chapter 33. Overview (pg 638 and fig 33.2). Concept 33.1(pg.642-643); Concept 33.2, (pg 643-4), fig 33.8; Concept 33.3. flatworms (pg. 646-648); Concept 33.4(pg 650-651 top left), fig 33.16; Concept 33.5(pg.653-655); Concept 33.6 (pg.655-656); Concept 33.7 (pg.656-658); Concept 33.8 (pg.665-666). Chapter 34. Overview. Concept 34. (pg. 671-674); Concept 34.3, Derived characters of Vertebrates (pg.678); Concept 34.4, Chondrichthyans, Ray-finned and lobe-finned fishes (pg. 680-682). Concept 34.5, Derived Characters of Tetrapods (pg.684), Amphibians (pg. 685-686). Concept 34.6, Derived characters of amniotes (pg.688), reptiles (pg. 688-689), birds (pg.691-692). Concept 34.7, Derived Characters of Mammals (pg.694), Monotremes, Marsupials and Eutherian mammals (pg.695-697). Unit 4: Animal structure and function.

Chapter 40. Overview. Concept 40.1(pg.820-822): Concept 40.2 (pg.823-827): Concept 40.3.Bioenergetics, Influences on Metabolic rate (pg.828-830); Concept 40.4 (pg 831-833); Concept 40.5,Thermoregulation, Ectotherms and Endotherms (pg833- 834). Chapter 41. Overview. (pg.844): Concept 41. 3 (pg.853-855): Concept 41.4 (pg.855-862): Concept 41. 5 (pg.862-864). Chapter 42. Overview. Concept 42. 1 (pg.867-87 1 ): Concept 42.2 (pg.87 1-874): Concept 42.3 (pg.874-878): Concept 42.4 (pg.879-883): Concept 42.5 (pg.884-887): Concept 42.6 (pg.888-890): Concept 42.7(pg.891- 893). Chapter 44. Overview. Concept 44.1 (pg.922-927): Concept 44.2 (pg.927-928); Concept 44.3 (pg.928-931); Concept 44.4 (pg.931-934).

Chapter 45. Overview. Concept 45.1 (pg.943-944): Concept 45.4(pg 953-957).

Chapter 48. Overview. Concept 48.1 (pg. 1012-1015); Concept 48.3 (pg 1017-1019); Concept 48.4. (pg. 1021-1022).

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Unit 5: Ecology.

Chapter 50. Concept 50.1 Organisms and the environment (pg 1081); subfields of ecology (pg 1082). Concept

50.2 Interactions limit distribution (pg 1083-1092). Aquatic biomes (pg 1094-1097).Terrestrial biomes (pg

1098-1103).

Chapter 52. Concept 52.1 Population density, dispersion and demography(pg 1136-1140).Concept 52.3

Population growth-logistic model (pg 1146-1147).Concept 52.5Populations regulated by biotic and abiotic. (pg

1148-1152).Concept 52.6 Human population growth (pg 1152-1156).

Chapter 53.Concept 53.2 Dominant and keystone species (pg 1165-1169).Concept 53.4 Biogeographic factors

and biodiversity. (pg 1175-1178).

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Practicals (3 hours each)

1. Plant diversity. Life cycle stages of Chara, mosses, ferns and conifers.

2. Plant tissues. Leaf epidermis and trichomes, root epidermis and root hairs, parenchyma, collenchyma,

sclerenchyma, xylem and phloem, meristem root tip.

3. Structure of Roots and Stems. Roots: Monocots and Dicots; mycorrhizae.

Stems: Monocots and Dicots; secondary growth in Dicots.

4. Structure of Leaves and Flowers. Leaves: Monocots and Dicots; adaptations for arid conditions.

Flower: Regular and irregular.

Seeds (Maize and Beans): fruit (Apple).

5. Animal diversity: lower invertebrates. Cnidaria (Hydra): Platyhelminthes (Planaria and Clonorchis); Nematoda (Ascaris) and Annelida

– Dissection and section of earthworm.

6. Animal diversity: higher invertebrates. Mollusca (Helix and Anadonta); Crustacea (crayfish); Insects – dissection of the grasshopper:

Echinoderm (starfish).

7. Mammalian Digestive system. Dissection of Rat digestive system. Histology of the stomach, ileum, pancreas and liver.

8. Mammalian thoracic blood system and respiratory system. Dissection of the rat thorax – showing heart and thoracic vessels; lungs. Alveoli structure.

9. Mammalian reproductive and excretory system.

Dissection of the rat abdomen – showing excretory, reproductive (in male and female) and

abdominal blood vessels.

10. Animal cells and tissues; Oman Ecology (1) Epithelia (cuboidal, ciliated columnar, squamous); Connective (adipose, areolar, dense white

fibrous, cartilage, compact bone); Muscle (cardiac, skeletal muscle, smooth muscle); neurons.

Ecology of Oman: DVD on the Empty Quarter (Rub Al-Kali).

11. Blood system; Oman Ecology (2) Blood cell types from a blood smear; ABO Rh blood groups.

Dissection of the heart.

Ecology of Oman: DVD on Dhofar mountains and sea.

12. Gulf Ecology (3) DVD on modern developments in Arabia (mainly Emirates) affecting the ecology.


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Learning Outcomes

By the end of the course, students should be able to:

1. Plant Diversity, Structure and Function • Explain the evolution of plants and how they are adapted to life on land.

• Explain functions of plant cells and tissues in relation to their structure.

• Explain the mechanism of water and food transport in plants.

• Understand plant nutrition and the adaptations shown to increase survival.

• Understand the processes involved in angiosperm pollination, seed formation and dispersal.

2. Animal Diversity, Structure and Function

• Understand the evolutionary developments within the protostomes and the chordates. • Recognize the most main phyla of invertebrates and their structural features in relation to their

physiological function and environments.

• Understand homeostasis and the mechanisms that permit animals to regulate internal environments.

• Correlate digestion with the structure and function of the digestive organ system.

• Relate how vertebrate digestive systems have adapted to diet.

• Understand how the different structures of the blood system are related to their function.

• Understand how the blood system supplies nutrients and remove waste materials.

• Explain how gas exchange surfaces function in different animal phyla.

• Understand the process of osmoregulation and why some animals do not osmoregulate.

• Understand the different types of excretory systems and how they function.

• Learn how the nervous and endocrine systems regulate animal physiology.

3. Ecology of animals and plants • Understand the concepts of habitats and niches.

• Explain the factors affecting the distribution and abundance of a species.

• Understand the concept of a food web, and of dominant and keystone species within that web.

• Explain the factors affecting the biodiversity of a community and the importance of species

conservation.


BIOL 3005: Ecology

Course outline



BIOL 3005: Ecology

Course outline

Dr Derek Roberts

BIOL 3005: Ecology

Course Summary This is a 3 credit introductory course on ecology that is a prerequisite for later ecology

courses. It consists of 2 lectures and 1 practical per week.

The lectures will concentrate on population ecology: considering the factors that control

the distribution of species and their abundance, and considering some practical applications of

population ecology (in fisheries, pest control and species conservation). The final section of the

lectures will briefly look at community ecology.

The practicals will include:

� Field trips to carry out experiments in different types of habitats.

� Lab experiments on population ecology.

� Computer simulations looking at complex problems in population ecology.

� Videos showing communities in different tropical habitats.

Learning Outcomes By the end of the course, students should be able to:

1. Understand the concepts of habitats and niches.

2. Understand the major factors limiting the distribution of species.

3. Understand the factors that control the abundance of species.

4. Understand the problems involved in maximizing fisheries.

5. Understand the different types of pest control and the problems associated with each type.

6. Understand why species head towards extinction and how they can be saved.

7. Understand the factors controlling biodiversity.

8. Understand the concepts of food webs, trophic levels and dominant species in a community.

Course assessment The course will be graded A to F. This assessment will be based on the following:-

∗ Assessment of practicals by quizzes and lab reports. 10 %

∗ Practical exam (2 hours) will cover videos, simulations and experiments. 20 %

∗ Theory tests (2) 30 %

∗ Final theory exam (3 hour) 40 %

Course coordinator Dr. Derek Roberts (room 2012, in new Biology Dept.).

Course prerequisite BIOL 2102: Biology II (diversity)

Course textbook Krebs CJ: “Ecology”. Pearsons publ. (6

th edit).

Lectures (28 lectures)

1. Introduction. What is ecology? Habitats and niches? Community and population

ecology. 1 Lecture

2. Distribution limited by • Dispersal. Effect of alien introductions and human hunting. Modes of dispersal. Barriers.

Recolonisation. Economic importance of dispersal abilities.

• Habitat selection. Examples of mosquitoes, herbivorous insects, bird courtship and

nesting behaviour, rodents in the Mojave desert.

• Predation. Examples of mussels and crabs; wallabies and foxes; seaweeds and sea urchins.

Effect of prey on predator distribution.

• Parasites and pathogens. Examples of avian malaria and chestnut blight.

• Allelopathy on plant distribution.

• Competition. Examples of fruit pigeons, salamanders and European crossbills.

• Temperature and water. Variations in temperature. Physiological limits. Microhabitats.

Combination of temperature and humidity.

• Plants limited by light. C3, C4 and CAM plants.

• Relationship between distribution and abundance. 7 Lectures

3. Population abundance: Introduction. Births, deaths, immigration/emigration.

Survivorship curves. Intrinsic rate of increase. Logistic curves. 2 Lectures

Competition. Competitive exclusion principle; separation between niches; alien

introductions; Grime’s theory of plant strategies. 1 Lecture

Predation. Characteristics shown by lab experiments; results of field studies; predator-

prey strategies. 2 Lectures

Herbivory. Plant chemical defenses. Examples of tobacco and oak; spines; herbivores on

the Serengeti; do plants benefit from herbivores? 2 Lectures

Parasites. Effect of a disease; parasite survival in a population; factors affecting your

parasite load; control of rabies; control using myxomatosis. 2 Lectures

4. Applied problems in populations: a) Fish harvesting: the fishing problem; fishery

strategies; reasons for collapse of different fisheries. 1 Lecture

b) Pest control: chemical control using insecticides; biological control, genetic methods of

control, cultural methods. 2 Lectures

c) Species conservation: Problems of small populations; habitat destruction and

fragmentation, hunting, introduction of foreign species and chain extinctions. 2 Lectures

5. Community ecology: Defining and recognising a community.

Primary & secondary succession; climax vegetation.

Biodiversity and heterogeneity; gradients and hotspots; factors controlling diversity.

Trophic levels and Food webs; keystone species; dominant species.

Disturbed (non-equilibrium) communities. 6 Lectures

Practicals

Practicals will consist of:

A. Community ecology will be studied by Field trips. These will include:

� Terrestrial ecology (near SQU) will use traps and field sampling to show the importance of

microhabitats, such as sun and shade, on the distribution of animals.

� Freshwater ecology (in Wadi Al-Khod and the SQU pond) will show the importance of

microhabitats, and the effect of flowing water and stagnant water on animal distribution.

� Marine ecology (Asifa) will show the importance of microhabitats and the effect of the tide

(and thus exposure to the air) on intertidal animals.

Field trips will be followed by lab practicals to analyse the samples collected. The practicals

will be written up as reports.

B. Wildlife videos (BBC Wild Africa series) will show the communities (and the adaptations of

plants and animals to the habitat) for:

� Deserts.

� Savanna,

� Rain forest.

� Freshwater.

� Mountains.

C. The problems of population ecology will be investigated by Computer simulations

(SimBiotic software). These simulations run experiments on the computer in which the student

alters the parameters to investigate the significance of particular factors on the population

abundance of a particular community. The communities investigated will include:

� Sampling plants using quadrats.

� Sampling animals using mark-recapture.

� The Competitive exclusion principle.

� Relation between competition and predation.

� Predation by wolves on moose.

� Community ecology in the intertidal zone.

The simulations involve collection and analysis of data by the students, so the student can predict

what is expected to happen and see the actual result.

D. Practicals will investigate:

� Barn Owl prey will be investigated by dissection of owl dropping to see how this key

predator varies in different part of the USA.

� A field experiment (within SQU) will investigate bird strategies in foraging for food and

in flocking defense against predators. This involves collection of data that will be analysed

and written up as a report.

Theory of Practical Exam. At the end of the course, there will be a theory of practical exam covering all of the above labs

(including the videos). Students will be given data from the labs and asked to discuss and analyse.


Practical details NOTE: Practicals will not run in this order, since field trips have to fit in with

physical constraints (outside temperature, low tides, buses, etc).

A. Habitat DVDs & computer simulations of populations:

Practical 1: Dhofar mountains and seas (DVD from BBC “Wild Arabia” series).

Practical 2: a) Deserts (DVD from BBC “Wild Africa” series)

b) Quadrat sampling of prairie grassland (SimBiotic computer simulation).

Practical 3: a) Savannas (DVD from BBC “Wild Africa” series).

b) Sampling pigeons by mark-recapture technique (SimBiotic computer simulation).

Practical 4: a) Rain forests (DVD from BBC “Wild Africa” series).

b) Niches and competition among rabbits (SimBiotic computer simulation).

Practical 5: a) Mountains (DVD from BBC “Wild Africa” series).

b) Species relationships–competition and predation (SimBiotic simulation).

Practical 6: a) Freshwater lakes and rivers (DVD from BBC “Wild Africa” series).

b) Predation by wolves on Moose (SimBiotic computer simulation).

Practical 7: a) Coasts (DVD from BBC “Wild Africa” series).

b) Keystone species in an intertidal community (SimBiotic simulation).

B. Field trips:

Practical 8: Acacia woodland field trip. a) Distribution of tree species inside and above a small wadi.

b) Effect of sun and shade on the invertebrates in different microhabitats (using

pitfall traps, water traps and looking under stones and among rotting wood).

Practical 9: Freshwater field trip. Diversity of animals in running water, and in water pools with and without fish.

Practical 10: Intertidal rocky shore field trip. Transects from High water to Low water mark during an ultra-low tide to show the

species distributions and microhabitats.

C. Laboratory experiment:

Practical 11: Dissection of Barn owl droppings to identify the relative importance of their

different prey and regional differences.


Possible Practical Schedule

Week 1 (Thur 10th Sept): Pract 1 Dhofar mountains and seas DVD

Week 2 (Thur 17th Sept): Pract 2 Deserts DVD & Quadrat sampling simulation.

Week 3 (Thur 24th Sept): Eid Al-Adha?

Week 4 (Thur 1st Oct): Pract 3 Savannas DVD & Mark-recapture simulation.

Week 5 (Thur 8th Oct): 1

st Theory Test

Week 6 (Thur 15th Oct): Islamic New year ?

Week 7 (Thur 22nd Oct): Pract 11 Analysis of barn owl droppings.

Week 8 (Thur 29th Oct): Pract 4 Rainforest DVD & Niches simulation.

Week 9 (Thur 5th Nov): Pract 5 Mountains DVD & Competition simulation.

Week 10 (Thur 12th Nov): 2

nd Theory Test

Week 11 (Sat 19th Nov): Pract 8 Acacia woodland (SQU) field trip.

Week 12 (Thur 26th Nov): Nation Day holiday?

Week 13 (Thur 3rd Dec): Pract 6 Freshwater DVD & Moose predation simulation.

Week 14 (Thur 10th Dec): Pract 10 Intertidal (Asifa) field trip.

Week 15 (Thur 17th Dec): Pract 9 Freshwater (Wadi Saal) field trip.

Week 16 (Thur 24th Dec): Theory of Practical Exam.


Course Assessment Week 5 = 1

st Theory test

Week 7 = 1st Quiz (Quadrat sampling + Mark recapture simulations)

Week 9 = 2nd Quiz (Barn owls + Niches simulation).

Week 10 = 2nd Theory Test

Week 13 = Submit report on Acacia woodland

Week 14 = 3rd Quiz (Competition + Moose predation simulation)

Week 15 = 4th Quiz (Intertidal Asifa field trip)

Week 16 = Theory of Practical Exam

Week 18 = Final Theory Exam

BIOL 3009 1 |

BIOL 3009: Introduction to Environmental Science

Number of Credits: 3

Instructional Format: Two lectures and one practical per week

Contact Hours/Week: 5

Prerequisite: BIOL 2102

Textbook: Cunningham, W.P. and Cunningham, M.A. 2013. Principles of

Environmental Science: inquiry and application. The 7th

edition. McGraw Hill.

Instructor: Dr. Hassan Ali Al-Reasi

Office: 1065 (1st floor, The New Science building)

Telephone: 24146871 or Extension: 6871 (on campus)

E-mail: [email protected] or [email protected]

Course Description:

This is an introductory course emphasizing the study of environmental issues from a scientific

perspective. It is designed to provide students with up-to-date information on the fundamental

aspects of environmental science. This knowledge along with hands-on skills will enable them to

understand how humans can use resources sustainably with minimal impact on the environment.

Examples of environmental concerns/problems in Oman will be introduced as brief case studies

and students will assess the risks associated with these problems and evaluate solutions for

resolving and preventing them. Topics include: Earth systems and resources, the living world,

populations, land and water use, energy resources and consumption, pollution, and global climate

change.

Learning outcomes:

The following goals are anticipated to be achieved by students enrolling in the BIOL 3009:

1. Define terminology and discuss the basic physical and biological principles related to the

environmental issues/problems.

mailto:[email protected]


BIOL 3009 2 |

2. Help students to develop appreciation for the vital roles played by the environment and

increase their awareness about the sustainable consumption of resources and the importance of

conservation.

3. List and discuss different renewable and nonrenewable energy resources, their current

situations, limitations and the future energy demand.

4. Become familiar with environmental concerns affecting our local (Oman) and regional

ecosystems and learn how to tackle them using scientific inquiry-based approaches.

5. Understand the basis of global environmental issues (e.g. global warming, increasing human

population, pollution, waste) and discuss the factors responsible for such issues and their

consequences.

6. Develop/strengthen critical thinking and encourage students apply the scientific method in

designing experiment, collecting and analyzing data.

7. Enhance student's skills in writing, oral communication and group discussion of Omani

environmental issues.

Assessment:

Grading scheme

2 Theory tests 30% (15% each)

Lab reports and quizzes 20%

Assignments/essays 3%

Presentation 7%

Final Examination 40%

Proposed exam dates:

Test 1 October 20, 2015

Test 2 November 24, 2015

BIOL 3009 3 |

Table of contents (Lectures)

Please refer to the following chapters of: Cunningham, W.P. and Cunningham, M.A. 2013.

Principles of Environmental Science: inquiry and application. The 7th

edition. McGraw Hill. More

details on the lectures are provided in PowerPoint (PPT) files on the E-learning website for BIOL

3009. And please take notes in the classes or during lectures.

Chapter 1: Understanding our environment

1.1 Understanding our environment

1.2 Crises and opportunities

1.3 Human dimensions of environmental science

1.4 Science helps us understand our world

3

3

4

7

14

Chapter 2: Environmental systems: matter and energy and life

2.5 From species to ecosystems

2.6 Biogeochemical cycles and life processes

26

38

41

Chapter 3: Evolution, species interactions and biological communities

3.3 Population growth

50

63

Chapter 4: Human populations

4.1 Past and current population growth are very different

4.2 Perspectives on population growth

4.3 Many factors determine population growth

4.4 Fertility is influenced by culture

4.5 A demographic transition can lead to stable population size

76

77

79

81

87

89

Chapter 5: Biomes and biodiversity

5.4 Biodiversity

5.5 Benefits of biodiversity

5.6 What threatens biodiversity?

5.7 Biodiversity protection

96

110

110

112

122

BIOL 3009 4 |

Chapter 7: Food and agriculture

7.1 Global trends in food and nutrition

7.2 How much food do we need?

7.3 What do we eat?

7.4 Living soil is precious resource

7.5 Agricultural inputs

7.6 How have we managed to feed billions?

7.7 Sustainable farming strategies

7.8 Consumer action and farming

152

154

157

160

163

166

171

173

176

Chapter 8: Environmental health and toxicology

8.1 Environmental health

8.2 Toxicology

8.3 Movement, distribution and fate of toxicants

8.4 Mechanisms for minimizing toxic effects

8.5 Measuring toxicity

8.6 Risk assessment and acceptance

8.7 Establishing public policy

180

182

188

192

195

195

200

201

Chapter 9: Climate

9.1 What is the atmosphere?

9.2 Climate changes over time

9.3 How do we know the climate is changing faster than usual?

205

207

210

213

Chapter 10: Air pollution

10.1 Air pollution and health

10.2 Air pollution and the climate

10.3 Health effects of air pollution

10.4 Air pollution control

229

231

237

240

243

Chapter 11: Water: resources and pollution

11.1 Water resources

250

252

BIOL 3009 5 |

11.2 Major water compartments

11.3 Water availability and use

11.4 Freshwater shortages

11.5 Water management and conservation

11.6 Water pollution

11.7 Pollution control

253

255

257

262

264

274

Chapter 13: Energy

13.1 Energy resources and uses

13.2 Fossil fuels

13.3 Nuclear power

13.4 Renewable energy

13.5 Energy from biomass

13.6 Wind and solar energy

302

303

305

310

313

316

318

Chapter 14: Solid and hazardous wastes

14.1 What waste do we produce?

14.2 Waste disposal methods

331

333

334

BIOL 3009 6 |

Table of contents (Practical sessions)

Practical 1: Laboratory safety practices and laboratory report write-up format

Sample report: dissolved oxygen of aquatic environment

Practical 2: Calculating your Ecological Footprint

Practical 3: Decomposition of biodegradable plastics

Practical 4: Determination of phosphate (PO42-) in water and wastewater samples

Practical 5: Environmental Forensics-1 (pH, total dissolved solids, TDS, and

turbidity measurements of water and wastewater)

Practical 6: Educational videos-Water desalination (advantages and disadvantages

Practical 7: Introduction to basic statistical analyses and data presentation in

environmental science

Practical 8: Field trip (Al-Ansab wetlands)

Practical 9: Sampling air for particulate matter (PM) and greenhouse gas emission

from passenger cars

Practical 10: Environmental contamination (2 weeks experiment)

Practical 11: The rate of photosynthesis of mung bean (Vigna radiata) seedlings

after exposure to oil-contaminated soil

Practical 12-13: Presentations delivery

7

11

14

18

22

26

32

34

49

52

55

59

64

1


College of Science


COURSE OUTLINE for BIOL 3011 PLANT PHYSIOLOGY

Course code : BIOL3011

Course title : Plant Physiology

Pre-requisite : BIOL 2102

Credits : 3 CU

Format : Two lectures (50 min) and 1 (3 hrs) laboratory / week

Coordinator : Dr Sardar A Farooq (Office Room # 2023; Tel. # 6882)

Email: [email protected]

Textbook : Plant Physiology (3rd

Edition) by Taiz and Zeiger

Course Outline

The course consists of the following units, which will give students an understanding of

the basic principles of Plant Physiology.

1. Plant water relations

2. Uptake and transport of water and nutrients

3. Photosynthesis

4. Reproductive growth and development

At the beginning of each topic students will be given a topic outline, lecture and

laboratory titles and the objectives the student is expected to attain during the topic.

Course Assessment

The written and practical ability of students will be assessed as follows:

Assessment of written ability Test 1 15% (Week 6)

Test 2 15% (Week 12)

Final examination 40%

Assessment of practical ability Mid-semester laboratory Test-I 10%

End of semester laboratory Test-II 10%

Laboratory Quizzes/ reports 10%


2

Learning outcomes:

By the end of the course, students should be able to:

Describe plant water relations: distinguish between diffusion, bulk flow and osmosis.

Identify the components of water potential and its measurement

Illustrate the transpiration, absorption of mineral nutrients and identify deficiency

symptoms of mineral nutrients

Relate the importance of chloroplast pigments in photosynthesis.

Compare the cyclic and non-cyclic photophosphorylation.

Distinguish between C-4 pathway for carbon fixation and carbon fixation in CAM

(succulent) plants.

Examine the physiological effects of various plant growth regulators,

Compare the actions of auxins and cytokinins, gibberellins, ethylene and ABA;

From the laboratories the students should be able to get the practical knowledge on the

following aspects:

1. Estimate osmotic potential in plant cells

2. Estimate the rate of transpiration and stomatal density

3. Compare the rates of transpiration by CoCl2 method in mesophytes, xerophytes.

5. Identify the mineral deficiency symptoms

6. Isolate chloroplast pigments

7. Extraction and absorption spectrum of chlorophyll pigments

8. Estimate the rate of photosynthesis

9. Demonstrate bioassays of gibberellins and auxins

Detailed Syllabus (Objectives and Lecture/Lab Titles)

Unit 1: Plant water relations

Objectives - To understand the following:

Properties of water

The process of diffusion and bulk flow

Osmosis, osmotic pressure and the Vant Hoffs equation

The components of water potential

Measurement of water potential and water content

3

Lecture titles

1 Structure and properties of water

2 Translocation of water

3 Water potential

4 The measurement of water in plants

Unit 2: Uptake and transport of water and nutrients


Absorption of water and transpiration

Absorption of mineral nutrients

Deficiency symptoms of mineral nutrients

Lecture titles

5 Transpiration

6 Uptake of water by roots

7 Uptake of mineral nutrients

8 Ion absorption

9 Mineral nutrition of plants

Unit 3: Photosynthesis


The structure of the chloroplast

Chloroplast pigments

Photophosphorylation and electron transport

The Calvin cycle

Photorespiration

The C-4 pathway for carbon fixation

Carbon fixation in CAM (succulent) plants

Transport of photosynthates

Lecture titles

10 Chloroplast structure and pigments

11 Photophosphorylation

12 Calvin cycle

13 Photorespiration

14 Carbon fixation in C4 plants

15 Crassulacean acid metabolism

16 Transport of photosynthates

4

Unit 4: Plant hormones and development

Objectives: To understand the following:

The physiology of flowering

Plant growth regulators

The seed dormancy and germination

Lecture titles

17 Flowering

18 Plant growth regulators

19 Auxins

20 Cytokinins

21 Gibberellins

22 Ethylene

23 Abscisic acid (ABA)

24 Seed dormancy and Seed germination

Laboratories

1 Measurement of osmotic potential in plant cells

2 Measurement of water content and water potential

3 Transpiration and stomatal density

4 Relative rates of transpiration (CoCl2 method)

5 Munch pressure flow

6 Mineral deficiency symptoms

7 Chromatography of chloroplast pigments

8 Separation of chlorophyll pigments

9 Extraction and absorption spectrum of chloroplast pigments

10 Evolution of oxygen during photosynthesis

11 Measurement of photosynthesis in leaf discs

12 Effect of gibberellins on stem elongation

13 Plant hormones and leaf abscission

Video films:

The students will be asked to watch the following videos available in the library:

1672 Photosynthesis- an advanced study

1845 Photosynthesis

3032 Diffusion

3033 Photosynthesis & Respiration

3415 Photosynthesis & Energy of life

4387 Cell biology

4601 Life functions

6374 Plant problems with water



BIOL 3023: Animal physiology

Course Outline

Dr Aziz Al-Habsi

BIOL 3023: Animal physiology - 4 credits

Course outline Course Description A basic introductory course covering the different organ systems to see how each functions.

It concentrates on human physiology in relation to structure.

The lectures start with homeostasis and give a brief introduction to the human cell. The

main section discusses each of the different organ systems (nervous system, muscle systems, sense

organs, endocrine system, cardiovascular system, immune system, respiratory system, digestive

system, renal system and reproductive system), to see how each functions.

The laboratories start with tissue histology and a series of rat dissections to demonstrate the

main organ systems. The following labs are mainly experiments that the students will carry out on

themselves to investigate different aspects of human physiology. There are also a number of

computer simulations, covering experiments too complex to be carried out by the students.

