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Course Outlines of BS Microbiology

SEMESTER 1

S. No. Course Code Course Title Credit Hour

1 MIC-301 General Microbiology-I 3(2-1)

2 BCH-301 Introductory Biochemistry 4(3-1)

3 MIC-303 Cell Biology 3(3-0)

4 MTH-321 Mathematics-I 3(3-0)

5 ENG-321 Functional English 3(3-0)

6 ISL-321 Islamic Studies 2(2-0)

Total Credit 18

SEMESTER 2

S. No. Course Code Course Title Credit Hour

1 MIC-302 General Microbiology-II 3(2-1)

2 MIC-304 Microbial Anatomy and Physiology 3(2-1)

3 MIC-306 Microbial Taxonomy 3(3-0)

4 MIC-308 Basic Pathology 3(2-1)

5 ENG-322 English Comprehension and Composition 3(3-0)

6 PST-321 Pakistan Studies 2(2-0)

Total Credit 17

SEMESTER 3

S. No. Course Code Course Title Credit Hour

1 MIC-401 Immunology 3(2-1)

2 MIC-403 General Virology 3(2-1)

3 MIC-405 Fundamentals of Mycology 3(2-1)

4 MIC-407 Biosafety and Risk Management 3(2-1)

5 ENG-421 Communication Skills 3(3-0)

6 CSI-321 Introduction to Computing Applications 3(3-0)

Total Credit 18

SEMESTER 4

S. No. Course Code Course Title Credit Hour

2

1 MIC-402 Systemic Bacteriology 3(2-1)

2 MIC-404 Systemic Virology 3(2-1)

3 MIC-406 Techniques in Parasitology 3(2-1)

4 MIC-408 Fundamentals of Epidemiology & Public Health 3(3-0)

5 STA-421 Biostatistics 3(3-0)

6 ENG-422 Technical Writing 3(3-0)

Total Credit 18

SEMESTER 5

S. No. Course Code Course Title Credit Hour

1 MIC-501 Food and Dairy Microbiology 3(2-1)

2 MIC-503 Cell and Tissue Culture Technology 3(2-1)

3 MIC-505 Microbial Enzyme Technology 3(2-1)

4 MIC-507 Molecular Biology & Biotechnology 3(2-1)

5 MIC-509 Agricultural Microbiology 3(2-1)

6 MIC-511 Management of Infectious Waste 3(3-0)

Total Credit 18

SEMESTER 6

S. No. Course Code Course Title Credit Hour

1 MIC-502 Vaccinology 3(2-1)

2 MIC-504 Environmental Microbiology 3(2-1)

3 MIC-506 Medical Microbiology 3(2-1)

4 MIC-508 Veterinary Microbiology 3(2-1)

5 MIC-510 Pharmaceutical Microbiology 3(2-1)

6 MIC-512 Microbial Biodegradation and Bioremediation 3(3-0)

Total Credit 18

SEMESTER 7

S. No. Course Code Course Title Credit Hour

1 MIC-601 Clinical Microbiology 3(2-1)

2 MIC-603 Plant Microbiology 3(2-1)

3 MIC-605 Marine & Fresh water Microbiology 3(2-1)

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4 MIC-607 Industrial Microbiology 3(2-1)

5 MIC-609 Research Methodology 2(2-0)

6 ENG-611 English for Employment 3(3-0)

Total Credit 17

SEMESTER 8

S. No. Course Code Course Title Credit Hour

1 MIC-632 Internship 6(0-6)

Total Credit 6

Grand Total 130

DETAIL OF COURSES

SEMESTER 1

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MIC-301 GENERAL MICROBIOLOGY-I 3(2-1)

Aims and objectives:

The course is designed to enable the students to work with microorganisms.

The basic techniques of sterilization, culturing, isolation and determining different

characteristics of the microorganisms are included.

Course Detail

Fundamentals of microbiology.

Microorganisms and their respective place in the living world.

Differentiation between eukaryotic and prokaryotic cells.

Historical development of Microbiology and its scope.

Microscopy: An outline of the principles and applications of light and electron

microscope.

Morphology, arrangement and detailed anatomy of bacterial cell.

Bacterial taxonomy and nomenclature, basis of classification of bacteria.

Growth, nutrition (physical and nutritional requirement and nutritional types;

sources of energy, C, N, H, O, S, P, H2O, trace elements, growth factors) and

reproduction.

General methods of studying microorganisms: cultivation, isolation, purification

and characterization.

Control of microorganisms by physical and chemical methods.

Chemotherapeutic agents and antibiotics. Modes of action of antibiotics on

microorganisms.

Basic properties of fungi, protozoa and algae.

A brief introduction to structure and propagation of viruses and bacteriophages.

Practical

Laboratory safety: Containment and decontamination.

An introduction to microscopy.

Equipments / Materials / Glassware etc. used in microbiology

Sterilization: Moist and dry heat sterilization methods

Preparation, selection and sterilization of bacteriological media and glassware.

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Inoculation techniques. Pour plate, spread plate & streak plate methods

Recommended Books

1. Kathleen P. T., and Arthur, T. 2001. Foundations in Microbiology: Basic

Principles McGraw-Hill Companies/

2. Tortora, G. J., Christine, L. Case, C. L., Funke, B. R., Funke, B., Case, C., 2006.

Microbiology: An Introduction, Publisher: Pearson Education.

3. Alcamo, I. E., 2001. Fundamentals of Microbiology published by Jones and

Bartlett Publishers, USA.

4. Black, J. G., 2005. Microbiology: principles and explorations, by 6th Edition, J.

Wiley & Sons, USA.

5. Cappuccino, J. G. and Sherman, N. 2004, Microbiology: a laboratory manual.

Pearson Education, USA.

6. Talaro, K. P., 2006. Foundations in Microbiology: Basic Principles. McGraw Hill.

Publisher.

BCH-301 INTRODUCTORY BIOCHEMISTRY 4(3-1)

Aims & objective

The course will provide in depth knowledge about the polymerized organic

compounds of life. The dynamism of the life proceeds with inter-conversion of

the chemicals from feeding to the liberation of energy for work.

In this course the concepts of the chemical basis of life and all the mechanisms

involved in harvesting of energy for growth, duplication etc. is given.

Course Detail

A general introduction to science of Biochemistry, importance and scope of

Biochemistry, Form, function and brief classification of prokaryotes, cellular

architecture and diversity of eukaryotes, structure, physical properties and

importance of water, unique properties of carbon. Nature of organic matter,

isomerism, general reactions of different functional groups, biologically important

organic groups/solvents. Overview of biological molecules (biomolecules) and

their structures including proteins, carbohydrates, lipids and nucleic acid.

Prebiotic molecular evolution and rise of living systems, review of the variety and

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ecology of living world, evolution of life, use and significance of radioisotopes in

Biochemistry.

Practicals

Preparation of percent solutions (W/V, V/V and milligram percent), calculation of

percent concentration of given solution, preparation of molar solution, preparation

of normal/equivalent solutions, preparation of molal solutions, preparation of ppm

and ppb solutions. Preparation of solution from given stock solution by dilution

method, standardization of given solution. Determination of pH of different

samples and body fluids, preparation of buffers.

Recommended Books

1. Voet, D., Voet, J. G. and Pratt, C. W., 2002. Fundamentals of Biochemistry; John

Wiley and Sons. Inc., New York.

2. Berg, J.M., Tymoczko, J.L., Stryer, L., 2006. Biochemistry: International 6th

edition. W. H. Freeman and Co Ltd;

3. Cox, M. and Nelson, D. L., 2005. Lehninger Principles of Biochemistry 4th

edition, Palgrave Macmillan.

4. Murray, R., Granner, D., Mayes, P., and Rodwell, V., 2006. Harper's Illustrated

Biochemistry 27th

Edition. McGraw-Hill Education.

MIC-303 CELL BIOLOGY 3(3-0)

Aims & objectives:

The cell and its organization of architecture and the unified role it plays for the

ultimate sustainability of the organisms.

The various ultra-structural, molecular and functional aspects of the cells.

Course Detail

Introduction to cell biology.

Difference between prokaryotes and eukaryotes.

Physico-chemical properties of protoplasm.

Ultra-structure, chemical composition and functions of cell wall, cell membrane,

cellular organelles (mitochondria, endoplasmic reticulum, Golgi apparatus,

lysosome, glyoxysome, nucleus, ribosomes, etc.) cytoskeleton.

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Chemical composition and molecular structure of chromosomes.

E. coli and yeast as representative prokaryotic and eukaryotic models for

molecular differentiation.

Cell cycle and apoptosis.

Molecular mechanism of Replication.

Transcription and Translation.

Regulation of gene expression in prokaryotes and eukaryotes.

Mutations and chromosomal aberrations.

DNA damage and repair.

Signal transduction.

Cell culture

Types of recombination.

Gene sequencing.

Principles of Recombinant DNA technology.

Role of Recombinant DNA Technology in economic development.

Human Genome Project.

Recommended Books

1. Lodish, H., Matsudaira, P., Berk, A., Ploegh, H., Scott, M., Kaiser, C.A., Krieger,

M., Bretscher, A., 2007. Molecular Cell Biology. W. H. Freeman Company.

2. Walker, D., 2007. Cells and Life Processes. Smart Apple Media.

3. Alberts. B., 2007. Molecular Biology of the Cell Taylor and Francis, Inc.

4. Pollard, T. D., Lippincott-Schwartz, J., Earnshaw, W. C., 2007. Cell Biology:

Saunders W. B. Co.

5. Karp, G., 2007. Cell and Molecular Biology, Study Guide: Concepts and

Experiments.5 Edition. th

Wiley, John and Sons Incorporated

6. Kierszenbaum, A., 2007. Histology and Cell Biology: An Introduction to

Pathology Elsevier Health Sciences.

MTH-321 MATHEMATICS-I 3(3-0)

Aims & objectives

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This is the first course of the basic sequence, Calculus I-III, serving as the

foundation of advanced subjects in all areas of mathematics. The sequence, equally,

emphasizes basic concepts and skills needed for mathematical manipulation. Calculus I &

II focus on the study of functions of a single variable.

Course Detail

Limits and continuity.

Derivative of a function and its applications.

Optimization problems.

Mean value theorem (Taylor’s theorem and the infinite Taylor series with

applications) and curve sketching; anti-derivative and integral.

Definite integral and applications.

The fundamental theorem of Calculus.

Inverse functions (Chapters 1-6 of the text)

Recommended Books

1. Anton H, Calculus: A New Horizon (6th edition), 1999. John Wiley, New York.

2. Stewart J, Calculus (3rd edition), 1995, Brooks/Cole (suggested text)

3. Thomas G. B, Finney A. R., Calculus (10th edition), 2002. Addison-Wesley,

Reading, Ma, U.S.A.

ENG-321 FUNCTIONAL ENGLISH 3(3-0)

Aims & objectives

Enhance language skills and develop critical thinking.

Course Contents

Introducing ourselves

Describing things

Getting and giving information

Recounting past events

Talking about facts and opinions

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Agreeing and disagreeing

Compare and Contrast

Cause and effect

Using your imagination

Reporting

Writing Essays

Presentation skills

Assessment

ISL-321 ISLAMIC STUDIES 2(2-0)

Aims & objective

This course is aimed at:

To provide Basic information about Islamic Studies

To enhance understanding of the students regarding Islamic Civilization

To improve Students skill to perform prayers and other worships

To enhance the skill of the students for understanding of issues related to faith and

religious life.

Course Outlines

Introduction to Quranic Studies

Basic Concepts of Quran

History of Quran

Uloom-ul -Quran

Study of Selected Text of Holly Quran

Verses of Surah Al-Baqra Related to Faith(Verse No-284-286)

Verses of Surah Al-Hujrat Related to Adab Al-Nabi (Verse No-1-18)

Verses of Surah Al-Mumanoon Related to Characteristics of faithful (Verse No-1-

11)

Verses of Surah al-Furqan Related to Social Ethics (Verse No.63-77)

Verses of Surah Al-Inam Related to Ihkam(Verse No-152-154)

Study of Selected Text of Holly Quran

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Verses of Surah Al-Ihzab Related to Adab al-Nabi (Verse No.6, 21, 40, 56, 57,

58.)

Verses of Surah Al-Hashar (18,19,20) Related to thinking, Day of Judgment

Verses of Surah Al-Saf Related to Tafakar,Tadabar (Verse No-1,14)

Seerat of Holy Prophet (S.A.W) I

Life of Muhammad Bin Abdullah ( Before Prophet Hood)

Life of Holy Prophet (S.A.W) in Makkah

Important Lessons Derived from the life of Holy Prophet in Makkah

Seerat of Holy Prophet (S.A.W) II

Life of Holy Prophet (S.A.W) in Madina

Important Events of Life Holy Prophet in Madina

Important Lessons Derived from the life of Holy Prophet in Madina

Introduction to Sunnah

Basic Concepts of Hadith

History of Hadith

Kinds of Hadith

Uloom –ul-Hadith

Sunnah & Hadith

Legal Position of Sunnah

Selected Study from Text of Hadith

Introduction to Islamic Law & Jurisprudence

Basic Concepts of Islamic Law & Jurisprudence

History & Importance of Islamic Law & Jurisprudence

Sources of Islamic Law & Jurisprudence

Nature of Differences in Islamic Law

Islam and Sectarianism

Islamic Culture & Civilization

Basic Concepts of Islamic Culture & Civilization

Historical Development of Islamic Culture & Civilization

Characteristics of Islamic Culture & Civilization

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Islamic Culture & Civilization and Contemporary Issues

Islam & Science

Basic Concepts of Islam & Science

Contributions of Muslims in the Development of Science

Quranic & Science

Islamic Economic System

Basic Concepts of Islamic Economic System

Means of Distribution of wealth in Islamic Economics

Islamic Concept of Riba

Islamic Ways of Trade & Commerce

Political System of Islam

Basic Concepts of Islamic Political System

Islamic Concept of Sovereignty

Basic Institutions of Govt. in Islam

Islamic History

Period of Khlaft-E-Rashida

Period of Ummayyads

Period of Abbasids

Social System of Islam

Basic Concepts of Social System of Islam

Elements of Family

Ethical Values of Islam

Reference Books

1. Hameed ullah Muhammad, “Emergence of Islam” , IRI, Islamabad

2. Hussain Hamid Hassan, “An Introduction to the Study of Islamic Law” leaf

Publication Islamabad, Pakistan.

3. Dr. Muhammad Zia-ul-Haq, “Introduction to Al Sharia Al Islamia” Allama Iqbal

Open University, Islamabad (2001)

SEMESTER 2

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MIC-302 GENERAL MICROBIOLOGY – II 3(2-1)

Aims and objectives

Aims of this course to let the students know about the applications of the science

of microbiology in the different fields of life.

The course may initiate their interest in agricultural, industrial and/or

environmental microbiology.

Course Detail

Structure and chemical composition of nucleic acid. Role of RNA, DNA in

protein synthesis.

Cell division, mitosis and meiosis, bacterial mutation and variation. Introduction

to the genetical intermixing of bacteria including transformation, transduction and

conjugation.

Introduction to metabolism and role of phosphorus in energy transfer. Glycolysis

and T.C.A. cycle.

Microbiology of water and wastewaters. Water as a source of infection and

methods of water purification. Methods of sewage treatment and disposal.

Introduction to food and dairy microbiology. Methods of food preservation.

Differentiation between food intoxication and food-infection.

Microbiology of soil with particular reference to nitrogen cycle.

Microbiology of air.

Practical

Principles of Staining Procedures: Simple staining, Gram’s staining, Acid-fast

staining, cell-wall staining, flagellar staining, capsule staining, spore staining and

spirochaete staining.

Study of cell motility by hanging drop preparation.

Enumeration of bacteria in drinking water, milk, soil and air

Urine analysis (physical, chemical and microbiological).

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Recommended Books

1. Talaro, K. P., 2006. Foundations in Microbiology: Basic Principles. McGraw

Hill. Publisher.