Learning Outcomes: (see later page)

Course Format A 4-credit course consisting of 3 lectures and one 3-hour laboratory per week 6 contact hours.

Course Prerequisite: BIOL 2101: Biology I (4 credits)

Course Facilities: Textbook: Moyes and Schulte “Principles of Animal Physiology”.

Course assessment: The course will be graded A - F based on:

Lecture test x 2 (1 hour each) = 30 %

Laboratory practicals and quizzes. = 15 %

Final practical Exam = 15 %

Final theory Exam = 40 %

Course Co-ordinator: Dr. Aziz Al-Habsi (Room 2026, Biology Department)

([email protected])


Lectures (2 per week for 14 weeks)

1. Homeostasis and a Human Cell. Homeostasis and feedback mechanisms. An introduction to cell biology, especially

cellular transport (diffusion, osmosis, active transport, vesicles) and a summary of the

functions of the main organelles. (3 lectures)

2. The Nervous system. Neurons and neuroglia. The Resting and Action potentials. Graded responses.

Impulse transmission. The synapse. Integration by inhibition and summation. Spinal cord

and reflexes. The brain. The autonomic nervous systems. (4 lectures)

3. Sense organs. Sensory receptors in the skin and viscera. Graded responses and accommodation. Smell and

taste. Vision in the eye. Hearing and balance in the ear. (4 lectures)

4. Skeletal and smooth muscles. Skeletal muscle: sliding filament mechanism; muscle contraction; tetanus; recruitment;

muscle tension; fatigue; fast and slow fibres. Smooth muscle: properties and contraction.

(3 lectures)

5. Endocrine system. Types of chemical signals. Control of hormone secretion. Hormone elimination. Types of

hormone receptors and their functioning. The pituitary gland. Thyroid and parathyroid

glands. Adrenal glands. Control of blood sugar and diabetes. (4 lectures)

6. Cardiovascular system. Plasma, erythrocytes and leucocytes. Blood clotting. Blood flow through the heart. Cardiac

muscle. Control of the heartbeat by intrinsic and extrinsic factors. Capillaries, arteries and

veins. Blood pressure. Capillary exchange. Control of blood flow locally and regional

control by nerves and hormones. (5 lectures)

7. Lymphatic system. The lymphatic system and movement of lymph. (1 lecture)

8. Immune system. Innate immunity by barriers, chemicals and cells. Inflammation. Adaptive immunity.

Activation of lymphocytes. Inhibition of lymphocytes. Antibodies. T lymphocytes. Active

and passive immunity. Allergies and auto-immune diseases. HIV. (3 lectures)

9. Respiratory system. Functions of the upper respiratory tract. Ventilation and lung volumes. The alveoli and gas

exchange. Oxygen transport by haemoglobin: association and dissociation. Carbon dioxide

transport. Control of ventilation and factors affecting ventilation. (3 lectures)

10. Digestive system. Movement of food. Hormonal and nervous regulation of digestion. The role of the stomach,

liver, pancreas, small and large intestines in digestion. Digestion and absorption of

carbohydrates, proteins and lipids. (3 lectures)

11. Metabolism and temperature regulation. (1 lecture)

12. Urinary system; and ionic and water balance of the blood. The nephron: ultrafiltration; reabsorption of nutrients, ions and water; active secretion. Role

of the peritubular and vasa recta capillaries. Regulation of urine by hormones and

sympathetic system. Control of water, ions and pH in the body. (4 lectures)

13. Reproductive systems. The male system and spermatogenesis. Male hormones. The female system; oogenesis and

hormonal control of the ovarian and menstrual cycles. Embryo development. (3 lectures)

Practical schedule (one 3-hour lab/ week) This starts with tissue histology and a series of rat dissections to demonstrate the main organ

systems. Most of the following practicals involve the students carrying out physiological experiments on

themselves, with computerised analysis of their data. There are also some computer simulations to show

more sophisticated experiments.

Wk 1 Practical 1: Tissue types: cuboidal, ciliated columnar, squamous, adipose, areolar, dense

white fibrous, cartilage, compact bone, cardiac, skeletal muscle, smooth muscle, neurons.

Wk 2 Practical 2: a) Dissection of the rat: to show the digestive system.

b) Computer simulation of muscle physiology using PhysioEx.

Wk 3 Practical 3: Dissection of the rat thorax to show the respiratory and blood systems.

Wk 4 Practical 4: Dissection of the rat abdomen to show the reproductive, urinary and

abdominal blood systems.

Wk 5 Practical 5: Blood 1: a) Measurement of blood haematocrit.

b) Blood cell counting using a haemocytometer.

c) Computer simulation of thyroxine control (PhysioEx).

Wk 6 [1st Theory test: Introduction, Nerves, Senses and Muscles = 14 lectures]

Wk 7 Practical 6: Blood 2: a) Analysis of the student’s blood glucose and blood clotting.

b) Blood groups: ABO and rhesus.

c) Computer simulation of insulin control (PhysioEx).

Wk 8 Practical 7: Heart 1:

a) Dissection of the sheep heart to show blood flow.

b) Experiments on human blood pressure and pulse rate using the Dynapulse system.

Wk 9 Practical 8: Heart 2: a) Analysis of human ECG (electrocardiogram).

b) Experiments on polar heart rate using the EasySense system.

c) Computer simulation of the effects of drugs and nerves on the heart beat (PhysioEx)

Wk 10 Practical 9: Lungs 1:

a) Measurement of lung volumes with the EasySense respirometer.

b) Computer simulation of control of blood pH by respiration and excretion (PhysioEx).

Wk 11 [2nd

Theory test: Endocrine, cardiovascular, Lymphatic and Immune systems = 14 lect.]

Wk 12 Practical 10: Lungs 2: Control of respiration (using the EasySense system).

Wk 13 Practical 11: Gut histology: stomach, liver, pancreas; ovary histology.

Wk 14 Practical 12: Urinary system:

a) Analysis of normal and abnormal urine.

b) Computer simulation of the processes in a nephron and the control of urine production.

Wk 15 Practical exam (covers all 12 practicals).

---------------------------------------------------------------------------------------------------------------------

Assessment: Lab practicals (15%): The 3 rat dissections will each be marked afterwards.

There will be 3 quizzes on the remaining practicals;

One lab report (considered as a quiz) and the lab manual drawings will be

marked.

Practical Exam (15%): This will consist of probably 25 stations with 5 questions at each station

and 2 minutes to answer them. Whole exam will last around 50 minutes.

Course Learning Outcomes By the end of the course, students should be able to:

1. Identify the main organ systems in the human body, the type of tissues that they are

made up of, and list their functions.

2. Dissect a rat to show its digestive, blood, respiratory, reproductive and urinary

systems.

3. Perform experiments to demonstrate blood pressure, blood clotting, blood groups,

lung capacities, control of ventilation and urine analysis.

4. Discuss the mechanisms of muscle contraction and nerve conduction.

5. Explain how hormones control blood glucose and blood ions.

6. Discuss the control of the endocrine system, blood flow and the heart beat,

ventilation, digestion.

7. Explain how the immune system controls pathogens.

8. Explain how digestion and absorption take place in the gut.

9. Explain how the kidney works in excreting and controlling loss of nutrients.

10. Explain how hormones control the female ovarian and menstrual cycles.

Lecture Units - Learning Outcomes A. Introduction. 1. Define homeostasis.

2. Explain how negative feedback is involved in homeostasis.

3. Recognise the main components of a typical cell and the structure of the plasma membrane.

4. Explain how diffusion and osmosis occur and the factors affecting their rates.

5. Describe the different types of mediated transport: facilitated diffusion; active transport;

secondary active transport.

6. Describe how vesicles are used in endo and exocytosis.

B. The Nervous system. 1. Describe a neuron.

2. List the types of neuroglia and give their functions.

3. Explain how a cell produces a resting potential.

4. Describe leak channels, voltage-gated channels and ligand-channels.

5. Explain the processes by which an axon produces an action potential.

6. Define graded responses and the All-or-none Law.

7. Explain how an impulse is transmitted by continuous and saltatory conduction.

8. Describe electrical and chemical synapses.

9. Explain how an impulse crosses a chemical synapse and the significance of excitatory

and inhibitory neurotransmitters.

10. Explain the importance of pre-synaptic inhibition and post-synaptic summation.

11. Describe a reflex in the spinal cord and its significance.

12. List the main regions of the brain and give their functions.

13. Describe the autonomic nervous system and the differences between the sympathetic,

parasympathetic and enteric systems.

C. The Sense organs. 1. Describe the functions of the different types of skin receptors and visceral receptors.

2. Compare primary and secondary receptors.

3. Explain why accommodation occurs in receptors.

4. Describe how smell occurs in the nose and taste in the tongue.

5. Describe the structure of the eye and explain how light detection occurs.

6. Describe the structure of the ear and explain how detection of sound occurs.

7. Explain how the vestibule of the ear detects static equilibrium and the semicircular

canals detect kinetic equilibrium.

D. Skeletal and Smooth muscles. 1. List the functions of muscles.

2. Describe the structure of skeletal muscles.

3. Explain the sliding filament mechanism.

4. Explain how a muscle contraction starts (excitation-contraction coupling).

5. Explain the movement of the myosin heads during contraction (cross-bridge cycling).

6. Describe muscle twitches, summation and tetanus.

7. Explain passive and active tension and how the muscle force is controlled by recruitment and

arrangement of antagonistic muscles.

8. Define isotonic and isometric contractions.

9. Compare the different types of fatigue.

10. Explain how energy is supplied to fast and slow fibres.

11. Describe smooth muscle.

12. Explain how smooth muscle contracts and compare with skeletal muscle.

E. The Endocrine system. 1. List the types of chemical signals.

2. Explain the different methods of controlling hormone secretion.

3. Describe how hormones are transported in the blood and eventually eliminated.

4. Explain how attachment of a hormone to its receptor triggers a response.

5. List the hormones produced by the anterior and posterior pituitary.

6. Describe the functions of thyroxine and the result of abnormal production.

7. Explain how calcitonin, PTH, epinephrine and aldosterone function in the body.

8. Explain how hormones control blood sugar and how malfunction results in diabetes.

F. The Cardiovascular system. 1. List the functions of blood.

2. Describe the components of blood.

3. Explain how erythrocytes transport oxygen and how their abundance is regulated.

4. Describe the processes of blood clotting (platelet plugs and coagulation).

5. Describe the double circulation and the role of valves in controlling flow through the heart.

6. List the characteristics of cardiac muscle cells.

7. Explain how the heart beat is controlled by intrinsic and extrinsic factors.

8. Describe the different types of blood vessels (arteries, veins and capillaries).

9. Explain why blood pressure changes in different parts of the body.

10. Explain how capillaries exchange nutrients and gases.

11. Explain how the blood supply is controlled, both at a local and a regional level.

G. The Lymphatic system. 1. Describe the structure and function of the lymphatic system.

2. Explain how the lymph nodes and spleen act as mechanical filters.

H. Immune system. 1. Describe the different components of innate immunity.

2. Explain how inflammation occurs.

3. Explain how and why B lymphocytes are activated.

4. List the types of antibodies and give their actions.

5. Compare primary and secondary responses.

6. List the types of T lymphocytes and give their actions.

7. Explain activation of Cytotoxic T cells and compare with B lymphocyte activation.

8. Describe active and passive immunity.

9. Explain how allergies and auto-immune diseases are produced.

10. Explain how HIV exploits the complexity of lymphocyte activation.

I. Respiratory system. 1. Describe ventilation when resting and when active.

2. Explain the factors affecting lung capacity.

3. Explain how gas exchange takes place in the alveoli.

4. Explain the factors affecting oxygen dissociation and association with haemoglobin.

5. List the methods of carbon dioxide transport in the blood.

6. Explain how ventilation is controlled, both when resting and active, and the role of CO2 and O2

receptors.

J. Digestive system. 1. List the functions of the stomach, the liver, pancreas, and the small and large intestines.

2. Explain how the 3 stages of digestion (cephalic, gastric and intestinal) are controlled.

3. Explain how digestion and absorption occurs for carbohydrates, proteins and lipids.

K. Metabolism and temperature regulation. 1. Define basal metabolic rate and list the factors that affect it.

2. Define obesity; and hyperplastic and hypertrophic obesity.

3. Explain the set-point theory and how the body controls food intake.

4. List the processes that control body temperature.

L. Excretory system. 1. Describe the parts of a nephron and define cortical and juxtamedullary nephrons.

2. Explain how ultrafiltration takes place in renal corpuscles.

3. Explain how reabsorption takes place in the different parts of the nephron.

4. Explain how the vasa recta works as a counter-current.

5. Explain how urine volume is controlled.

6. List the factors affecting the volume of body fluids and explain the controlling mechanisms.

7. Explain how the body regulates the different cations in the blood.

K. Reproductive system. 1. List the components of the male reproductive system and give their functions.

2. Describe the processes of spermatogenesis and of oogenesis.

3. Explain the ovarian and menstrual cycles and how they are controlled.

4. Summarise the processes resulting in fertilisation and implantation of the embryo.

ooooooooooooOOOOOOOOOOOOOOOOOOoooooooooooo



BIOL 3025: The Invertebrates (3 credits)

Course outline

Dr. Derek Roberts

BIOL 3025: Invertebrates (3 credits)

Course outline

Course description: This is an intermediate level course, which covers the major invertebrate phyla. It

shows the diversity of structure and function, in relation to their habits and mode of life.

The lectures introduce the major phyla, covering their ecology, and their

comparative anatomy and physiology. The practicals show the characteristic features of

the most important invertebrates and include dissections to show their internal anatomy,

and videos on their ecology and biology.

Course objectives: To familiarise students with the characteristics and biology of the major phyla:

Cnidaria, Platyhelminthes, Nematoda, Annelida, Mollusca, Arthropoda (Crustacea,

Insecta and Arachnida) and the Echinodermata.

Learning outcomes By the end of the course, the students should be able to:

1. Identify the main invertebrate Phyla and their Classes.

2. Dissect representatives of the main phyla to display their internal anatomy.

3. Explain how invertebrates have solved the problems of feeding, locomotion,

respiration, excretion and reproduction.

4. Explain the evolutionary trends that have occurred in the invertebrate phyla.

Course format: 2 Lectures & 1 laboratory per week, giving 4 contact hours.

Course prerequisite: BIOL 2102: Biology II (4 credits)

Course assessment: The course will be graded A - F, using the following format:-

Lecture tests (2) 30 %

Laboratory practicals 10 %

Practical exam 20 %

Final Theory exam 40 %

Textbook: Brusca & Brusca: Invertebrates. Sinauer.

E-learning: The course is available on Moodle. In addition to the lectures and course outline, this contains PowerPoints and video clips to demonstrate behavioural and

ecological features, as well as past exam papers and tests.

Course Co-ordinator: Dr. Derek Roberts (room 1070, Biology Dept.)


Lectures (2/week for 14 weeks)

1. Introduction (1 lecture) The evolutionary trends that have occurred from the primitive Cnidaria to the advanced

Arthropoda.

2. Cnidaria (2 lectures) Characteristics; classification and structure of the Hydrozoa, Scyphozoa and Anthozoa;

nutrition (predators, filter feeders, symbiotic algae and digestion); reproduction and life

cycles.

3. Platyhelminthes (2 lectures) Characteristics; nutrition (predators and parasites); locomotion; reproduction and life

cycles of Clonorchis and Taenia; nervous and excretory systems.

4. Nematoda (2 lectures) Characteristics; locomotion; nutrition; excretion; nervous system; reproduction;

parasitism in humans.

5. Annelida (4 lectures) Characteristics and structure of the Polychaeta, Oligochaeta and Hirudinea; locomotion

(in the Polychaeta, earthworms and leeches); nutrition (predators and herbivores; filter

and deposit feeders); respiration and blood system; nervous system; reproduction and

development.

6. Mollusca (4 lectures) Characteristics of the Polyplacophora, Gastropoda, Bivalvia and Cephalopoda; nutrition

(herbivores, filter feeders, deposit feeders and predators, digestion); respiration in

bivalves, Gastropods and Cephalopods; blood system; nervous system; reproduction and

development.

7. Introduction to the Arthropoda (1 lecture) Characteristics and evolutionary relationships; advantages and disadvantages of the

exoskeleton.

8. Crustacea (Arthropoda) (3 lectures) Characteristics; nutrition (predators and herbivores, filter feeders and deposit feeders;

digestion); respiration (cutaneous, gills and air respiration); excretion and

osmoregulation; nervous system; reproduction and development.

9. Insecta (Arthropoda) (4 lectures) Characteristics; life cycles; nutrition (feeding and digestion); locomotion (running and

flight); respiration; blood, nervous and excretory systems; life on land.

10. Arachnida (Arthropoda) (2 lectures) Characteristics; feeding (predators, blood-suckers, omnivores); feeding in spiders

(hunting, raptorial and web spiders); digestive, respiratory and excretory systems.

11. Echinodermata (2 lectures) Characteristics; the water vascular system; locomotion; defense; feeding (predators,

scavengers, herbivores, filter and deposit feeding); digestion; excretion, respiration;

nervous system and reproduction.

Practicals (2 h/ week)

Practical 1: Cnidaria Hydrozoa: Pennaria colony; L.S. of Hydra; Physalia colony, Velella colony.

Jellyfish: Aurelia, Gonionemus and Polyorchis. Anemones: Metridium, corals.

Practical 2: Platyhelminthes & Nematoda Flatworms: Planaria; T.S. of Planaria;

Flukes: Echinostoma and Clonorchis; Tapeworms: Taenia and Echinococcus.

Nematoda: Dissection of Ascaris. T.S. Ascaris.

Practical 3: Annelida (A) Typical Polychaeta: Nereis - external features; a parapodium; dissection to show

internal structures; T.S. of body.

Practical 4: Annelida (B) Specialised Polychaeta: Fan worm, tube worm, sea mouse, scale worm.

Earth worm: Lumbricus- external features & T.S. Leech: Haemopis.

Practical 5: Mollusca (A) Polyplacophora: a chiton.

Gastropoda: Keyhole limpet (Prosobranchia); dissection of Helix (Pulmonata).

Practical 6: Mollusca (B) Gastropoda: Conch (Prosobranchia); sea slug (Opisthobranchia).

Bivalvia: Anadonta; Pecten. Cephalopoda: Dissection of the squid Loligo.

Practical 7: Videos on invertebrates “Introduction to invertebrates”; “Phylum Annelida”; “Phylum Mollusca”

Practical 8: Crustacea Artemia (brine shrimp); Lepas (goose barnacle); dissection of Astacus (crayfish);

swimming and walking crabs; Oniscus (woodlouse).

Practical 9: Insecta Dissection of the grasshopper (Romalea); grasshopper mouthparts.

Practical 10: Insecta & Arachnida Aquatic insects: mosquito larva, Corixid, dragonfly larva.

Arachnida: scorpion, web and hunting spiders, tick.

Practical 11: Echinodermata Brittle stars, crinoids, sea urchins, sand dollar and sea cucumber.

Dissection of the Starfish.

[Practical exam]

Lecture Learning Outcomes Introduction 1. List the trends that have occurred in the evolution of the invertebrates.

Cnidaria 1. List the characteristics of the Cnidaria and of its 4 main Classes.

2. Describe nutrition and reproduction in the Cnidaria.

Platyhelminthes 1. List the characteristics of the Platyhelminthes and of its 3 main Classes.

2. Describe nutrition, locomotion, reproduction and the nervous and excretory systems.

3. Explain how the flukes and tapeworms are adapted to a parasitic life.

Nematoda 1. List the characteristics of the Nematoda.

2. Describe locomotion, nutrition, excretion and the nervous system in Nematodes.

3. List examples of Nematodes that are human parasites and summarise their life cycles.

Annelida 1. List the characteristics of the Annelida and of its 3 main Classes.

2. Describe locomotion, nutrition, respiration, and the blood, excretory and nervous

systems of Annelids.

3. Compare reproduction in the 3 Annelid Classes.

Mollusca 1. List the characteristics of the Mollusca and of its 4 main Classes.

2. Describe nutrition, respiration and the nervous and reproductive systems of Molluscs.

Introduction to the Arthropoda. 1. Compare the Annelida, Onychophora and Arthropoda.

2. Explain the advantages and disadvantages of having an exoskeleton.

Crustacea 1. List the characteristics of the Crustacea.

2. Describe nutrition, respiration, reproduction and the blood system of Crustacea.

3. Explain why Crustacea are badly adapted for life on land.

Insecta 1. List the characteristics of the Insecta.

2. Compare the life cycles of the 3 insect Divisions.

3. Describe nutrition, locomotion and respiration in insects.

4. Explain why insects are well-adapted for life on land.

Arachnida 1. List the characteristics of the Arachnida.

2. Describe nutrition and respiration in Arachnids.

3. Explain the different methods by which spiders catch their food.

Echinodermata 1. List the characteristics of the Echinoderms and their 5 main Classes.

2. Explain the functioning of the water vascular system.

3. Describe locomotion, defense, nutrition, respiration, reproduction and the nervous

system in Echinoderms.


SULTAN QABOOS UNIVERSITY

College of Science Course Information Form

Department: Biology

Course Code: BIOL 3202 Credit & Contact Hours:

3 credits = 4 hours (2 lect + 1 lab)

Course Title: Molecular Biology

Prerequisite(s): BIOL 2102: Biology II Co-requisite(s):

Textbook(s: Essentials of Molecular Biology" by George M. Malacinski

Course Co-ordinator: Dr Raeid Abed

Description:

This course is an examination of fundamental biological processes with emphasis on events and

interactions at the molecular level, and applications of molecular biology in currently active areas

of research. The course will give the students a perception of macromolecules and their role in

eukaryotic versus the prokaryotic organisms at the molecular level. The course will concentrate

especially on the replication of DNA process, the transcription mechanism of RNA, translation

and protein sysnthesis, gene repair and gene regulation.

Aims & Objectives:

To familiarize the students with basic molecular processes and their regulation as well as to

teach them different molecular tools.

Learning Outcomes

Knowledge:

To understand the structure of nucleic acids and other macromolecules.

To understand the key genetic processes of DNA replication, transcription

and translation and their role in the follow of genetic materials.

To understand the mechanisms involved in protein synthesis, folding and

secretion

To know the different types of mutations and their causes as well as the

mechanisms of DNA repair and reversion.

To understand basic concepts in gene regulation and manipulation.

Skills:

To be able to perform different molecular techniques such as DNA extraction, DNA

quantification, restriction digestion, PCR, gel electrophoresis and sequencing.

Syllabus:

1) GENES AND GENE EXPRESSION Macromolecules and Genetic Information, Genes and the Steps in Information Flow

Prokaryotic and Eukaryotic Genetics, Macromolecules (proteins, carbohydrates, nucleic

acids), Non covalent bonds

2) DNA STRUCTURE DNA Structure: The Double Helix, DNA as a Double Helix, Size of a DNA Molecule

Inverted Repeats, Secondary Structure, and Stem-Loops, The Effect of Temperature on

DNA Structure

DNA Structure: Supercoiling, Topoisomerases: DNA Gyrase, Archaea and Reverse

Gyrase

3) DNA REPLICATION DNA Replication: Templates and Enzymes, DNA Polymerase and Primase

DNA Replication: The Replication Fork, Initiation of DNA Synthesis and

Leading/Lagging Strands, Bidirectional Chromosome Replication and the Replisome

The Replisome, Fidelity of DNA Replication: Proofreading, Termination of Replication

4) RNA SYNTHESIS: TRANSCRIPTION Overview of Transcription, RNA Polymerases, Promoters

Diversity of Sigma Factors, Consensus Sequences, and Other RNA Polymerases Sigma Factor Diversity, RNA Polymerases in Eukarya and Archaea

Transcription Terminators, Rho-Dependent Termination

The Unit of Transcription, Ribosomal and Transfer RNAs and RNA Longevity

Polycistronic mRNA and the Operon

5) PROTEIN SYNTHESIS The Genetic Code, Stop and Start Codons, Open Reading Frames, Other Genetic Codes

Codon Bias

Transfer RNA, Structure of tRNAs, Recognition, Activation, and Charging of tRNAs

Translation: The Process of Protein Synthesis, Ribosomes, Steps in Protein Synthesis

Initiation, Elongation, Translocation, and Termination, Role of Ribosomal RNA in Protein

Synthesis, Effect of Antibiotics on Protein Synthesis

6) Folding and Secreting Proteins Protein Folding, Protein Secretion and the Signal Recognition Particle, Secretion of

Folded Proteins: The TAT System

7) TOOLS FOR MANIPULATING DNA Restriction Enzymes and Hybridization, Mechanism of Restriction Enzymes

Modification: Protection from Restriction, Electrophoresis and Restriction Analysis of

DNA, Nucleic Acid Hybridization and the Southern Blot,

Sequencing and Synthesizing DNA, DNA Sequencing, RNA and Automated Sequencing

Synthetic DNA

Amplifying DNA: The Polymerase Chain Reaction, PCR at High Temperature

Applications and Sensitivity of PCR

8) Mutation, mutagenesis, and DNA repair, Types of mutation, Type of mutagenesis

Mechanisms of mutation and mutagenesis, DNA repair mechanisms

SOS repair

9) Reversion, What is the meaning of reversion, Reversion mechanisms, Ames test

10) Gene manipulation, Vectors, plasmids, bacteriophages, Types of plasmids, Mechanism of

DNA recombination, Types of bacteriophages and their use in gene manipulation

Instructional Methodology & Teaching Resources:

2 lectures and a 2 hour laboratory per week

Assessment:

Test 1 10%

Test 2 20%

Practical 30%

Finals 40%

BIOL 3410 : ANGIOSPERM BIOLOGY LECTURER : Dr Neelam Sherwani OFFICE : College of Science, Room 2034 (Telephone 24146883) COURSE CREDIT : 3 credits LECTURES : 2/week PRACTICAL(S) : 1/week SEMESTER : Spring and Fall PREREQUISITES : BIOL 2102 TEXT BOOK : "Biology of Plants" by Raven, Evert & Eichhorn (Freeman) and “Introductory Plant Biology” by Stern, Bidlack & Jansky, Mc Graw Hill Publisher COURSE DESCRIPTION : The course covers the morphology, evolution, classification and identification of the Angiosperms –“ The Flowering Plants”, which are by far the most important group of plants in the world. Important and dominant families of both dicots and monocots specially growing in the arid environment of Oman are dealt with.Special emphasis is given to the native flora of Oman

OBJECTIVES & LEARNING OUTCOMES : On the successful completion of the course the students will be expected: (1) to have a clear understanding of the fundamental significance of angiosperms from an ecological and economic perspective. (2) to have a clear knowledge of the major families and species of native plants growing around them. (3) to outline and understand important evolutionary features that have enabled angiosperms to become the predominant group of plants on the planet. ASSESSMENT : The course will be assessed (A--F). The assessment will be as follows: Assessment Date % Test I 1st Lecture of week 6 17.5% Test II 2nd Lecture of week 11 17.5% Lab Test Lab session of week 14 10% Field trips 10% Field Reports 5% Final As announced by A&R 40% ____________________________________________________ Total 100 Finally, your attendance is very crucial for you final assessments. My e-mail addresses if you require additional assistance is [email protected]

College of Science Department of Biology

__________________________________________________________________________

Course Code: BIOL 3441 Course Title:Microbiology

General Information


Instructional Format: lectures Contact Hours/Week: 4

Prerequisite: BIOL 2101 Co-requisite: NO

Assessment: A-F Grading (A–F, Pass/Fail): Textbook: Alcamo`s Fundamental of Microbiology 2004 Seventh Edition 9J.c.POMMERVILLE) References (optional):

1. Course Description

The course teaches basic modern microbiology. It covers nutrition, cultivation, isolation of microorganisms, control of microorganism, microbiology of water and wastewater, food microbiology, microbial ecology, soil microbiology, microbial deterioration of materials and basic morphology of viruses and their replication.

2. Course Objectives To exposure students to the world of microbiology which is the most applied of all biological sciences. It helps them to improve the quality of human life

3. Learning Outcomes[Use Bloom’s taxonomy]

Having successfully completed this course the students will be able to

1. Prepare media for the cultivation of microorganism and compare between

different categories of media.

2. Isolate microorganism in pure culture.

3. Identify bacteria through different staining procedures.

4. Examine and analyze water for portability and classify water as potable, safe,

polluted and contaminated.

5. Analyze and compare the antimicrobial properties of spices and commercial

antibiotics.

6. Prepare Produce inoculants and inoculate legume seeds in Rhizobium

biotechnology.

7. Identity and classify fungi on seeds, fruits and vegetables.

8. Quantify and enumerate microorganisms in a gram of soil or one ml of milk.

9. Evaluate the efficiency of sewage treatment plant.

10. Isolate and identify microorganisms in sewage water

11. Test the ability of soil microorganisms to produce enzymes

12. Compare between different types of viruses

4. Assessment

Assessment Criteria

Assessment: Tests :

1. Test 1 15%

2. Test 2 15%

3. Lab Test 15%

4. Lab quizzes 15%

5. Final Exam 40% Total 100%

1. Test 1

2. Test 2

3. Lab test

4. Final exam

5. Course Structure The course is designed to be delivered in one semester of 15 weeks with 4/5 contact hours per week (2/3 practical/tutorial and two theory). The course weight is 3/4 credit hours.

6. Topics

Part A Culture Media and Growth Measurements (Alcamo’s) (150 - 155)

Culture media contain the nutrients to grow bacteria (p.150)

Culture media can be devised to select and differentiate between bacteria

(p.150)

A Comparison of Bacterial Media, Table 4.4., p.151

Satisfying Koch’s Postulates, p.152

Population measurements are made using pure cultures, p.154

Types of media (lab manual, p.1)

Categories of Media( lab manual, p.2)

Sterilization (lab manual p.3), pouring the medium onto Petri dishes (lab manual

p.3). Streaking for isolation and identification (lab manual, p.3)

Colonial Morphology (lab manual, p.4 - 5)

Staining Techniques provide contrast (p.105 - 108)

Staining of Bacteria – Gram Staining (lab Manual, p.6)

Negative Staining of Bacteria, (lab 3, p.3)

The spore stain (lab manual, lab 3, p.3)

Part B Chapter 4

Bacterial Structure and Growth, p.121 – 160

Fig.4.1 – 4.22; Tables 4.1 – 4.4

Bacteria have a cylindrical shape, p.122

Cocci form a variety of arrangements, p.123

Spirals and other shapes also exist, p.123

The structure of bacteria, p.124

Bacterial flagella provide motility, p. 124

Pili are structures used for attachment, p.127

The Glycocalyx is a sticky layer coating many bacteria, p.128

The cell wall provides shape and protection, p.130

The cell membrane is a permeability barrier, p.133

The cytoplasm is the center of biochemical activity, p.134

Endospore are designed for dormancy, p.136

Bacterial Reproduction, p.141

A Bacterial Growth Curve illustrates the dynamics of growth, p.143

Temperature is one of the most important factors governing growth, p.145

Oxygen can support or hinder growth, p.146

Most bacteria prefer to grow at neutral pH, p.149

Population growth can be measured in several ways, p.155

Part C Chapter 26

Environmental Microbiology, p.949 – 975, fig 26.1 -26.16

Water pollution, p.950

Unpolluted and polluted water contain different microbial populations, p.951

Sewage water treatment plant at SQU. Lab manual, lab 5, p.16

Diseases can be transmitted by water, p.954

The treatment of water and sewage, p. 957

Water purification is a three-step process, p.957

Sewage treatment can be multi-step process, p.958

Biofilms are prevalent in the environment, p.961

The Bacteriological analysis of water tests for indicator organisms, p.962

The cycles of elements in the environment, p.964

The carbon cycle is influenced by micro, p.965

The sulfur cycle recycles sulfate molecules, p.968

The nitrogen cycle is dependent on microorganism, p.969

Part D Chapter 22 Physical Control of Microorganisms, p. 823 -848, Fig. 22.1 –

22.15

Physical control with heat, p.825

The direct flame represents a rapid sterilization method, p.827

The hot-air oven uses dry heat, p.828

Boiling water involves moist heat, p.829

The autoclave uses moist heat and pressure, p.829

Fractional sterilization uses free-flowing steam, p.833

Pasteurization does not sterilize, p.833

Physical control by other methods, p.836

Filtration traps microorganisms, p.836

Ultraviolet light can be used to control microbial growth, p.838

Other types of radiation also can sterilize materials, p.839

Ultrasonic vibrations disrupts cells, p.841

Preservation methods retard / spoilage by microorganisms, p.842

Part E Chapter 25 Microbiology of Food, p. 915 – 976, Fig. 25.1 – 25.16

Food Spoilage, p.916

Several conditions determine if spoilage can occur, p.917

The chemistry of spoilage produces specific products, p.919

Meats and fish can become contaminated in several ways, p.920

Poultry and eggs can spoil quickly, p.921

Breads and bakery products can support bacterial and fungal growth, p.921

Some grains are susceptible to spoilage, p.923

Milk and dairy products sometimes sour, p.923

Food preservation, p.925

Heat denatures proteins, p.926

Low temperatures slow microbial growth, p.929

Drying removes water, p.931

Osmotic pressure can help preserve food, p.931

Chemical preservatives are found in or are added to many foods, p.931

Radiation can sterilize food, p.933

Food borne disease can result from an infection or intoxication, p.934

HACCP systems attempt to identify potential contamination point, p.937

Part FChapter 12 Viruses and Virus-like Agents, p. 421 – 468, Fig. 12.1 – 12.24,Tables 12.1 – 12.6

The structure of viruses, p.427

Viruses occur in various shapes, p.428

Viruses lack cellular structures, p.428

Virus structure determines host range and specificity, p.430

The replication of viruses, p.432

The replication of bacteriophage is a five-step process, p.432

Animal virus replication has similarities to phage replication, p.435 – 440 (omit)

Acquired immune deficiency syndrome results from immune system dysfunction,

p.530

Some animal viruses can exist as provirus, p.439 (Chapter 12)

Other characteristics of viruses, p.440

Nomenclature and classification do not use conventional taxonomic groups,

p.440

Cultivation and detection of viruses are critical to virus identification, p.441

Virus-like agents, p.461

Viroids are infectious RNA particles, p.461

Prions are infectious proteins, p.461

Part G Chapter 15 The Fungi, p.555 -593

Characteristics of fungi, p.556

Fungi share a combination of characteristics, p.556

Fungal growth is influenced by several factors, p.558

Reproduction in fungi involves spore formation, p.561

The classification of fungi, p.563

The Zygomycetes have nonseptate hyphae, p.564

The Ascomycota are the sac fungi, p.565

The Basidiomycota are the club fungi, p.569

The Deuteromycota lack sexual reproduction phase, p.570

The yeasts are microscopic, unicellular fungi, p.574

Fungal diseases of humans, p.578 – 589

7. Laboratory component

Week 1 Preparation of selective ,differential & enriched media; sterilization with

Autoclave

Week 2 Staining of bacteria

Week 3 Negative staining of bacteria

Week 4 The enumeration of bacteria in raw and pasteurized milk

Week 5 A visit to the University Sewage plant

Week 6 Bacteriological examination of water and sewage water

Week 7 Antimicrobial properties of spices

Week 8 Mycology: Examination and identification of fungi

Week 9 Biotechnology: Inoculation and inoculants production. Isolation of

Rhizobium

Week 10 Biotechnology: Inoculation and inoculants production:Preparation of

carrier

Week 11 Microbiology of soil :a) Quantitative enumeration of microorganisms.

b) Ammonification c) Nitrate reduction and denitrification.

Week 12 Hydrolysis of polysaccharide , Proteins and lipids

Week 13 Fermentation of carbohydrates

Week 14 Biochemical characteristics of hydrogen sulfide production.

COURSE INFORMATION Biological Skills Biol4000

2015

Course Coordinator: Dr Michael Barry

CONTENTS

1. Introduction 2. Course overview 3. Learning resources 4. Assessment 5. Course calendar

1. Introduction This unit will provide students with the knowledge and skills to work as a professional biologist. The course will provide an overview of important generic topics that all biologists should be familiar with including the scientific method, the process of scientific research from conception to publication, the communication of science, ethics and occupational health and safety. Practical work will focus on the critical analysis of scientific controversies and on communication of science by oral, written and poster modes. Course: BIOL 4000 Generic Skills for Biologists Coordinator: Dr Michael Barry Department of Biology Room Email: [email protected] Telephone: 2414 2257

3

2. Course overview Summary This course is designed to strengthen your ability to critically analyse scientific data, to understand the scientific method and design testable hypotheses, and have a sound understanding of occupational health and safety and ethics as they relate to biological sciences. Your ability to communicate scientific ideas will also be developed. Finally, we will look at one or two “big picture” scientific controversies to understand how science works within the context of government regulations and public perception. Learning objectives On completion of this course the student should be able to:

• Describe the scientific method and differentiate between good quality science, poor quality science and pseudoscience.

• Understand the research process • Demonstrate awareness of occupational health and safety issues and ethics

as the relate to biological sciences • Communicates complex scientific ideas in written, oral and visual forms

3. Learning resources Text: You will receive a set of theory notes plus a tutorial booklet. There is also a textbook called “Study and communication skills for the biosciences” that you should get from the book store.

4

4. Assessment Practical: Assertion-evidence oral presentations 5% Mini-project:

• Data collection: 3% • Annotated literature review: 5% • Introduction: 5% • Methods & results: 5% • Discussion: 5% • Final complete version: 12%

Researcher interview presentations: 5% OH&S: 5% Poster: 10% Theory:

Final exam: 40%

ASSESSMENT POLICY

Plagiarism: Students found to have copied significant sections of text from textbooks, web, or other students will receive zero for that assignment

In class assessment: For in class activities that are assessed

students must attend ALL relevant classes to receive a mark. Students who miss any component of an assessed activity will receive zero unless a medical certificate is provided.

5

Generic Skills Timetable and Submission Dates 2015 Week Lecture Topic Tutorial Assessment Due 1 No class Overview 2 What is science:

Introduction to the philosophy of science. Short Video: Doing science

Using assertion-evidence system to make effective PowerPoint presentations

3 How science works. Examples of great scientists

Oral presentations Oral (5%)

4 Eid? Eid? 5 Video: Science wars Introduction to the

mini-project Plagiarism Note taking In text citations

6 Good science, Bad science & pseudoscience

Using Zotero to collect references

7 Ethics lecture 1 Video: There be dragons

Introductions, methods & results. Developing hypotheses for the mini-project

Submit collected data for mini-project (3%)

8 Ethics lecture 2 Video: The Tuskegee syphilis study

Ethics tutorial Introduction to the researcher interview

Submit annotated literature review for mini-project. 10 annotated references (5%)

9 Ethics lecture 3: Use of humans and animals in experiments Video: Animal rights

Analysing the data from mini-project

Introduction for mini-project (500 words) (5%)

10 Ethics lecture 4: Occupational health and safety

Occupational health & safety tutorial

OH&S report (in class) (5%)

11 Case study 1: GM foods Writing an abstract Key words Work on mini-project

Mini-project methods & results (5%)

12 Case study 2: Hormones in meat

Researcher interviews Presentations (5%)

13 Review of theory Introduction to poster design SETAC: Poster video

Discussion to mini-project (5%)

14 Work on posters Submit final report(12%)

15 Poster presentations Submit posters (10%)

16



Department: Biology

Course Code: BIOL 4009 Credit & Contact Hours: 3 credits = 4hrs (2 lect + 1 lab) Course Title: Waste management

Prerequisite(s): BIOL 3009 Co-requisite(s):None Textbook(s): Waste management practices – John Pichtel,Taylor &Francis Course Co-ordinator: Hameed Sulaiman

Description: The course introduces about wastes and overviews of waste management; Municipal

solid waste and its management; Historical aspects; Generation of solid wastes; sources and types

of solid wastes; composition of municipal solid wastes; generation rates; waste Management

hierarchy; waste minimization; prevention and reduction strategies; waste management methods

(recycling, reuse, composting, landfill, incineration), energy recovery from wastes. It also covers

introduction to hazardous wastes, life cycle assessment and integrated waste management.

Aims & Objectives: This is an application oriented course which covers the fundamentals of waste

generation, composition and characteristics, its environmental and health impacts and also deals

with the various waste management options.

Learning Outcomes

1. Knowledge:

To be able to classify solid waste and explain functional elements of solid waste

management.

To explain waste generation, composition and factors affecting them.

To understand and explain waste management hierarchy

To discuss the significance of recycling

2. Skills:

To assess the current situation of solid waste management in Oman

To carry out waste stream analysis

To apply waste management hierarchy and be able to decide the suitable waste

management options to the specific waste quantity and waste type.

To be able to do composting at pilot scale level.

Syllabus:

1.Introution to Solid Waste Management(SWM)

Classification of solid waste

SWM scenario in Oman

2.Waste generation aspects

Waste generation and composition

Waste characteristics

Environmental and health impacts

Case study in Oman and other developing countries

3.Waste processing techniques

4.Sourse reduction, Product recovery and Recycling

Recycling program elements

Commonly recycled materials

Case study on recycling

5.Recovery of biological conversion products

Composting

Biogasification

6.Incineration and energy recovery

7.Hazardous waste

8.Integrated Waste Management(IWM)

Basics of IWM

Life cycle assessment


Lectures and group discussion, Demonstrations through YOU TUBE, Case study analysis. Field

visit. Evaluation

The course will be graded using an A (exceptional performance) to F (unacceptable performance)

system. Final grade will be based on the following evaluations (components depend on the

course).

Evaluation Weight

Short presentations 10%

Group assignments 5%

Presentation(Poster

+ oral)

15%

Mid- Exam 30%

Final Exam 40%

COURSE INFORMATION VERTEBRATE ZOOLOGY: Biology 4021


500mm

A Coelacanth, Latimeria chalumnae, the lobe-finned fish thought to have been extinct for hundreds of millions of

years before it was discovered in South Africa in the 1940’s

CONTENTS

1. Introduction 2. Course overview 3. Learning resources 4. Assessment 5. Course calendar

1. Introduction Welcome to vertebrate zoology! In this course we will study an amazing and diverse group of organisms ranging from tiny fish to elephants, but all with one thing in common: a backbone. We will ask the question, how are these groups related and what were their common ancestors like. We will look closely at the adaptations and specialisations that make each group unique. Course: BIOL 4021: Vertebrate Zoology Coordinator: Dr Michael Barry Department of Biology Room Email: [email protected] Telephone: 2414 6858

3

2. Course overview Summary This course will give you an overview of the major groups within the subphylum Vertebrata including those groups which are closely related to the vertebrates. You will learn how vertebrates are classified and the characters that are used to make these classifications. We will examine theories of how the vertebrates evolved and their classification within Classes. Finally, we will look at the remarkable adaptation of vertebrates that have made the adaptable and successful group on the planet. Learning objectives On completion of this course the student should be able to:

• relate metazoan evolutionary milestones to the geological timescale; • describe the theories relating to the origin of the vertebrates; • give a basic account of vertebrate systematics; • show an understanding of evolutionary relationships within the vertebrates; • describe patterns of anatomy and physiology within the vertebrates; • display awareness of vertebrate conservation;

3. Learning resources Texts: Collect from bookstore: ZOOLOGY by Miller & Harvey 7th Edition McGraw Hill BIRDS OF OMAN: H & J Ericson Vertebrate Zoology Lecture notes: These notes summarise the main points that will be covered in the lectures but in no way replace attendance at lectures. Additional materials will be provided in the lectures that are examinable. Student need to take their own notes based on information that is presented in class and written on the board.

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4. Assessment Theory: Term tests 1 & 2: 16% each Final theory exam: 40% Practical: Mini-quizzes: 5% Lab manual assessment: 5% Bird community analysis report +notebook: 6% Final laboratory exam: 12%

COURSE CALENDAR Week 1 Introduction 2 Geological time scale Animal classification

Patterns of biological organisation

3 The Chordates The Chordates 4 EID EID 5 The fishes The fishes 6 The fishes The fishes 7 Evolutionary theory Amphibians 8 Amphibians Amphibians 9 Reptiles Reptiles 10 Reptiles Reptiles 11 Birds Birds 12 Birds Birds 13 Mammals Mammals 14 Mammals Mammals 15 Mammals Mammals 16 Revision Revision



BIOL 4023: Entomology (3 credits)

Course Outline

Course Co-ordinator: Dr Derek Roberts



BIOL 4023: Entomology Course description

Course Summary This is a 3 credit introductory course on the insects. It consists of 2 lectures and 1 practical

per week.

The lectures will concentrate on insect anatomy and physiology, although ecology and

behaviour will also be covered.

The practicals will cover:-

∗ Experiments on insect ecology and on their physiology.

∗ Dissections showing insect anatomy.

∗ Living and preserved specimens showing morphological adaptations to their environment.

In addition, each student will produce an insect collection, demonstrating Omani insect

diversity (this is submitted at the end of the semester).

Learning Outcomes By the end of the course, students should be able to:

1. Identify the main orders of insects.

2. Prepare a taxonomic collection showing the diversity of Omani insects.

3. Collect insects in different habitats using different collecting methods

4. Dissect different types of insects to demonstrate their comparative internal anatomy.

5. Explain how an insect is adapted for a particular type of feeding and locomotion.

6. Discuss how insects are able to find, eat and digest their food.

7. Explain how insects solve the problems of flight and of running.

8. Discuss how reproduction takes place in different insects.

9. Outline the 3 main types of life cycles in insects.

10. Explain how the tracheal system works and the different possible adaptations required for

aquatic respiration.

11. Discuss how excretion and the blood systems work in insects.

12. Explain how insects are able to see.

13. Compare the different types of insect control, demonstrating their relative advantages.

Course assessment The course will be graded A to F. This assessment will be based on the following:-

∗ Assessment of practicals (drawings, reports and dissections) 10 %

∗ Practical exam (2 hours) 10 %

∗ Insect collection 10 %

∗ Theory tests (2) 30 %

∗ Final theory exam (3 hour) 40 %

Course coordinator Dr. Derek Roberts (room 2012, in Biology Dept.).

Course prerequisite BIOL 2102: Biology II (diversity)

Course textbook Gjullan & Cranston - Insects: an outline of Entomology. Chapman & Hall.



BIOL 4023: Entomology Course outline

This course will give an introduction to the insects, concentrating on their anatomy and

physiology, but also covering their diversity, ecology and behaviour.

Lectures

1. Nutrition. Finding food by plant-feeding and blood-sucking insects; Feeding using chewing and

sucking mouthparts; Predators - raptorial and active hunting insects; Parasitic insects -

mosquitoes, fleas, lice and myiasis; herbivorous insects - leaf chewers, plant borers and

sap-suckers; Filter-feeders: blackfly larvae, caddisfly larvae, mosquito larvae; Digestive

system - the functions of the foregut, midgut, hindgut and fat body. 7 Lectures

2. Locomotion. Walking and modifications of the legs for jumping, grasping, digging and swimming.

Crawling. Mechanism of flight and the problems of controlling flight direction, turbulence,

stability and speed. Migratory flight. 4 Lectures

3. Reproduction. Reproductive systems and egg maturation. Mating and sperm transfer. Oviposition +

structure of the egg. Development - growth, life cycles and adult emergence. Physiological

age: its application in agricultural + medical entomology, and in climatic modelling. Social

insects - nests, polymorphism, group defense and communications. 6 Lectures

4. Respiration. Respiration: the tracheal system, regulation of oxygen availability and ventilation.

Aquatic respiration: siphons, plastrons, air stores and tracheal gills. 3 Lectures

5. Other systems. The cuticle: its structure and moulting. The blood system: the circulation and the functions

of haemolymph. Excretion: malphigian tubules + cryptonephric excretion. 2 Lectures

6. Nervous system. Vision using apposition and superposition compound eyes; colour vision.

Mechanoreceptors: trichoid sensillae, Johnston’s organ and tympanal organs.

Chemoreceptors. Structure of the nervous system. Pheromones. 2 Lectures

7. Insect pest control. Beneficial and harmful insects; medical entomology. Economic injury levels. Pest control

by insecticides, cultural methods, biological control, mass trapping, and sterile male release.

Integrated pest management of potatoes and maize. 4 Lectures

ooooooooooooOOOOOOOOOOOOOOOOOOoooooooooooo

Insect collection

Each student will produce an insect collection as a project. This will be discussed during the

first practical. The collection will be assessed at the end of the course on the basis of:-

∗ The diversity of the insects collected.

∗ Their correct identification.

∗ The insect display: mounting and labeling the insects.

oooooooooooooooOOOOOOOOOOOOOOOooooooooooooooo

Practicals

1. The insect collection: techniques for collecting and preserving insects;

use of keys for insect taxonomy.

2. Nutrition: adaptations for different types of feeding as:

- predators (wasp, dragonfly, mantid, giant water bug, antlion larva);

- filter-feeding (blackfly larva) and

- nectar-feeding (honeybee).

3. Dissection of a grasshopper to show its digestive and nervous systems;

Chewing mouthparts.

4. Mouthparts and feeding: Rate of feeding in the housefly;

mouthparts of housefly, honeybee, assassin bug and the horsefly.

5. Parasitic insects: ectoparasites (mosquito, bedbug, flea and human louse) and

endoparasites (horse bot).

6. Flight activity (part 1): A field study to show:

a) the effects of circadian rhythms on flight activity and

b) the effect of trap bias on the apparent abundance of insects.

Part 1: using hand nets to collect insects.

7. Flight activity (part 2): using suction traps and light traps to collect insects.

8. Video: “Little creatures who run the world (ants)”

9. Aquatic insects: Comparison of distribution and abundance of aquatic insects:

in open water, among vegetation and on the bottom of a freshwater pond.

10. Respiration:-

- The tracheal system of a flying insect.

- Ventilation in a grasshopper.

- Respiratory adaptations in aquatic insects, using a siphon (mosquito larva and

water scorpion), spiracular gills (blackfly pupa) and tracheal gills (damselfly larva,

mayfly larva and dragonfly larva).

11. Excretion; and the brain and sense organs of a grasshopper.

ooooooooooooOOOOOOOOOOOOOOOOOOOoooooooooooo

BIOL 4030 BACTERIOLOGY

LECTURER : Prof. Saif Al-Bahry

OFFICE : College of Science, Room 2029 (Telephone 24146868)

COURSE CREDIT : 3 credits

LECTURES : 2/week

PRACTICAL(S) : 1/week

SEMESTER :Spring

PREREQUISITES : BIOL 3441

TEXT BOOK : "Microbiology, Concept and Application" by Michael Pelczar, 1993,International Edition, Mc Graw Hill Publisher.

COURSE DESCRIPTION : The course covers basic concepts of bacteriology through bacterial cellstructure, survival, colonization and genetics. This course willemphasize on the bacteria, their role in environment and men.Spread and control of bacteria will be dealt in some details.

OBJECTIVES & LEARNING OUTCOMES: On the successful completion of the course the students will be expected:

(1) to know the details of bacterial structure, genetics, survival andcolonization, and some types of bacterial infections and diseases,(2) to understand host-parasite interactions and their implications,(3) environmental aspect and biotechnology, and (4) to able tohandle and identify bacteria with special reference to pathogenicbacteria.