2. Black, J. G., 2005. Microbiology: principles and explorations, by 6th

Edition, J.

Wiley & Sons, USA.

3. Tortora, G. J., Funke, B. R. and Case, C. L. 2008. Microbiology: an introduction

9th

Edition, Pearson Education, USA.

4. Pepper, I.L., C.P. Gerba, and J.W. Brendecke. 2004. Environmental

Microbiology - A Laboratory Manual. Second Edition. Academic Press, San

Diego.

5. Pepper, I. L., C. P. Gerba and M. L. Brusseau. 2006. Environmental and

Pollution Science, Second Edition. Academic Press, San Diego.

MIC-304 MICROBIAL ANATOMY AND PHYSIOLOGY 3(2-1)

Aims & objectives

Identify the basic components of all cells.

Distinguish the features of prokaryotic cells.

Distinguish the characteristics of eukaryotic cells.

Understand the use and characteristics of microscope.

Course Detail

Detailed organization of microbial cells.

Chemical composition and biosynthesis of macromolecules in microbial cells.

Genomic organization of prokaryotes.

Regulation of gene expression (operon, catabolite repression).

Uptake and secretion of molecules.

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Aerobic and anaerobic respiration and fermentation.

Cell metabolism: protein, nucleic acid and fat.

Microbial enzymes and metabolites. Classifications, chemistry, mechanism of

action and inhibition.

Practicals:

1. Isolation of polysaccharides from bacteria.

2. Isolation of lipids from bacteria.

3. Estimation of total protein from bacterial cell.

4. Isolation and purification of a bacterial enzyme.

Recommended Books

1. Atlas, R. M. 1998. Microbiology: fundamentals and applications. MacMillan

Publishing Co. U.S.A.

2. Levin, B., 1996. Genes VI. Oxford University, Oxford.

MIC-306 MICROBIAL TAXONOMY 3(3-0)

Aims & objectives:

Identify the objectives of classification

Identify traits used to classify microorganisms

Locate microorganisms in the realm of living world

Course Detail

Basic concepts and aims of classification.

Classical and molecular basis of classification of prokaryotes.

Bacterial nomenclature.

Classification of Enterobacteriaceae, spore formers, Actinomycetes

(Mycobacterium & Nocardia), Spirochaetes (Treponema &Leptospira).

Detailed classification of viruses, fungi, protozoa and Algae.

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A brief introduction of Rickettsia, Chlamydia and Mycoplasma.

An introduction to Prions and Viroids.

Recommended Books

1. Nigel, J. J., Dimmock, N. J. J., Keith, L., Andrew, E., 2001. Introduction to

Modern Virology. Blackwell Science, Inc.

2. Garrity, G. M., Krieg, N. R., Brenner, D. J., 2006. Bergey's Manual of Systematic

Bacteriology: The Proteobacteria, Vol. 2. Williams and Wilkins Co, Baltimore.

3. Ogunseitan, O., 2000. Microbial diversity. John Wiley and Sons.

MIC-308 BASIC PATHOLGY 3(2-1)

Aims and Objectives:

1. Concept of disease and basic terminology

2. Concept of various types of cancers

3. To know the basic practical techniques used in Pathology

Course Contents:

1. Scope of Pathology & concept of disease

2. Definitions and terminology: Ischemia, Hypoxia, Necrosis, Infarction, Atrophy,

Hypertrophy, Hyperplasia, Metaplasia, Aplasia, Anaplasia.

3. Response of body to injury and infection: Acute inflammation, chronic inflammation,

Immunity, Allergy, Hypersensitivity.

4. Specific: Ulcer (Peptic, Duodenal), Hypertension, Leukemia or Blood Cancer

(Malignant Carcinoma, Sarcoma & Lymphomas), Diagnosis and treatment of Cancer in

general, fate, survival and prognosis with tumors.

Practicals:

1. Study of Pathological Slides of various Pathological Conditions: Acute inflammation,

Chronic inflammation, Chronic specific inflammation, Different types of Degeneration,

Thrombosis, Embolism, Infarction, Necrosis, Gangrene, Hyperplasia, Metaplasia,

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Pigmentation, Calcification, CVC, Papilloma, Adenoma, Chondroma, Fibroma,

Leomyoma, Neofibroma, Sq. Cell Carcinoma etc. etc.

2. Examiantion of different body fluids in various Pathological Conditions: Urine

complete Examination, stool Examination, Blood Complete Examination,Semen

Examination, Cerebrospinal Fluid Examination, BloodSugar, Blood Urea, Blood

Cholesterol etc.

3. Tests for various Specimens of Clinical Importance: Techniques of Clinical Blood

Examination for various disases, GastricAnalysis, Tests for liver function, Renal function

test, Tests for endocrineabnormalities, Biopsies and cytologic techniques.

Recommended Books:

1. Kumar Cotran Robins, Basic Pathology,6th edition, W B Saunders Company,

Philadelphia, (1992).

2. Walters and Israel, General Pathology, Churchill Livingstone, London, (1998).

3. Peter S Macfarlane, Robin Reid, Robin Collander, Pathology Illustrated, Churchill

Livingstone, London (1998).

4. Robbins Pathology, W B Saunders Co, London, 2nd Ed., 1962.

5. Walter G B, General Pathology, Churchill Livingstone, New York, 1996.

ENG-322 ENGLISH COMPREHENSION AND COMPOSITION 3(3-0)

Aims:

To enable the students to:

• Read the lines (literal understanding of text), read between the lines (to interpret

text) and read beyond the lines (to assimilate, integrate knowledge etc.)

• Write well organized academic texts including examination answers with

topic/thesis statement/supporting details

• Write argumentative essays and course assignments

Reading and Critical Thinking

1. Read academic texts effectively by:

• Using appropriate strategies for extracting information and salient points according

to a given purpose

• Identifying the main points supporting details, conclusions in a text of intermediate

level

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• Identifying the writer’s intent such as cause and effect, reasons, comparison and

contrast, exemplification

• Interpreting charts and diagrams

• Making appropriate notes using strategies such as mind maps, tables, lists, graphs.

• Reading and carrying out instructions for tasks, assignments and examination

questions

2. Enhance academic vocabulary using skills learnt in Compulsory English I course

3. Acquire efficient dictionary skills such as locating guide words, entry words, choosing

appropriate definition, and identifying pronunciation through pronunciation key,

identifying part of speech, identifying syllable division and stress patterns

Writing Academic Texts

Students will be able to:

1. Plan their writing: identify audience, purpose and message (content)

2. Collect information in various forms such as mind maps, tables, charts, lists

3. Order information such as:

• Chronology for a narrative

• Stages of a process

• From general to specific and vice versa

• From most important to least important

• Advantages and disadvantages

• Comparison and contrast

• Problem solution pattern

4. Write argumentative and descriptive forms of writing using different methods of

developing ideas like listing, comparison, and contrast, cause and effect, for and

against

� Write good topic and supporting sentences and effective conclusions

� Use appropriate cohesive devices such as reference words and signal markers

5. Redraft checking content, structure and language, edit and proof read

Grammar in Context

• Phrase, clause and sentence structure

• Combining sentences

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• Reported Speech

Methodology

In this curriculum, students will be encouraged to become independent and efficient

readers using appropriate skills and strategies for reading and comprehending texts at

intermediate level. Moreover, writing is approached as a process. The students will be

provided opportunities to write clearly in genres appropriate to their disciplines.

Recommended Readings:

1. Eastwood, J. (2004). English Practice Grammar (New edition with tests and answers).

Karachi: Oxford University Press.

2. Fisher, A. (2001). Critical Thinking. C UP

3. Goatly, A. (2000). Critical Reading and Writing: An Introductory Course. London:

Taylor & Francis

4. Hacker, D. (1992). A Writer’s Reference. 2nd

Ed. Boston: St. Martin’s

5. Hamp-Lyons, L. &Heasley, B. (1987). Study writing: A course in written English for

academic and professional purposes. Cambridge: Cambridge University Press.

6. Howe, D.H, Kirkpatrick, T.A., & Kirkpatrick, D.L. (2004). Oxford English for

Undergraduates. Karachi: Oxford University Press.

7. Murphy, R. (2003?). Grammar in Use. Cambridge: Cambridge University Press.

8. Smazler, W.R. (1996). Write to be Read: Reading, Reflection and Writing. Cambridge:

Cambridge University Press.

9. Wallace, M. (1992). Study Skills. Cambridge: Cambridge University Press.

10. Yorky, R. Study Skills.

PST-321 PAKISTAN STUDIES 2(2-0)

Aims and objectives

Develop vision of historical perspective, government, politics, contemporary

Pakistan, ideological background of Pakistan.

Study the process of governance, national development, issues arising in the

modern age and posing challenges to Pakistan.

Course Outline

1. Historical Perspective

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a. Ideological rationale with special reference to Sir Syed Ahmed Khan, Allama

Muhammad Iqbal and Quaid-e-Azam Muhammad Ali Jinnah.

b. Factors leading to Muslim separatism

c. People and Land

i. Indus Civilization

ii. Muslim advent

iii. Location and geo-physical features.

2. Government and Politics in Pakistan

Political and constitutional phases:

a. 1947-58

b. 1958-71

c. 1971-77

d. 1977-88

e. 1988-99

f. 1999 onward

3. Contemporary Pakistan

a. Economic institutions and issues

b. Society and social structure

c. Ethnicity

d. Foreign policy of Pakistan and challenges

e. Futuristic outlook of Pakistan

Books Recommended

1. Akbar, S. Zaidi. Issue in Pakistan’s Economy. Karachi: Oxford University Press,

2000.

2. S.M. Burke and Lawrence Ziring. Pakistan’s Foreign policy: An Historical analysis.

Karachi: Oxford University Press, 1993.

3. Mehmood, Safdar. Pakistan Political Roots & Development. Lahore, 1994.

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SEMESTER 3

MIC-401 IMMUNOLOGY 3(2-1)

AIMS & OBJECTIVES:

• Present a general perspective of acquired immunity

• To examine the nature of antibodies and process whereby antibodies are induced in

response to antigens.

• Discuss the process of immunization

Course Detail

• Introduction: chronological development and scope of immunology.

• Immunity and immune responses: Definitions and types (specific and non-specific).

Humoral and cellular immunity.

• Complement system.

• Cells and tissues of immune system.

• The antigens: structure (simple and complex molecules, proteins and polysaccharides)

and immunogenicity.

• Tissue antigens: the Allo- and heterophile antigens. The ABO and Rh blood group

systems, their chemical basis, inheritance & clinical significance.

• Immunoglobulins: structure and function; classes, subclasses, types and subtypes;

immunoglobulin genetics.

• Immuneresponse to an antigen.

• Introduction to antigen-antibody reactions: methods for detecting antigens and

antibodies (agglutination, precipitation, complement fixation, EIA, etc.).

• HLA & MHC and its role in immune response, disease and its significance in tissue

transplantation.

• Immunoregulation and tolerance.

• Cancer immunology.

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• Introduction to immunopathology: hypersensitivity reactions, autoimmune diseases and

immunodeficiencies.

• Immunization (methods of immunization, vaccines and adjuvants).

Practicals

1. Differential leukocyte count.

2. Blood grouping (ABO & Rh).

3. Agglutination test (Widal test).

4. Precipitation tests.

5. Complement fixation test.

6. Gel diffusion test.

Recommended Books:

1. Janis Kuby. Immunology 6th

Edition.W.H. Freeman Company New York.

2. Male, Brostoff, Roth &Roit. Immunology 7th

Edition. Mosby.

MIC-403 GENERAL VIROLOGY 3(2-1)

AIMS & OBJECTIVES:

• To identify major components of viruses

• System of traits used for classification of viruses

• Describe how viruses interact with cells

• Examine the ways that viruses persist in host cells

Course Detail

• Principles of electron microscopy.

• Nature of animal and plant viruses.

• Classification: structural and functional groups.

• Cell culture: various types of cell lines (plants and animals).

• Replication of viruses (RNA & DNA).

• Principles of viral diagnostic procedures.

• Introduction to bacterial viruses.

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• Receptors for bacteriophages, somatic, non-somatic viruses and sex specific viruses.

Adsorption sites and mode of replication.

• Transducing viruses of eukaryotes and cross-phylogenetic transfer.

• Prion and viriod.

Practicals

1. Detection and quantification of viruses.

2. Hemagglutination Inhibition assay.

3. Chick embryo inoculation.

4. Plaque assay.

5. Transmission electron microscopy (field trip).

6. Sample preparation for electron microscopy.

7. Isolation and identification of phages from various sources.

Recommended Books

1. Cann, A. J., 2001. Principles of Molecular Virology Academic Press

2. Griffin, R., Martin, M. A, Straus, H., Griffin, D. E., Robert, G., LMICRO, A., Howley,

P. M., Roizman, B., Straus, S. E., David, M., 2001.Fundamental Virology

Lippincott Williams and Wilkins.

3. Brian, W., Mahy, B., Mahy, W., 2001. A Dictionary of Virology. Academic Press

Incorporated.

4. Flint, S. J., Racaniello, V. R., Enquist, L. W. and Skalka, A. M. 2003. Principles of

Virology: Molecular Biology, Pathogenesis, and Control of Animal Viruses.

CMICROridge University Press.

5. Nigel J. J., Dimmock, K. L. and Andrew E., 2001. Introduction to Modern Virology

Blackwell Science, Inc.

6. Zuckerman, A. J., Banatvala, J. E., Pattison, J. R., Griffiths, P., Schoub, B., 2004.

Principles and Practice of Clinical Virology, 5th Edition.John Wiley and Sons

Limited.

MIC-405 FUNDAMENTALS OF MYCOLOGY 3(2-1)

AIMS & OBJECTIVES:

• Describe how to classify fungi.

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• Examine fungal metabolism.

• Define mycotoxins.

• Role of fungi in plant and animal diseases.

Course Detail

• Introduction to mycology.

• Fundamentals of fungal classification.

• Structure and physiology of fungi.

• Physical and nutritional factors affecting the growth of fungi.

• Structural development and reproduction in fungi including cell cycle.

• Fungal metabolism (with reference to food and beverages).

• Economic impact of fungal plant diseases and their control.

• Fungi of medical importance.

• Mycotoxins.

• Use of fungi in biotechnology.

Practicals:

1. Isolation and identification of fungi from:

Environment

Rhizosphere

Clinical samples.

2. Effect of temperature on growth of fungi.

3. Determination of antifungal activity of (nystatin, actidion, amphoteracin B etc.)

Recommended Books

1. Hocking, A.D., Pitt, J.I., Samson, R.A., Thrane, U., 2006. Advances in Food

Mycology, Springer.

2. Tkacz, Jan S., Lange, L., 2004. Advances in Fungal Biotechnology for Industry,

Agriculture, and Medicine.Springer.

24

3. Eugene, N., Milton, P. G. and Allen, K., 2004. Agrobacterium tumefaciens: From Plant

Pathology to Biotechnology. APS Press.

4. Gioconda, S-B. and Richard, C. A., 2008. Pathogenic Fungi: Insights in Molecular

Biology. Caister Academic Press.

MIC-407 BIOSAFETY AND RISK MANAGEMENT 3(2-1)

Objectives:

To have the practice to conduct on microbes.

Details of Courses

• Detailed concept of Risk and Hazardous: Environment, Factors, Chemicals, Biological

Radiations.

• Risk Management: Preventions, Surveillance, Monitoring Committee.

• Judicial Rights / Penalties.

• Concepts of Biosafe Environment: Terrestrial, Marim, Atmosphere.

• Designing of Labs based on Biosafety and Containment Parameters.

• Details of Biological Containment: Plants, Animals, Microbes.

Recommended Books:

1. Biological Safety. Principles and Practices, 4th edition, 2006.by D. O. Fleming and

D.L. Hunt (ed.). ASM Press, Washington, D.C.

2. Biological Weapon Defence: Infectious diseases and counter bioterrorism. 2004. L. E.

Lindler, F. J. Lebeda, G. W. Korch. Humana Press.

3. Biodefence. M. S. Bronze and R. A. Greenfield. 2005. Horizon Biosciences.

4. Laboratory Biosafety Manual, 3rd edition, 2004. WHO, Geneva.

5. Biosafety in Microbiological and Biomedical laboratories. Centers for Disease Control

and Prevention and National Institutes of Health.5th

edition, 2007.

6. Laboratory biosafety guidelines. Kennedy, M.E., et al., eds. 3rd ed. Ottawa: Office of

Laboratory Security, Public Health Agency of Canada, 2004

ENG-421 COMMUNICATION SKILLS 3(3-0)

Aims:

To enable the students to meet their real life communication needs

Contents:

25

• Oral presentation skills (prepared and unprepared talks)

• Preparing for interviews (scholarship, job, placement for internship, etc.)

• Writing formal letters

• Writing different kinds of applications (leave, job, complaint, etc.)

• Preparing a Curriculum Vitae (CV), (bio-data)

• Writing short reports

Recommended Readings:

1. Ellen, K. 2002. Maximize Your Presentation Skills: How to Speak, Look and Act on

Your Way to the Top

2. Hargie, O. (ed.) Hand book of Communications Skills

3. Mandel, S. 2000. Effective Presentation Skills: A Practical Guide Better Speaking

4. Mark, P. 1996. Presenting in English.Language Teaching Publications.

CSI-321 INTRODUCTION TO COMPUTING APPLICATIONS 3(3-0)

Generation of computer:

1st

to 4th

generation with their characteristics.

Basic concept of computer:

Introduction , different components of computer, basic design of computer.

Introduction to operating system

Introduction to OS, different management (processor, memory, device, file),

Processor management-Process concept, Threads, CPU Scheduling

Process scheduling, Deadlocks, Process synchronization.

Memory management –Memory allocation rule, Swapping, Overlay, Paging, Demand

paging, segmentation, virtual memory.

Device management, File management.

Practical

Usage of MS DOS commands: basic concept of internal & external commands, directory

&file commands, copying, erasing, renaming, displaying files, introduction to pipes

&filters, concept of batch file. Wndows operation: Customizing the interface, windows

explorer, computer upkeep & utilities

Office operation

26

Microsoft word:- concept of toolbar ,character ,paragraph& document formatting,

drawing tool bar, header, footer ,document editing ,page setup, short cut keys, text &

graphics.

Microsoft excel:- concept of spread sheets, creating worksheet ,well formatted

documents, concept of row, column ,cell &formula bar, using function ,using shortcuts

,chart, conditional formatting, goal seek, validation rule. Microsoft power point:- slide

presentation, slide layout & design , custom animation, image importing, slide transition.

SEMESTER 4

MIC-402 SYSTEMIC BACTERIOLOGY 3(2-1)

Aims and objectives

Pathogenesis of microorganisms

Mechanism of infection

Molecular mechanism of Pathogenesis

Course Detail

Introduction: Host-pathogen interactions.

Determination of pathogenicity and molecular mechanisms of pathogenesis.

Chemotherapy and drug resistance.

Study of bacterial infections with emphasis on mechanisms of pathogenesis of the

following groups: Streptococcus, Staphylococcus, Niesseria, Pseudomonas,

Corynebacterium, Bordetella, Vibrio, Enterobacteraceae, Clostridium, Bacillus,

Campylobacter, Aeromonas and Helicobacter, Legionella, Mycobacterium,

Actinomycetes/ Nocardia, Chlamydia and Mycoplasma.

Zoonotic infections.

Study of rickettsial and chlamydial diseases including epidemic and endemic

typhus,

Classical and newly emerging bacterial diseases.

27

Practical

Collection and transportation of clinical samples:

Infections of ear, nose, throat, eye, GIT, urogenital tract and bone

Isolation and identification of selected pathogens.

Pure culture study of (on the basis of morphological, cultural and biochemical

characteristics): E. coli, Salmonella sp, Shigella sp, Staphyloccus aureus, S.

epidermidis and S. fecalis, Corynebacterium.

Antibiotic assays by disc diffusion methods and dilution method.

Determination of MIC, MBC and E-Test.

Recommended Books:

1. Hawkey, P and Lewis, D., 2004. Medical Bacteriology: A Practical Approach.

2nd

Edition .Oxford University Press;

2. Mims, C Dockrell, H., Goering, R., Roitt, I Wakelin, D. and Zuckerman, M., 2004.

Medical Microbiology.3rd

Edition. Mosby.

3. Stephen, J., Mims, C.A., Nash, A. 2000. Mims' Pathogenesis of Infectious Disease.5th

Edition. Academic Press Inc., U.S.A.

4. Greenwood, D., Slack, C. B. R., and Peutherer, J. F., 2002. Medical Microbiology: A

Guide to Microbial Infections: Pathogensis, Immunity, Laboratory Diagnosis and

Control. 16th

Edition. Churchill Livingstone.

5. Cowan, S. T., Steel, K. J., Barrow, G. I and Feltham, R. K. A., 2004. Cowan and

Steel's Manual for the Identification of Medical Bacteria. 3rd

Edition CMICROridge

University Press.

MIC-404 SYSTEMIC VIROLOGY 3(2-1)

AIMS & OBJECTIVES:

• To identify major families of viruses

• System wise diseases of viruses

• Describe how viruses infect host and cell interactions

28

• Examine the ways that viruses persist in host cells

How viral diseases prevented and their control?

Course Detail

Introduction to viral families, (dsDNA, ssDNA, dsRNA, and ssRNA).Viral diseases and

pathogens, gastrointestinal infections, respiratory infections, infections of liver and

systemic spread, HIV and AIDS, Carcinogenesis and tumor viruses, Vaccines and

Antivirals, Vaccine preventable diseases of infants and children, Prion diseases and

emerging viral infections

Practical:

Practical 1: Layout of virology laboratory, construction, equipment and precautionary

measures

Practical 2: Isolation of bacteriophages from different samples

Practical 3: Cultivation of viruses in embryonated eggs through different routes

Practical 4: Propagation of viruses in cell culture

Practical 5: Calculation of end point 50 (LD 50, EID 50, CCID 50 and TCID 50)

Recommended Books

1. Cann, A. J., 2001. Principles of Molecular Virology Academic Press

2. Griffin, R., Martin, M. A, Straus, H., Griffin, D. E., Robert, G., LMICRO, A., Howley,

P. M., Roizman, B., Straus, S. E., David, M., 2001.Fundamental Virology

Lippincott Williams and Wilkins.

3. Brian, W., Mahy, B., Mahy, W., 2001. A Dictionary of Virology. Academic Press

Incorporated.

4. Flint, S. J., Racaniello, V. R., Enquist, L. W. and Skalka, A. M. 2003. Principles of

Virology: Molecular Biology, Pathogenesis, and Control of Animal Viruses.

CMICROridge University Press.

5. Nigel J. J., Dimmock, K. L. and Andrew E., 2001. Introduction to Modern Virology

Blackwell Science, Inc.

6. Zuckerman, A. J., Banatvala, J. E., Pattison, J. R., Griffiths, P., Schoub, B., 2004.

Principles and Practice of Clinical Virology, 5th Edition.John Wiley and

Sons Limited.

MIC-406 TECHNIQUES IN PARASITOLOGY 3(2-1)

29

AIMS & OBJECTIVES:

Introduction to protozoa & parasites

Host parasite interactions, life cycles and pathogenesis

Diagnosis and treatment of major diseases

Techniques for isolation & identification

Course outline

Protozoology: Brief history of protozoology, ecology and host parasite

relationship (parasitism and symbiosis).

Amoeba: Nonpathogenic and pathogen amoeba. Morphology and life cycle of

amoeba pathology. Symptomatology Laboratory Diagnosis of) Giardia (G. Limblia)

Flagellates of genital tract Trichomonas (T. tenax, T. hominis, T. vaginalis) Malaria

parasite (Plasmodium vivax, P. malariae, P. ovale,) Genaral life cycle of Malarial

parasite in man and anopheles mosquito, sequal of malaria, Toxoplasma gondi, life

cycle, Symptomatology, Transmission and Lab diagnosis of Toxoplasmosis.

Helminthology: Genaral introduction of helminthes and classification, medically

important hemimths. Immunity in Taenia saginata, T. solium, Echinococcusgranulosis,

Trematodes, Schistosomes (S. haematobium, S. mansoni, S. Japonicum)

Nematodes.Ascaris lumbriicoides, Ancylostomaduodenale, Strongyloidesstercoralis,

Enterrobius

Medical entomology: Role of arthropods in the spread and causation of

parasite diseases.

Practicals:

1. Isolation and identification techniques for major human blood & tissue protozoa

2. Isolation and identification techniques for major human helminths

3. Identification of arthropod vectors of major human diseases

Recommended Books

1. Medical Parasitology (Gillespie and Hawkey)

2. Modern Parasitology (F.E.G Cox)

3. Essential of Parasitology (Schimidt).

4. Parasitology (K.D Chatterjee)

30

MIC-408 FUNDAMENTALS OF EPIDEMIOLOGY & PUBLIC HEALTH 3(3-0)

Learning objectives

• Define epidemiology.

• Describe the different mathematical tools of epidemiology.

• Define and examine descriptive and analytical epidemiology.

Course Detail

• Introduction to epidemiology: Types of epidemiology, clinical, occupational,

experimental, interrelation of factors.

• Epidemiological methods; incidence, prevalence, morbidity, mortality, susceptibility

• Types of studies; cross sectional, cohort, case control.

• Epidemiologic consideration in disease process.

• Health information and biostatistics.

• Sampling methodology: procedure, sample size, cluster sampling, sampling error,

bias, risk, data collection of infectious disease cases, antibiotic resistance profile

of infectious agents.

• Screening tests, accuracy of screening tests, predictive value, reliability.

• Hypothesis testing, statistical significance, (p values, confidence interval etc.)

• Epidemiological polarization.

• Disease pattern in community & Social diversity.

• Cyclicity of diseases: Chicken Pox, measles, Rota virus infections, mumps.

• Flu, common cold and prevailing pandemics and epidemics.

• Surveillance prevention, control and eradication of disease.

• Status of health services in Pakistan: comparison with other counties.

• Detailed study of predisposing factors in developed countries and a comparison with

the existing factors in Pakistan.

- Specificity and sensitivity of different tests

31

Recommended Books

1. Salyers, A. A. and Whitt, D. D., 2002. Microbiology: Diversity, Disease, and the

Environment. John-Wiley and Son Limited.

2. Ziegler, A., and Koenig, I. R., 2006. A Statistical Approach to Genetic

Epidemiology: Concepts and Applications. John-Wiley and Son Limited.

3. Haines, J. L., Pericak-Vance, M. A., 2006. Genetic Analysis of Complex disease.

Wiley, John and Sons Incorporated.

4. Adami, H.O., Hunter, D., Trichopoulos D., 2002. Textbook of Cancer

Epidemiology.Oxford Press.

5. Seedhouse, D., 2003. Health Promotion: Philosophy, Prejudice and Practice,

2nd Edition. John Wiley and Sons limited.

STA-421 BIOSTATISTICS 3(3-0)

Aims and objectives

It will help the students to analyze data pertaining to their research work

To assess the significance of their experimental designs. Without statistical

analysis research articles are not accepted for publication by the scientific

journals.

Students must have sound knowledge of the statistical programs.

Course Detail

Introduction to Biostatistics and its scope in Microbiology.

Collection of Primary and Secondary data.

Editing of data.

Presentation of data: Tabulation, Classification, Visual Presentation (Diagrams

and Graphs).

Measures of Central Tendency: Arithmetic Mean by direct and short-cut method,

Geometric Mean, Harmonic Mean, Mode, Median, ED50

(LD50

in detail ),

Quantile.

32

Measures of Dispersion: Range, Quartile Deviation, Mean Deviation, Standard

Deviation by direct and short-cut method, Variance, and their Coefficient.

Correlation: Simple Correlation Table, Rank Correlation, Partial and Multiple

Correlations.

Regression and method of least square.

Probability: Concept of Probability, Laws of Probability.

Permutation and Combination.

Probability distributions: Binomial distribution, Poisson distribution and their

fitting to observed data, Normal distribution.

Sampling and Basic Design

Hypothesis Testing.

Chi-square test, Student’s t-test, Analysis of variance.

Laboratory Experiments pertaining to the course.

Recommended Books

1. Stanton, A.G., 2001. Primer of Biostatistics.McGraw Hill.

2. Jekel, J., Elmore, J.G., Katz, D.L., 2001. Epidemiology, biostatistics and preventive

medicine. W. B. Saunders.

3. Quinn, G., 2002. Experimental Design and Data Analysis for Biologists.CMICROridge

University Press.

4. Fernholz, L.T, Morgenlhaler, S., Stahel, W., 2000. Statistics in Genetics and in

Environmental Sciences, BirkhauserVerlag.

5. Kuzma, J. W. and Bohnenblust, S. E. 2001, Basis Statistics for the Health Sciences,

McGraw-Hill International Education.

ENG-422 TECHNICAL WRITING 3(3-0)

Aims:

33

To enable the students to:

• Read Academics text critically

• Write well organized academic text e.g. assignments, examination answers

• Write narrative, descriptive, argumentative essays and reports (assignments)

Contents:

1. Critical Reading

Advanced reading skills and strategies building on Foundations of English I &

II courses in semesters I and II of a range of text types e.g. description,

argumentation, comparison and contrast

2. Advanced Academic Writing

Advanced writing skills and strategies building on English I & II in semesters

I and II:

o Writing summaries of articles

o report writing

o Analysis and synthesis of academic material in writing

o Presenting an argument in assignments/term-papers and examination

answers

Recommended Readings:

1. Aaron, J. 2003. The Compact Reader. New York: Bedford

2. Axelrod, R. B and Cooper, C.R. 2002. Reading Critical Writing Well: A Reader and

Guide

3. Barnet, S. and Bedau, H. 2004. Critical Thinking, Reading and Writing: A Brief Guide

to Writing. 6th

Ed.

4. Behrens & Rosen. 2007. Reading and Writing Across the Curriculum.

5. Gardner, P. S. 2005. New Directions: Reading, Writing and Critical Thinking

6. George, D. and Trimbur, J. 2006. Reading Culture: Context for Critical Reading and

Writing.6th

Ed.

7. Goatly, A. 2000. Critical Reading and Writing: An Introductory Course. London:

Taylor & Francis

8. Grellet, F., Writing for Advanced Learners of English. CUP

9. Jordan, K. M. and Plakans, L. 2003. Reading and Writing for Academic Success

34

10. Jordon, R. R. 1999. Academic Writing Course.CUP.

11. Smith, L. C. 2003. Issues for Today: An Effective Reading Skills Text

12. Withrow, J., Effective Writing. CUP

SEMESTER 5

MIC-501 FOOD & DAIRY MICROBIOLOGY 3(2-1)

AIMS & OBJECTIVES:

• Discuss the major roles of microorganisms in production, reservation and spoilage of

food and agricultural practices.

Course Detail

• Scope of food and agriculture microbiology.

• World food problems.

• Microorganisms important in food industry.

• Principles of food spoilage and their preservation.

• Spoilage and preservation of food products.

• Food preservation in warm countries.

• Food hygiene, sanitation and legislation.

• Quality assurance in food industries.

• Recent advances in food industry.

• Technology of food processing.

• Preservative agents for improving the quality, shelf-life and organolaptic properties

of foods.

Neutralizers, stabilizers, firming agents, coating and wrapping agents.

Food Preservation Technology.

Principles and methods of food preservation.

Bacteriology of preserved foods.

Packaging and related problems.