ASSESSMENT :The course will be assessed (A--F). The assessment will be as follows:Assessment Date %Test I 1st Lecture of week 5 15Test II 1st Lecture of week 10 20Lab Test (Unknown) Lab session of week 13 5% Lab Safety 5%Lab Quizzes 10Lab Report 5Final As announced by A&R 40

___________________________________________________________________________Total 100

If you are unable to present for any test, it is your responsibility to get in touch with me and present anacceptable excuse one day before the exam. If I am not available on my office telephone, you can alwaysleave a massage with Biology Department secretaries at extension 1437. Also, to avoid embarrassment,please do not ask to change the exam days listed above. Finally, your attendance is very crucial for you finalassessment.My e-mail addresses if you require additional assistance. [email protected],

TABLE OF CONTENTS Page

DETAILED SYLLABUS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 - 1SECTION ONE: BACTERIAL CELL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 - 1SECTION TWO: BACTERIA: THEIR INTERACTION WITH MAN AND ENVIRONMENT1 - 1SECTION THREE: SPREAD AND CONTROL OF BACTERIA . . . . . . . . . . . . . . . . . . . . . 1 - 2

LECTURES OUTLINE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 - 1PREFACE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 - 2SECTION ONE: BACTERIAL CELL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 - 3

PROCARYOTIC CELL STRUCTURE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 - 3BACTERIAL GENETICS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 - 3CULTIVATION AND GROWTH OF MICROORGANISMS . . . . . . . . . . . . . . . . . . 2 - 3CLASSIFICATION OF BACTERIA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 - 3

SECTION TWO: BACTERIA: THEIR INTERACTION WITH MAN AND ENVIRONMENT2 - 41.NORMAL FLORA OF THE HUMAN BODY . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 - 4THE MICROORGANISM AS A PATHOGEN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 - 4NOSOCOMIAL INFECTIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 - 4FOODBORNE AND WATERBORNE DISEASES . . . . . . . . . . . . . . . . . . . . . . . . . . 2 - 5

SECTION THREE: SPREAD AND CONTROL OF BACTERIA . . . . . . . . . . . . . . . . . . . . . 2 - 6CHEMICAL AGENTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 - 6ANTIBIOTICS AND OTHER CHEMOTHERAPEUTIC AGENTS . . . . . . . . . . . . . 2 - 6

LABORATORY MANUAL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - IPREFACE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - IISAFETY CONSIDERATIONS AND GENERAL RULES . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - IIILAB SCHEDULE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - VI

DEMONSTRATION OF BACTERIAL CAPSULE (GLYCOCALYX) . . . . . . . . . . 3 - 1STUDY OF RESERVE MATERIALS IN BACTERIAL CELLS . . . . . . . . . . . . . . . 3 - 2

A. DEMONSTRATION OF METACHROMATIC GRANULES . . . . . . . . . 3 - 2THE DETECTION OF MOTILITY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 3DEMONSTRATION OF BACTERIAL CELL WALL . . . . . . . . . . . . . . . . . . . . . . . 3 - 4PRODUCTION OF INDOLE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 5THE MR-VP AND SODIUM CITRATE UTILIZATION TEST . . . . . . . . . . . . . . . . 3 - 6DETECTION OF CATALASE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 7THE EFFECT OF ULTRAVIOLET RADIATION ON MICROORGANISMS

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 8DEMONSTRATION OF ANTIBIOSIS OR ANTAGONISM AMONG MICROBES

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 9ANTIGEN-ANTIBODY REACTIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 10

Agglutination Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 10ISOLATION AND IDENTIFICATION OF BACTERIA . . . . . . . . . . . . . . . . . . . . . 3 - 12

GENERAL INSTRUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 12For Identification of Unknown Bacteria . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 12

FAMILY: PSEUDOMONADACEAE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 14Genus - Pseudomonas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 14

FAMILY: CYTOPHAGACEAE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 16Genus - Cytophaga . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 16

FAMILY: SPIRILLACEAE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 17

Genus - Spirillum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 17FAMILY: VIBRIONACEAE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 17

Genus - Vibrio . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 17FAMILY: ENTEROBACTERIACEAE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 19

Genera - Escherichia and Enterobacter . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 19Genus - Proteus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 21

FAMILY: MICROCOCCACEAE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 22Genus - Micrococcus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 22Genus - Staphylococcus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 23

FAMILY: NEISSERIACEAE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 25FAMILY: STREPTOCOCCACEAE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 27

Genus - Streptococcus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 27CORYNEFORM GROUP OF BACTERIA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 29

Genus - Corynebacterium . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 29FAMILY: BACILLACEAE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 31

Genus - Bacillus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 31Genus - Clostridium . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 33

MAINTENANCE AND PRESERVATION OF BACTERIAL STOCK CULTURES. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 35

Lyophilization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 35Freezing bacterial cells in -70 oC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 36

CERTAIN CHARACTERISTICS OF SELECTED BACTERIA . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 37

RECORD SHEET . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 - 40

APPENDIX . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 - AAPPENDIX - A: LIST OF CULTURES BACTERIA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 - BAPPENDIX B: STAINING SOLUTIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 - CAPPENDIX C: REAGENTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 - EAPPENDIX D: MEDIA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 - F

BIOL 4030, BACTERIOLOGY SYLLABUS

1 - 1

DETAILED SYLLABUS

SECTION ONE: BACTERIAL CELL

Lecture Pages Topics1 107-128 Prokaryotic cell structure

2 Prokaryotic cell structure (cont.)



5 349-372 Bacterial genetics

6 Bacterial genetics (cont.)

7 Bacterial genetics (cont.)

8 175-182 Cultivation and growth of microorganisms

9 Cultivation and growth of microorganisms (cont.)

10 Cultivation and growth of microorganisms (cont.)

_____ Test I

11 242-264 Classification of Bacteria

12 Classification of Bacteria (cont)

13 Classification of Bacteria (cont)

SECTION TWO: BACTERIA: THEIR INTERACTION WITH MAN AND ENVIRONMENT

14 454-470 Normal Flora of the Human Body

15 Normal Flora (cont.)

16 476-491 The Bacteria as Pathogens

17 590-598 Nosocomial infections

18 Nosocomial infections (cont)

_____ Test II

BIOL 4030, BACTERIOLOGY SYLLABUS

1 - 2

19 646-680 Airborne diseases

20 680-693 Foodborne and Waterborne Diseases

21 Foodborne and Waterborne Diseases (cont.)

22 743-750 Wound and skin nfections

SECTION THREE: SPREAD AND CONTROL OF BACTERIA

23 221-234 Chemical Agents

23 Chemical Agents (cont)

24 556-581 Antibiotics and Other Chemotherapeutic Agents

25 Antibiotics and Other Chemotherapeutic Agents (cont.)

26 Antibiotics and Other Chemotherapeutic Agents (cont.)

_____ Final exam

Sultan Qaboos University Department of Biology

COURSE OUTLINE for BIOL 4034 Biochemistry

Course code : BIOL 4034

Course title : Biochemistry Pre-requisite : BIOL 2101/ CHEM 3322/27 Credits : 3 CU Format : 2 (1 hr) Lectures + 1 (3 hrs) Laboratory / week Lecturer : Dr. Elsadig A. Eltayeb (Office # 2005),

e-mail: [email protected]

Textbook: Biochemistry, 5th edition, by Jeremy Berg, John Tymoczko and Lubert Stryer

Course Description

This course covers carbohydrate metabolism; glycolysis, Krebs' cycle, oxidative phosphorylation, pentose phosphate pathway and gluconeogenesis, glycogen metabolism. Energetics and significance of metabolism. β-Oxidation of fatty acids and glycerol. Fatty acid biosynthesis. Nucleic acid structure and function. Amino acids and proteins. Enzymes, structure, reaction rate and kinetics of enzymatic catalysis.

Expected Outcomes Students who successfully complete this course will be able to; • Know the major metabolic pathways for carbohydrate catabolism under aerobic or

anaerobic conditions, Gluconeogenesis, fructose and galactose and glycogen metabolism.

• Know the metabolic pathways for lipid oxidation and biosynthesis. • Analyze the nitrogen path from atmospheric gas to its incorporation into biological

molecules and amino acid and protein synthesis. • Adopt a problem-solving approach to experimental data especially with enzyme

kinetics. • Application of adequate knowledge of basic biochemical experimental techniques

used in biochemical research and other studies, such as chromatography, spectrophotometry and electrophoresis.

• Formulate correctly methods for the preparation of their own reagent solutions for their experiments.

• Perform, analyze, and interpret data from practical experiments. • Effectively communicate their biochemistry learning by both written and spoken

words. • Relate biochemistry to cellular and organismal processes. • Contrast important biochemical features that distinguish prokaryotes from

eukaryotes and plants from animals.

1


• Interpret and communicate biochemical information from a variety of sources. • Plan, execute and present an independent piece of work (e.g. a project). • Appreciate the different approaches taken in the various areas of biochemistry. • Evaluate the primary literature in particular areas of biochemistry.

Evaluation System The course will be graded using an A (exceptional performance) to F (unacceptable performance) system. Final grade will be based on the following evaluations (below is an example; components depend on the course). If possible include exam dates.

Evaluation Weight Exam Dates Lab Quizzes 15% In-Term Exam I 15% In-Term Exam II 15% Lab Reports 15% Final Exam 40%

Missing quizzes and tests: A student who misses an examination or quiz without a valid reason will be graded as having scored zero. If the student has an acceptable excuse, the final mark will be the percentage scored out of the components completed; or at the discretion of the instructor a makeup exam may be given.

Attendance: A student will be sent a Warning Notice on missing 10% (7 contact hours) of the course and a Failure Notice on missing 20% (15 contact hours) or more according to University Regulations. Note that there are 5 contact hours a week.

Course Syllabus

The syllabus format is flexible but should include: Names of the main course units; topics within the unit with reference to pages and figures in the textbook and/or other assigned material. Instructors can include weekly schedules.

A. Carbohydrates; Carbohydrate metabolism; 1. Glycolysis, phases of glycolysis, the fate of pyruvate under aerobic and anaerobic

conditions. 2. Regulation of the glycolytic pathway in detail. 3. Krebs’ cycle. The reactions of the cycle, energetics and metabolic significance of

2

carbohydrates are covered in some detail including the oxidative phosphorylation and chemiosmosis.

4. Metabolism of fructose and galactose and the deficiency of the enzyme galactose 1-phosphate uridyl transferase.

5. Gluconeogenesis. Reactions and reaction products all the way to glucose synthesis. 6. Regulation of gluconeogenesis. 7. Glycogenesis, synthesis and elongation of glycogen chains. 8. Glycogenolysis. Skeletal glycogen degradation and liver glycogen degradation. 9. Regulation of glycogen metabolism (synthesis and degradation). 10. The pentose phosphate pathway and the fate of glucose 6-phosphate (organs active in the

P.P.P.) 11. Regulation of the pentose phosphate pathway.

B. Lipids;

1. Release of fatty acids from triacyl glycerol (Hormone action). 2. Activation of fatty acids and their transport into the mitochondria. 3. Lipid metabolism via the β-oxidation of odd- and even-numbered fatty acids. 4. Oxidation of glycerol. 5. Oxidation of unsaturated fatty acids. 6. Energetics and significance of lipid metabolism. 7. Biosynthesis of fatty acid. 8. Biosynthesis of phospholipids. 9. The relationship of fatty acid synthesis to carbohydrate metabolism.

C. Proteins and Enzymes

1. The biochemistry of amino acids. 2. Nitrogen fixation into biological molecules. 3. Essential and Non-essential amino acids. 4. Pathways leading to the biosynthesis of some of the non-essential amino acids. 5. Biosynthesis of an essential amino acid. 6. Levels of protein structure. 7. The α-Helix and the β-pleated sheet. 8. The machinery of protein biosynthesis. 9. The process of protein biosynthesis. 10. Prokaryotic and eukaryotic protein biosynthesis. 11. Energetics of the process of protein biosynthesis. 12. Posttranslational changes of proteins

D. Enzymes 1. Enzyme classification, nomenclature and properties. 2. Feedback inhibition; types of feedback inhibition for branched pathways. 3. Proteolytic activation of proteins and enzymes

3

4. The diversity of enzyme function, reaction rates and reaction order. 5. Kinetics of enzymatic catalysis. 6. The Michaelis-Menten equation. 7. Enzyme inhibitors and the kinetics of inhibited and uninhibited enzymes catalysed

reactions. 8. Applications of enzymatic analysis in medicine and industry. 9. Mechanisms of enzyme action of selected enzymes (Carboxypeptidase, Ribonuclease and

Lysozyme).

4

SULTAN QABOOS UNIVERSITY COLLEGE OF SCIENCE

DEPARTMENT OF BIOLOGY

Course code : Biol 4041 Course title : Histology Pre-requisite : Biol 2101/2102/2103 Credits : 3 CU Format : 2 (1 hr) Lectures + 1 (2-3 hrs) Laboratory / week Lecturer : Dr. Taher A. Ba-Omar (Office #1072),

e-mail: [email protected] Textbook Basic Histology, 9th edition, 1998, Junqueira, Carnereio & Kelley Course Outlines The course is designed to introduce students to the general topics of animal histology. The course is divided into 3 major parts:

1. Introduction: an introduction to histology

2. General Histology: This part deals with the general tissue which are present in most organs such as, epithelial tissue, connective tissue, muscluar tissue and nervous tissue.

3. Special Histology: This part deals with specific organs and their specific tissues such as gastrointestinal system, urinary system, respiratory system etc

Objectives of the Course At the end of this course students are expected to know the major tissues of the animal body and the types of tissue present in different organs. They are also expected to identify different organs of the body by means of their specific tissues and learn how to prepare slides of different animal tissue and organs.

1


Course Assessment This course will be assessed as follow:

Laboratory work and Seminars (5+5) 10% Practical Tests (2 ) 20% Theory Tests (2) 30% Final Examination 40%

Schedule of Theoretical Tests : ( 15% Each)

Test No.1 Test No.2

Schedule of Practical Tests : (10% Each)

Practical Test No.1 Practical Test No.2

The following topics will be covered during the lectures sessions:

Introduction and Tissue Classification Epithelial Tissue Connective Tissue

Connective Tissue Proper: loose and Dense Connective Tissue Special Connective Tissue:

Adipose Tissue Cartilage

Test I Bone Blood

Nervous Tissue Muscular Tissue

Test II Digestive System Respiratory System Urinary System

You are responsible for all information presented during lecture and lab sessions. Lecture

and lab attendance are both required.

2

Practical Work 1. Learn how to prepare histological slides: Fixation, tissue processing, embedding

sectioning and staining. (Practicals # 1) 2. Study of prepared slides of epithelial tissue (Practical # 2) 3. Study of prepared slides of connective tissue (general connective tissue, cartilage and bone)

(Paractical # 3)

4. Learn how to prepare blood smearing and study of prepared blood cells slides (Practical # 4)

5. Practical Test I (Practical # 5) 6. Study of prepared slides of nervous and muscular tissue (Practical # 6) 7. Study of prepared slides of digestive system (Practical # 7) 8. Study of prepared slides of respiratory system (Practical # 8) 9. Study of prepared of slides of urinary system (Practical # 9) 10. Practical Test II (Practical # 10) 11. Seminars (Practical #11-14) Seminars will be held at the end of the semester (Date will be announced during the semester)

Attendance of Seminars is compulsory

3



BIOL 4042: Parasitology (3 credits)

Course Outline

Dr Derek Roberts

Course Outline Course Description This is an intermediate level 3 credit course that investigates parasitology from a

biological, rather than medical, point of view, but concentrates on human parasites. It considers

the problems that a parasites faces in being a parasite and how parasites have overcome them.

The lectures start with an introduction on the importance to humans of parasitology, and

then briefly considers the main parasites in the Protozoa, Platyhelminthes and Nematoda. It

considers the main vectors that transmit parasites from 1 person to another and considers how

vectors and other factors control the abundance of parasites, both in humans and free-living

stages. It looks at the physiological and immunological adaptations required to be a successful

parasite. Finally, the lectures consider chemotherapy and vector control of parasites.

The practicals cover the characteristics and identification of the main human parasites.

There will also be videos and practicals on live animal parasites.

Learning Outcomes: (see later page)

Course Format A 3-credit course consisting of 2 lectures and one 2-hour laboratory/week → 4 contact hours.

Course Prerequisite: BIOL 2102: Biology II (4 credits)

Course Facilities: Textbook: Bush AO et al: “Parasitism: the diversity and ecology of animal parasites”.

Cambridge University Press, 2001.

SQU On-line: The course will be available in Moodle. This will give:

∼ Course outline

∼ Lecture outcomes

∼ Lecture notes

∼ Relevant PowerPoints.

∼ Past exam and test papers

∼ Other facilities such as video clips.

Course assessment: The course will be graded A - F based on:

Lecture test x 2 (1 hour each) = 30 %

Laboratory practicals, quizzes & assignment. = 15 %

Final practical Exam = 15 %

Final theory Exam = 40 %

Course Co-ordinator: Dr Derek Roberts (Room 1070, Biology Dept)

([email protected])

Lectures (28 lectures in 14 weeks) 1. Introduction.

Scope of the course; Effect of parasites on human populations and on an individual;

Man as a host; Reproductive strategies. 2 lectures

2. Protozoan (Protista) parasites. Flagellates: biology, Giardia, Trypanosoma cruzi and T. brucei, Leishmania.

Amoebas: biology,Entamoeba,

Sporozoans: biology, Plasmodium, Toxoplasma. 4 lectures

3. Platyhelminth parasites (Flukes & Tapeworms). Flukes : biology, Schistosoma, Clonorchis.

Tapeworms: biology, Diphyllobothrium, Taenia, other major tapeworms. 4 lectures

4. Nematode parasites (Roundworms). Biology, gut nematodes, filarial nematodes, other nematodes. 3 lectures

5. Vectors of parasites. Effect of the vector on the parasite’s epidemiology. Vector efficiency. Vector types:

mosquitoes, sandflies, blackflies, horseflies, tsetse flies, Triatomid bugs. 3 lectures

6. Epidemiology. Prevalence and parasite load; factors regulating parasite abundance in the host; effect of

climatic factors on infective larvae. 4 lectures

7. Defenses against host immune systems. Human defenses against parasites; parasite defense against humans; insect defenses

against parasites and the parasite response. 2 lectures

8. Physiological adaptations in parasites. Invasion of the host: accidental ingestion, insect transmission and active penetration;

entering your cells. Reproductive physiology. Parasite nutrition and metabolism.

3 lectures

9. Control of parasites. Chemotherapy: characteristics of a drug and its mode of action, examples. Vector

control: types of vector control, problem in using vector control; examples. 3 lectures

------------------------------------------------------------------------------------------------------------------

There will be 2 Tests on the lectures:

Test 1(Week 7*) will cover the first 3 topics: Introduction, Protozoans, Platyhelminthes.

Test 2 (Week 11*) will cover the next 3 topics: Nematodes, Vectors, Epidemiology.

*Week may vary depending on public holidays.

The Final Exam will cover all sections equally.

Examples of the tests and Final will be available on Moodle.

Practicals (2 hours each) Practicals will cover:

� Slides showing the different parasites and their immature stages.

� Specimens showing the major insect vectors.

� Live invertebrate parasites, which you will dissect out.

� DVDs covering individual diseases.

Each practical will normally start with a short DVD (25 minutes) from the BBC “Kill or

cure” series on diseases, followed by slides/ specimens/ live material.

Practical 1: Introduction. DVD on “Sleeping sickness” from BBC Survival series.

Practical 2: Protozoa. Specimens of Giardia, Leishmania, Plasmodium, Trichomonas,

Toxoplasma and Trypanosoma. DVD on “Malaria” from BBC Kill or cure series.

Practical 3: Trematoda (A). Specimens of Clonorchis and Fasciola life cycles.

DVD on “Chagas disease” from BBC Kill or cure series.

Practical 4: Trematoda (B). Specimens on Echinostoma, Paragonimus, Schistosoma life

cycles. DVD on “Kala-azar” from BBC Kill or cure series.

Practical 5: Cestoda (A). Specimens on Moniezia and Taenia life cycles.

DVD on “Trematodes” from BBC Kill or cure series.

Practical 6: Cestoda (B). Specimens on Dypilidium, Diphyllobothrium, Echinococcus and

Hymenolepis. DVD on “Bilharzia” from BBC Kill or cure series.

Practical 7: Nematoda. Specimens on Ancylostoma, Ascaris, Enterobius, Loa,

Trichinella and Trichuris.

DVD on “Filariasis” from BBC Kill or cure series.

Practical 8: Insect vectors. Specimens of mosquitoes (Anopheles, Aedes, Culex), blackflies

(Simulium), sandflies (Phlebotomus), tsetse flies (Glossina), kissing bug (Triatoma).

DVD on “Intestinal worms” from BBC Kill or cure series.

Practical 9: Live parasites (A). Live earthworms and insects such as termites will be

dissected to observe Protozoans. DVD on “Onchocerciasis” from BBC Kill or cure.

Practical 10: Live parasites (B). Dissection of live marine gastropods to observe flukes.

DVD on “Guinea worm” from BBC Kill or cure series.

Practical Exam will cover all the practicals as a series of stations.

Course Outcomes At the end of the course, the student will be able to:

1. Explain why parasites are important to humans.

2. Identify the main parasites affecting humans and their immature stages.

3. Describe the biology & life cycles of parasitic Protozoa, flukes, tapeworms and nematodes.

4. Identify the main insect vectors and explain how they transmit parasites.

5. Explain the factors controlling the abundance both inside and outside the host.

6. Describe innate and adaptive immunity in humans and explain how a parasite overcomes

these defenses.

7. Describe the physiological adaptations needed by a parasite to be successful.

8. Explain how parasites can be controlled by chemotherapy and vector control.

Outcomes for the Lecture Topics Introduction 1. Explain how parasites may affect an individual and how they affect human populations.

2. List the strategies used by a parasite to increase transmission to a new human.

Protozoan parasites 1. Describe the biology of the parasitic flagellates, amoebas and sporozoans.

2. Describe the life cycles and medical importance of the main Protozoan.

Platyhelminth parasites 1. Describe the biology of the parasitic flukes and tapeworms.

2. Describe the life cycles and medical importance of the main flukes and tapeworms.

Nematode parasites 1. Describe the biology of the parasitic gut, filarial and other nematodes.

2. Describe the life cycles and medical importance of the main nematodes.

Vector biology 1. List the characteristics of an efficient vector and explain how the vector affects the

epidemiology of the disease.

2. Describe the biology of the main insect vectors.

Epidemiology 1. Define prevalence and parasite load and explain the factors that affect them.

2. Explain the factors regulating parasite abundance in humans.

3. Explain how climatic factors affect the abundance of infective larvae.

Immune defenses 1. Describe the main innate and adaptive human defenses against parasites.

2. Explain the methods used by parasites to survive your immune defenses.

3. Describe the defenses of an insect vector against the parasite.

Physiological adaptations of a parasite 1. Describe the 3 mechanisms by which a parasite can enter your body.

2. Explain the problems that an intracellular parasite has to solve to enter the correct host cell.

3. Describe the adaptations that a parasite needs in its reproduction, nutrition and metabolism.

Control of parasites 1. List the characteristics of an ideal drug for chemotherapy.

2. Explain the different mechanisms by which drugs can work.

3. Explain the different types of vector control and the problems faced by each.

4. Describe examples of vector control programs used against the major parasites.


College of Science


Course outline for BIOL4046 Fundamental Biotechnology

Description :

This course describes the major principles and the applications of gene manipulation technology

in human, animal, plants and microbes. The topics include various concepts in biotechnology

with emphasis on molecular biotechnology techniques and their role in modern biotechnology.

Class discussions will be held to familiarize the students with the legal and ethical issues involved

with the widespread application of modern biotechnology.

Course credit: 3

Format: 2 lecture/week, 1 laboratory for three hours per week


Prerequisite BIOL3202 Molecular Biology

Textbook: "Molecular biotechnology-principles and applications of recombinant DNA”

By: Bernard R. Glick and Jack J. Pasternak

Learning outcome: At the end of the course the students will be anticipated to understand the

scientific basis behind molecular manipulation and to know how to apply this knowledge in

practice. This includes practical skills in DNA cloning, protein purification and gene expression

analysis.


First exam 15%

Second exam 15%

Final exam 40%

2 Lab test 25%

Lab Quizzes 5%

COURSE SYLLABUS

1- Definitions

A - Use of Biotechnology in our life (medicine, Agriculture and Food industry).

B -Biological systems used in biotechnology.

C -Substrates for biotechnology.

2- Recombinant DNA Technology (Chapter 4)

A- Restriction Endonucleases.

B- Plasmid Cloning Vector.

C- Creating and screening Libraries.

D- Cloning DNA Sequences that Encode Eukaryotic Proteins.

E- Vectors and Cloning Large Pieces of DNA.

F- Gate Way Cloning Systems.

H- Agrobacterium Plasmids.

I- Genetic Transformation of Prokaryotes and Eukaryotes.

3- Manipulation of Gene Expression in Prokaryotes (Chapter 6)

A- Gene Expression from Strong and Regulatable Promoters.

B- Fusion Protein

C- Unidirectional Tandem Array.

D- Translation Expression Vectors.

E- Increase Protein Stability.

F- Protein Folding.

G- Overcoming Oxygen Limitation.

H- DNA integration into Host Chromosome

I- Increase secretion.

J- Metabolic Load.

4- Heterologous Protein Production in Eukaryotic Cells. (Chapter 7)

A- Saccharomyces cerevisae Expression System.

B- Pichia pastoris and Other Yeast Expression System.

C- Baculovirus-Insect Cell Expression systems.

D- Mammalian Cell Expression Systems.

5- Direct Mutagenesis and Protein Engineering. (Chapter 8).

A- Direct Mutagenesis Procedures (Oligonucleotide-directed mutagenesis,

Oligonucleotide-directed mutagenesis with plasmid DNA, PCR-amplified

Oligonucleotide-directed mutagenesis…etc.).

B- Protein Engineering (adding disulfide bonds, changing Asparagines to other amino

acids…etc.

6- Applications of Biotechnology in Medicine.

7- Applications of Biotechnology in Plants.

8- Applications of Biotechnology in Microbes.

9- BioEthics.

Laboratory Manual

Part I

Molecular Cloning.

Laboratory I:

1- Searching for DNA sequence from the Databases.

2- Primer Design using the software.

3- PCR using a genomic DNA.

Laboratory 2:

1- Running the PCR product through the agarose gel electrophoresis.

2- Extraction of the PCR products from the Gel.

Laboratory 3:

1- Quantification of the purified PCR products using the agarose gel method.

2- Ligation to the pGEMT-easy vector contains the LacZ inducible promoter and the

beta-galactosidase gene.

Laboratory 4:

Genetic transformation of the ligation products using heat shock method and

electroporation.

Laboratory 5:

1- Screening for positive clones using the blue/white colony method.

2- Selection and growing of the positive colonies.

Laboratory 6:

1- Plasmid extraction using the column method.

2- Confirming the positive clones using the using the EcoRI which realize the insert

from the plasmid.

3- Gel Electrophoresis.

Part II: Recombinant Protein Production and Purification.

Laboratory 7: Production and Purification of Green Fluorescent Protein (GFP) from bacteria using the

pGLO Expression system and the hydrophobic interaction chromatography column.

Laboratory 8: Continue….Production and Purification of Green Fluorescent Protein (GFP) from

bacteria using the pGLO Expression system and the hydrophobic interaction

chromatography column.

Laboratory 9:

Continue…Visualizing the GFP in PAGE (Native and denatured forms)

Part III: Gene Expression Analysis

Laboratory 10:

RNA isolation from Plant Tissue.

Laboratory 11:

Reverse transcriptase PCR (RT-PCR) using the RNA sample.

Laboratory 12:

Semi-quantitative RT-PCR. Detection the gene expression difference by agarose gel

electrophoreses and image analysis.



Department: Course Code: BIOL4054 Credit & Contact Hours: 3 credits and 4 contact hours (2 lectures and 1 laboratory) Course Title: Marine Biology

Prerequisite(s): BIOL3005 Co-requisite(s): Textbook(s): Morrissey, J.F. & Sumich, J.L.,2011. An Introduction to the Biology of Marine Life, 10th Edition, Jones and Bartlett, Sudbury, Massachusetts. http://biology.jbpub.com/marine10e/ Course Co-ordinator: Prof. David Clayton

Description: An introduction to oceanography and the major marine environments and their biological groups, with emphasis on adaptations and interactions. Biomass and productivity at primary, secondary and tertiary trophic levels are reviewed with limiting factors and competition. Applied aspects of the course include resource management.

Aims & Objectives: To show students that marine biology is a multidisciplinary, dynamic and active field that uses a wide range of techniques to explore the interaction between marine organisms and with their environment.

Learning Outcomes Knowledge:

Students who successfully complete this course will be able to; 1. List the major habitats and marine phyla present in the oceans;

2. Describe how marine organisms interact and with each other and their physical

environment

3. describe some ecological processes that influence marine community structure More specifically this includes:

4. The ecology and biodiversity of the marine environment including physical parameters. 5. The distribution and abundance of marine organisms and their adaptation to the marine environment. 6. The structure and function of marine primary producers and their importance in the marine ecosystem. 7. The taxonomy, life history, structure and function of marine invertebrates. And vertebrates and their role in

the marine environment.

8. How the ocean provides humans with resources.

Skills:

After course completion students will be able to:

identify major groups of marine organisms

selectively use a variety of sources in researching a marine biological topic.

critically analyze and evaluate marine data sets


2 lectures and a 2 hour laboratory per week Series of assignments designed for students to collect and manipulate web based sources of information. DVD that includes: Textbook PowerPoint presentations and chapter summaries Lecture PowerPoint presentations and associated video material Additional reading support material including both scientific texts and newspaper articles

Syllabus: The Ocean Habitat The Changing Marine Environment, The World Ocean, Properties of Seawater, The

Ocean in Motion, Classification of the Marine Environment.

Phytoplankton Phytoplankton Groups and Special Adaptations for a Planktonic Existence, HABs.

Zooplankton Zooplankton groups, General diurnal and seasonal vertical migration, Patchiness of

Epipelagic Zooplankton,

Marine Plants Multicellular autotrophs in the sea, Anthophyta, The Seaweeds, Diversity of Life Cycles,

Geographical Distribution.

Primary Productivity Measurements of Primary Production, Factors That Affect Primary Production

including Pycnoclines and Upwelling, Seasonal Patterns of Marine Primary Production, El

Niño/Southern Oscillation (ENSO), Indian Monsoon, Global Marine Primary Production

Nekton Inhabitants of the Pelagic Division, Generalized Large-Scale Distribution of Epipelagic Species,

Locomotion, Hydrodynamic Drag, Body Shape Speed, Buoyancy, Selective Advantages of Schooling

Behavior, Migration, Functions, Extensive Oceanic Migrations Role of Tagging and Telemetry

Benthos Seafloor Characteristics, Sources of Marine Sediment, Vent and Seep Communities,

Chemosynthesis and Primary Production, Animal-Sediment Relationships, Intertidal Communities,

Larval Dispersal, Shallow Subtidal Communities. Types of Estuaries, Estuarine Circulation, Salinity

Adaptations, Estuarine Habitats and Communities, Salt Marshes, mangals, Seagrasses.