Agriculture microbiology, pesticides, microbial insecticides, ruminants

andmicroorganisms,

35

Practicals

1. Isolation of starter culture from: Cheese and Yogurt.

2. Isolation of phages from lactobacilli.

3. Enumeration of bacteria from: Poultry, Beef, Milk, Eggs and Fish.

4. Field trips to: Brewery industry and Milk plant.

Recommended Books

1. Jay, J. M., Loessner, M. J. and Golden, D. A., 2006. Modern Food Microbiology. 7th

Edition, Springer Science, Inc., U.S.A.

2. Karl, R. and Matthews, M. P., 2006. Doyle Microbiology.ASM Press.

3. Han, J., 2005. Innovations in Food Packaging, Elsevier Science and Technology

Books.

4. James, G., 2006. Brennan Food Processing Handbook. Wiley, John and Sons,

Incorporated.

MIC-503 CELL & TISSUE CULTURE TECHNOLOGY 3(2-1)

AIMS & OBJECTIVES:

• Nutritional Discuss the process of tissue culture technology.

• To study requirements.

Course Detail

• History and application of cell culture.

• The eukaryotic cell: general structure and function, cell cycle, chromosomes,

polyploidy, polytene and karyotypes.

• Nutritional requirements, growth and metabolism of cells, serum and growth control,

topoinhibition, source substitutes, pH regulation.

• Outlines of methodology of plant, insect and animal cell and tissue culture.

• Cell culture, cell types and morphology of cells in culture.

• Primary and secondary culture, cell strains and established cell lines.

• Establishment of cell lines.

36

• Establishment of clones of plant and animal cells.

• Lymphoid cells culture.

• Transformed cells: growth control of mouse fibroblasts and malignancy, the normality

of 3T3 fibroblasts cell lines from tumors.

• Genetics of cells in culture. Origin of mutant cell lines. Negative selection:

heterokaryons, malignancy of hybrids.

• Differentiated, serum dependent normal cells. Role of cyclic nucleotides.

• Selective cell line and their specialized uses (HeLA, Vero, 3T3 fibroblast, WEHI, etc.)

• Tissue culture and virology (CPE, Plaque Assay).

• Applications of plant tissue culture.

• Stem cell technology.

Practical

1. Preparation of glassware and media.

2. Starting a primary culture (tissue digestion, cell count and cell culture).

3. Establishing a cell line.

4. Cryopreservation of cell line.

5. Plant cell culture.

Recommended Books

1. Smith, R., 2000. Plant Tissue Culture. Academic Press.

2. Freshney, II., .2000. Culture of animal cells: A manual of basic techniques Wiley, John

and Sons

3. Masters, J. R., 2000. Animal cell culture.Oxford University Press.

4. Lanza, R. P., Lanza, B., Atala, A., 2001. Methods of tissue engineering Academic

Press Inc.

5. Doyle, A., Griffiths, J. B., 1998. Cells and tissue culture: Laboratory. Procedures in

biotechnology.Wiley, John and Sons.

6. Barnum, S., 2004. Biotechnology: An Introduction (with Infotrac) Brooks /Cole.

7. Halford, N., 2006. Plant Biotechnology: Current and Future Applications of

Genetically Modified Crops .John Wiley and Sons Limited.

37

MIC- 505 Microbial Enzyme Technology 3(2-1)

Course Outline

1. Introduction; Enzyme biosynthesis and genetic information

2. Enzyme nomenclature

3. Isoenzymes

4. Structure-function relationship

5. Optimal temperature; Arrhenius plot; Optimal pH

6. Enzyme catalysis and mechanism of action

7. Enzyme-substrate complex; active site

8. Allosteric enzymes

9. Auxiliary enzymes

10. Immobilized enzymes, applications; bioreactors, biosensors

11. Enzyme purification; purposes and strategies

12. Enzyme inhibition; drug, pesticide, herbicide inhibitors

13. Enzymatic analysis

14. Enzyme units; specific activity; Factors influencing enzyme activity

15. Enzyme Technology; Production of industrial enzymes in fermentation

Practical

1. Isolation of amylase producing microorganisms from soil samples.

2. Screening of amylase activity.

3. Identification of the amylase producing bacteria.

4. Isolation and purification of a bacterial enzyme.

5. Determination of enzyme activity.

Recommended Books

Nicholas Price, Lewis Stevens. 1999. Fundamentals of Enzymology. Oxford University

Press.

Martin F. Chaplin, C. Bucke. 1990. Enzyme Technology. Cambridge University Press.

José-Luis Barredo. 2005. Microbial Enzymes and Biotransformations. Humana Press.

C. P. Hollenberg (Author), H. Sahm (Editor). 1987. Microbial Genetic Engineering

and Enzyme Technology (Biotec, Vol 1). G. Fischer Verlag.

MIC-507 MOLECULAR BIOLOGY & BIOTECHNOLOGY 3(2-1)

Course Detail

Nature of genetic material, nucleic acids, DNA replication

Organization of Chromosomes: Genome size and complexity, the supercoiling of DNA,

the structure of prokaryotic and eukaryotic chromosome, Polytene chromosomes,

euchromatin and heterochromatin, satellite DNA, centromere and telomere structure.

38

Gene organization and expression in prokaryotes and eukaryotes.Introduction to Genes

and Proteins, Genome Sequences, ORFs, Genes, Introns, Exons, Splice Variants,

DNA/RNA, Secondary structure, Triplet Coding, Protein sequences, Protein Structure,

Secondary, Tertiary and Quaternary structures.Mendelian Laws of inheritance, gene

interactions. Extra chromosomal inheritance, mitochondrial and chloroplast genetic

systems: sex linked inheritance.

Gene linkage and chromosome mapping: Linkage and recombination of genes in

chromosomes, crossing over and its molecular mechanism, gene mapping by three point

test crosses, mapping by tetrad analysis, somatic cell hybridization for gene linkage

studies, recombination within genes.

Mutation: Spontaneous versus induced mutations, types of mutations, the molecular

basis of mutations, mechanisms of DNA repair, mutations, frequency, correlation

between mutagenicity and carcinogenicity, mutagenic agents, chemical and radiation.

Properties of microorganisms useful to the bio-industry. Biotechnology, brewing,

antibiotic production, recombinant protein production, vaccine production and waste

treatment industries.

Scope of fermentation biotechnology In Pakistan

Scientific disciplines used in microbial biotechnology.

Practical:

- Major biotechnological techniques used in Microbiology

- Biotechnological tools used in disease diagnosis

- Any additional techniques subject to the availability of facilities

Recommended Books:

1. Microbial Genetics- Maloy, S.R. Crown, J.E., and Freifelder, D.

2. Genetics- Hartl, D.L.

3. Genetics: Analysis and Principles- Brooker, R.J.

4. The Science of Genetics- Antherly A.G. Girton, J.R.

5. Microbial Genetics- Freifelder, D.

6. Genetics: Analysis of Genes and Genomes- Hartl, D.L. Jones, E.W.

MIC-509 AGRICULTURAL MICROBIOLOGY 3(2-1)

39

Learning Objectives

-Discovery how microbial ecologists view relationship of microorganisms

• Examine the major kinds of interactions microorganisms enter into

• Examine the habitats where we find microorganisms

• To discuss microbial plant diseases and their importance.

• To identify fungal and bacterial diseases.

• Discuss control of plant diseases.

Course Detail

• Study of major microbial plant diseases in Pakistan.

• Nature and classification of plant diseases.

• Fungal diseases: Rusts, Smuts, Wilts and Root rots.

• Diseases of fruits and vegetables.

• Bacterial diseases: Blights, Cankers, Leaf spots and Rots.

• Viral diseases: Mosaics, Dwarfs, Stunts, Yellows Leafcurl,

Witches Broom, Ring spots and Wilts.

• Cultural practices in disease control, chemical control.

• Elements of soil formation and conservation.

• Soil microbial population and methods of study with their advantages and

disadvantages.

• Role of microorganisms in mineral transformations with special and detailed emphasis

on Carbon and Nitrogen transformations. Brief introduction to Sulphur and Phosphorus.

• Introduction to soil ecology. Plant-microbe interactions and microbe-microbe

interactions and their impact on soil fertility and formation of compost and humus.

• Biotechnological potentials of soil microorganisms.

• Importance of the subject in the agricultural development of Pakistan.

Practical contents:

Different culture methods of soil microbes (plate culture, slope culture and broth

culture)

Qualitative examination of soil microflora

40

Enumeration of soil bacteria by direct microscopic count

Soil fungi count by dilution plating method

Examination of rhizosphere

Isolation of fungal and bacterial phyto-pathogens from diseased plants

Plant disease diagnostic techniques: study of symptoms, signs

how to prepare fungicide (Bordeaux mixture)

Preparation of bio-fertilizer

Recommended Books

1. Tate, R. L., 2000. Soil Microbiology.Wiley, John and Sons, Inc.

2. Davet, P. 2004. Microbial ecology of soil and plant growth.Science Publishers.

3. Elass, V., 2006. Modern Soil Microbiology.2nd Edition.

4. Sylvia, D. M., Fuhrmann, J. J., Hartel, G., Zuberer, D. A. 1998. Principles and

applications of soil microbiology, Oxford University Press.

5. Diane Tice, D., 2005. Principles and Applications of Soil Microbiology.2nd Edition.

6. Hull, R., 2001. Matthews’ Plant virology.Academic Press.

7. Prell, H. H., Day, P. R., 2001. Plant-fungal pathogen interactions: A classical and

molecular view. Springer Verilog.

MIC-511 MANAGEMENT OF INFECTIOUS WASTE 3(3-0)

Detail of Course

• An introduction to the management of infectious material/waste.

• Various types of infectious materials: handling and methods of their disposal.

• Infectious diseases and methods of spread of agents involved.

• Laboratory and Hospital acquired infections: possible sources and causes.

• Hazardous groups of microorganisms including genetically modified organisms.

• Basic containment rules and laboratory containment levels.

• Control measures and maintenance of control. Guidelines for workers in

pathological Labs.and post mortem rooms.

• Rules for safe conduct of field work expeditions in outdoor activities.

41

• Risk assessment: recognition of hazards, competence, elimination of hazards,

collection of data etc.

• Risk group personnel: their education, training and monitoring.

• Radiation hazards and disposal of radioactive wastes.

- Tours to different hospitals for practical orientation of students

Books Recommended

1. World Health Organization. 2001. WHO biosafety manual, WHO, Geneva.

2. Gillespie, S., and Hawkey, P. 2006. Principles and Practice of Clinical

Bacteriology, 2nd Edition.John Wiley& Sons, Inc U.S.A.

3. Frosch, M., Martin C. and Maiden, J., 2006. Handbook of Meningococcal Disease:

Infection Biology, Vaccination, Clinical Management. John Wiley & Sons, Inc

U.S.A.

4. Hacker, J. and Heesemann, J., 2002. . Molecular infection Biology: Interactions

between Microorganisms and Cells, John Wiley& Sons, Inc U.S.A.

5. Santoro, M.A., Gorrie, T.M., 2005. Ethics and the Pharmaceutical Industry,

CMICROridge University Press

6. Fay, A., Rozovsky, J. D., Woods, Jr., J.M. and Bellamy, M., 2005. The Handbook

of Patient Safety Compliance: A Practical Guide for Health Care Organizations.

John Wiley and Sons limited.

SEMESTER-6

MIC-502 VACCINOLOGY 3(2-1)

Learning Objectives:

On completion of this course, students should be able to:

1. Get insights into manipulation of immune system for vaccine development.

2. Exploit natural disease resistance as a tool to find out vaccine targets.

3. Obtain detailed knowledge of different types of vaccines, characteristics of

successful vaccines and their mode of protection.

4. Prepare vaccine at industry level and implement vaccination program.

42

Unit 1: Introduction, immunity & its types, immunization: passive and active

immunization, vaccines: introduction & types of vaccines with their merits & demerits,

Whole cell live attenuated & killed bacterial & viral vaccines, purified macromolecules

as vaccines, toxoids and antitoxins, attenuation, vaccine production methods, different

routes of vaccine administration, current vaccination practices.

Unit 2:EPI vaccines: production and testing of tetanus toxoids, diphtheria toxoids,

pertussis vaccine, BCG vaccines; preparation of Hepatitis B vaccine, tissue culture

derived rabies vaccine and AIDS vaccine.Adjuvants: classification and properties;

carriers- types and functions; vehicles: types, functions and mode of action;

biodegradable polymers- microspheres, liposomes and ISCOMs.

UNIT 3: Recombinant vaccines: polynucleotide as vaccines; vector vaccines; naked

DNA vaccines; biosynthetic and chemically synthesized vaccines; subunit vaccine; anti

idiotype vaccines; fussion vaccines; mixed particle vaccines; human mucosal vaccines;

combination vaccines; edible vaccines produced in transgenic plants and

microencapsulation, multivalent subunit vaccines, recent research and development of

AIDS vaccines.

Practical:

Purification of antibody, preparation of different bacterial and viral antigens, raising of

hyperimmune sera, seed cultivation, purification & quantification of important bacteria

and viruses for vaccine production, use of cell culture in attenuation of pathogenic

microorganisms and vaccine production, use of adjuvants, study of immunogenicity of

prepared vaccines in experimental animals.

Recommended Books

1. Janis Kuby, Immunology. 5th

Edition. W H Freeman and company New York.

2. Gregory G. et al; 1995 Vaccines; new generation immunological adjuvants. SeriesA:

Life Sciences; Volume: 282.

3. Heing K. and T. L. Philip: 1986 Vaccines: New concepts and developments-

proceedings of the 10th international convocation on immunology; July 14 – 17 buffalo,

New York. Longman scientific and technical 1998; New York.

43

4. Gregory G., C.A.Anthony and P.George; 1990. Vaccines: recent trends andprogress.

Series A: Life sciences: vol; 215 plenum press, New York

5. David male,Jonathan Brostoff,David B Roth, Ivan Roitt “Immunology”7th

edition

2006, Mosby, Europe Ltd, London.

MIC-504 ENVIRONMENTAL MICROBIOLOGY 3(2-1)

Learning Objectives

• Discuss role of microbial activities on chemical and geologic processes.

• Examine the roles microorganisms play in pollution.

Course Detail

• Introduction to environmental biotechnology.

• Microbial techniques for pollution control.

• Role of microorganisms for the production of food and fodder products from

agricultural and forestry wastes.

• Biological and chemical pesticides: their advantages and disadvantages.

• Microbial degradation of toxic and poorly degradable (recalcitrant) compounds.

• Bioremediation of environment contaminated with wood preservatives, petroleum

products, hydrocarbons, fuels and industrial wastes etc.

• Bioaccumulation of heavy metals and phytoremediation.

• Applications of recombinant microorganisms in reducing environmental pollution.

• Microbes as a tool for the assessments of risks associated with the environment.

• Recent advances in agricultural and environmental biotechnology.

Practical

1. Isolation of Oil degrading bacteria from environment.

2. Isolation of microorganisms from industrial effluent.

3. Detoxification of metal ions through microbes.

4. Effects of industrial effluents on germination and growth of seedlings.

Recommended Books

1. Ho- Yu, M., 2004. Environmental Toxicology, 2nd

edition, CRC press

2. Kofi asanteduah, D., 2002. Public health risk assessment for human exposure to

chemicals, Springer.

44

3. Caravati, E. M., Michael, A., and Lippincott, M., 2003. Medical Toxicology,

Williams and Wilkins.

4. Tickner, J. A., 2002. Precaution, environmental science, and preventive public policy,

2002, island press.

MIC-506 MEDICAL MICROBIOLOGY 3(2-1)

Course details:

Preparation of container and swabs for collections of specimens for microbial

examination.

Portal regulation and transport of specimen.

Flowchart of lab diagnostic procedures.

Documentation of specimen in laboratory.

Infection syndrome and diagnostic procedure.

Strategy of antimicrobial therapy.

Prophylactic mass immunization.

Nosocosmial infection and sterility testing of I.V. fluids and processing of various

Samples for various hospital infections.

Preservation of pure culture: Periodic subculture methods, cold storage, freezing,

deep

Freezing, lyophilization methods.

Blood culture, cell tissue and organ culture.

Total and viable counts of bacteria.