Coral Reefs

Anatomy and Growth, Coral Distribution, Coral Ecology, Coral Reef Formation, Reproduction in Corals,

Zonation on Coral Reefs, Coral Diseases. Coral Reef Fishes, Symbiotic Relationships, Coloration,

Spawning and Recruitment, Sexual Systems in Reef Fishes.

Marine Resources

A Brief Survey of Marine Food Species, Major Fishing Areas of the World Ocean, Fishing Down the

Food Web, Mariculture, The Problems of Overexploitation, The Tragedy of the Commons, International

Regulation of Fisheries, A Brief History of Whaling, Regulations and the International Whaling

Commission, Developing a Sense of Stewardship , Ocean Pollution.


COURSE OUTLINE for BIOL4054 Marine Biology Course Description

An introduction to oceanography and the major marine environments and their

biological groups, with emphasis on adaptations and interactions. Biomass and

productivity at primary, secondary and tertiary trophic levels are reviewed with

limiting factors and competition. Applied aspects of the course include resource

management and pollution control Pre Requisite: BIOL3005. Incompatible:

MASF3026.

Expected Outcomes

Students who successfully complete this course will be able to;

• List the major habitats and marine phyla present in the oceans;

• Describe how marine organisms interact and with each other and their physical environment • • describe some ecological processes that influence marine community structure More specifically this includes:

. The ecology and biodiversity of the marine environment including physical parameters.

. The distribution and abundance of marine organisms and their adaptation to the marine environment.

. The structure and function of marine primary producers and their importance in the marine ecosystem.

. The taxonomy, life history, structure and function of marine invertebrates.

. The taxonomy, life history, structure and function of marine vertebrates and their role in the marine environment. . How the ocean provides humans with resources.

Textbook Morrissey J.F. & Sumich, J.L., 2012. An Introduction to the Biology of Marine Life, 10th Edition, Jones and Bartlett, Sudbury, Massachusetts. Additional web information at: http://biology.jbpub.com/marine10e/

Evaluation System

The course will be graded using an A (exceptional performance) to F (unacceptable performance) system. Final grade will be based on the following evaluations. If possible include exam dates.

Evaluation Weight Exam Dates

Assignments 20% Delivered to deadlines/deduction for late submission

Quizzes 10% Week 5 - 4th

October, and Week 14 - 6

th December

Mid-Examination 20% Monday 9th

November 2.15-3.45pm (Wk. 9)

Final Examination 40% Tuesday 5

th January 2016: Comprehensive

covering the full course

Laboratory Reports 10% Delivered to deadlines / deduction for late submission

Missing quizzes and tests:

Students who misses an examination or quiz without a valid reason will be graded as having

scored zero. If there is an acceptable excuse, the final mark will be calculated out of the

percentage scored the components complete o,r at the discretion of the instructor a makeup

exam may be given.

Attendance: There will be lecture and Laboratory sign in sheets from which attendance records will be calculated. Punctuality in attending all scheduled classes is expected. Any necessary absences, especially of examinations, should be notified before the event and in the case of any unexpected absence, a written and appropriately signed explanation should be provided as soon as possible.

A student will be sent a Warning Notice on missing 10%(7 contact hours) of the course and a

Failure Notice on missing 20% (13 contact hours) or more according to University Regulations.

Note that there are 4 contact hours a week.

Plagiarism: Students are reminded of the university regulations and penalties concerning presentation of work that is not your own. Submitted work should appropriately cite/reference source material.

Course Syllabus

The DVD contains: The slides and chapter summaries from the course textbook.

1. The lectures and videos that will be presented in the course. Note that these may be subject to change as new/revised material is incorporated.

the lecture sequence does not strictly follow that of the textbook

2. A resource folder containing articles relevant to the course. 3. The Assignments that are to be carried out during the course.

Tide calculation and SDT profile Google earth Fish Key and Fish database Nekton tracking

4. Articles selected from the Journal of Marine Biology for a seminar presentation

Lectures

1) The Ocean as a Habitat 2) Phytoplankton 3) Zooplankton 4) Marine Plants 5) Primary Productivity 6) Nekton 7) El Nino 8) Marine Environments 9) Coral reefs10) Management of Resources

Note: A rough guide to relevant pages from textbook is provided in lectures. Also look at the chapter Study Guides for revision. Additional material may be supplied in the lectures.

Laboratories

Note: the laboratories may be field or laboratory based exercises the order of which may change to accommodate the tide cycle and availability of Al Jamiah, the university research vessel and other course schedules Some field trips will have to be held on Saturdays. Some laboratory periods will be used for lectures and the midterm examination and for presentation of some assignment results.

Possible field trips (that will be held on Saturdays) include: The dates depend on the tidal cycle

Oceanography Beach benthos Mangroves Rocky shore Laboratories Include but may not be limited to:

Phytoplankton Zooplankton Swimming with fish Reproductive strategy Fish identification Key

Assignments.

Note: Each student will have their own data set for their assignments and accordingly will have unique results and presentations.

Seminar

Each student is expected to read two artilces from the list provided to :

a. give a short (7.5 minutes) presentation and to answer questions (2.5 min) on one of them.

b. ask questions about the second paper which will be presented by another student.

Complete a rating sheet for each presentation

Lecturer: Professor David Clayton. In Dean’s Office Admissions & Registration. Office hours open, but best to email or call ahead of time: [email protected]. Phone 1807.

Technician: Dr Amina Al Farsi



Course Outline


3 credits = 4 hours (2 lect + 1 lab) Course Title: Biological Data Handling Prerequisite(s): None Co-requisite(s): None Textbook(s): Biostatistical Analysis (Fifth Edition), 2010. J.H.Zar; Pearson Educational Course Coordinator: Prof. Reginald Victor

Description: This is the first course in biostatistics for biologists with very little background in mathematics. It deals with the application of statistical procedures to biological problem solving. It covers a wide range of parametric procedures used in biological research. The lectures begin with characterisation of biological data and takes the students through descriptive statistics, normal distribution, comparison of means for two and multiple samples to regression. The laboratories support the lectures and train the students to use basic statistical packages for solving problems. The students are also required to collect data, analyse and interpret results.

Aims & Objectives: This is a compulsory course for all Biotechnology and Environmental Biology students. It is designed to help students understand and analyze biological data properly. The techniques learnt here will be very useful for analyzing the data collected during research projects.

Learning Outcomes 1. Knowledge:

To understand the nature of biological data and data distributions

To understand the reason behind the application of appropriate procedures to analyze and interpret data

To understand the significance of statistical analyses in biological research. 2. Skills:

To design experiments and collect data that are amenable to data analysis.

To think critically and avoid the inappropriate uses of statistical procedures

To analyze data cost effectively using Microsoft Excel and other open access programs available for free on the internet.

Syllabus:

1. Introduction - Types of biological data, accuracy and significant figures, populations, samples

from populations, random sampling.

2. Measures of central tendency- dispersion and variability. Mean, median, mode, the range, the

mean deviation, the variance, the standard deviation, the coefficient of variation, coding data,

effects of coding.

3. Frequency distribution – For Ratio scale, Interval scale, Ordinal scale and nominal scale data

4. The normal distribution - Symmetry and Kurtosis, proportions of a normal curve -Z scores,

assessing normality, confidence limits

5. The t-distribution -Two tailed and one tailed hypotheses concerning the mean, confidence limits

for the population mean, reporting variability about the mean.

6. The t-test - Paired and unpaired t-tests

7. The analysis of variance - Single factor ANOVA -the F test, basic assumptions under ANOVA,

loss of replications, ANOVA with two treatments.

8. Multiple comparisons - The Tukey test -for equal and unequal sample sizes

9. Data transformations - Arcsin, logrithmic and square root transformations

10. Correlation, regression and line fitting through graph points. - Pearson's correlation coefficient,

simple linear regression, testing the significance of regression.

Instructional Methodology & Teaching Resources: Two lectures and two laboratory hours/ week Course Assessment: Final Examination: 40% Mid-term Test (x2): 30% Homework (25 problems): 15% Assignments & Quiz: 15% Grade Scale: F - A; F = Fail, D= Course requirements achieved; C= Good achievement; B= Very good achievement; A= Excellent achievement. Given grades are D, D+, C-, C, C+, B-, B, B+, A-, A.


College of Science


BIOL 4432 Introductory Genetics

Fall 2011

Course Outline Coordinator : Dr. Aisha Alkhayat Al Shehi

Office: 1071 Biology Department

Phone: ext 1446

Credit hours : 3

Format : Lectures, Laboratories and Tutorials

Textbook : Genetic, Analysis and Principles by Robert J Brooker 3rd Ed.

Course Description: This is an introductory course in Genetics. Students will learn the basic principles of Genetics. The

course will emphasize transmission of traits and different modes of inheritance. Overview of the

chromosome structure and function, in addition to principles of genomics and population genetics

will be covered. Tutorials will be used to reinforce the concepts and applications of genetics

principles. Laboratory periods will emphasize tutorials and hands on experiments for classical as well

as molecular genetics.

Course Content: The following general concepts will be covered:

Overview of Genetics (chapter 1)

Patterns of Inheritance

Mendelian Inheritance (chapter 2)

Reproduction and Chromosome Transmission (chapter 3)

Extension of Medelian Inheritance. (chapter 4)

Non-Medelian Inheritance (chapter 7)

Variations of chromosome structure and function (Ch 8)

Genomics (chapter 20 &21)

Population genetics (chapter 24)

Assessment Midterm Tests (2) 30 %

Laboratory (Reports and Assignments & Final) 30 %

Final Examination 40 %

Mid term Tests

Test 1 wk 7

Test 2 wk12

PRACTICALS (2010)

Week 1 No lab

Week 2 Human Genetics I,

Week 3 Human Genetics I

Week 4 Human Handedness

Week 5 Solving Human Genetics Problems

Week 6 Chromosomes I: Chromosomes in Mitosis (Onion root tip)

Week 7 Chromosomes II: Human chromosomes - Karyotyping

Week 8 Chromosomes III: Salivary gland chromosomes of Drosophila

Week 9 Drosophila handling, sexing and set up crosses

Week 10 Follow up on Drosophila crosses.

Week 11 Probability, Chi-square and Analysis of maize cobs.

Week 12 Molecular Genetics I

Week 13 Molecular Genetics II

Week 14 Molecular Genetics III

Week 15 Lab Exam

Learning outcomes from the practical: 1. Be able to follow instructions independently

2. Carry out independent projects to demonstrate various rules of genetics by doing Drosophila

crosses.

3. identify different types of Drosophila mutants and phenotypic properties of the fruit fly.

4. Isolate polytene chromosomes from larval stages.

5. Perform molecular genetics techniques e.g

a. DNA extraction

b. Gel electrophoresis

c. DNA fingerprinting

d. PCR

e. Restriction analysis

Learning outcomes for the Genetics course BIOL4432 1. Define the concept of the gene

2. Define the following terms: true-breeding, hybridization, monohybrid cross, P generation, F1

generation, and F2 generation

3. Use a Punnett square to predict the results of a monohybrid cross, stating the phenotypic and

genotypic ratios of the F2 generation

4. Distinguish between the following pairs of terms: dominant and recessive; heterozygous and

homozygous; genotype and phenotype.

5. State Mendel’s law of independent assortment and describe how this law can be explained by the

behavior of chromosomes during meiosis

6. Use the rule of multiplication to calculate the probability that a particular F2 individual will be

homozygous recessive or dominant.

7. Use the laws of probability to predict, from a trihybrid cross between two individuals that are

heterozygous for all three traits, what expected proportion of the offspring would be: a. homozygous

dominant for the three traits b. heterozygous for all three traits c. homozygous recessive for two

specific traits and heterozygous for the third

8. Give an example of incomplete dominance and explain why it does not support the blending

theory of inheritance

9. Explain how phenotypic expression of the heterozygote differs with complete dominance,

incomplete dominance, and codominance

10. Describe how environmental conditions can influence the phenotypic expression of a character.

Explain what is meant by “a norm of reaction.”

11. Given a simple family pedigree, deduce the genotypes for some of the family members

12. Define the following terms: (linkage, centimorgam, crossing-over, cis-conformation, trans-

conformation

13. Distinguish linked and unlinked genes from observing results of a cross and studying the ratios.

14. Describe how cross-over happen at the 3 chramatid stage.

15. Illustrate (explain) the effect of different types of mutations.

16. List the different types of gene interaction.

17. Recognize the difference between the interaction of alleles of the same gene (dominance, co-

dominance, incomplete dominance, recessive lethal alleles).

18. Identify phenotypes produced because of interaction of different genes complementation,

epistasis, suppressors, modifiers, synthetic lethal.

19. Explain modified F2 ratio in various gene interaction.

20. Predict different types of gene interaction by examining F2 ratio.

21. List different types of changes in chromosome numbers

22. List different types of changes in chromosome structure and their causes

23. Recognize different types of euploidy and how they arise in the cell

24. describe gene interaction in population

25. Study the effect of variation on allele frequencies

26. Predict allele frequencies based on Hardy-Weinberg formula

BIOL4500 Dr. Senan Baqir

1

Sultan Qaboos University Cell Biology

College of Sciences BIOL4500


Course credit : 3 Credits

Lectures : Mon 08:00 – 08:50 & Wed 08:00 – 08:50

Practical/labs : Sun 14:15 - 17:05 PM

Venue : Lectures D09 Labs: 1031

Final exam : Thu, January 07, 2016 (11:30-02:30)

Prerequisites : BIOL 2101

Course coordinator : Dr. Senan Baqir Room 2039, Ext. 6893

: E-mail: [email protected]

Office hours : Mon 13:00 – 14:00

E-Learning : BIOL4500 Dr. Baqir PW: WOW

Course Description

This course is designed to introduce the student to the principles of eukaryotic cell

biology. Emphasis is placed on the study of structure and function of cells and subcellular

components and cell regulation. The course covers cell components and membranes,

protein sorting, cell-cell interactions, cell signaling, cell cycle regulation, cryobiology of

the cell, stem cells, and cancer. The course includes practical classes using cell biology

techniques including light and electron microscopy, spectrophotometry, flow cytometry

and centrifugation. In these labs students will be learning methods for disrupting tissues

and cells, cell and organelle separation, cell counting, lipid extraction and study the

properties of cell membranes.

Learning outcomes

Upon successful completion of Cell biology (BIOL4500) course students should be able

to:

1. Identify the structures of eukaryotic cell organelles

2. Discuss the functions of the various cell organelles, their intercommunication and

their contribution to the overall functioning of the cell.

3. Describe the molecular mechanisms that are the basis for the cellular processes that

were studied (protein processing and sorting to the correct location within or outside

the cell, membrane synthesis and cell-cell and cell-extracellular matrix interactions)

4. Outline the mechanisms of cell proliferation, cell cycle regulation, cell signaling, cell

survival, differentiation and cell death.

5. Recognize the consequences of defects in basic cell regulatory mechanisms illustrated

by apoptosis and cancer.



2

6. Introduction to state of the arts technologies, such as those used in stem cell research

and cellular cryobiology

7. Review current original literature related to topics discussed in the lectures and give a

presentation in a seminar of peers, including the use of visual aids.

8. Recognize the different experimental approaches used for the study of cell structure

and function and how these approaches can be applied to specific problems in cell

biology

9. Carry out practical work related to cell counting, cell separation, organelle isolation,

enzyme assay, examining membrane properties, isolation of membrane components

and produce word-processed reports of the work

Course Objectives

1) To develop an understanding of the structure and functions of the sub-cellular

components of eukaryotic cells.

2) To introduce students to the tools, methods and recent techniques used in the

study of cell biology.

3) To understand molecular events that is associated with cell growth, replication

and differentiation.

4) To understand the biology of cell cryopreservation

5) To introduce students to current application of cellular biotechnology such as

stem cell applications.

Text book, articles, papers & supplemental material:

Text book: The Cell: A Molecular Approach (2013): G.M. Cooper and R. E.

Hausman, 6th ed., ASM Press (SQU 1207030056)(ISBN 978-0-87893-964-0)

Book companion website: http://sites.sinauer.com/cooper6e/

Scientific papers: Review articles will be named after each class

Lecture notes: Handouts (H/O) will be posted on E/Learning

Movies & Video Clips: Presented during the class and labs

E-Learning, SQU Website

Glossary: P773-795

Penalties & Bonuses:

During the lab and lectures students might get a penalty/bonus of 20% in the next quiz


3

Course Evaluation: (Scale A-F)

Assessment Percentage Date Week

Theory test 1 15% 11/10/15 6

Theory test 2 15% 08/11/15 10

Essay and seminar 10% 12-13

Lab quizzes and reports 20% -------

Bonuses 0-5% Prior to final -------

Final exam 40% 07/01/16 18

Lectures Outline:

Section 1: Cell Organelles

The Nucleus

o Structure of the Nuclear Envelope

o The nuclear pore complex

o Selective transport of proteins to and from the nucleus o Regulation of nuclear protein import o Internal Organization of the nucleus

o Functional domains within the nucleus

Nucleus: Biotech Applications

o Enucleation

o Nuclei staining

o Cell Fusion

o Nuclei Sexing

The Nucleolus & Ribosome

o Ribosome characteristics & function

o Ribosomal RNA genes

o Ribosome assembly

Ribosomal Biotechnology

o Ribosome display (RD) technology

o Methodology

o Schematic presentation (RD)

o Antibody-Ribosome-mRNA production

Chloroplasts


4

o Chloroplast characterizes and function

o Chloroplast structure

o Stroma & Thylakoid what for?

o Chemiosmotic generation (chloroplast & mitochondria)

o Characteristics of Chloroplast Genome

o Chloroplast DNA

Section 2: Bioenergetics and Metabolism

The Mitochondria

o Definition

o Structure of the mitochondria

o Mitochondria function and availability

o The genetic system of mitochondria

o Description of mtDNA

o Metabolism in the mitochondria

o Mitochondria Vs. Chloroplast

o Mitochondria & Microtubes

o Mitochondria Motion

o Where do the mitochondria come from?

o Mitochondrial diseases

o What are mitochondrial diseases?

o Dynamics of mitochondrial disease

o Biotechnology application of mtDNA

Plastids & Peroxisomes

o Plastid Characteristics

o Plastid development

o Plastid development and differentiation

o Peroxisomes Characteristics

o Peroxisomes function

o Peroxisomes assembly

Section 3: The Extracellular Matrix and Cell-Cell Interactions

o The Extra Cellular Matrix (ECM)

o Structural Proteins of the ECM

o Polysaccharides of the ECM

o Adhesion Proteins of the ECM

o Attachment of cells to ECM-Integrins

o Cells Matrix junctions - Focal Adhesion & Hemidesmosomes

o Cell Adhesion Proteins – Selectins, Integrin, Ig Superfamily & Cadherins


5

Section 4: Protein Regulation, Sorting and Transport

Endoplasmic Reticulum

o The Endoplasmic reticulum and protein secretion

o Targeting proteins to the Endoplasmic Reticulum

o Insertion of proteins into the ER membrane

o Protein folding and processing in the ER

o The smooth ER and lipid synthesis

o Export of proteins and lipids from the ER

Lysosomes

o Lysosomal acid hydrolases

o Endocytosis and lysosome formation

o Phagocytosis and Autophagy

Section 5: Cell Cryobiology

Cell Cryobiology and Crypreservation

o Applications of cell crypreservation

o Fundamentals of cell cryobiology

o Cryoprotective agents (CPA)

o Cryopreservation procedure

o Cryopreservation Methods

o Techniques for loading freezing straws

o Cell Freezing

Section 6: Cell Regulation and Signaling

Cell Signaling Molecules and Receptors

o Signaling Molecules and Their Receptors

o Models of Cell-Cell Signaling

o Steroid Hormones and the Nuclear Receptor Superfamily

o Functions of Cell Surface Receptors

o G-Protein Coupled Receptors

o Receptors Protein-Tyrosin

o Cytokine Receptors and Nonreceptors Protein-Tyrosin Kinases

Programmed Cell Death

o Caspases and Apoptosis

o Regulators and Effectors of Cellular Apoptosis


6

o Cell death receptors and Caspase activation

o Signaling Cell Survival

Section 7: Genomic Structure and Cell Regulation

o Transcription

o Eukaryotic Repressors

o Relationship of chromatin structure to Transcription

o Histone Acetylation

o Histone Methylation and phosphorylation

o Nucleosome Remodeling

Section 8: Stem Cell Biology

o Stem Cells Proliferation

o Stem Cells Usage and Characteristics

o Stem Cells Nuclei Staining

o Directed In Vitro Differentiation

o Stem Cells Genetic Markers

o Stem Cell Replication and EB Formation

o Medical Applications of Stem Cell

Stem Cell Biotechnology

o Generation & Derivation of ES Cells

o Importance of Stem Cells

o Stem cells Therapeutic Applications

o ES Cells Derivation and Pluripotency

o Stem Cells and Biotechnology

o Stem Cells Tissue Bio-Engineering

o ES Cells in Therapeutic Cloning

o Stem Cells Challenges

Section 9: Cancer & Carcenogenesis

o Types of Cancer

o Development of Cancer

o Causes of Cancer

o Properties of Cancer Cells

o Oncogenes

o Cell Transformation by RSV and ALV

o Oncogenes in Human Cancer

o Oncogenes and Cell Survival

o Tumor Suppressor Genes

o Suppression of Tumorigenicity by Cell Fusion


7

Laboratory Schedule:

Week no. Lab. No. Experiment

1. No Lab

2. 1 Pipetting, weighments, Cell count

3. 2 Organelle Isolation: Mitochondria (Part I)

4. 3 Organelle Isolation: Mitochondria (Part II)

5. 4 Assay of Cell Fractions for SDH: Mitochondria (Part II)

6. 5 Lipid Extraction

7. Theory test 1 8. 6 Electron Microscopy

9. 7 Cell Cryopreservation

10. 8 Flow Cytometery

11. 9 Cell & tissue culture visitation

12. Theory test 2 13. Seminars

14. Seminars

15. Final Exam

Expectations: You will come to the lab prepared having already red the lab manual. You

should expect a surprise quiz at any time during the lab. You will be required to record

your results and to produce a lab report from each lab.

General:

Students should return the text book on the final day of the exam

BIOL 4501 1 |

BIOL 4501: Principles of Toxicology


Instructional Format: Two lectures and one practical per week

Contact Hours/Week: 4

Prerequisite: BIOL 2101

Textbook: Klaassen CD and Watkins III JB. 2010. Casarett and Doull's

Essentials of Toxicology. The 2nd

edition. McGraw Hill.

Instructor: Dr. Hassan Ali Al-Reasi

Office: 1065 (1st floor, The New Science building)

Telephone: 24146871 or Extension: 6871 (on campus)

E-mail: [email protected] or [email protected]

Course Description:

This course provides the basic understanding of the science of toxicology. It covers the

fundamental toxicological concepts including dose‐response relationships, mechanisms of toxicity,

risk assessment, adsorption, distribution, metabolism and excretion (ADME) of toxicants,

biotransformation of xenobiotics, and toxicokinetics. Selected examples of nonorgan-directed

toxicity and target organ toxicity will be discussed. In addition, a brief description of the

applications of toxicology will be introduced with some examples from Oman.

Learning outcomes:

Upon successful completion of the BIOL 4501, the students should be able to:

1. Summarize the fundamental toxicological concepts, list and differentiate interactions between

toxicants/drugs.

2. Demonstrate understanding of some molecular mechanisms behind the toxicological endpoints

in the human body caused by exposure to certain toxicants/toxins.



BIOL 4501 2 |

3. Recognize the importance of risk assessment for evaluation and determination of a hazard

imposed by a toxicant on human or environment.

4. Use standard experiments, collect, analyze and interpret data to demonstrate toxicity of

selected chemicals.

5. Utilize online chemical databases to acquire and organize the relevant information on

toxicological properties of chemicals

6. Become familiar with the importance of the ethical issues associated with the use of humans

and animals in toxicological research

Assessment:

Grading scheme

2 Theory tests 30% (15 % each)

Lab reports and quizzes 20%

Presentation 10%

Final Examination 40%

Proposed exam dates:

Test 1 October 18, 2015

Test 2 November 22, 2015

BIOL 4501 3 |

Table of contents (Lectures)

Please refer to the following chapters of: Klaassen CD and Watkins III JB. 2010. Casarett and

Doull's Essentials of Toxicology. The 2nd

edition. McGraw Hill. More details on the lectures are

provided in PowerPoint (PPT) files on the E-learning website for BIOL 4501. And please take

notes in the classes or during lectures.

Chapter 1: History and scope of toxicology

History of toxicology

Modern toxicology

After world war II

1

1

3

3

Chapter 2: Principles of toxicology

Introduction to toxicology

Classification of toxic agents

Spectrum of undesired effects

Characteristics of exposure

Dose-response

Variation in toxic responses

Descriptive animal toxicity tests

Toxicogenomics

5

6

7

7

9

9

15

15

17

Chapter 3: Mechanisms of toxicity

Delivery: from the site of exposure to the target

Reaction of the ultimate toxicant with the target molecule

Conclusions

21

22

26

44

Chapter 4: Risk assessment

Introduction and historical context

Definitions

Decision making

Hazard identification

47

47

48

49

49

BIOL 4501 4 |

Dose-response assessment

Risk characterization

Exposure assessment

Information resources

Risk perception and comparative analyses of risk

Summary

51

53

54

54

54

55

Chapter 5: Absorption, distribution, and excretion of toxicants

Introduction

Cell membranes

Absorption

Distribution

Excretion

Conclusions

57

58

59

60

63

65

68

Chapter 6: Biotransformation of xenobiotics

General principles

Hydrolysis, reduction and oxidation

Conjugation

71

72

72

88

Chapter 7: Toxicokinetics

Introduction

Classic toxicokinetics

Physiologic toxicokinetics

99

99

100

103

Chapter 8: Chemical carcinogenesis

Overview

Multistage carcinogenesis

Mechanisms of action of chemical carcinogens

Test systems for carcinogenicity assessment

Chemical carcinogenesis in humans

109

110

100

103

117

118

BIOL 4501 5 |

Table of contents (Practical sessions)

Practical 1: Laboratory safety practices and laboratory report write-up format

Sample report: Determination of copper toxicity to Daphnia magna in two

concentrations of dissolved organic matter (DOM)

Practical 2: Introduction to dose-response experiments

Practical 3: Dose-response experiment for the effect of copper (Cu2+) and

salinity and interaction of Cu2+ and salinity on seed germination and root

elongation of mung bean (Vigna radiata) - Examining the additive effect

Practical 4: Examining the antagonistic effect of humic substances on copper

(Cu2+) toxicity to seed germination and root elongation of mung bean (Vigna

radiata)

Practical 5: Data analyses of mung bean (Vigna radiata) experiments

Practical 6: Dose-response experiments for determination of lethal

concentration (LC50) of copper (Cu2+) to brine shrimp (Artemia sp.)

Practical 7: Dose-response experiments for determination of lethal

concentration (LC50) of copper (Cu2+) to water flea (Daphnia magna)

Practical 8: Scavenging of hydrogen peroxide (H2O2) by green tea

antioxidants (GTA)

Practical 9: Material Safety Data Sheets (MSDS) and Toxicology Databases

Practical 10: Introduction to presentation

Practical 11: Presentations delivery



6

10

19

23

29

35

36

40

43

46

49

51

51

51


Course Outline for BIOL4600

Course Description

The course consists of the following units, which will give students an understanding of biofuels as a renewable energy source. First, second and third generation biofuels will be discussed as well as advanced biofuels. Economic and social impacts, both globally and locally, will also be discussed.