Epidemiology markers of microorganisms: Serotyping and Bacteriophage.

Diagnosis, treatment and control of common infections and infestations.

Specific serological methods of diagnosis.

Test of sensitivity to anti-microbial agents and their preparation.

Specific culture and drug sensitivity methods.

Practicals:

Antibiotic sensitivity (one organism).

Collection and processing of specimens like blood, urine, stool, pus etc. and

Isolating the causative organism (any one material).

45

Detection of antibody levels of sera taken from patients suspected to

be suffering from a bacterial infection (one sample).

Antigenic characterization of an unknown organism (one sample).

Animal inoculation.

Antibiotic sensitivity (one organism).

Recommended Books:

1. Topley and Wilson’ principles of Bacteriology, virology and immunology

Vol.-1-IV

2. Text Book of microbiology- Ananthanaryan and Panikar.

3. Medical microbiology- Greenwood, Stack and Penthre.

4. Medical microbiology- Mims et al.

MIC-508 VERTERINARY MICROBIOLOGY 3(2-1)

Course Detail

• Study of major animal diseases in Pakistan. Etiology, Symptomatology, Immunology,

Epidemiology, diagnosis, and prevention.

• Tuberculosis, Anthrax, Brucellosis, Johne’s Disease, Bovine Mastitis, tick fever,

Salmonellosis (including Pullorum).

• Rabies, Foot and Mouth Disease. New castle Disease, Infectious laryngotracheitis,

Fowl pox, Sore Mouth of sheep and goats, avian influenza, infectious bursal disease

(Gumboro), hydropericardium syndrome (Angara).

• Importance of Zoonoses in Pakistan.

• Quarantine and international control of animalslivestock farming.

Practicals:

- Isolation, identification and characterization of important Veterinary pathogens

Books Recommended

1. Quinn, P. J., Leonard, F. C., Markey, B. K., 2002. Veterinary Microbiology and

microbial diseases. Blackwell Science Inc.

46

2. Kornerup, A., Hansen, K., 1999. Handbook of laboratory animal bacteriology.

CRC Press, LLC.

3. Mettenleiter, T. C and F. Sobrino, F., 2008. Animal Viruses: Molecular Biology

Caister Academic Press.

4. Aarestrup, F. M., 2005. Antimicrobial Resistance in Bacteria of Animal Origin

American Society for Microbiology.

5. Acha P.N. and Szyfres, B., 2003. Zoonoses and communicable Diseases common

to Man and animals, VolumeI, II, III, Pan American Health Organization.U.S.A.

6. Martin E., Jones, H., William T. and Hubbert, V. H., 2005. Zoonoses: Recognition,

Control and Prevention, Blackwell Publishing.

MIC-510 PHARMACEUTICAL MICROBIOLOGY 3(2-1)

Aims and Objectives: At the end of course, students should be able to describe

Define the term selective toxicity

Elaborate on the sources of anti-microbial compounds

Elaborate on the mechanisms of anti-microbial compounds

Design a rational hospital / national antibiotic policy

Define GMP

Describe the potential sources of microbial contamination in the pharmaceutical

industry

Describe the method to control microbial contamination in industry

Design clean rooms and microbiology quality control lab

Define and explain fermentation

Describe fermentation methods to produce antibiotics

Course contents:

Introduction to chemotherapy and selective toxicity, anti-microbial agents, their

sources and mechanism of actions, anti-microbial resistance and mechanisms of

resistance (genetic and acquired), anti-microbial susceptibility testing, hospital antibiotic

policies, anti-viral chemotherapy and problems in anti-viral.

47

Introduction to sterilization, disinfection and antisepsis, methods of sterilization

and sterility testing, pyrogens and pyrogens testing, factory and hospital hygiene and

Good Manufacturing Practices, sources and control of microbial contamination during

manufacturing, manufacture of sterile products, Design clean rooms and microbiology

quality control lab, introduction to fermentation and its types, fermentation methods to

produce antibiotics (penicillins, cephalosporins, gentamicin, erythromycin, tetracyclines,

rifamycin, griseofulvin).

Introduction to recombinant DNA technology, its role in pharmaceutical industry,

pharmaceutical products made by genetic engineering e.g. cytokines (interferon),

hormones (insulin, somatotropin and somatostatin), molecular diagnostics.

Practicals:

1. Microbiological assay of drugs and vitamins

2. Pyrogen testing through LAL test

3. Anti-microbial susceptibility testing (Disc diffusion method)

4. Determination of MIC (Broth dilution method) and MBC

Recommended Books:

1. Tortora, Case, Funke. Microbiology: An Introduction. 11th

Edition. Addison Wesley

Longman, Int. California.

2. Janis Kuby, Immunology. 5th

Edition. W H Freeman and company New York.

3. Hugo and Russell, Pharmaceutical microbiology. 7th

edition 2004.Blackwell Science

Ltd London.

MIC-512 MICROBIAL BIODEGRADATION AND BIOREMEDIATION 3(3-0)

Course Contents

Introduction of Bioremediation and Biodegradation- the basic problem, biological and

non-biological treatments, detoxification, activation, lag phase, kinetics

48

The Microbiology of Bioremediation And Biodegradation – concepts, natural

bioremediation, bioavailability, types of bio treatment processes, composting technology,

co-substrates

Metabolic and co-metabolic biodegradation – general concepts on metabolic and co-

metabolic biodegradation of environmental contaminants as well as metabolic pathways

involved

Future Directions in Bioremediation – areas of current research, engineering

technologies, development of strains

Recommended Books

Rittman, B. 2001. Environmental Biotechnology, Principles and Application.

McGraw Hill, New York.

Chaudry, G.R. (1995), Biological degradation and Bioremediation of Toxic

Chemicals, Chapman and Hall.

Focht, D.D. (1996), Principles of Biodegradation, Chapman and Hall

Madingan, M., Martinko, J. and Parker, J. (1997) Biology of microorganisms:

Prentice Hall International (UK) Ltd.

SEMESTER 7

MIC-601 CLINICAL MICROBIOLOGY 3(2-1)

Course Detail

• An introduction to clinical bacteriology

• Hazards in clinical microbiology laboratory

• Role and importance of normal flora in different parts of body

• Respiratory tract infections.

• Infections of eye, ear and skin

• Fluids from infected joints, CSF, pleural and peritoneal fluids

• Differential diagnosis of selective systemic bacterial infections of GIT, genito-

urinary, cardiovascular and central nervous system.

• Nosocomial infections: prevention and control

49

• Principles of latest diagnostic procedures

• Post-operative infections

Practical

1. Good laboratory practices.

2. Collection and processing of different clinical specimen.

3. Isolation and identification of pathogens from different clinical specimen.

4. Antibiotic sensitivity test by various techniques.

Recommended Books

1. Gladwin, M., Trattler, B., Trattler. B., 2004. Clinical Microbiology Made Ridiculously

Simple, 3rd Edition, Med Master, Incorporated.

2. Jones, S. L., and Ed. Jones, R., 2001. Clinical Laboratory Pearls.Lippincott Williams

and Wilkins.

3. Murray, P.R., Rosenthal, K.S., Pfaller, M.A., Rosenthal, K.S., 2005. Medical

Microbiology: Elsevier Health Science.

4. McClatchey, K. D., Keren, D. F., Hackel, E., Lewandrowski, K. and Alkan, S., 2001.

Clinical Laboratory Medicine.Lippincott Williams and Wilkins.

5. Hawkey, P and Lewis, D., 2004. Medical Bacteriology: A Practical Approach.

2nd

Edition .Oxford University Press.

MIC-603 PLANT MICROBIOLOGY 3(2-1)

Learning Objectives

Fundamental and applied aspects of plant microbiology.

Discus interaction between plants and microorganisms.

Discus the role of PGPRs in plant/crop management.

Course Detail

Introduction to plant microbiology

Discuss in detail plant microbe interaction and plant microbe-microbe interaction

Plant defenses mechanisms towards pathogenic microorganisms (emphasis on

bacteria and fungi)

Bacterial ice nucleation role in plant

50

Microbiology of pulp and paper

Microbial role in root nodulation (emphasis at nitrogen fixing bacteria)

Decomposition of plant litter and wood decay process

Major microbial enzyme systems/pathway for induction of plant defense

Plant growth promoting bacteria (types and classification)

Colonization of plant roots by PGPRs and its role in plant growth and plant

defense

Agrobacterium biology and plant transformation

Gene transfer in plants via microorganisms (Agrobacterium tumefaciens) and

Plant mutants that resist Agrobacterium-mediated gene transfer

Study of plant cell receptor and bacterial receptor in gene transfer process

Microbial role in plant biotechnology

Microbial and plant Biotechnology for Biofuels and Bioproducts.

Recent advances in plant microbiology

Practicals:

1. Isolation of plant growth promoting bacteria from plant and soil

2. Study the effect of PGPR on plant seedling growth

3. In-vitro study of bio-control bacteria

4. Study of microbes in plant root nodulation

Recommended Books

1. Bakker, P.A.H.M., Raaijmakers, J.M., Bloemberg, G., Höfte, M., Lemanceau,

P., Cooke, B.M. (2007).New Perspectives and Approaches in Plant Growth-

Promoting Rhizobacteria Research. Springer Press.

2. Siddiqui, Z.A (2006). PGPR: Biocontrol and Biofertilization. Springer Verilog.

3. Jones, H (1996). Plant Gene Transfer and Expression protocols (Methods in

Molecular Biology). Humana Press.

4. Yoshihiro N, Mari N, Satoshi Y and Masaki I (2012). Transgenic plants,

Advances and Limitations, Chapter 9, Methods to Transfer Foreign Genes to

Plants. CRSS Press

MIC- 605 MARINE AND FRESH WATER MICROBIOLOGY 3(2-1)

51

Course Details:

• Introduction to marine microbiology.

• Zonation and stratification in marine environment.

• Movement of water in marine environment.

• Laws of ecology with particular reference to marine ecosystem: environmental

factors (biotic and abiotic) and their influence on the distribution of

microorganisms.

• Enumeration of bacteria: sampling and samplers, processing and actual enumeration

procedures.

• Marine microorganisms: some important groups of marine microorganisms.

• Detailed study of biogeochemical cycling of C, N, S& P.

• Advantages and disadvantages of marine microorganisms including their

importance in marine biotechnology.

• Some common diseases of marine fauna.

Introduction to fresh-water environment and its microbiology.

• Stratifications in lakes and ponds.

• Laws of ecology with particular reference to fresh-water ecosystem: environmental

factors (biotic and abiotic) and their influence on the distribution of

microorganisms.

• Enumeration of bacteria: sampling and samplers, processing and actual enumeration

procedures.

• Fresh-water microorganisms: some important groups of fresh-water

microorganisms.

• Advantages and disadvantages of fresh-water microorganisms including their

importance in fresh-water biotechnology.

• An introduction to aqua-culture and some common microbiological problems.

• Some common diseases of fresh-water fauna.

52

Practical

1. Study of microbial population from fresh water.

2. Study of Microbial counts.

3. Biological oxygen demand of fresh water sample.

4. Effect of physical factors on microbial fresh water flora.

Recommended Books

1. Paul, J., 2001. Marine Microbiology (Methods in Microbiology Vol. 30).

Academic Press, Inc.

2. Kirchman, D. L., Kirchman, D. L., 2000. Microbial ecology of the ocean.Wiley,

Johns and Sons Inc.

3. Munn, C., 2003. Marine microbiology: Ecology & application. Lavoisier.

4. Paul F. and Andrew H. K., 2007. Evolution of Primary Producers in the

Sea.Academic Press.

5. Horst, D. S. and Matthias Z., 2006. Marine Geochemistry. Springer

6. Stuart, F. and Robert L. S., 2002. Aquatic Ecosystems: Interactivity of

Dissolved Organic Matter. Academic Press.

MIC-607 INDUSTRIAL MICROBIOLOGY 3(2-1)

Course Detail

• Properties of microorganisms useful to the bio-industry. Biotechnology, brewing,

antibiotic production, recombinant protein production, vaccine production and

waste treatment industries.

• Scope of fermentation biotechnology In Pakistan

• Scientific disciplines used in microbial biotechnology.

• Immobilized enzymes and microbial cells and their applications

• Principles of Biochemical Engineering and historical perspective.

• Large-scale microbial fermentation, the principles and problems.

• An introduction to downstream processing.

53

• Strain Development spectrum of for microbial, Isolation and identification of

industrially important microorganisms. Different approaches improvement of

industrial microbes. Empirical and Semi-empirical strain development,

mutagenesis, screening and selection.

• Use of auxotroph and analogue resistant mutants in strain development.

• Growth and Development of Microorganisms in Bioreactors.

• Quorm (r) myco-protein, a product produced by continuous flow fermentation.

• Continuous culture technologies for strain improvement.

• Metabolic Control Analysis: principles and means of rational strain development.

Practicals

1. Citric Acid production.

2. Ethanol production.

3. Lactic Acid.

4. Estimation of Microbial cell mass.

5. Mutagenesis (Physical and Chemical).

6. Field trips:

Industrial alcohol production from sugar cane; Citric acid production.

Amino acid biosynthesis in Corynbacteriunglutamicum.

Tryptophan biosynthesis in Neurosporacrassa.

Recommended Books

1. David, B., Jewell, T.R. 2000. Biotechnology: demystifying the concept, Oxford

University Press.

2. Sedivy, J. M., Joyner, A. L. 2000. Gene targeting, Oxford University Press.

3. Baumberg, S. 1999. Prokaryotic gene expression, Oxford University Press.

MIC-609 RESEARCH METHODOLOGY 2(2-0)

Objectives

The course will provide participants with an introduction to the knowledge and

skills necessary to develop a research proposal and subsequently to conduct a research

54

study. It will help: to develop research abilities in the activities of research design and

practice; to develop skills in reading research papers and in writing reviews with critical

thinking skills & to evaluate a range of specific literature via the ability to reason clearly

and think critically; to introduce students to research design, research methods, and the

process of doing research and reporting the results

Course Contents

Introduction to Research, Research Design & Research Methods; Scientific

Research: Science, Scientific Methods, Techniques & Pre-requisites for Scientific

Research, Critical Thinking and Developing the Research Question: Defining the

Research Problem; Selecting the Research Method; Research Proposal: its importance -

A pre-requisite for Research; Research Proposal Writing Techniques: Importance of

Research Design, Review of Literature, Objectives, Methodology; How to put things

together? Introduction, Material Methods, Review of Literature, Bibliography, Literature

Search: Database, Search Engines; Analytical tools in research: qualitative and

quantitative methods; Sampling: the logic of sampling, concepts and terminologies,

population and sampling frames, types of sampling design/; Data Collection: Techniques

in data collection: Quantitative & Qualitative Data; Experimental Research, Case Studies,

Surveys, Interviews, Questionnaire; Data Analysis: Data Interpretation: Current data

interpretation with comparative studies (Inter-laboratory comparison), Inference based on

findings; Research Presentation Techniques – Data presentation

Recommended Books:

Designing and Conducting Mixed Methods Research, Creswell, J. W. & Plano

Clark, V.L. Thousand Oaks, Sage CA, USA, 2007.

Case Study Research: Design and Methods, Robert Yin, 3rd Edition, Sage

Publishers. USA, 2003.

Students project in Environmental Science, Harrad, S., Batty, H., Diamon, M. and

Arhonditsis, G, John and sons Ltd., Chichester, England, 2008.

ENG-611 ENGLISH FOR EMPLOYMENT 3(3-0)

What is your dream job?