1. Overview of biofuel and bioenergy production 2. First, second and third generation biofuels 3. Microbial production of biofuels 4. Advanced biofuels: alternatives to ethanol such as biobutanol 5. Concept of “biorefineries” 6. Social and economic effects of biofuel based industries

At the beginning of each topic students will be given a topic outline.

Course code : BIOL4600 Course title : Biofuels Pre-requisite : BIOL 4030 Credits : 3 CU Format : 2 (75 min) Lectures Lecturer : Dr. Mohab Ali Al-Hinai (Office # 1075), Tel. 2296

e-mail: [email protected]

Textbook : Introduction to Biofuels. David M. Mousdale, CRC Press (2010). ISBN 978-1439812075

Reference book : Biofuels and Bioenergy from Biomass and Biowastes.

Samir K. Khanal et al., ASCE Publishing (2010). ISBN 978-0784410899

Course learning Outcomes By the end of the course, students should be able to: Distinguish between first, second and third generation biofuels and describe the advancement made at each level. Understand how plant biomass, such as cellulose, hemicellulos and lignin, be converted to


soluble sugars to support biofuel production. Describe how biofuels are produced by microbial processes such as yeast and bacteria. Know and describe the increasing portfolio of advanced biofuels that are alternatives to ethanol such as biobutanol and biohydrogen. Understand and grasp the economic and social advantages and disadvantages of biofuel production and biorefineries. Understand the difficulty in sustaining biofuel production The course will also consist of a group project. The students will be asked to come up with a biofuel inspired project that is relevant to the Omani need.

Evaluation System

The course will be graded using an A (exceptional performance) to F (unacceptable performance) system. Final grade will be based on the following evaluations (below is an example; components depend on the course). If possible include exam dates.

Evaluation Weight Exam Dates Test 1 20% Week # 6 Test 2 20% Week # 12 Project 20% Week # 14 Final Exam 40%

Detailed Syllabus (Lecture) Unit 1: Overview of biofuel and bioenergy production Introduction Why biofuels? Current status of biofuel generation Suitability of biofuel industries

Unit 2: First, second and third generation biofuels Ethanol as the leading first-generation biofuel History of ethanol as a biofuel Environmental aspects of ethanol as a biofuel Cellulosic ethanol as a second-generation biofuel Cellulose, hemicellulose and lignin as feedstock for biofuel production Cellulases, Hemicellulose and lignin-degrading enzymes Third-generation biofuel produced from algal mass

Unit 3: Microbial production of biofuels Production of ethanol by yeast Conventional vs. nonconventional yeast for biofuel/ethanol Metabolic engineering of yeast for the production of cellulosic ethanol Production of biofuels by bacteria Genetic and metabolic engineering of bacteria for enhanced biofuel production Unit 4: Advanced biofuels: alternatives to ethanol such as biobutanol Introduction to alternatives to ethanol as a biofuel Biobutanol and the Acetone-Butanol-Ethanol (ABE) fermentation Biohydrogen Microbial fuel cells Unit 5: Concept of “biorefineries” Introduction to the biorefinery concept Feedstock and substrates for biorefineries Important biorefinery products Economics of biorefineries Unit 6: Social and economic effects of biofuel based industries The market forces that affect biofuel production Impact of oil prices on the future of biofuels Cost for biofuel production Governmental and economic factors Social and environmental factors of biofuel-based industries


Course Outline for BIOL4700 Environmental Biotechnology

Course Description The course will give students an understanding of Environmental Biotechnology as a means to improve environmental quality. Topics to be discussed include:

1. Areas of application of Biotechnology 2. Genetically modified organisms 3. Microbial metabolism, microbial growth medium, microbial growth kinetics 4. Environmental monitoring 5. Sewage treatment 6. Bioremediation 7. Biotechnology and sustainable technology

8. Agricultural and marine biotechnology

At the beginning of each topic students will be given a topic outline.

Course code : BIOL4700 Course title : Environmental Biotechnology Pre-requisite : BIOL3441 Credits : 3 CU Format : 2 (75 min) Lectures Lecturer : Dr. Mohab Ali Al-Hinai (Office # 2009, New Annex)

e-mail: [email protected] ext.6874

Textbook : Environmental Biotechnology. Second edition. Alan Scragg. Oxford University Press. ISBN978-0-19-926867-2

Reference book : Environmental Biotechnology. 2010. M.H. Fulekar. CRC

press. ISBN 978-1-57808-582-8

Course learning Outcomes By the end of the course, students should be able to: Understand the areas where biotechnology can be applied to improve environmental quality. Understand and describe specific microbial metabolism that maybe applied in areas related to environmental biotechnology. Additionally, microbial growth medium requirements as well


growth kinetics will be discussed. Describe and understand the various environmental monitoring procedures. Understand the various sewage treatments methods and how can one modify them to make them more efficient. The course will also discuss various methods of bioremediation and the students should be able to describe the various methods used, Describe and understand the role of agricultural and marine biotechnology in help sustaining the environment. The course will also consist of a group project. The students will be asked to come up with a project that is relevant to the Omani need for environmental biotechnology.

Evaluation System

The course will be graded using an A (exceptional performance) to F (unacceptable performance) system. Final grade will be based on the following evaluations (below is an example; components depend on the course). If possible include exam dates.

Evaluation Weight Exam Dates Test 1 20% Week # 6 Test 2 20% Week # 12 Project 20% Week # 14 Final Exam 40%

Detailed Syllabus (Lecture) Unit 1: Introduction to Environmental Biotechnology Introduction Biodiversity Areas of application of Biotechnology Genetically modified organisms and the environment

Unit 2: Microbes and the environment Microbial structure, cell shape and size

Direct & Indirect methods for determination of cell number and activity Microbial metabolism and growth requirements Microbial growth kinetics Relationship to the environment Identification of microorganisms

Unit 3: Environmental monitoring Sampling

Physical, chemical and biological analysis The role of recombinant DNA technology in environmental monitoring. Determination of biodegradable organic material Monitoring pollution Bioindicators, Biomarkers, and Biosensors

Unit 4: Sewage and waste treatment Sewage and waste treatment methods

Modification of existing processes Sludge treatment and disposal Anaerobic digestion Agricultural and industrial waste

Unit 5: Bioremediation Synthetic and petrochemical compounds Bioremediation strategies In situ and ex situ bioremediation techniques

Phytobioremediation Metal and gaseous bioremediation Biochemical pathways of bioremediation

Unit 6: Biotechnology and sustainable technology Bulk and fine chemicals Microbial polymers and plastics Industrial processes and clean technology Biofuels Natural resource recovery Unit 7: Agricultural and marine biotechnology Transgenic plants and animals

Safety of transgenic organisms Disease control Pharmaceuticals Polymers Microalgae Marine pollution

Ecotoxicology BIOL5010 2014

Course Coordinator: Dr Michael Barry LECTURE NOTES PART 1

2

1. Introduction Ecotoxicology is a multidisciplinary subject that incorporates ecology, toxicology, modelling, pharmacology, biochemistry and chemistry. The aim is to measure the effects of chemicals on ecosystems and the organisms that live in them.

2. Course overview Summary The first part of the course will cover the major classes of environmental pollutants and the modes of actions. Secondly, we will look at how chemicals are transported in the environment and the factors that influence mobility and persistence. Thirdly, we will consider how toxicity can be measured from the gene to the ecosystem. Fourthly, we will look at ways in which the impact of toxicants can be monitored in the environment. Finally we will consider the quantification of risk and how it is communicated to scientists, regulators and the public. 3. Learning objectives On completion of this course the student should be able to:

o Have a sound knowledge of the major classes of environmental pollutants and their modes of toxicity.

o Understand how pollutants enter the environment, how they are transported and their environmental fate.

o Be competent at calculating measures of toxicity and understand the basics of ecotoxicological testing.

o Have an understanding the differences between cellular, whole organism, population and ecosystem-level toxicity.

o Be able to design a simple biomonitoring survey. o Understand the principles of ecological risk assessment and apply them to

specific chemicals and environments 4. Teaching arrangements This course will be delivered using the following means:

• Lectures: Monday: 9:0-9:50 Wednesday: 9:0-9:50 • Practical: Tuesday: 2:15 - 4:05

3

5. Resources Text: -Principles of Ecotoxicology by CH Walker, SP Hopkin, RM Sibly, DB Peakall Readings: You will receive either hardcopy or on-line readings from time to time. Moodle: A Moodle page for Ecotoxicology is available. A password will be provided in the class. 6. Assessment

Form of assessment Weighting Week

Theory Tests 2 X 12% 5 & 10

Presentations 2X 2% TBA Lab report 1 (tadpole experiment) 7% 8 Lab report 2 (tomato experiment) 7% 10

Assignment 5% 9

Small activities 5% TBA

Lab exam (Theory) 8% Week 15

Final exam 40%

4

7. Lecture and Practical Topic Guide WEEK

Beginning LECTURE THEME PRACTICAL

1

Introduction

2

• Basic principles Start tadpole experiment

3

• Metals Start plant growth experiment

4

Emerging toxins • Pharmaceuticals • Nanoparticles

Arsenic in soil and water

5 .

Emerging toxins • Polyfluorinated

compounds • Polybrominated

compounds

Metals & water hardness

6

Physiological & energetic effects Effects of chemicals on populations

Analysis of tadpole experiment

7 .

Endocrine disrupting chemicals Analysis of plant experiment

8

Behavioural toxicity EPA ECOTOX database

9

Indirect effects Community level effects

Fish behaviour experiment

10

Pesticides Toxswa: Fate of pesticide in water

11 .

Pesticides Risk assessment

12

Predicting pesticide behaviour in the environment from physico-chemical properties

Risk assessment

13

Biomarkers No lab

14

Revision Lab test

15


College of Science


Course Outline


3 credits = 4 hours (2 lect + 1 lab) Course Title: Desert Biology Prerequisite(s): BIOL 3005 Ecology Co-requisite(s): None Textbook(s): Theory and principles are adopted from various books and examples are based on Arabian deserts; a course manual/handouts will be given as and when appropriate Course Coordinator: Prof. Reginald Victor

Description: This is a core course for Environmental Biology Majors. It describes the nature of the desert environment and the uniqueness of its plant and animal communities. Specifically, the adaptations of plants and animals to tolerate the desert environment, their reproductive strategies, functional aspects including desertification and the human dimension and their evolutionary ecology are covered in lectures. Field trips include visits to various types of deserts and non-destructive sampling methods are used to examine the desert plants and animals under field and laboratory conditions. .

Aims & Objectives: To introduce the students to desert biology and ecology and equip them with the basic knowledge to work in applied fields relating to desert areas such as biodiversity, conservation, land degradation and restoration and sustainable development.


To know the environmental conditions governing deserts in general and Arabian deserts in particular and to understand the biology of desert communities

2. Skills:

To recognize the identity of important plant and animal species in Oman deserts

To conduct field studies in the desert environment

Syllabus:

1. Definition of deserts and a brief introduction to the deserts of the world 2. Types of deserts 3. The desert climate 4. Principles of adaptation to deserts 5. Flora and fauna - morphological, physiological and behavioural adaptations 6. Reproductive strategies of plants and animals 7. General structure of some typical plant and animal communities 8. Functional aspects of desert communities 9. Evolutionary ecology of deserts 10. Man and the desert Note: Examples used for illustrating the theory (as many as possible) will be from Oman so that the students will have an opportunity to study them in the field.

Instructional Methodology & Teaching Resources: Two lectures and two laboratory hours/week; field work during weekends Course Assessment: Final Examination: 40% Mid-term Test (x2): 30% Field Study Reports: 15% Assignments & Quiz: 15% Grade Scale: F - A; F = Fail, D= Course requirements achieved; C= Good achievement; B= Very good achievement; A= Excellent achievement. Given grades are D, D+, C-, C, C+, B-, B, B+, A-, A.


College of Science


Enzyme Biochemistry

BIOL5031

Prepared by: Dr. Sirin Adham

For undergrad students

Course credits: 3

Formate: 2 lectures 1 hour each & 1 lab per week for

3 hours

Text Book: Biochemistry by Jeremy M. Berg, fifth edition.

Description: This course aims to teach biotechnology students the fundamental

information about enzymes in terms of their mode of catalysis, regulation, their role in

controlling the different cellular functions including growth, differentiation, cell

motility, cytokinesis, and transport of materials throughout the cell. There will be a

full description of enzyme kinetics in theory and in practical lab experiments.

Objectives: One important aim of this course is to allow the students to understand

the importance of enzymes applications and the related use of enzymes in the

different fields of biotechnology including drug discovery. The students will be

learning how to measure the different parameters of enzymatic reactions, they will

apply different changes to the enzymatic reactions and measure the different variables

of Michaelis-Menten equation, and in addition to that they will learn how enzymes get

inhibited by different chemicals and investigate the different types of enzymatic

inhibitors. This course depends on analysing the data by the use of computer

software's such as Sigma plot and Excel so the students will learn how to analyze their

data independently.

ASSESSMENT: The course will be assessed from A - F. The assessment will be

as follows:

Two theory tests: 30

Lab test: 10

Lab report: 20

Final Examination : 40

First Exam: 8-OCT-2012

Second Exam:5-11-2012

Florida

Cross-Out

COURSE SYLLABUS This course intends to cover the main concepts of enzymes and their mode of action

in the different cellular activities. It will show the students that enzymes are of many

differnt types and they belong to a wide range of different groups and each enzyme

group has its own specificity in the cellular functions.

1- Enzymes: Basic Concepts and Kinetics

General Aspects of enzymatic reactions and transition states

A: Enzymes Are Powerful and Highly Specific Catalysts

B: Free Energy Is a Useful Thermodynamic Function for Understanding Enzymes

C: Enzymes Accelerate Reactions by Facilitating the Formation of the Transition

State

D: The Michaelis-Menten Model Accounts for the Kinetic Properties of Many

Enzymes

E: Enzymes Can Be Inhibited by Specific Molecules

F: Vitamins Are Often Precursors to Coenzymes.

Summary points

1.1 Transition state stabilization

1.2 Enzyme Classes

1.2.1. Oxidoreductases: This is a very broad class of enzymes that catalyze the

many oxidation-reduction reactions found in biochemical pathways.

Oxidoreductases catalyze reactions in which at least one substrate gains

electrons, becoming reduced, and another loses electrons, becoming

oxidized.

1.2.2. Transferases: This class of enzymes catalyze the transfer of a specific

functional group between molecules. Important subsets of transferases

include a) Kinases that transfer phosphate groups,

usually from ATP to another molecule (such as hexokinase and

glucokinase, that phosphorylate glucose and protein kinases that

phosphorylate protein hydroyxl groups), b) Aminotransferases (see right)

that transfer amino groups that are important in amino acid metabolism, c)

Acyltransferases that transfer fatty acyl groups and d)

Glycosyltransferases, which transfer carbohydrate residues.

1.2.3. Hydrolases: Hydrolysis reactions refer to the cleavage of bonds by the

addition of a water molecule. A very important class of hydrolases are the

proteases involved in cleaving peptide bonds, as we will be discussing

shortly.

1.2.4. Lyases: This class refers to those enzymes involved in cleaving bonds by

means other than hydrolysis or oxidation. Examples include aldolases

(such as fructose diphosphate aldolase, which is involved in glycolysis)

and thiolases (such as b-ketoacyl-CoA thiolase involved in the breakdown

of fatty acids). Lyases also include enzymes involved in elimination of

groups from two adjacent carbon atoms to form double bonds.

1.2.5. Isomerases: At many stages of metabolism, rearrangement of the atoms of

a molecule is required to create an isomer of the starting compound.

Enzymes generally catalyzing the rearrangement of the bond structure are

called isomerases, while those specifically catalyzing the movement of a

phosphate from one group to another are known as mutases. For example,

triose phosphate isomerase (right) catalyzes the interconversion between

dihydroxyacetone phosphate and D-glyceraldehyde 3-phosphate, which is

essential for continuing glycolysis following splitting of six carbon sugars

into two three carbon sugars by fructose diphosphate aldolase.

1.2.6. Ligases: Ligases are involved in synthesizing bonds between carbon

atoms and carbon, nitrogen, oxygen or sulfur atoms in reactions that are

coupled to the cleavage of the high energy phosphate of ATP or another

nucleotide. Pyruvate carboxylase, a key enzyme in gluconeogenesis, is

one important ligase in metabolism.

2- Catalytic Strategies: A Few Basic Catalytic Principles Are Used by Many Enzymes

A: Covalent catalysis. In covalent catalysis, the active site contains a reactive group,

usually a powerful nucleophile that becomes temporarily covalently modified in the

course of catalysis. The proteolytic enzyme chymotrypsin provides an excellent

example of this mechanism.

B: General acid-base catalysis. In general acid-base catalysis, a molecule other than

water plays the role of a proton donor or acceptor. Chymotrypsin uses a histidine

residue as a base catalyst to enhance the nucleophilic power of serine.

C: Metal ion catalysis. Metal ions can function catalytically in several ways. For

instance, a metal ion may serve as an electrophilic catalyst, stabilizing a negative

charge on a reaction intermediate. Alternatively, the metal ion may generate a

nucleophile by increasing the acidity of a nearby molecule, such as water in the

hydration of CO2 by carbonic anhydrase. Finally, the metal ion may bind to substrate,

increasing the number of interactions with the enzyme and thus the binding energy.

This strategy is used by NMP kinases.

D: Catalysis by approximation. Many reactions include two distinct substrates. In

such cases, the reaction rate may be considerably enhanced by bringing the two

substrates together along a single binding surface on an enzyme. NMP kinases bring

two nucleotides together to facilitate the transfer of a phosphoryl group from one

nucleotide to the other (Section 9.4.3).

Summary Points on Enzyme Catalysis:

1) Understand what is meant by transition state stabilization.

2) Know which amino acid residues can be involved in acid-base catalysis.

3) Understand that covalent catalysis results from the transient formation of a covalent

bond involving a nucleophile and an electrophile.

4) Recognize the general classes of enzymes, including oxidoreductases, transferases,

hydrolases, lyases, isomerases and ligases.

5) Recognize the physiological importance of Proteases.

6) Understand that proteases use nucleophilic attack by either covalent catalysis or

activation of a water molecule, along with acid-base catalysis.

7) Know what is meant by a serine protease.

8) Have a general understanding of covalent catalysis by Trypsin.

9) Understand that the specificity pocket allows different members of the trypsin

family of proteases to use the same catalytic mechanism for proteolysis but with very

different sequence specificities.

3- Regulatory Strategies: Enzymes and Hemoglobin

A: Allosteric control. Allosteric proteins contain distinct regulatory sites and

multiple functional sites. Regulation by small signal molecules is a significant means

of controlling the activity of many proteins. The binding of these regulatory

molecules at sites distinct from the active site triggers conformational changes that are

transmitted to the active site.

B: Multiple forms of enzymes. Isozymes, or isoenzymes, provide an avenue for

varying regulation of the same reaction at distinct locations or times. Isozymes are

homologous enzymes within a single organism that catalyze the same reaction but

differ slightly in structure and more obviously in KM and Vmax values, as well as

regulatory properties. Often, isozymes are expressed in a distinct tissue or organelle or

at a distinct stage of development.

C: Reversible covalent modification. The catalytic properties of many enzymes are

markedly altered by the covalent attachment of a modifying group, most commonly a

phosphoryl group. ATP serves as the phosphoryl donor in these reactions, which are

catalyzed by protein kinases. The removal of phosphoryl groups by hydrolysis is

catalyzed by protein phosphatases. This chapter considers the structure, specificity,

and control of protein kinase A (PKA), a ubiquitous eukaryotic enzyme that regulates

diverse target proteins.

D: Proteolytic activation. The enzymes controlled by some of these mechanisms

cycle between active and inactive states. A different regulatory motif is used to

irreversibly convert an inactive enzyme into an active one. Many enzymes are

activated by the hydrolysis of a few or even one peptide bond in inactive precursors

called zymogens or proenzymes.

10.1Aspartate Transcarbamoylase Is Allosterically Inhibited by the End

Product of Its Pathway

10.2 Hemoglobin Transports Oxygen Efficiently by Binding Oxygen

Cooperatively

10.3 Isozymes Provide a Means of Regulation Specific to Distinct Tissues and

Developmental Stages

10.4 Covalent Modification Is a Means of Regulating Enzyme Activity

10.5 Many Enzymes Are Activated by Specific Proteolytic Cleavage

10.5.1. Chymotrypsinogen Is Activated by Specific Cleavage of a Single Peptide

Bond.

10.5.2. Proteolytic Activation of Chymotrypsinogen Leads to the Formation of a

Substrate-Binding Site.

10.5.3. The Generation of Trypsin from Trypsinogen Leads to the Activation of Other

Zymogens.

10.5.4. Some Proteolytic Enzymes Have Specific Inhibitors

10.5.5. Blood Clotting Is Accomplished by a Cascade of Zymogen Activations

3- What is the role of enzymes to control the cell functions what is the major

role in signal transduction pathway.


College of Science


BIOL5040

Microbial Genetics and

Genetic Engineering

Prepared by

Dr. Sirin Adham


COURSE CREDIT : 3

FORMAT : 2 lecture/week, 1 lab for three hours per week

PREREQUISITE BIOL3441; BIOL4034 or equivalent.

1. Molecular biotechnology principles and application

2.“Prokaryotic genetics genome organization, Transfer and

plasticity. ByF. Joset et al. 1994.”

3. “Molecular genetics of bacteria. 3rd Edition. By J. Dale. 1999."

DESCRIPTION :

The course is going to focus on the advances that are taking place in the field of genetic

engineering, new methods new applications in order to make the students up to the day

knowledge. We will cover the main methods used in genetic engineering as the basis for all the

molecular techniques that takes place in plant, microbial or animal cloning.

OBJECTIVES: At the end of the course the students will be anticipated to understand how the

directed mutagenesis can be performed to change the behavior of the different proteins and

enzymes. How to detect using molecular techniques the expression of any particular gene, how to

silence any gene of interest and how epigenetics control gene expression in eukaryotic cells. The

applications of molecular biology techniques in diagnostics, therapeutics and industry will be

discussed.


First exam 15

Second exam 15

Final exam 40

Lab test 20 Lab Quiz + Seminar 10

COURSE SYLLABUS

This course intends to cover structures of prokaryotic and Eukaryotic genome and its

related genetic entities, modification and regulation of protein expression, and modern

techniques used in genetic engineering. In brief, the course will be covered the following

areas:

1. Structure of prokaryotic genome and autonomously genetic entities: Bacterial

chromosome, plasmids, bacteriophages, and transposable elements.

2. Modification of genome through directed mutagenesis: Mutation & mutants, DNA

repair, genetic recombination, natural and artificial gene transfer.

3. Gene expression and regulation: Promoters, repressors, regulation and integration of

Regulatory systems.

4. Modern techniques and concepts used in molecular diagnostics.

The following topics are going to be taught during the lecture:

We will cover mainly the following topics:

1-Directed mutagenesis techniques

2-Protein engineering

3-Mechanisms of gene silencing

4-Recombinant Protein production by microorganisms, insects..etc

5-DNA repair mechanisms in prokaryotes and eukaryotes

6-Bacterial secretion systems

A. Genome structure and function

B. Autonomous genetic identities

8-Epigenetics and its regulators

9-Advanced Molecular techniques "yeast two hybrid system".

SULTAN QABOOS UNIVERSITY COLLEGE OF SCIENCE DEPARTMENT OF BIOLOGY Course Code : Biol5042 Course Title : Embryology Pre-requisite : BIOL2102/2103 Credits : 3 CU Format : 2 (1 hr) Lectures + 1 (2 - 3 hrs) Laboratory / week Lecturer : Prof. Taher A. Ba-Omar (Office #1072)

e-mail: [email protected] Textbook PATTEN'S FOUNDATION OF EMBRYOLOGY, 6th Edition, 2002, by Bruce M. Carlson,. McGraw-Hill Publishing Co. Course Outlines The course is designed to introduce student to the general topics of animal embryology. It is divided into 3 major parts:

1. Introduction: An introduction to embryology, reproductive organs and gametogenesis (spermatogenesis and oogenesis cell division).

2. General Embryology: Fertilization, cleavage, gastrulation, neuralation, germ layer formation and their derivatives.

3. Special Embryology: Organogenesis such as nervous system, gastrointestinal system, cardiovascular system etc.

The emphasis will be on mammalian embryology especially human embryology. Objectives of the Course At the end of this course students are expected to know the major events that took place during embryogenesis and organogenesis. They are also expected to identify and locate certain organs of the developing embryo. 1


Course Assessment This course will be assessed as follows :- Theory Tests (X 2) 30% Practical Tests (X2) 20% Lab work (Reports & Seminars) 10% Final Theory Exam (Comprehensive) 40% Schedule of Theoretical Tests:

Theory Test No. 1 (15% ) Date of test1 Theory Test No. 2 (15% ) Date of test 2

Schedule of Practical Tests:

Practical Test No.1 (10%) Date of Practical Test1 Practical Test No.2 (10%) Date of Practical Test1

The following topics will be covered during the lectures sessions

Introduction Reproductive organs and sexual cycle Gametogenesis (spermatogenesis and oogenesis) Fertilization Cleavage and Blastula Gastrulation and the establishment of germ layers Theory Test I Neuralation, the neural crest and somites formation Extraembryonic membrane and placenta Basic body plan of young mammalian embryos Development of muscular tissue Development of skeletal tissue Theory Test II The Digestive and Respiratory Systems of the Body Cavities The Development of the Circulatory System The Development of the Urogenital System

You are responsible for all information presented during lecture and lab sessions. Lecture

and lab attendance are both required.

2

Practical Work The study will be of prepared slides of different animal embryos including; amphibian (frog) and

avian (chick) embryos. Projects and seminars will be conducted during the semester.

I. The followings topics will be covered during laboratory sessions: 1. Mammalian gametogenesis : ovary & testis Practical # 1 2. Frog embryo: Cleavage, blastula and gastrula Practical # 2 3. Open fertilized eggs Practical # 3 4. 24 old chick embryos Whole mount (WM) & (primitive streak ) Practical # 4 5. Practical test I Practical # 5 6. 36 hr old chick embryos Whole mount (WM) and transverse

sections (TS) through eyes, heart and trunk Practical # 6 7. 48 hr old chick embryo Whole mount (WM) and transverse sections (TS) through eyes, heart and trunk Practical # 7 8. 72 hr old chick embryo Whole mount (WM) and transverse sections (TS) through eyes, heart and trunk Practical # 8 9. Video Practical # 9 10. Practical test II Practical # 10 11.. Seminars and Project presentations Practical # 11-14

Seminars will be held at the end of the semester (Date will be announced during the semester)

Attendance of Seminars is compulsory.