Job searches: internal job market (newspapers, internet, job fair/talent hunt at

universities)

55

Reading advertisements

Researching the company and its ethos

Filling an application form

Introduction to resumes

Practicing with a resume

CV writing

Practicing with format 1 of a CV (no personal statement)

CV writing

Practicing with format 2 of a CV (with introductory personal statement)

Writing a cover letter

Preparing for interviews 1: content / questions

Preparing for interviews 2: body language, comportment, grooming appearance

Preparing for interviews 3: Practicing mock face-to-face interviews

Job searches: overseas job market

Writing resumes and CVs: overseas job market

Practicing with CVs: overseas job market

Job interviews (face-to-face and Skype / telephone): overseas job market

SEMESTER 8

MIC-632 INTERNSHIP 6(0-6)

Dr Muhammad Hidayat Rasool

Chairman

Department of Microbiology

Government College University Faisalabad

Phone: +92-41-9201205; 0301-7102378; 0336-7102333

Email: drmhrasool@gcuf.edu.pk

1

COURSES FOR

M. Phil. / PhD

MICROBIOLOGY

DEPARTMENT OF MICROBIOLOGY

FACULTY OF SCIENCE AND TECHNOLOGY

GC UNIVERSITY FAISALABAD

2

General Rules and Guidelines

The M Phil Microbiology degree Programme will be of minimum two years (Four

Semesters) and maximum three years (six semesters).

The programme will comprise of both course work as well as research work.

For award of M. Phil degree, candidates will need to complete total 30 credit

hours comprising 24 credit hours of course work along with 6 credit hours for

research work / thesis (As per HEC Criteria & GC University rules and

regulations).

The course work will be further divided as

- Major Courses = Two third (16 Credit Hours)

- Minor Courses = One third (08 Credit Hours)

- Research and Thesis = 06 Credit Hours

The minor courses will include courses like Biostatistics, Biochemistry or to be

selected by a student in consultation of his / her supervisory committee from any

other department of Life / Biosciences within Faculty of Science & Technology

like Bioinformatics & Biotechnology, Pharmacy, Physiology, Biochemistry,

Botany, Wild life & fisheries, Food Science and Environmental Sciences.

One or more deficiency courses may also be enrolled by a student if necessary but

these courses will be additional to the prescribed course work and their marks will

not be counted towards CGPA.

Each student will be allotted a three member supervisory committee comprising a

Supervisor and two members.

Each student will have to prepare his / her course work in consultation with

supervisory committee and get it approved from Departmental Board of Studies

as well as from Directorate of Advanced Studies before the enrolment of 2nd

Semester.

The student will have to compile his / her synopsis for research, get it approved

from supervisory committee and then will be scrutinized by Faculty Scrutiny

Committee and finally will be defended in an open seminar.

3

No student will be allowed to enroll third semester if they have not submitted

their final approved synopsis in Directorate of Advanced Studies.

The students will conduct their Research work in 3rd

& 4th

semester and write up a

dissertation / thesis which will be checked and duly approved by supervisory

committee.

Student will have to submit the semi-final copy of thesis to Directorate of

Advanced Studies on due dates along with the Plagiarism Report duly signed by

the supervisory committee.

Final copy of thesis shall be submitted afterward to Controller of Examination

along with the panel of experts from the respective supervisor. The controller

office will get approval of one expert from the list by Vice Chancellor. One copy

of final thesis along with the letter of approval will be sent to the external

examiner for Viva.

After oral examination the result duly signed by internal supervisory committee

and external examiner will be sent to Controller of Examination who will

officially notify the result of the student.

The student will then submit copies of thesis in hard binding as well as soft copy

to the Controller of Examination for their record and distribution to HEC,

University Library, Directorate of Advanced Studies and respective Department.

Admission Criteria

The admission Criteria in M. Phil Microbiology Programme will be as per HEC

requirements and according to the rules and regulations of GC University Faisalabad.

Sixteen years of schooling or 4 year education (124 credit hours) after

HSSC/F.Sc/Grade 12 will be required for admission in the M. Phil.

Candidates with BS/BSc (Hons.) Microbiology or MS/MSc Microbiology will be

preferred. Moreover, those having degrees of Pharm-D, DVM, BSc (Hons)/ BS in

Biological/Life Sciences are also eligible to apply. However, the students without

basic degree in Microbiology may have to enroll some deficiency courses in

4

addition to their prescribed course work as approved by the Chairman and

Supervisory Committee.

The GAT-General (www.nts.org.pk/gat/gat.asp) conducted by the National

Testing Service with a minimum 50% cumulative score will be required at the

time of admission to M. Phil. The GAT-General test is valid for a period of two

years.

Admissions will be made purely on merit basis after every two semesters (once a

year) and number of seats will be ten (10) for admission in 1st Batch (Fall 2012)

which may be increased in future.

For award of M. Phil degree, candidates need to complete 24 credit hours of

course work along with a minimum of 6 credit hours for research work/thesis.

Any change can be made in these rules from time to time as per HEC Criteria and

GC University rules & regulations with the approval from departmental Board of

Studies.

5

COURSE OUTLINE

Sr. No. Course Code Course Title Credit Hours

1 MIC-700 Introductory Microbiology (Deficiency

course for Non-Microbiologists)

3(2-1)

2 MIC-701 Advanced General Microbiology (Elective) 3(2-1)

3 MIC-702 Advanced Bacteriology (Core) 3(2-1)

4 MIC-703 Advanced Virology (Core) 3(2-1)

5 MIC-704 Advanced Mycology (Core) 3(2-1)

6 MIC-705 Advanced Parasitology (Elective) 3(2-1)

7 MIC-706 Advanced Epidemiology & Public Health

(Elective)

3(2-1)

8 MIC-707 Public Health Microbiology (Elective) 3(2-1)

9 MIC-708 Advanced Immunology (Core) 3(2-1)

10 MIC-709 Microbial Physiology (Elective) 3(2-1)

11 MIC-710 Microbial Genetics (Elective) 3(2-1)

12 MIC-711 Molecular Biology of Bacterial Viruses

(Elective)

3(2-1)

13 MIC -712 Advanced Anaerobic Microbiology

(Elective)

3(2-1)

14 MIC-713 Tissue Culture Technology (Elective) 3(2-1)

15 MIC-714 Microbiological Techniques (Deficiency

course for Non-Microbiologists)

3(1-2)

16 MIC-715 Molecular Biology Techniques (Elective) 3(1-2)

17 MIC-716 Recombinant DNA Technology (Elective) 3(2-1)

18 MIC-717 DNA Damage, Repair and Carcinogenesis

(Elective)

3(3-0)

19 MIC-718 Vaccinology (Elective) 3(2-1)

20 MIC-719 Industrial & Pharmaceutical Microbiology

(Elective)

3(2-1)

21 MIC-720 Food & Dairy Microbiology (Elective) 3(2-1)

6

22 MIC-721 Environmental Microbiology (Elective) 3(2-1)

23 MIC-722 Bioinformatics, Genomics & Proteomics 3(2-1)

24 MIC-723 Research Methodology (Elective) 2(2-0)

25 MIC-724 Advanced Biorisk Management 3(2-1)

Mandatory Requirements for M. Phil

1 MIC-728 Seminar (General) 1(0-1)

2 MIC-729 Seminar (Research) 1(0-1)

3 MIC-730 Thesis 6(0-6)

Mandatory Requirements for PhD

1 MIC-758 Seminar (General) 1(0-1)

2 MIC-759 Seminar (Research) 1(0-1)

3 MIC-760 Thesis

Note:

All the students admitted in M. Phil programme have to enroll four core courses

of 3 credit hours each (as mentioned in the above list) which will be offered in Ist and 2

nd

Semesters. In addition to this they will enroll elective courses offered in a particular

semester from the above mentioned list in consultation to the Chairman of the

Department and Supervisory Committee in order to complete their course work. The

Seminar of 1 credit hour and Research and Thesis of 6 credit hours is compulsory of all

the students.

7

M. Phil. Microbiology with major in (Health Microbiology) for

Medical Graduates

General Rules and Guidelines

This programme will be specific for Medical Graduates (MBBS, BDS).

It will be of minimum two years (Four Semesters) and maximum three years (six

semesters).

The programme will comprise of both course work as well as research work.

For award of M. Phil degree, candidates will need to complete total 30 credit

hours comprising 24 credit hours of course work along with 6 credit hours for

research work / thesis.

The course work will be further divided as

- Major Courses = Two third (16 Credit Hours)

- Minor Courses = One third (08 Credit Hours)

- Research and Thesis = 06 Credit Hours

The minor courses will include Biostatistics, General Pathology, Clinical

Biochemistry or to be selected by a student from allied disciplines in which M.

Phil. programme for Medical Graduates is being carried out like Physiology,

Biochemistry, Pharmacology, Nutrition etc etc. or from any other department of

Life / Biosciences at GCUF.

One or more deficiency courses may also be enrolled by a student if necessary but

these courses will be additional to the prescribed course work and their marks will

not be counted towards CGPA.

Each student will be allotted a supervisory committee comprising a Supervisor

and 2nd

member from major discipline (Microbiology) and 3rd

member from allied

discipline(s) in 1st semester.

8

Each student will have to prepare his / her course work in consultation with

supervisory committee and get it approved from Departmental Board of Studies

as well as from Directorate of Advanced Studies before the enrolment of 2nd

Semester.

The student will have to compile his / her synopsis for research, get it approved

from supervisory committee, then will be scrutinized by Faculty Scrutiny

Committee and finally he / she has to defend it in an open seminar.

No student will be allowed to enroll third semester if they have not submitted

their final approved synopsis in Directorate of Advanced Studies.

The students will conduct their Research work in 3rd

& 4th

semester and write up a

dissertation / thesis which will be checked and duly approved by supervisory

committee.

Student will have to submit the semi-final copy of thesis to Directorate of

Advanced Studies on due dates along with the Plagiarism Report duly signed by

the supervisory committee.

Final copy of thesis shall be submitted afterward to Controller of Examination

along with the panel of experts from the respective supervisor. The controller

office will get approval of one expert from the list by Vice Chancellor. One copy

of final thesis along with the letter of approval will be sent to the external

examiner for Viva.

After oral examination the result duly signed by internal supervisory committee

and external examiner will be sent to Controller of Examination who will

officially notify the result of the student.

The student will then submit copies of thesis in hard binding as well as soft copy

to the Controller of Examination for their record and distribution to HEC,

University Library, Directorate of Advanced Studies and respective Department.

Admission Requirements

Candidates holding MBBS / BDS degrees with minimum 2nd

division.

9

Anyone who has been expelled by any university or college for mis-conduct or

for use of unfair means in the examinations or any offence involving moral

turpitude or for any valid reasons shall not be entitled to admission.

The GAT-General (www.nts.org.pk/gat/gat.asp) conducted by the National

Testing Service with a minimum 50% cumulative score will be required at the

time of admission to M.Phil. The GAT-General test is valid for a period of two

years.

Admissions will be made purely on merit basis after every two semesters (once a

year) and number of seats will be Five (05) for admission in 1st Batch (Fall 2012)

which may be increased in future.

For award of M. Phil degree, candidates need to complete 24 credit hours of

course work along with a minimum of 6 credit hours for research work/thesis.

Any change can be made in these rules from time to time as per HEC Criteria and

GC University rules & regulations with the approval from departmental Board of

Studies.

10

COURSE OUTLINE

Sr. No. Course Code Course Title Credit Hours

1 MIC-700 Introductory Microbiology (Deficiency

course for Non-Microbiologists)

3(2-1)

2 MIC-701 Advanced General Microbiology (Elective) 3(2-1)

3 MIC-702 Advanced Bacteriology (Core) 3(2-1)

4 MIC-703 Advanced Virology (Core) 3(2-1)

5 MIC-704 Advanced Mycology (Core) 3(2-1)

6 MIC-705 Advanced Parasitology (Elective) 3(2-1)

7 MIC-706 Advanced Epidemiology & Public Health

(Elective)

3(2-1)

8 MIC-707 Public Health Microbiology (Elective) 3(2-1)

9 MIC-708 Advanced Immunology (Core) 3(2-1)

10 MIC-709 Microbial Physiology (Elective) 3(2-1)

11 MIC-710 Microbial Genetics (Elective) 3(2-1)

12 MIC-711 Molecular Biology of Bacterial Viruses

(Elective)

3(2-1)

13 MIC -712 Advanced Anaerobic Microbiology

(Elective)

3(2-1)

14 MIC-713 Tissue Culture Technology (Elective) 3(2-1)

15 MIC-714 Microbiological Techniques (Deficiency

course for Non-Microbiologists)

3(1-2)

16 MIC-715 Molecular Biology Techniques (Elective) 3(1-2)

17 MIC-716 Recombinant DNA Technology (Elective) 3(2-1)

18 MIC-717 DNA Damage, Repair and Carcinogenesis 3(3-0)

11

(Elective)

19 MIC-718 Vaccinology (Elective) 3(2-1)

20 MIC-719 Industrial & Pharmaceutical Microbiology

(Elective)

3(2-1)

21 MIC-720 Food & Dairy Microbiology (Elective) 3(2-1)

22 MIC-721 Environmental Microbiology (Elective) 3(2-1)

23 MIC-722 Bioinformatics, Genomics & Proteomics

(Elective)

3(2-1)

24 MIC-723 Research Methodology (Elective) 2(2-0)

25 MIC-724 Seminar (Compulsory) 1(1-0)

26 MIC-725 Special Problem (Elective) 1(0-1)

27 MIC-726 Research & Thesis (Compulsory) 6(0-6)

Note:

All the Medical Graduates (MBBS & BDS) admitted in this programme have to

enroll four core courses of 3 credit hours each (as mentioned in the above list) which will

be offered in Ist and 2

nd Semesters. In addition to this they will enroll elective courses

relevant to Medical / Health Microbiology from the above mentioned list in consultation

to the Chairman of the Department and Supervisory Committee in order to complete their

course work. The Seminar of 1 credit hour and Research and Thesis of 6 credit hours is

compulsory of all the students.

12

MIC-700 INTRODUCTORY MICROBIOLOGY (THEORY) 3(2-1)

Learning objectives:

On completion of this course, students should be able to:

1. Understand the importance of microorganisms

2. Understand the structure, functions, nutrition, growth, metabolism, evolution,

taxonomy, diversity, and chemotherapy of microorganisms.

3. Use the techniques to deal with the safe culturing, detection, and typing of microbes.

The Study of microbial structure; Prokaryotic cell structure and function; Eukaryotic cell

structure and function; Microbial nutrition; Microbial growth; Microbial metabolism;

Microbial genetics; Control of microorganisms by physical and chemical agents;

Microbial evolution, taxonomy, and diversity; The archaea; The protists; Characteristics

of viruses; The fungi (Eumycota); Biogeochemical cycling and introductory microbial

ecology; Microbial interactions; Nonspecific (innate) host resistance; Specific (adaptive)

immunity; Pathogenicity of microorganisms; Antimicrobial chemotherapy; Role of

microbes in industry.

MIC-700 INTRODUCTORY MICROBIOLOGY (PRACTICAL) 3(2-1)

Preparation and maintenance of culture media; selective, enrichment and differential

media. Culturing of microbes and their stock management; Cultural, Morphological and

Biochemical characteristics for the isolation and purification of microorganisms from

various environments; Typing of pathogens; sero-types, Phage-types and Pathotypes.

Suggested Readings:

1. Camille, L. and M. Simonet, 2012. Bacterial Pathogenesis: Molecular and

Cellular Mechanisms. Caister Academic Press, UK

2. Cappuccino J.G. and N. Sherman, 2004. Microbiology: A Laboratory Manual.

Pearson Education, NJ, USA

13

3. Jawetz, E., 2000. Medical Microbiology. 21st Ed., Prentice-Hall Intl. Ltd.,

London, UK

4. Talaro, K.P. and A. Talaro, 2002. Foundation in Microbiology. McGraw Hill,

New York, USA

5. Tortora, G.J., B.R. Funke and C.L. Case, 2004. Microbiology - An Introduction,

8th

Ed., Pearson Edu. Inc., California, USA

MIC-701 ADVANCED GENERAL MICROBIOLOGY (THEORY) 3(2-1)

Learning objectives:

On completion of this course, students should be able to:

1. Understand the importance of microorganisms.

2. Understand the structure, functions, nutrition, growth, metabolism, evolution,

taxonomy, diversity, and chemotherapy of microorganisms.