3

COURSE INFORMATION: 2015

Freshwater Ecology BIOL 5052


2

CONTENTS

1. Introduction 2. Course overview 3. Learning resources 4. Assessment

1. Introduction Welcome to freshwater ecology! Freshwater ecosystems are facing many challenges and threats from overuse of water for agriculture, industry and domestic supply, to habitat loss, introduced species and pollution. The United Nations has warned that freshwater is one of the world scarcest resources. Oman has limited freshwater resources but the ecosystems that do exist are beautiful and contain diverse wildlife. The aim of this course is to give you and introduction to the science of limnology (freshwater ecology) and overview of freshwater resources in the Sultanate. Course: BIOL 5052 Freshwater Ecology Coordinator: Dr Michael Barry Department of Biology Room Email: [email protected] Telephone: 2414 6858

3

2. Course overview Summary The lecture course is divided into 4 main sections as follows:

1. An introduction to the properties of water, the hydrological cycle and catchments

2. The physical and biological properties of standing waters 3. The physical and biological properties of flowing waters 4. Impacts of humans on aquatic systems

Learning objectives On completion of this course the student should be able to:

• Describe the relationship between catchment properties and water resources

• Describe the main biological and physical features of standing waters • Describe the main biological and physical features of flowing waters • Demonstrate understanding of how human activities can modify aquatic

ecosystems • Demonstrate competence in sampling methods for aquatic systems

3. Learning resources Text: Stream Ecology Allan & Castillo 2nd Ed

4

Autumn Semester, 2015

WEEK Beginning PRACTICAL

1 (8/9) No Lab

2 (15/9)

Review field equipment/Prepare for field work (15/9) Field trip Jebel Akdar (Saturday-19/9)

3 (22/9) Chemical/microbial analyses

4 (29/9) EID?

5 (6/10) Zooplankton

6 (13/10) Test 1

7 (20/10) Start leaf pack experiment

8 (27/10)

No lab Field trip Wadi Abyat (Saturday 31/10)

9

Chemical analysis

10 End leaf pack experiment

11 Macroinvertebrates

12 Test 2

13 No lab/Possible trip to reservoir or Al Ansab wetlands

14 Seminars

15 Lab Test

5

Assessment

Form of assessment Weighting

Practical

Jebel Akdar Report 6%

Wadi Abyat Report 7%

Leaf Pack Report 4%

Oral presentation 5%

End of term lab quiz 8%

Attendance & participation in lab & field work 2%

Theory

Theory tests (x2) 28%

Final 40%

Information Booklet for

(BIOL 5101 and BIOL 5103)

This document was originally

subsequently edited by Dr.



Information Booklet for Biology Project Students

(BIOL 5101 and BIOL 5103)

This document was originally prepared by Dr. Derek Roberts and

. Michael Barry and Professor Reginald Victor

Biology Project Students

Derek Roberts and was

Professor Reginald Victor

BIO 5101: Research Project I (3 credits)

Course Objectives: This course has the following objectives:

• Familiarize students with the theory, concepts and methodology needed to

do a research project

• Train students to find research literature using library and online resources

• Develop the skills and knowledge to carry out field/laboratory work,

operate equipment, collect and process samples and other relevant

procedures.

• Initiate experiments and collect data.

• Present a progress report, including a preliminary literature survey, and

demonstrate the ability to continue with BIOL 5103 in the following

semester.

BIOL 5103: Research Project II (3 credits)

This is a continuation of BIOL 5101, which is therefore a pre-requisite.

Course Objectives: The student is expected to:

• Complete literature review.

• Complete the field or laboratory work.

• Analyze data.

• Interpret and discuss results.

• Present research findings in a departmental seminar.

• Submit a final thesis covering all aspects of the project.

Pre-requisites and co-requisites:

To register for BIOL5101 students must have completed or enrol

concurrently in the following courses:

• BIOL4000 Generic skills (Note this is only offered in Fall)

• BIOL 4100 Biological data handling

Requirements and expectations of students

Project can be the most rewarding and enjoyable part of your

undergraduate studies. It will help you decide if you wish to pursue a

career as a researcher. Employers look favourably on students who have

done project because it demonstrates independent thinking and initiative,

the ability to analyse data and to organise the results in to a report.

General requirements and expectations:

There are no formal lectures assigned to the project. However, students

will be expected to manage their own time and perform the required work

in consultation with their supervisor. The general expectations include:

o Arrange regular meetings with your supervisor.

o Follow instructions but feel free to make suggestions and discuss

the proposed work

o Collect relevant literature for your topic.

o Read the literature and keep written notes on points relevant to

your research

o Show initiative and try to solving practical problems with minimum

help.

o Follow instructions from assigned technicians and follow safe

laboratory procedures.

The following is a summary of assessable activities that are

undertaken during the project in a given semester:

BIOL5101

• Present a 10 minute seminar on their project topic in week 6 or 7.

Students will be assessed on both the scientific content and the

quality of presentation. The seminar will cover:

o Background of the project

o Aims and objectives

o Methods used

o Preliminary results, if any

o A timetable for proposed activities

• A progress report on the project. The progress report will include:

o A detailed literature review of between 5-8 pages 1.5

spaced.


o Methods for all work done or planned. Indicate clearly which

work was done by you and which was done by others. (E.g. if

you sent samples for analysis, it should be clearly indicated

where and by whom).

o Available results.

o Summary of achievements, obstacles encountered and

planned activities.

o References in required format

• Attend a 10 minute Viva where you will be asked to explain your

work, justify your methods and explain how you have dealt with any

difficulties.

• Your good laboratory practice, cleanliness and safety will be

assessed by the assisting technician and supervisor.

BIOL5103

Students will complete the following assessable activities during

the semester:

• Present a 15 minute seminar on their project topic in week 13 or 14.

Students will be assessed primarily on the scientific content of

the presentation. The seminar will cover::


o Materials and methods

o Results

o Discussion

• A final report on the project. The progress report will include:

o Abstract

o A detailed literature review of between 5-8 pages 1.5 spaced


o Materials and methods. Clearly indicate all work done by you

and done by others. (e.g. if you sent samples for analysis,

clearly indicate where and by whom).

o Results

o Discussion

o References in required format.

• Attend a 15 minute Viva where you will be expected to demonstrate

an understanding of your project, your achievements and

limitations.

• Your good laboratory practice, cleanliness and safety will be

assessed by the assisting technician and supervisor.

Course Evaluation

Both courses will be evaluated A to F based on the following:

BIOL 5101:

� Seminar for project proposal (10%). To be given in Week 4 OR 5 before all

available Biology staff and interested students. Each student will be given 10

minutes for presentation and five minutes for answering questions. The

seminar should include the scope, aims and objectives (hypotheses being

tested if any), methods used, experimental design (number of replicates,

analysis, etc.) and expected results. The function of the seminar is to show

that the project is viable and the students understand what they are doing.

� Supervisors report (25%). This evaluates the student’s progress during the

semester. See Appendix I for the format.

� Progress report written by the student (30%). The student will submit 3

typed copies to the Course coordinator by Week 14. See Appendix II for the

format.

� Oral Examination (30%). The student will be interviewed by the project

committee (Course coordinator + two other academic staff) for 20-30 minutes

to ensure that the students understands the background of their projects,

the methods being used and their preliminary results. Problems encountered

and the proposed future work will also be covered.

� Good Laboratory Practices and Safety (5%). Spot (unannounced checks will

be made by a team (the project coordinator, the Superintendent and the

Biology safety officer) to all student workplaces to ensure that the student is

keeping their work area clean and tidy, and that they are following the safety

guidelines.

BIOL 5103:

� Seminar on project results (20%). To be given in Week 13 before all the all

available Biology staff and interested students. Each student will be given 15

minutes and five minutes for answering questions. The seminar should briefly

cover the background, objectives and methods It will concentrate on the

results and the discussion. Note: the discussion should give a synthesis of the

significance of the results and how they fit in with previous studies. See

Appendix III for how the seminar will be graded.

� Supervisors report (15%). This evaluates the student’s progress during the

semester. See Appendix I for the format.

� Thesis (30%). The student will submit three typed copies to the Course

coordinator by Week 14. See Appendix IV for the format.

� Oral Examination (30%). The students will be interviewed by the project

committee (Course coordinator + other academic staff) to assess their

understanding and competence in carrying out their project. Afterwards, the

students should carry out any corrections demanded by the committee and

resubmit two corrected copies of their thesis (one for their supervisor and

1one for the Department).

� Good Laboratory Practices and Safety (5%). Spot (unannounced checks will

be made by a team (the project coordinator, the Superintendent and the

Biology safety officer) to all student workplaces to ensure that the student

is keeping their work area clean and tidy, and that they are following the

safety guidelines.

What is a Project?

The aim of project is to provide training for students in scientific research.

The aim in not to produce research that is ready for publication, although

sometimes student work may become part of a larger project that will eventually

achieve some form of publication through a conference or journal.

The project can be defined as a practical investigation carried out by a

student to inquire into some aspect of biology and conducted largely on his/ her

initiative. A project should involve practical work in the field or laboratory.

Investigations involving careful observation, description and analyses can also

make suitable projects. Basic features of all projects are:

a) Identification of a problem in the area of interest and selection of a limited

topic for investigation.

b) Investigation of the knowledge already available, including a survey of the

literature.

c) Experimental design, including the apparatus required; the methods of data

recording and the analysis of the results.

d) Carrying out the practical work.

e) Collecting and presenting the data.

f) Conclusions from the practical work, with due regard for accuracy and

significance.

g) Relating your conclusions to the background knowledge and producing

suggestions for further investigations.

h) Bibliography and acknowledgements, including all sources which have been

mentioned in the thesis.

Supervision of the project:

Each student has a supervisor, whose role is that of a guide to the student.

The supervisor has to make sure that the execution of the project is possible

without practical difficulties. Make sure that all the equipment and supplies are

available in the Department. Once the research topic is chosen, the supervisor

will give advice on the experimental design, the methods, the collection and

analysis of the data and discussing the results. A supervisor may supervise one or

two students while consultants may supervise with a co-supervisor.

In BIOL 5101, the supervisor will:

a) Advise the student on the scientific methods to be used in the project.

b) Examine the student's general background knowledge in the research area.

c) Report on the student's progress during the semester to the Project

Committee.

In BIOL 5103, the supervisor will advise on:

a) Data analysis.

b) Interpretation and discussion of the results.

c) Seminar presentation.

d) Presentation of the thesis.

The supervisor will also submit a report on the student's performance.

Although it is the supervisor's responsibility to advise on the project and

assist in getting it started, it is the student's responsibility to carry out the

project. Students should therefore develop a degree of independence both in

carrying out the project and in solving the problems encountered. On the other

hand, the student should keep the supervisor informed about the problems and

progress of the project and should meet with the supervisor at regular intervals.

Facilities: Laboratory space

Working space should be allocated by the Supervisor in his Research

Laboratory. If he/she does not have space, he/she can also try and help find space

in other laboratories of the department as long as it does not interfere with the

work of teaching labs and technicians. After the project students list is available

with complete information on the type of projects and facilities required, the

Laboratory Superintendent can be approached with a request for technical

assistance. Students can make these arrangements by themselves or seek

Supervisor’s help. Students may also be allowed to work in other research labs and

prep rooms, with the permission of the person in-charge.

In all laboratories, the following rules must be observed:

a) Always wear your laboratory coat

b) Do not drink or eat in the lab; do not store food or drinks in cupboards or

refrigerators meant for chemicals, glassware and equipment. Failure to observe

this could be hazardous to your health.

c) Respect the work of your classmates and do not touch their experiments.

Before you turn off a tap or electric switch, make sure that they are not part of

someone else's experiment.

d) Do not borrow your neighbor's equipment. If you need beakers, slides, ethanol,

etc, please ask the technician in-charge.

e) Do not invite friends into the project lab; they will not know the lab rules and

may unknowingly cause problems.

f) Be careful of fire hazards. Do not leave Bunsen burners unattended; store

flammable liquids safely after use.

g) Be prepared for accidents; know the position of the eye wash and first aid

kits. If there is an accident or any damage to equipment, the nearest technician

should be notified immediately.

Working hours

No students may remain in the lab after normal working hours (8 am to 4 pm),

without prior permission of the Head of Department and the labs will also be

closed during the weekend and public holidays. So students should take these into

account when designing their experiments. Special permission from the Head of

Department may be obtained to work during weekend. However, arrangements

should be made with the Laboratory Superintendent for opening and closing the

labs. Alternatively, the supervisor may take the responsibility to monitor the

student while weekend or holiday time work is necessary.

Equipment

The technician assigned to a student project will be responsible for supplying

equipment, chemicals etc. as needed.

Some equipment such as microscopes, pH meters etc. can be signed out for

the duration of the project. However, more specialized equipment such as

research microscopes, ovens, incubators, centrifuges, electrophoresis units,

microtomes etc. must be shared with other students and staff. Any problems with

the equipment, such as exhausted batteries, faulty electrical connections, should

be reported to the technician in-charge of your project as soon as possible.

Consumables, such as chemicals and glassware, will be supplied as needed by

the technician in-charge of the project. Students will sign for these.

The student is responsible for keeping their work place and equipment in a

clean and tidy state. At the end of the project, students must return the

equipment in good condition. All breakages should be notified to the technician in-

charge immediately

Technical Assistance

The technician assigned to your project will be able to give advice for many of

your technical problems. However, for assistance in using specialized equipment,

such as preparing SEM material, using the photomicroscopes, etc, contact the

Laboratory Superintendent. Please note that the technicians will only demonstrate

the techniques to be used, they will not do your project for you. Once you have

mastered the equipment, it is the student's responsibility to carry out the

technical part of their project (e.g. preparing histological sections).

Field Trips:

Students doing field work should produce a timetable with their supervisor,

who may then arrange for University transport via the College Administrator. All

University transport must be booked at least four weeks in advance. Please note

that female students must be accompanied by a female academic or non-academic

staff during all field trips. Trips longer than one day require University permission,

so that the Head of Department must be consulted via the Course Co-coordinator

well in advance.

If the field trip involves heavy work, such as lifting equipment, setting up nets

and traps, then technical assistance may be provided on a regular basis. However,

please remember that the technician is only there to assist and not to carry out the

practical work.

Appendix I

BIOL5101 Research Project

Supervisors Evaluation

Name of supervisor

Name of student

Aspect Evaluation (A-F)

1 Ability to do independent literature research

2 Ability to work with limited supervision & show

initiative

3 Ability to solve problems arising during the project

4 Worked consistently on the project

5 Shows good laboratory practice

Comments

Appendix II

BIOL 5101 Research Project

Format for Progress Report

Title page. This is similar to the title page in Project II, see appendix IV

Introduction.

This section should be fairly brief. It will consist of:

i) A brief review of relevant studies previously conducted in the subject area, in order to show what work has already been done and how the present research is related to these other studies.

ii) The objectives of the project should be clearly stated, preferably as a list of specific points.

Methods.

Results.

Describe clearly what you have achieved, giving your results in the form of tables and figures. Relevant photos may also be included. If you have done any preliminary analysis of your data, then this should be given. Raw data should not be in the Results section, but if you wish, you may include them as an Appendix at the end of the report.

Expected Work.

Provide a list of activities yet to be done for the successful completion of your project at the end of Semester 10. You should also give a rough timetable to show when you expect to complete each of the remaining stages of your project. E.g. dates for completion of each experiment; date for completion of analysis of data, etc.

Report Submission.

Submit 3 copies of your Progress report before the exams start at the end of Semester 9 to the Course Co-coordinator. The report should be typed on a word processor. The pages should be A4 size, with the typing double-spaced on one side of each page.

Apart from the top copy, the other two copies may be photocopies, but make sure that any photos are clearly legible when photocopied.

Appendix III

BIOL 5103 Research Project : Format for Thesis

Title page. See format in Appendix IV

Acknowledgments.

Table of contents; followed by List of Figures and List of tables.

Abstract. One page summarising what you did, your results and what they

showed.

Introduction. This section will be similar to your report for BIOL 5101 :

i) A brief review of relevant studies previously conducted in the subject area, in order to show what work has already been done and how the present research is related to these other studies.

ii) The objectives (hypotheses)of the project should be clearly stated,

preferably as a list of specific points.

Methods.

Results.

Describe clearly what you have achieved, giving your results in the form of tables and figures (but do not duplicate the same data in both tables and figures). Relevant photos may also be included. Be careful in graphs: it is not wise to use colours that cannot be distinguished when photocopied in black & white. It is better to use black lines of different types (dotted, dashed, etc). Graphs would normally have standard errors on them. Where relevant, clearly state how you analysed your data.

Do not discuss your results here. Only explain what they show.

Raw data should not be in the Results section, but if you wish, you may include them as an Appendix at the end of the report.

Discussion.

Here you should not only discuss the relevance of what your results show, but also how they compare with studies by previous researchers. You should try to synthesise, not just list other research (not Author A showed this; Author B showed that, Author C showed this) - show what they had in common with your work and what were their differences, and explain why.

Thesis Submission. Submit 3 copies by the end of Week 14 to the Course Co-

coordinator. The report should be typed on a word processor. The pages should

be A4 size, with the typing double-spaced on one side of each page. Apart from

the top copy, the other two copies may be photocopies, but make sure that any

photos are clearly legible when photocopied.

Previous examples of theses. Samples of theses written by students of

earlier cohorts are available in the Coordinator’s office. You are welcome to

borrow these via your supervisor.

Appendix IV: Title page for Thesis

Name of

BIOL 5103: Research Project II

Appendix IV: Title page for Thesis



Title of Thesis

Name of Student & ID

Supervisor:

BIOL 5103: Research Project II

Final Thesis

Date: (e.g. June 2016)

Key Dates

Task Date

Project 1

Submit short summary of planned project

(<150 words) and copy of Power Points for

seminar.

Week 6 or 7: 1 day before seminar

Project 1 seminar (10 minutes + 5 minutes

questions)

Week 6 or 7

Stop all lab work End of Week 13

Submit progress report End of Week 15

Project 1 vivas Week 16

Project 2

Stop all lab work End of week 12

Submit abstract of seminar (<150 words)

and copy of Power Points for seminar.

Week 13: 1 day before seminar

Project 2 seminar (15 minutes + 5 minutes

questions)

Week 14

Submit final report End of week 15

Project 2 vivas Week 16

College of Science Department of Biology ___________________________________________________________________________ Course Code: BIOL 5120 Course Title: Microbial Biotechnology General Information Number of Credits: 3 Instructional Format: Lecture and Lab Contact Hours/Week: 4 (2 lectures and 1 lab) Prerequisite: BIOL 3441, BIOL 4044 Co-requisite: Assessment: Test 1: 15%; Test 2: 15%; Lab quiz: 10%; Lab reports: 10%;

Lab test: 10%; Final: 40% Grading (A–F, Pass/Fail): A-F Textbook: Microbial Biotechnology: Fundamentals of Applied

Microbiology by Alexander N. Glazer and Hiroshi Nikaido, Second edition, Cambridge University press, 2007.

References (optional):

1. Course Description This course covers the applications of microorganisms or microbiological processes for the benefit of human beings. The lectures start with how microbial diversity is useful to mankind. It also explains the significant role of microbes in vaccine production, plant microbe interactions, development of microbial insecticides, production of microbial polysaccharides and polymers. Useful primary and secondary metabolites produced by microbes are discussed. This course also covers the environmental applications of microorganisms.

2. Course Objectives This course explains how microorganisms are commercially exploited to produce useful products to human beings. This course gives a better understanding of how microorganisms are used to produce synthetic and recombinant vaccines, production of disease resistance plants and mode of action of microbial insecticides and their benefits. It describes the production of polysaccharides and bio plastics produced by microbes. This course gives a description of organic acids, amino acids and antibiotics produced by microorganisms. Furthermore it provides knowledge about the microbial degradation of wastes, heavy metals and xenobiotics.

3. Learning Outcomes [Use Bloom’s taxonomy] (a) Students understand the commercial applications of microorganisms

(b) They also acquire knowledge about environmental applications of microbes (c) They will be able to isolate enzyme and antibiotic producing organisms

(d) They acquire the ability to isolate the bacteria of interest

(e) Able to screen and enrich the bacteria

4. Assessment

Assessment Criteria

Learning outcome:








5. Course Structure The course is designed to be delivered in one semester of 15 weeks with 4 contact hours per week (2 practical and two theory). The course weight is 3 credit hours.

6. Topics [A breakdown of the syllabus into major components listed logically and by weekly coverage if need be. This should be detailed enough to enable another instructor to teach the course at the same level.] Unit Topics Sections Lectures/Weeks 1 Microbial

diversity Prokaryotes and Eukaryotes Two groups of prokaryotes Principal modes of metabolism

1/1

Taxonomic diversity of bacteria with uses in Biotechnology Culture collection and preservation of microorganisms

2/2

2 Recombinant and synthetic vaccines

Problems with traditional vaccines Input of biotechnology on vaccine development

2/3

Improving the effectiveness of subunit vaccines

1/4

3 Plant-microbe interactions

Production of transgenic plants Direct introduction of cloned genes into plants

1/4

Herbicide-resistant plants 2/5

Insect-resistant plants Virus-resistant plants

Plants resistant to fungi and bacteria Stress tolerant plants

1/6

4 Microbial Insecticides

Bacillus thuringiensis Crystalline inclusion bodies Mechanism of action of BT insecticide B. thuringiensis β – exotoxin

1/6

Mechanism of δ – endotoxin action Role of BT toxins in nature Impact of non-target organisms

1/7

5 Microbial polysaccharides and polymers

Polysaccharides Bacterial polysaccharides Roles of microbial polysaccharides in nature

1/7

Xanthan gum Structure and properties of xanthan Production of xanthan gum

1/8

Polyesters Occurrence Synthesis of novel polyesters through co metabolism PHA as biodegradable thermoplastics Genetis engineering of plants for the production of PHA Obstacles

2/8&9

6 Primary metabolites: Organic acids and amino acids

Citric acid L- Glutamate

2/9&10

Need for amino acids other than glutamate Auxotrophic mutants Regulatory mutants

1/10

7 Secondary metabolites

Antitumour agents Peptidase inhibitors Inhibitors of cholesterol biosynthesis

1/11

Immunosuppressants Antibacterial agents Primary goals of antibiotic research Physiology of antibiotic production

2/11&12

8 Environmental applications

Degradative capabilities of microorganisms Behaviour of organic compounds in the environment Waste water treatment

2/12&13

Microbial degradation of xenobiotics Microbial basis of biodegradation Types of bioremediation In situ bioremediation In situ remediation of oil spills

2/13&14

Composting Landfarming Above ground bioreactors Genetic and metabolic aspects of biodegradation

1/14

Microorganisms in mineral recovery Diversity of bacteria that cause bioleaching How bacteria leach metals from ores Microorganisms in the removal of heavy metals

2/15


Week Content 1 Microbiology lab practices and safety rules 2 Yogurt fermentation with Lactobacillus cultures 3&4 Production and assay of penicillanase 5&6 Isolation of antibiotic producing organisms 7 Comparative evaluation of antimicrobial chemical agents 8 Phenol coefficient 9 Enrichment culture technique: Isolation of phenol utilizing

microorganisms 10 Industrial visit 11 Isolation of phosphate utilizing bacteria 12 Isolation of amylase producing bacteria from soil 13 Laboratory production and assay of amylase 14 Lab test


College of Science


BIOL 5132 TISSUE CULTURE

Course Description

This course is aimed at understanding the concepts of plant and animal tissue culture and their

applications in in vitro biotechnology. The topics include Plant tissue culture, micropropagation,

organogenesis, somatic embryogenesis, in vitro haploid production, somaclonal variation,

protoplast isolation, culture and somatic cell hybridization. Genetic transformation in plants and

animal cell culture.

Credit Hours : 3

Format : Two one hour lectures and Three hour laboratory per week

Prerequisites : BIOL 4045

Textbook #1 : Plant Biotechnology by H.S. Chawla.

Laboratory book : Plant Tissue culture Concepts by Dennis J. Gray.

Text book #2 : Stem Cells by A. M. Wobus (2006)

Reference E-book : Principles of Tissue Engineering by Lanza R. (2007)

Coordinator : Dr. S. A. FAROOQ

Room 1099 Ext. 1487

and

: Dr. S. Baqir

Room 1068 Ext. 1450

Course Assessment

The course will be assessed (Grading Scale A-F) as follows:

Laboratory Reports - 10%

Laboratory test - 10%

Mid-term Test (Plant) - 15%

Mid-term Test (Animal) - 15%

Quizzes/Seminar - 10%

Final Examination - 40%

Students Should not damage the textbooks by writing , underlining or highlighting. If they do so,

they would be penalized.

Students must return the textbook on the day of final examination.

Students must submit laboratory work in time.

Lecture Schedule

Plant Tissue Culture:

Introduction to Plant Tissue culture

Applications of plant tissue culture

Plant Tissue culture Media & Culture Techniques

Totipotency & Organogenesis

Micropropagation

Nonzygotic embryogenesis

Cell Suspension culture and

Secondary metabolite production

Production of Haploids

Gene transfer in Plants

Animal Tissue Culture

Section 1: Tissue culture introduction

History

Cell Technology

Regulatory considerations

Technology platforms to clinical setting

Principles of Animal Tissue Culture

Initiation of the Culture

Subculture and propagation

Sourcing cell lines and strains

Growth cycle

Passage number and generation number

Contamination

Characterization

Immortalization & Transformation

Cytotoxicity & Mutagenesis

Tissue Structure and Molecules

Cell Division in tissues

Cell Adhesion molecules

Culture Media

Tissue cell types

Section 2: Stem Cells

Introduction

Definition

Embryonic stem cells

Adult stem cells

Postnatal stem cells

Self Renewal and Pluripotency

Background

Extrinsic factors

Intrinsic Factors

Summary

Embryoid Bodies (EBs)

The genesis of embryoid bodies

ESC Lines influence on embryoid bodies formation

Pre gestrulation-like development of EBs

Markers of Adult Tissue-based Stem Cells

Common attributes of Stem Cells

Organ-Specific Stem Cells

Section 3: Tissue Engineering

Introduction

Relevance

Section 4: Future Directions

Smart biomaterials

Bioreactors

Section 5: Ethics in Tissue Culture/Engineering

Social challenges

Bioethical Concerns

Religious prospective

Laboratory Schedule

Week 1 Plant tissue culture video and Preparation of media (pages 21-38)*

Week 2 Effect of Cytokinin and Auxin on organogenesis in Petunia (pages 167-173)*

Week 3 Somatic embryogenesis from cotyledon explants of Peanut (pages 213-229)*

Week 4 Micropropagation of African Violet

Week 5 Embryo culture of maize

Week 6 Effect of Auxin & Cytokinin on Shoot organogenesis in Cauliflower

Week 7 Trip to Tissue culture lab, Jumah / Agrobacterium mediated Gene transfer in

plants. (pages 321-328)*

Week 8 Techniques in handling the laboratory mouse

Week 9 Mechanical/enzymatic disintegration of animal tissues

Week 10 Primary tissue cultures (Mouse)

Week 11 Cell separations and characterization

Week 12 Tissue cryopreservation

Week 13

Week 14

Week 15 Lab Test

From week 4 in every lab you have to examine your cultures and if required subculture them

* Read pages from spiral bound book Plant tissue culture concepts & Laboratory exercises.


___________________________________________________________________________

Course Code: BIOL 5144 Course Title:Applied Mycology

General Information


Instructional Format: lectures Contact Hours/Week: 4

Prerequisite: BIOL 3441 Microbiology Co-requisite: NO

Assessment: A-F Text Book:

The Fungi by M.J. Carlie, S.C. Watkinson & G.W. Gooday Second Edition Reprinted 2007


This course describes fungal diversity, the role of fungi in ecosystems, fungi and biodeterioration, how fungi cause infection and penetrate plant tissues, fungi that cause diseases in humans and animals, fungi and biotechnology, fermentation technology, enzyme technology, the production of economically important primary and secondary metabolites by fungi : citric acid, antibiotics, ergot alkaloids, fungicides and gibberellins

2. Course Objectives To exposure students to the world of mycology which is the most applied of all biological sciences. It helps them to improve the quality of human life.