3. Use the techniques to deal with the safe culturing, detection and typing of microbes.

Unit 1: Introduction to the science of Microbiology, history and scope of Microbiology,

major divisions of Microbial World and relationship among them, nomenclature and

classification of microorganisms.

Unit 2: Microscope & Microscopy: types and working of light microscopes ( bright field

microscope, dark field microscope, phase contrast microscope, polarizing microscope,

inverted microscope, fluorescent microscope) & electron microscope (scanning and

transmission).

Unit 3: Dyes & staining: light & color, absorption spectrometry, general chemistry of

dyes, indicators, nature of staining processes, factors that influence staining, staining the

living cells, different types of staining (simple staining, differential staining, special

staining, negative staining etc.)

Unit 4: Concept of sterilization, disinfection and antisepsis, pasteurization, tyndalization

etc. methods of disinfection and sterilization with their merits & demerits.

MIC-701 ADVANCED GENERAL MICROBIOLOGY (PRACTICAL) 3(2-1)

Laboratory Safety Rules with special reference to Microbiology lab, Introduction to

different Equipments / materials used in microbiology lab, Microscope and microscopy:

parts and working, Sterilization: Use of autoclave and hot-air-oven (sterilization of glass

14

ware & culture media), Staining of bacteria (Simple staining, Gram’s staining, acid fast

staining, spore staining, capsule staining, flagellar staining).

Recommended Books

1. Tortora, Case, Funke. Microbiology: An Introduction. 11th

Edition. Addison Wesley

Longman, Int. California.

2. Prescot L.M., Harley G.P Klein D.A “Microbiology” 2nd- edition Mc Graw Hill

Company Inc

3. Alcamo, Introduction to Microbiology. 6th

edition 2003. John Bartlett Publishers.

4. Cappuccino, Sherman, Microbiology: A Laboratory Manual. 7th

edition 2004. Pearson

Education Inc.

MIC-702 ADVANCED BACTERIOLOGY (THEORY) 3(2-1)

Learning Objectives:

On completion of this course, students should be able to:

1. To learn the properties and technical cultural, morphological and molecular

characteristics essential for the identification of Gram positive, Gram negative,

aerobic and anaerobic bacteria.

2. To become competent enough to deal with the collection, examination and the

identification of normal bacterial microflora from the environment, healthy and

disease specimen.

3. To apply the practical hands-on training in the characterization of specific

bacterial species required for the fields of clinical microbiology and quality

control in the major food, textile and pharmaceutical industries.

Unit 1: General Bacteriology: Introduction, General and cellular morphology of bacteria,

structure and function of bacterial cell and its components, classification of bacteria,

bacterial growth and growth curve, growth rate and generation time, physical and

nutritional requirements of bacterial growth and their classification, culture media and

their types, bacterial cultures and their maintenance.

Unit 2: Medical Bacteriology: Study of medically important bacteria and diseases caused

by them (mode of transmission, pathogenesis, clinical signs, diagnosis, treatment and

control). Gram positive cocci - Staphylococci and Streptococci, Gram negative cocci -

15

Neisseria, Gram positive rods - Bacillus, Clostridium, Corynebacterium, Gram negative

rods - Pseudomonas, Vibrio, Yersinia, Bordetella, Brucella, Haemophilus, Escherichia,

Salmonella, Shigella, Proteus, Klebsiella, Serratia, Bacteriods - Helicobacter, and

Chlaymdia, Acid fast bacteria - Mycobacterium, Filamentous bacteria - Actinomycetes,

Cell wall less bacteria - Mycoplasma. Zoonosis & Zoonotic infections, Classical & newly

emerging bacterial diseases, Probiotics.

MIC-702 ADVANCED BACTERIOLOGY (PRACTICAL) 3(2-1)

Selection, preparation & sterilization of different culture media (simple, differential,

selective & enrichment media), Selective isolation of bacteria in different environments

(aerobic, anaerobic, microaerophilic & in CO2 tension), pour plate, spread plate & streak

plate methods, Biochemical tests for the identification of bacteria, Determination of

bacterial motility, Total & viable count of bacteria, Microbiological examination of

water, milk & soil samples, Collection & transportation of clinical samples; ear, nose,

throat, eye, GIT, UGT & bones, Isolation & characterization of some important human

pathogenic bacteria.

Recommended Books

1. Tortora, Case, Funke. Microbiology: An Introduction. 11th

Edition. Addison Wesley

Longman, Int. California.

2. Prescot L.M., Harley G.P Klein D.A “Microbiology” 2nd- edition Mc Graw Hill

Company Inc

3. Alcamo, Introduction to Microbiology. 6th

edition 2003. John Bartlett Publishers.

4. Cappuccino, Sherman, Microbiology: A Laboratory Manual. 7th

edition 2004. Pearson

Education Inc.

5. Breed R.S. et al. (2002). Bergey’s Manual of Determinative Bacteriology. The

Wiliams and Wilkins Co. Baltimore.

Hawkey, P and Lewis, D., 2004. Medical Bacteriology: A Practical Approach. 2nd

Edition

.Oxford University Press;

16

6. Mims, C Dockrell, H., Goering, R., Roitt, I Wakelin, D. and Zuckerman, M., 2004.

Medical Microbiology. 3rd

Edition. Mosby.

7. Stephen, J., Mims, C.A., Nash, A. 2000. Mims' Pathogenesis of Infectious Disease. 5th

Edition. Academic Press Inc., U.S.A.

8. Greenwood, D., Slack, C. B. R., and Peutherer, J. F., 2002. Medical Microbiology: A

Guide to Microbial Infections: Pathogenesis, Immunity, Laboratory Diagnosis and

Control. 16th

Edition. Churchill Livingstone.

9. Cowan, S. T., Steel, K. J., Barrow, G. I and Feltham, R. K. A., 2004. Cowan and

Steel's Manual for the Identification of Medical Bacteria. 3rd

Edition Cmicroridge

University Press.

MIC-703 ADVANCED VIROLOGY (THEORY) 3(2-1)

Learning Objectives:

On completion of this course, students should be able to:

1. The structural and functional properties of all the important viruses.

2. The genetic mechanisms of virus replication and virulence.

3. The diagnostic techniques and mechanisms of viral diseases.

4. Treatment, prevention and viral disease control regimens.

Unit 1: General Virology: Introduction, origin and nature of viruses, general properties

and symmetry of viruses, composition of viruses, nomenclature and classification of

viruses, electron microscopy of virus particles, methods of determination of particle size,

effect of chemical and physical agents on viruses, virus-host cell interactions, techniques

of isolation, cultivation and identification of viruses (laboratory animals, embryo

inoculation and cell culture), replication of bacteriophages and human viruses. Antiviral

drugs, prions & viriods.

Unit 2: Medical Virology: Study of medically important viruses and diseases caused by

them (mode of transmission, pathogenesis, clinical signs, diagnosis and control). DNA

viruses, Parvoviridae (parvoviruses), Hepdnaviridae (HBV), Herpesviridae (HSVI,

HSVII, EBV, CMV, VZV, HHV 6,7, and 8), Poxviridae, (Small pox, vaccinia) RNA

17

viruses: Parmyoxoviridae (Measles and Mumps), Orthomyxoviridae (Influenza A, B, C),

Rhabdoviridae (Rabies virus), Filoviridae (Marburg and Ebola), Reoviridae (Rotavirus),

Picornaviridae (Polio, Hepatitis A virus, rhinoviruses), Togaviridae (Rubella), Flaviviride

(yellow Fever virus), Classic & emerging viral hemorrhagic fever viruses (Dengue virus,

Crimean Congo hemorrhagic fever virus), Hepatitis C virus, Retroviridae (HIV-AIDS).

MIC-703 ADVANCED VIROLOGY (PRACTICAL) 3(2-1)

Collection, transport & processing of samples for virus isolation and preservation,

filtration, centrifugation, demonstration of inclusion bodies, equipments needed for virus

work, electron microscopy, quantification of viruses and determination of LD 50,

methods of cultivation of viruses in embryonated eggs, cultivation of bacteriophages,

washing of RBC and preparation of antigens.

Recommended Books

1. Cann, A. J., 2001. Principles of Molecular Virology Academic Press

2. Griffin, R., Martin, M. A, Straus, H., Griffin, D. E., Robert, G., LMICRO, A., Howley,

P. M., Roizman, B., Straus, S. E., David, M., 2001. Fundamental Virology Lippincott

Williams and Wilkins.

3. Brian, W., Mahy, B., Mahy, W., 2001. A Dictionary of Virology. Academic Press

Incorporated.

4. Nigel J. J., Dimmock, K. L. and Andrew E., 2001. Introduction to Modern Virology

Blackwell Science, Inc.

5. Zuckerman, A. J., Banatvala, J. E., Pattison, J. R., Griffiths, P., Schoub, B., 2004.

Principles and Practice of Clinical Virology, 5th Edition. John Wiley and Sons Limited.

6. Cann, A. J., 2005. Principles of Molecular Virology. .Elsevier Science and Technology

Books.

7. Wagner, E. K., Hewlett, M. J., 2003. Basic Virology, Blackwell Publishers.

8. Howley, P. M., Roizman, B., Straus, S. E., Martin, M. A., Griffin, D. E., 2001.

Fundamental Virology, Lippincott Williams and Wilkins.

MIC-704 ADVANCED MYCOLOGY (THEORY) 3(2-1)

Learning Objectives:

18

On completion of this course, students should be able to:

1. Identification of fungi and recognition of their unique features and properties.

2. Fungal growth, nutrition and metabolism.

3. Major Fungal diseases and their health and economic impacts.

4. Role of Fungi in the recent development of biotechnology.

5. Key fungal fermentation products and their role in food and beverage industry.

Unit 1: General Mycology: Introduction to fungi, general characteristics and

classification, Yeast, Molds and Mushrooms, Morphology and cultural characteristics of

pathogenic fungi, Mycotoxins and mycotoxicosis, diagnosis of fungal infections,

isolation and identification of fungi.

Unit 2: Medical Mycology: Systemic study and an account of the diseases caused by

fungi in man: superficial / cutaneous mycosis (tineas / ringworm infections), sub-

cutaneous mycosis (sporotrichosis, chromomycosis, and mycetoma), systemic mycosis

(Cocidiodomycosis, Histoplasmosis) and opportunistic mycosis. Immunogenic

phenomenon of mycosis, prevention and treatment of mycotic infections. Fermentation

Mycology, Use of fungi in health biotechnology (Production of antibiotics, enzymes,

Single Cell Protein).

MIC-704 ADVANCED MYCOLOGY (PRACTICAL) 3(2-1)

Preparation and sterilization of fungal media, staining methods for fungi (Acid fast,

Lactophenol Cotton Blue), preparation of slides for fungal examination (direct staining &

slide culture methods), cultural characteristics, reproduction & identification of some

yeasts & molds of medical importance.

Recommended Books

1. Tortora, Case, Funke. Microbiology: An Introduction. 11th

Edition. Addison Wesley

Longman, Int. California.

2. Hocking, A.D., Pitt, J.I., Samson, R.A., Thrane, U., 2006. Advances in Food

Mycology, Springer.

3. Tkacz, Jan S., Lange, L., 2004. Advances in Fungal Biotechnology for Industry,

Agriculture, and Medicine. Springer.

19

4. Eugene, N., Milton, P. G. and Allen, K., 2004. Agrobacterium tumefaciens: From Plant

Pathology to Biotechnology. APS Press.

5. Gioconda, S-B. and Richard, C. A., 2008. Pathogenic Fungi: Insights in Molecular

Biology. Caister Academic Press.

MIC-705 ADVANCED PARASITOLOGY (THEORY) 3(2-1)

Learning Objectives:

On completion of this course, students should be able to:

1. Isolation & identification of parasites and recognition of their unique features and

properties.

2. Parasitic growth, nutrition and metabolism.

3. Major protozoan and helminth diseases and their health and economic impacts.

4. Treatment, prevention of major diseases and role of vectors in diseases

History & scope of Parasitology, Nomenclature & classification of parasites, Host

parasite relationships.

Protozoology: Study of medically important protozoa (Intestinal, urogenintal, blood &

tissue) Amoeba: Nonpathogenic and pathogen amoeba. Morphology and life cycle of

amoeba pathology. Symptomatology Laboratory Diagnosis of) Giardia (G. Limblia)

Flagellates of genital tract Trichomonas (T. tenax, T. hominis, T. vaginalis) Malaria

parasite (Plasmodium vivax, P. malariae, P. ovale,) Genaral life cycle of Malarial

parasite in man and anopheles mosquito, sequal of malaria, Toxoplasma gondi, life

cycle, Symptomatology, Transmission and Lab diagnosis of Toxoplasmosis.

Helminthology: Genaral introduction of helminthes and classification, medically

important hemimths. Immunity in Taenia saginata, T. solium, Echinococcus granulosis,

Trematodes, Schistosomes (S. haematobium, S. mansoni, S. Japonicum) Nematodes.

Ascaris lumbriicoides, Ancylostoma duodenale, Strongyloides stercoralis, Enterrobius.

Medical Entomology: Medically important insects & arachnids, Role of arthropods in

the spread and causation of infectious diseases, Diagnosis & treatment of parasitic

infections.

20

MIC-705 ADVANCED PARASITOLOGY (PRACTICAL) 3(2-1)

Collection, transport & processing of specimens for parasitic examination, Isolation and

identification techniques for major human blood & tissue protozoa, Isolation and

identification techniques for major human helminths, Identification of arthropod vectors

of major human diseases.

Recommended Books

1. Medical Parasitology (Gillespie and Hawkey)

2. Modern Parasitology (F.E.G Cox)

3. Essential of Parasitology (Schimidt).

4. Parasitology (K.D Chatterjee)

MIC-706 ADVANCED EPIDEMIOLOGY & PUBLIC HEALTH (THEORY) 3(2-1)

Learning objectives:

On completion of this course, students should be able to:

1. Understand the scope and concepts of epidemiology.

2. Understand the methods to study the epidemiology of infectious diseases of animals

and man.

3. Apply the epidemiological information of an infectious disease for its control and

eradication.

Unit 1: Introduction to epidemiology and course objectives, definitions, future prospects,

population concept, host & parasite relationship, natural history of disease and levels of

prevention, introduction to infectious disease epidemiology, disease measures; morbidity

mortality rates and adjustment, causation in epidemiology and in other fields, diagnostic

tests, study design; randomized trials, study design & analysis; cohort studies, case

control and cross-sectional studies, concept of risk, measures of risk and applications,

bias, confounding & interaction.

Unit 2: Introduction to chronic disease epidemiology and life course models,

epidemiology and public policy, case studies of important disease syndromes and entities,

21

methods include definitions and nomenclature, outbreak investigations, disease

surveillance, case-control studies, cohort studies, laboratory diagnosis, molecular

epidemiology, dynamics of transmission, and assessment of vaccine field effectiveness,

case studies will focus on acute respiratory infections, diarrheal diseases, hepatitis, HIV,

tuberculosis, sexually transmitted diseases, malaria, and other vector-borne diseases.

MIC-706 ADVANCED EPIDEMIOLOGY & PUBLIC HEALTH (PRACTICAL) 3(2-1)

Designing of questionnaire for surveillance of infectious diseases; Collection of

epidemiological data from hospitals, clinics, diagnostic laboratories etc; Storage,

management and analysis of epidemiological data; Hands on training of computer

software for epidemiology.

Recommended Books

1. Salyers, A. A. and Whitt, D. D., 2002. Microbiology: Diversity, Disease, and the

Environment. John-Wiley and Son Limited.

2. Ziegler, A., and Koenig, I. R., 2006. A Statistical Approach to Genetic Epidemiology:

Concepts and Applications. John-Wiley and Son Limited.

3. Haines, J. L., Pericak-Vance, M. A., 2006. Genetic Analysis of Complex disease.

Wiley, John and Sons Incorporated.