3. Learning Outcomes[Use Bloom’s taxonomy]

Having successfully completed this course the students will be able to

1. Prepare media for the cultivation of microorganism and compare between

different categories of media.

2. Isolate microorganism in pure culture.

3. Identify bacteria through different staining procedures.

4. Examine and analyze water for portability and classify water as potable, safe,

polluted and contaminated.

5. Analyze and compare the antimicrobial properties of spices and commercial

antibiotics.

6. Prepare Produce inoculants and inoculate legume seeds in Rhizobium

biotechnology.

7. Identity and classify fungi on seeds, fruits and vegetables.

8. Quantify and enumerate microorganisms in a gram of soil or one ml of milk.

9. Evaluate the efficiency of sewage treatment plant.

10. Isolate and identify microorganisms in sewage water

11. Test the ability of soil microorganisms to produce enzymes

12. Compare between different types of viruses

4. Assessment

Assessment Criteria

Assessment : Tests:

1. Test 1 15%

2. Test 2 15%

3. Lab Test 15%

4. Project 15%

5. Final Exam 40%

Total 100%

1. Test 1

2. Test 2

3. Project

4. Final exam

5. Course Structure The course is designed to be delivered in one semester of 15 weeks with 4/5 contact hours per week (2/3 practical/tutorial and two theory). The course weight is 3/4 credit hours.

6. Topics

Page

1. The Fungi as a Major Group of Organisms

The Fungi 1

The Classification of Organisms into Major Groups 3

The Study of Fungi 5-7

2. Fungal Diversity

The Oomycetes 25-32

The Zygomycetes 38-43

The Ascomycetes 44-54

The Basidiomycetes 57-67

The Mitosporic Fungi 69-70

The Yeasts 70-73

The Lichens 76-79

3. Fungi and Biotechnology 461

Fermentation Technology 462-475

Enzyme Technology 476-478

The Cultivation of Fungi for Food 492-496

The Production of Fungi of Primary Metabolites of Economic Importance

507-510

4. Parasites and Mutualistic Symbionts 363

Fungi and Plants 363-419

Medical Mycology 432-443

Veterinary Mycology 443-444

5. Handout Articles

Mycotoxins Contaminating Cereal Grain Crops:

Their Occurrence and Toxicity

171-188

Production of Organic Acids and Metabolites of Fungi for Food Industry

387

1. Introduction

2. Organic Acids

2.1 Citric Acids

2.1.1 Raw Materials

2.1.2 Production Processes

2.1.3 Surface Fermentation

2.1.4 Submerged Fermentation

2.1.5 Aspergillus niger Fermentation

2.1.6 Yeast

2.1.7 Overproduction of Citric Acid

2.1.8 Immobilization

2.1.9 Applications

2.2 – 2.2.5 Gluconic Acid

2.3 – 2.3.1 Fumaric Acid

2.4 Itaconic Acid

2.5 – 2.5.2 Kojic Acid

2.6 Malic Acid ))

2.7 Lactic Acid

2.8 – 2.8.1 Tartaric Acid

2.9 Succinic Acid

3. Fungal Metabolites

3.1 Amino Acids

3.2 Vitamins

3.2.1 Vitamin B2 (Riboflavin)

3.2.2 Vitamin B6 (Niacin)

3.2.3 Vitamin A

3.2.4 Vitamin D

3.3 Flavors and Nucleotides

3.3.1 Flavors

3.3.2 Aroma Compound

3.4 Lipids and Fatty Acids

3.5 Polysaccharides

3.5.1 Pullulan

3.5.2 Scleroglycan

3.5.3 New Polysaccharide from Yeast

3.6 Other Metabolites

4. Conclusion

387

387

388

388

389

389

390

390

392

392

393

394

395-397

397-398

398

401

401

403

404

404

405

405

406

406

407

407

408

408

408

409

410

411

412

412

414

414

414

The Role of Thermophilic Fungi in Agriculture 707

I Introduction 707

II History 707

III Colonization and Heating of Agriculture 712

A. Water Activity 712

B. Aeration 712

C. Nutrition 713

IV Colonization of Substrates 713

A. Grain 713

B. Hay 713

C. Other Substrates 715

V Composting of Plant and Animal Wastes 716

A. Heat Production by Composting Organic Matter 718

B. Mode of Substrate Degradation 718

C. Soil Modification with Compost 719

VI Colonization in Natural Habitats 720

VII Conclusion 721

Biotechnological Potential of Thermophilic Fungi

I Introduction 729

II Characteristics endowed on thermophilic molds 730

A. Simple Nutritional Requirements 730

B. Wider Extrcellular Enzymatic Activity 730

C. High Growth rates 732

D. Higher Temperature Requirements 732

E. Thermostability of the Macromolecules 732

F. Stress Resistance 734

III Potential Biotechnologies 734

A. Extracellular Enzymes 735

1. Amylases

2. Proteases

3. Lipases

4. Xylanases

5. Cellulases

735

735

736

737

738

B. Exopolysaccharides 742

C. Bioconversion of Sterols and steroids and binding of steroids 742

D. Upgradation of animal feeds and sep 742

E. Antibiotics and volatile sporostatic factors 745

F. Phenolics, organic acids, and amino acids 745

G. Thermophilic mold enzymes in processing of oil seeds 745

H. Experimental system for genetic manipulation 745

IV Conclusions 746

References 746

7. Laboratory component

Week 1 Characteristics features of Oomycetes

Week 2 Characteristics features of Zygomycetes

Week 3 Characteristics features of Ascomycetes ,Plectomycetes

Week 4 Characteristics features of Ascomycetes ,Dscomycetes

Week 5 Characteristics features of Basidiomycetes , Hymentomycetes

Week 6 Characteristics features of Basidiomycetes , Ustomycetes and

Teliomycetes

Week 7 The mitosporic fungi ,Hyphomycetes 1

Week 8 The mitosporic fungi ,Hyphomycetes 2 and coelomycetes

Week 9 The lichens

Week 10 Aflatoxin quantification by monoclonal antibodies.

Week 11 Nematophagous fungi

Week 1 to week 10 * Group project on isolation and identification of fungi using morphological characteristic and molecular techniques.

SULTAN QABOOS UNIVERSITY College of Science

Course Information Form

Department: Biology Course Code: BIOL5400 Credit & Contact Hours: 3 credits = 5 hours (2 lect + 1 lab) Course Title: Introduction to Bioinformatics Prerequisite(s): BIOL3201 Molecular Biology Co-requisite(s): BIOL4500 Cell Biology or equivalents. Textbook(s): Practical Bioinformatics by Michael Agostino Course Coordinator: Aliya Alansari Description: Bioinformatics is the science of organizing, storing, extracting, analyzing and interpreting biological data.

The course introduces the main principles of Bioinformatics. It includes database

searching, sequence analysis, and structure prediction.

Aims & Objectives: Train the students to develop hands-on skills in biological data storage, retrieval, analysis and interpretation. Learning Outcomes

1. Knowledge: • Be familiar with Biological data storage and different analysis approaches. 2. Skills: • Able to retrieve different types of biological data from specialized databases. • Know who to analyze biological data using specific tools and can interpret the results.

Grading Scheme : The grading scheme will be the university letter grading scheme (A to F)

Assessments: Theoretical exam 15% Theoretical exam II 15% Project 15% Assignments 15% Final Exam 40%

Syllabus: Introduction

Biological data (Genomes, genes, RNA and protein); storage, searches and analysis.

Biological Databases and Information retrieval Non-sequence Databases

Primary and Secondary databases Structure databases Genomic databases Metabolic pathways databases Genome databases Search engines

Sequence Alignment and database searching Simple Alignments Gaps

Scoring Matrices Global and Local Alignments

Database Searches Alignment Scores and Statistical Significance

Multiple Sequence Alignments Analyzing sequences

DNA sequences Eukaryotic Gene structure

Promoter elements sequences Regulatory Protein binding sites

Open Reading Frames identification Termination sequences Introns and exons

Translation Molecular biology Tools

Polymerase chain reaction DNA sequence editing Restriction enzyme digests

Protein sequences

Post-Translational Modification Prediction Hydrophilicity and Hydrophobicity

Protein structure

Secondary Structure Tertiary Structure

Instructional Methodology & Teaching Resources: Lectures Web based exploration Labs Problem-based learning Project and presentation

SULTAN QABOOS UNIVERSITY College of Science

Course Information Form

Department: Biology Course Code: BIOL5402 Credit & Contact Hours: 3 credits = 5 hours (2 lect + 1 lab) Course Title: IMMUNOLOGY Prerequisite(s): BIOL 3441 Microbiology Co-requisite(s): BIOL4500 Cell biology Textbook(s): Roitt's Essential Immunology Course Co-ordinator: Aliya Alansari Description: The course consists of lectures, practical(s), assays, seminars and a visit to an immunology laboratory. The course provides a broad overview of immunology. It covers the historical background and the immune system in health and disease. Topics include Innate and Adaptive Immunity, Antibody- and cell-mediated immune responses, Cytokines, Antigen, Antigen Processing and Histocompatibility Antigens, Complement, Regulation of the immune response, Tolerance, Organ Transplantation, Immunity and infection, vaccination, Defects in the immune system, Inflammation, Hypersensitivity, Autoimmunity and Immnoassays.

Aims & Objectives: Understand how the immune system works in health and disease. And apply some of the Immunological test in different investigations.


Assessments: Theoretical exam I 15% Theoretical exam II 15 % Reports 5% Practical test 15% Literature review & 10% Presentation Final Exam 40%

Learning Outcomes 1. Knowledge: Explain the basic components of the immune system and its role in host defense Describe the consequences of immune system failure or dysfunction Recognize the value of immunological tools 2. Skills: understand the basic principles of the immunological tests, carry the tests and interpret the results. Syllabus:

1. Antigens and Receptors 2. Barriers to Infection 3. Cells of the Innate Immune System 4. Innate Immune Function 5. Molecules of Adaptive Immunity 6. Cells and Organs 7. Generation of Immune Diversity: Lymphocyte Antigen Receptors 8. Lymphocyte Development: B Cells and T Cells 9. Lymphocyte Activation 10. Lymphocyte Function 11. Regulation of Adaptive Responses 12. How Innate and Adaptive Immune Responses Maintain Health 13. Hypersensitivity responses 14. Immunodeficiency 15. Autoimmunity 16. Transplantation 17. Measurement of Immune Function

Instructional Methodology & Teaching Resources: Lectures Labs Short animations Paper presentation Invited speakers talks

College of Science Department of Biology ___________________________________________________________________________ Course Code: BIOL 5411 Course Title: Fermentation Technology General Information Number of Credits: 3 Instructional Format: Lecture and Lab Contact Hours/Week: 5 (2 lectures and 1 lab) Prerequisite: BIOL 4030 Co-requisite: none Assessment: Test 1: 15%; Test 2: 15%; Lab quiz: 10%; Lab reports: 10%; Lab

test: 10%; Final: 40% Grading (A–F, Pass/Fail): A-F Textbook: “Principles of fermentation technology”. Peter F. Stanbury, Allan

Whitaker & Stephen J. Hall. 2nd edit. Butterworth-Heinemann. References (optional):

1. Course Description This course provides knowledge about the industrial applications of microorganisms in production and treatment processes. This course also adds technical information on fermenter design, operation and growth kinetics of microbes involved in the fermentation processes. Types of fermentations and the commercial products derived from microbes are also discussed in this course. Students will get hands on experience in the microbial production of biopolymer, enzymes, bioactive compounds and biomass. Based on the skills acquired in this course, graduate students would have a mini project / review writing/ assignment as an additional component.

2. Course Objectives This course provides an understanding of the exploitation of microorganisms in the manufacture of bulk commodity biological products. This course highlights the application of biological and engineering principles involving in microbial fermentation systems. The lectures will emphasize and place perspectives on biological systems with industrial practices. Topics to be discussed include microbial growth techniques, isolation, media composition, sterilization, inoculum development, process design, fermentation, downstream processing of products including separation and purification technology,.

3. Learning Outcomes [Use Bloom’s taxonomy] (a) Students will be able to recognize the fundamentals of microbial fermentation

(b) Can isolate industrially important organisms from soil

(c) Production of microbial biomass, metabolites and enzymes

(d) Know the different types of downstream processing

(e) Based on the skills acquired in this course, students will be able to optimize different bacterial

fermentation conditions

4. Assessment

Assessment Criteria

Learning outcome:








5. Course Structure The course is designed to be delivered in one semester of 15 weeks with 5 contact hours per week (1practical and two theory). The course weight is 3 credit hours.

6. Topics [A breakdown of the syllabus into major components listed logically and by weekly coverage if need be. This should be detailed enough to enable another instructor to teach the course at the same level.] Unit Topics Sections Lectures/Weeks 1 Design of

fermenter and kinetics

Types and modes of operation, design and construction of bioreactors for different products

2/1

Fundamentals of process control and monitoring

2/2

Microbial kinetics

Batch, fed-batch and continuous cultures – Phases of batch growth

2/3

Kinetics of cell growth – Yield concept and productivity.

2/4

2 Downstream processing

Characteristics of biotechnological products. Primary separation – removal of insoluble materials

1/5

Cell disruption - Product isolation 1/5 Purification techniques – Product

polishing.

2/6

3 Fermented food products

Dairy products: Milk processing - Cheese - principles of cheese making

1/7

and food additives

Production of additives - organic acids (acetic acid, lactic acid and citric acid)

2/7&8

Production and characterization of bacteriocins

1/8

Production, purification and characterization of xanthan

2/9

4 Bioactive compounds and enzymes

Antibiotics (penicillin, streptomycin, tetracycline),

2/10

DNAses, cellulases 2/11 Proteases, lipases 2/12 Extremozymes 2/13 5 MEOR

biproducts Biosurfactants, 1/14

Biopolymers, gases, acids, solvents 3/14&15


Week Content 1 Measurement of biomass 2 Seed culture and inoculum preparation 3 Production of polysaccharide by bacteria 4 Measurement of cell dry weight, reducing sugar,

polysaccharide production and yield 5 Standardization of best carbon source for polysaccharide

production 6 Isolation of cellulase producing organisms 7 Enrichment culture technique 8 Fermentative production of bacterial cellulases 9 Standardization of cellulase fermentation conditions( Carbon

and nitrogen) 10 Standardization of cellulase fermentation conditions

(Temperature and pH) 11 Enzyme kinetics of cellulase via initial rate determination 12 Bacteriocin production by Lactobacillus sp. 13 Determination of Bacteriocin activity 14 Biosurfactant production 15 Lab test

Protein Production and Characterization (BIOL5501)

Instructor: Mahmoud Yaish, [email protected]

Description:

The course is designed for advanced undergraduate and postgraduate students. This course will give students a

theoretical overview and intensify the practical aspect of protein purification, analysis and applications.

Objectives:

To provide a theoretical and practical aspect of protein purification, separation, detection and measurement.

Goal:

The students will be able to analyze protein and improve their practical skills and solve problems related to the

optimization of protein extraction, purification and analysis.

Assessment and learning outcomes:

At the end of the course the students will be anticipated to understand the scientific basis behind protein

production and purification at the laboratory as well as at the industrial levels. This includes practical

skills in automatic chromatography purification, protein engineering and bioinformatics.

Perquisites:

Fundamental Biotechnology (BIOL 4046) and Biochemistry (BIOL 4034).

Content of the Course:

1- Protein Description and Classification.

2- Protein Purification.

A- Extraction of Protein (total extraction, membrane protein extraction).

B- Quantification of extracted proteins.

C- Purification and concentration by ultrafiltration and precipitation with sodium sulfate.

D- Immunoaffinity chromatography.

E- Affinity chromatography.

F- Removal of detergents from the extracted proteins.

G- Dialysis.

3- Detection of the Extracted Protein.

A- SDS Polyacrylamide Gel Electrophoresis (SDS-PAGE).

B- Native Gels Electrophoresis.

C- Gradient SDS Polyacrylamide Gel Electrophoresis.

D- Staining techniques.

E- Isoelectric Focusing and 2-dimentional PAGE.

F- ELISA technique.

G- Western Blot.

4- Electrobloting of Proteins from Polyacrylamide Gels.

5- Production of Recombinant Protein in Bacteria.

A- Cloning strategy.

B- Expression.

C- Purification.

6- Measuring the Enzymatic Activity.

7- Storage and Stabilization of the Protein.

A- Freezing.

B- Lyophilaization.

8- Overview on Protein Advanced Techniques.

A- Sequencing.

B- Protein NMR.

C- Protein Array.

D- Protein Nanotechnology and Application.

Format of the course:

6 hour lecture and laboratory/week.

Distribution of the marks:

Midterm Exam: 25%

Final: 40%

Report: 10%

Seminar: 10%

Attendance: 10%

Quizzes 5%

Sultan Qaboos University College of Science

Department of Biology BIOL 5600 Techniques in Molecular Diversity

Course Coordinator : Dr. Aliya Alansari

Office : College of Science Room 1025

Credit hours : 3

Contact hours : 2 per week for 15 weeks

Lectures : 1 per week

Practical : 2 per week (5h)

Prerequisite : BIOL3202 Molecular Biology

Course Description : The course will provide the student with hands on experience of laboratory

and in silico techniques currently used in detecting and analyzing molecular diversity.

Applications in different areas, including molecular identification of genetic variations,

species, individuals, sex and pathogens, DNA barcoding, forensic genetics, conservation

forensics, population genetics, and molecular medicine, will be covered.


Assessment for the course will be as follows: Lab Notebook 20%

Practical skills 20%

Theoretical tests (2) 20%

Reports (5) 20%

Project 20%

Learning Outcomes:

Successful students in this course will be able to:

• Identify and describe the suitable techniques and analyses used to address a question based on molecular diversity.

• Design, prepare for and perform the techniques • Analyze and Interpret data from different molecular fields and communicate the findings • review and evaluate the literature to develop a proposal for addressing a research question using molecular

techniques


___________________________________________________________________________

Course Code: Biol 5610 Course Title: Environmental Impact Assessment

General Information


Instructional Format: 2 (1 hr) Lectures + 1 (2-3 hrs) Laboratory / week Contact Hours/Week: 5 hrs Prerequisite: Biol 3009 Co-requisite: None

Assessment: Group works, Presentation-case studies, Exams (Midterm and Final)

Grading (A–F, Pass/Fail): A-F Textbook: None References (optional): UN university open resource module


The course deals in general the overview of Environmental Impact Assessment. A note on the purpose and utility of EIA.Then in detail the EIA process (Methods) from Screening to EIA reporting in accordance with the general EIA framework. Also will highlight the Law, policy and institutional arrangements for EIA in Oman. The course also covers few case studies around the world from development projects.

2. Course Objectives

This is an advanced course that covers the purpose and methodology of preparing environmental impact assessments (EIA), generally case studies will be used to illustrate the main topics.

3. Learning Outcomes

On completion of the course the students should be able to:

1. Appraise the purpose and role of EIA in the decision-making process;

2. Explain different elements and the steps in the EIA process

3. Connect the various elements of the EIA process from the screening to the

review process;

4. Analyse the environmental issues relevant to the development projects

5. Identify the potential impacts and significance of development project.

6. Evaluate the project appraisal of EIA case studies

4. Evaluation

The course will be graded using an A (exceptional performance) to F (unacceptable

performance) system. Final grade will be based on the following evaluations

(components depend on the course).

Evaluation Weight

Presentation 15%

Case study-Term

paper

15%

Mid- Exam 30%

Final Exam 40%

5. Course Structure

The course is designed to be delivered in one semester of 15 weeks with 4/5

contact hours per week (2/3 practical/tutorial and two theory). The course

weight is 3/4 credit hours.

6. Topics

[A breakdown of the syllabus into major components listed logically and by weekly coverage if need

be. This should be detailed enough to enable another instructor to teach the course at the same level.]

Unit Topics Sections Lectures/Week

1 Introduction Introduction to EIA 2

Sustainable development 1

Role of EIA 2

2. EIA

Legislation

General guidelines 2

EIA legislation in Oman 2

3. EIA

Process

EIA process framework 1

4 Screening Methods of screening 2

Screening list 1

5. Scoping Purpose of scoping in EIA 1

Elements in the scoping process I 2

Elements in the scoping process II 2

6 Impact

assessment

Identification of Impacts 2

Impact prediction 2

Impact evaluation 2

Impact significance 1

7 Impact

mitigation

Mitigation framework 1

Mitigation measures 2

8 EIA review Review process in EIA 1


Week Content

1 Introduction to group discussion-Rules and roles of the

members

2 Comparative EIA legislation-Presentation

3 Screening criteria analysis-Group exercise

4 Screening exercise-Presentation

5 Scoping activity(Identification of potential impacts)

6 Synthesis of long and short lists for scoping

7 Impact assessment methods I

8 Impact assessment methods II

9 Impact assessment methods II

10 Impact evaluation methods

11 Impact significance analysis

12 Impact significance appraisal

13 Reporting

SULTAN QABOOS UNIVERSITY COLLEGE OF SCIENCE

DEPARTMENT OF BIOLOGY Course Code : BIOL6205 Course Title : DEVELOPMENTAL BIOLOGY Pre-requisite : BIOL5042 Embryology Credits : 3 CU Format : 3 (1 hr) Lectures / week Course Coordinator : Prof. Taher Ba-Omar

[email protected] Lecturers : Prof. Abdulkader Elshafie Prof. Saif Al-Bahry Dr. Mahmoud Yaish

Prof. Taher Ba-Omar Textbook : DEVELOPMENTAL BIOLOGY 6th edition by Scott Gilbert Description : This course has three main components. Part I. Development in Bacteria and Fungi

Growth of cell and cell Cycle, Growth rates as a variable, cellular differentiation. Regulation of

bacterial differentiation. Sporulation and endospore formation. Differentiation of photosynthetic

bacteria. Fundamental and applied aspects of bacterial spores.The fungal cell and tissues ;

vegetative multicellular system; sexual development in Oomycetes, Basidiomycetes and

Ascomycetes. Conidiogenesis in mitosporic fungi.

Part II. Development in Plants

Growth, development and differentiation, Development of roots and shoots, Cell differentiation,

Cell death in plants, Development of flower and homeotic flower mutants, Pollination and

apomixis, Embryogenesis, Dormancy, Post embryo vegetative development.


Part III. Development in Animals

Analysis of Biological Development, Role of cells in development, The Impact of Molecular and

Cellular Biology, Gametogenesis, fertilization and cleavage, Gastrulation, Neurulation, Cell

Motility, Cell Adhesion and Morphogenesis, Cell Differentiation, Hormonal Control of

Development, Apoptosis, Development and Cancer.

Schedule for the Lectures:

Development in Bacteria and Fungi (10 Lectures)

Development in Plant (10 Lectures)

Development in Animal (20 Lectures)

Grading The course is graded A – F. The grade distribution among various course elements such as seminars, tests, assessments, homework and final examination is left to the discretion of the instructor.

Assessment

Development in Bacteria and Fungi 25%

Development in Plant 25%

Development in Animal 50%

Schedule for the tests : To be arranged with the lecturers

Test-I (Bacteria and Fungi development)

Test-II (Plant development)

Test-III (Animal Development)

Test-IV (Animal Development)



Course Outline


3 credits = 4 h/wk Course Title: Biostatistics Prerequisite(s): BIOL 4100 or An equivalent course in Statistics Co-requisite(s): None Textbook(s): Biostatistical Analysis, 5th Edition, J.H.Zar Course Coordinator: Prof. Reginald Victor

Description: This is an advanced course that covers complex models in parametric procedures including multivariate statistical techniques. It also covers non-parametric procedures that are equivalent of their parametric analogues with particular reference to large data sets

Aims & Objectives: This course builds on the basic knowledge of statistics and goes on to advanced techniques that are normally required by research students in biology with minimum or no mathematical background. It emphasizes on application rather than theory and informs on the appropriateness and validity of procedures used.


To learn how to successfully analyze and interpret data collected during postgraduate research

2. Skills: a. Ability to independently plan experiments, and collect and analyze data using

appropriate statistical methods b. Ability to use statistical software packages for advanced statistical analysis.

Syllabus: The syllabus is determined on the basis of the students’ previous knowledge in statistics and is tailor-made to match their research needs. Students are required to do several assignments, often in their own area of research.

Instructional Methodology & Teaching Resources: Lectures and practical workshops Course Assessment: Final Open-book Examination (maximum time 24 hours): 50% Homework problems): 25% Assignments: 25% Grade Scale: F - A; F = Fail, D= Course requirements achieved; C= Good achievement; B= Very good achievement; A= Excellent achievement. Given grades are D, D+, C-, C, C+, B-, B, B+, A-, A. Passing Grade: MSc students: B; PhD students are encouraged to Audit

New Gene Discovery (BIOL6220)

Instructor: Dr. Mahmoud Yaish. [email protected]

Description:

This is an advanced course designed for postgraduate students. This course describes the

new molecular techniques which are used to identify functional genes. In addition, this

course explains the application of this technology in the agricultural and the medical

sectors.

Objectives:

To learn how to identify functional genes and effective mutations by using molecular and

computational biology tools.

Goals:

1- Provide the student with enough knowledge about the concept and the different

types of molecular markers.

2- Teach the students how to design molecular markers.

3- Describe the latest technology in reverse genetics and deferential gene expression

analysis which leads to discover genes.

4- Train the student on bioinformatics tools which are required to screen for

molecular markers linked to a trait of interest in plants and animals.

Assessment and learning outcomes: At the end of the course the students will be anticipated to understand the scientific basis behind

the discovery of the functional genes and how to apply this knowledge in practice. This includes

practical skills in bioinformatics at gene mapping and gene expression analysis.

Prerequisite: Genetics (BIOL 4432), Fundamentals Biotechnology (BIOL 4044).

Course Contents:

1- Eukaryotes Chromosome Mapping By Recombination.

A- The Discovery of the Inheritance Patterns of Linked Genes.

B- Recombination.

C- Linkage Maps.

D- Using the Chi-Square Test in Linkage Analysis.

E- Using LOD Scores to Assess Linkage in Human Pedigrees.

F- Accounting For Unseen Multiple Crossovers.

2- Development of DNA Markers.

A- The Concept of Molecular Markers.

B- Type of DNA Markers (AFLP, ISSR, RAPD, RFLP and SNAP).

C- Linkage Analysis and Construction of Genetic Map in Plants Using Mapmaker

Software.

D- Mapping of Quantitative Trait Loci (QTL).

E- Multigenerational QTL Mapping (Recombinant Progeny).

F- Molecular Markers Using Mitochondrial and Plastidic DNA.

G- Molecular Markers to Study Biodiversity (Bar-coding) and Quality Control.

3- Protein Markers.

A- Allozyme.

B- Differential Protein Accumulation. One and Two-Dimensional Gel

Electrophoresis.

C- Protein Sequencing and Gene Prediction.

4- Differential Gene Expression as a Tool for Gene Discovery.

A- Expressed Sequence Tag (EST).

B- Microarray.

C- Quantitative Real Time PCR.

5- Reverse Genetics.

A- Reverse Genetics Versus Forward Genetics as Tools of Gene Discovery.

B- Genomic Projects.

C- Site-Directed Mutagenesis.

D- Random Point Mutations.

E- Insertion Lines.

F- RNA-Interfering Technology.

6- Mapping of Genes Involve In Human Disease Using Chips Technology.

Format of the course

The course will cover two theoretical classes of 1 hours/week and 3 practical hours/week.

Documents

Sultan Qaboos University College of Science Department of ... · Textbook: Biology. Neil A. Campbell and Jane B. Reece. (7th edition. ) 2005. Benjamin Cummings References (optional):