4. Seed house, D., 2003. Health Promotion: Philosophy, Prejudice and Practice, 2nd

Edition. John Wiley and Sons limited.

5. Robine, J.M., Jagger, C., Mathers, C.D., Crimmins, E.M. and Suzman, R.M., 2002.

Determining Health Expectancies. John Wiley and Sons limited.

6. Tan, J., 2005. E-Health Care Information Systems: An Introduction for Students and

Professionals. John Wiley and Sons limited.

MIC-707 PUBLIC HEALTH MICROBIOLOGY (THEORY) 3(2-1)

Learning objectives:

On completion of this course, students should be able to:

1. Understand the scope and concepts of public health microbiology.

22

2. Have the knowledge of microbial diseases of public importance transmitted through

water, food, dairy products, meat, eggs, vegetables, fruits, air etc.

3. Apply the knowledge for control of microbial disease in the population. .

Scope of public health microbiology; water-borne microbial diseases and their control;

use of microbes in waste water treatment; role and significance of microorganisms in

food; food-borne microbial diseases and their control; Bacterial, viral and fungal diseases

transmitted through dairy products, meat, eggs, vegetables, fruits and their control; role of

vaccines in public health; sexually transmitted microbial diseases and their control; Air-

borne microbial diseases; Vector-borne microbial disease; bacterial, viral and fungal

diseases of zoonotic importance; Nosocomial infections; Bioinformatics and public

health microbiology.

MIC-707 PUBLIC HEALTH MICROBIOLOGY (PRACTICAL) 3(2-1)

Identification of microorganisms and/or their products in food, dairy products, meat,

eggs, vegetables, fruits and air; Detection of antibiotic residues in foods; Demonstration

of food and water sanitation.

Recommended Books:

1. Burlage, R.S., 2011. Principles of Public Health Microbiology. Jones and Bartlett

Learning, Canada.

2. Harrigan, W., 1998. Laboratory Methods in Food Microbiology.Academic Press, U.K.

3. Jay, J. M., M. J. Loessner, and D. A. Golden, 2005. Modern Food Microbiology. 7th

.

Ed. Springer Science Publishers, U.S.A.

4. Manwar, A. W. 2010. Air Microbiology: An environmental and Health Perspective.

Cinnamonteal Print and Publishers, GOA.

5. Spencer, J. F. T. and A. L. R. Spencer, 2010. Public Health Microbiology: Method and

Protocols. Humana Press, Totowa, New Jersey.

23

MIC-708 ADVANCED IMMUNOLOGY (THEORY) 3(2-1)

Learning Objectives:

On completion of this course, students should be able to:

1. It will provide students with detailed knowledge of the cells and organs of the

immune system, their organization and diversity, and their specialized functions at

different anatomical locations.

2. Student should be able to understand cross talk of immune cell receptors and

cytokines in cellular interactions and co-ordination of immunological

mechanisms.

3. Student should be able to perform practical immune-assays.

Unit 1: Introduction: general considerations, types of immunity (innate / non-specific);

Physical factors: intact skin, mucus membrane, cilia of respiratory tract, mucus etc.

Humoral factors: lysozyme, complement, interferon etc., (acquired / specific); Passive

immunity; natural and artificial, active immunity; natural and artificial, components of

immune system (cells and organs of immune system), Ontogeny of immune system.

Unit 2: Antigen: definitions, characteristics, classification, specificity, bacterial and viral

antigens and their properties. Immunoglobulins: definitions, characteristics,

classification, structure and function. Antigen-antibody interactions / immunodiagnostics

(primary, secondary and tertiary binding tests).

Unit 3: Antigen processing and presentation, Complement system and complement

pathways, Cytokines: production and their therapeutic applications, Autoimmunity and

autoimmune diseases, Hypersensitivity and its types, drug allergy mechanisms,

Monoclonal antibody: its production and uses, recent advances in immunology.

MIC-708 ADVANCED IMMUNOLOGY (PRACTICAL) 3(2-1)

24

Collection of blood, RBC washing, separation of serum, Precipitation tests, agglutination

tests: slide & tube agglutination tests, viral haemagglutination and haemagglutination

inhibition test, immunodiffusion tests: Agar gel precipitation test,

Immunoelectrophoresis: counter current immunoelectrophoresis test, complement

fixation test, ELISA, fluorescent antibody technique, animal inoculation, preparation of

hyperimmune sera, purification of antibody, demonstration of immediate type

hypersensitivity in guinea pig / rabbits.

Recommended Books

1. Janis Kuby, Immunology. 5th

Edition. W H Freeman and company New York.

2. David male, Jonathan Brostoff, David B Roth, Ivan Roitt “Immunology”7th

edition

2006, Mosby, Europe Ltd, London.

3. Essentials of Immunology by Riott I .M. 1998. ELBS, Blackwell Scientific Publishers,

London.

4. Immunology 2 nd Edition by Kuby J. 1994. W.H. Freeman and Co. New York.

5. Immunology - Understanding of Immune System by Claus D. Elgert. 1996. Wiley -

Liss, New York.

6. Cellular and Molecular Immunology. 3rd Edition by Abbas.

7. Immunobiology: The Immune System in Health and Disease. 3rd Edition by Travers.

8. Manual of Clinical Laboratory and Immunology 6th Edition. 2002 by Noel R. Rose,

Chief Editor: Robert G. Hamilton and Barbara Detrick (Eds.), ASM Publications.

25

MIC-709 MICROBIAL PHYSIOLOGY (THEORY) 3(2-1)

Learning Objectives:

On completion of this course, students should be able to:

1. Develop an understanding of the cellular and intracellular organization of the

microbial cells.

2. Understand how microbes transport major and minor nutrients for cellular growth

and differentiation?

3. Key Enzymes and Metabolic pathways that enable microbes to grow and

outcompete other organisms under a variety of favorable and adverse

environmental conditions including extremes of temperature, pressure, moisture,

ionic concentrations etc.

4. Role of microorganisms as tools in genetic engineering, biological

transformations and a variety of industrial and environmental applications.

5. Cell to cell communication and new insights into microbial pathogenesis.

Unit 1: Physiological aspects of microbial growth cycle, Nutritional requirements of

microorganisms: energy, carbon, nitrogen, inorganic elements, growth factors; vitamins,

minerals, amino acids, purines & pyrimidines & other organic compounds. Physical

requirements of microorganisms; temperature, pH, osmotic pressure, radiations.

Unit 2: Microbial fermentation, Photosynthetic microorganisms, photosynthetic

pigments, and generation of reducing power by cyclic and non-cyclic

photophosphorylation, electron transport chain in photosynthetic bacteria, carbon dioxide

fixation pathways. Bacterial aerobic respiration, components of electron transport chain,

free energy changes and electron transport, oxidative phosphorylation and theories of

ATP formation, inhibition of electron transport chain. Electron transport chain in some

heterotrophic and chemolithotrophic bacteria. Bacterial anaerobic respiration:

Introduction. Nitrate, carbonate and sulfate as electron acceptors. Electron transport

26

chains in some anaerobic bacteria. Catalase, super oxide dismutase, mechanism of

oxygen toxicity.

Unit 3: Bacterial Permeation; structure and organization of membrane (Glyco-conjugants

and proteins in membrane systems), fluid mosaic model of membrane. Methods to study

diffusion of solutes in bacteria, passive diffusion, facilitated diffusion, different

mechanisms of active diffusion (Proton Motive Force, PTS, role of permeases in

transport, different permeases in E. coli. Transport of amino acids and inorganic ions in

microorganisms and their mechanisms. Molecular mechanisms in sporulation of bacteria.

MIC-709 MICROBIAL PHYSIOLOGY (PRACTICAL) 3(2-1)

Microbial assays: general application and their practical significance, study of bacterial

growth cycle, effects of different physical factors and nutrients on the growth of bacteria,

isolation of photosynthetic bacteria, glucose uptake by E. coli / Saccharomyces

cerevisiae; active and passive diffusion, effect of UV, gamma radiations, pH,

disinfectants, chemicals and heavy metal ions on spore germination of Bacillus spp.

Recommended Books

1. Microbial Physiology and Metabolism by Caldwell D.R. 1995Brown Publishers.

2. Microbial Physiology by Moat A.G. and Foster J. W. 1999. Wiley.

3. Advances in Microbial Physiology. Volumes. Edited by A.H. Rose. Academic Press,

New York.

4. Applied Microbial Physiology by Rhodes.

5. Microbial Physiology by Benjamin

MIC-710 MICROBIAL GENETICS (THEORY) 3(2-1)

Learning Objectives:

On completion of this course, students should be able to:

1. Analyze, interpret and evaluate a range of scientific literature in microbial

genetics.

2. Understand how microorganisms maintain and transfer genetic information.

3. To understand how microorganisms evolve through mutations and the exchange

of genetic information.

27

4. To understand how genes are expressed and regulated in microorganisms.

5. To understand how microbial genetics was used to answer many of the

fundamental questions in biology and current research problems.

6. Define and manipulate the main features of viral, prokaryotic and eukaryotic

genomes.

Unit 1: DNA structure and mutagenesis: Historical developments in genetics, discovery

of DNA and experimental evidence, structure of circular DNA molecule, primary,

secondary, tertiary and quaternary structure of DNA, Watson and Crick model of double

stranded DNA, DNA replication: DNA replication mechanism, enzymes involved in

DNA replication and models of DNA replication. Molecular basis of spontaneous and

induced mutations, physical and chemical mutagenic agents, types of mutation: point,

frame shift, lethal, conditional lethal, inversion and deletion, null mutation, reversion of

mutations, intra and intergenic suppression mutations.

Unit 2: Prokaryotic transcription and translation, organization of transcriptional units and

regulation of gene expression, mechanism of transcription of prokaryotes-structure and

function of RNA polymerase, ribosomes and their organization in prokaryotes,

polycistronic mRNA in bacteria, initiation of translation in bacteria, small sub-units, its

accessory factors, SD sequence in bacteria, initiator tRNA, elongation of translation,

translocation and termination mechanisms, post-translational modification, salient

features of genetic code. Regulation of gene expression in prokaryotes; E. coli lac operon

model.

Unit 3: Genetic recombination, genetic recombination processes, transposons; insertion

sequences and composite transposons, phages as transposons, replicative, non-replicative

and conservative transposition. Mutations i.e. deletions, inversions and frame shift due to

transposition, mechanism of transposition. Phage Genetics: T4 virulent phage, lamda

temperate phage: structure, genetic map, lytic and lysogenic cycle, lysogenic repression

and phage immunity.

MIC-710 MICROBIAL GENETICS (PRACTICAL) 3(2-1)

Isolation & purification of chromosomal & plasmid DNA and study of DNA profile,

confirmation of nucleic acid by spectral study, quantitative estimation by diphenylamine

test, DNA denaturation and determination of Tm and G+C content, agarose gel

28

electrophoresis of DNA, effect of UV radiations to study the survival pattern of E. coli,

restriction digestion and agarose gel electrophoresis of DNA.

Recommended Books

1. Microbial Genetics by Maloy ET. Al. 1994. Jones and Bartlett Publishers.

2. Molecular Genetics of Bacteria by J. W. Dale. 1994. John Wiley and Sons.

3. Modern Microbial Genetics. 1991 by Streips and Yasbin. Niley Ltd.

4. Microbial Genetics by Frefielder. 4th

Edition.

5. Molecular Genetics of Bacteria, 1997 by Larry, Snyder and Wendy, Champness, ASM

Publications.

MIC-711 MOLECULAR BIOLOGY OF BACTERIAL VIRUSES (THEORY) 3(2-1)

Learning Objectives:

On completion of this course, students should be able to:

1. To gain theoretical foundations and research experience needed to become an

independent and original investigator of bacterial viruses.

2. To identify bacterial viruses from environment and to develop their therapeutic

application for the pathogenic bacteria.

Introduction; historical perspectives, the bacterial host cell infective unit. Classification

of bacteriophages. Properties and growth pattern in temperate and lytic cycle.

Bacteriophage bioinformatics and genomics. Bacteriophages in environment, food

fermentation and medicine. Phage therapy. Induction in phage lambda. One step growth

curve; multiplicity of infection; synthesis of virus progeny. Metabolism and DNA

replication in the infected cell; Mutation in mixed infection; genetic recombination;

genetic fine structure and molecular basis of mutation. Radiobiology; lysogeny;

transduction; transformation comparative bacterial virology; Biotechnological and

therapeutic role of bacteriophage.

MIC-711 MOLECULAR BIOLOGY OF BACTERIAL VIRUSES (PRACTICAL) 3(2-1)

Isolation and identification of phages. Bacteriophages plaque assay, determination of one

step growth curve; preparation and maintenance of phage lysate; study of gene;

recombination; photo reactivation,; bacteriophage typing of bacteria.

Recommended Books:

29

1. McGrath, S and D. V. Sinderen 2007 Bacteriophage: Genetics and Molecular

biology. Caister Academic Press. Norfolk. UK.

2. Tropp, B. E., 2007. Molecular biology; genes to protein. 3rd

Edition. Jones and

Bartlett Publisher International, London, UK

3. Clark, D., 2005. Molecular biology. Elsevier Academic Press, California USA.

4. Cairns, J., G. S. Stent and J. D. Watson, 2000. Phage and origin of Molecular

biology. Cold Spring Harbor Laboratory Press, New York, USA.

MIC -712 ADVANCED ANAEROBIC MICROBIOLOGY (THEORY) 3(2-1)

Learning Objectives:

On completion of this course, students should be able to:

1. To learn characteristics, mode of reproduction and essential growth requirements

for the isolation and identification of anaerobic bacteria from environment, food

and health related issues.

2. To gain understanding and awareness of anaerobic bacteria in infection,

antibiotics resistance and their diagnosis.

Introduction to anaerobic microbiology, Diversity and importance of anaerobic bacteria,

Taxonomy and ecology of various genera of anaerobic bacteria and microaerophiles,

Anaerobic versus aerobic bacteria, Biochemistry and Physiology of anaerobic bacteria,

Role of anaerobes in biosphere, Oxygen lethality theories, Oxygen as an oxidant and as

toxic agent, Free radical formation and molecular oxygen reduction, Reducing

environments and origin of life hypothesis, Basic redox chemistry, The role of SOD`s in

bacteria and higher organisms, Diversity of energy sources of anaerobic bacteria,

Mechanism of hydrogen activation, Iron-sulphur cluster biosynthesis, Oxygen and

anaerobes, Electron transport system in anaerobes, Inorganic sulphur oxidation, Principle

anaerobic infections of man and animals and their diagnosis, Anaerobic fermentation,

Chemical and fuel production by anaerobic bacteria, Industrial importance and

applications of anaerobes. Exploitation of anaerobic bacteria as probiotics.

MIC -712 ADVANCED ANAEROBIC MICROBIOLOGY (PRACTICAL) 3(2-1)

30

Preparation of different culture media for anaerobic bacteria, Cultivation

methods/systems for anaerobes (Anaerobic jars, Depletion of oxygen, addition of

reducing agents, CO2 incubators, Paraffin plug technique, Chromium sulphuric method

etc.,) Methods of measuring respiratory activity by the following procedures :- a)

Barber's Method. b) Thumburg Method. c) Measurements of oxidation reduction

intensity. Colorimetric determination of oxidation reduction potential, Titration of toxins

and antitoxins, Identification of anaerobes by Hungatc technique vs. tube technique, Pure

culture studies of anaerobes.

Recommended Books:

1. Salminen, S. and A. von Wright, 2004.Lactic acid bacteria: microbiology and

functional aspects. Marcel Dekker, Inc., New York, USA.

2. Paul N, Levett, 1991. Anaewrobic bacteria: A functional biology. Wiley-Blackwell

publishers.

3. . Ljungdahl, L. G., et. al., (Editors) 2003, Biochemistry and physiology of anaerobic

bacteria. 1st Edition, Springer Publishing company, New York, USA.

4. Herbert, H.P. Fang, 2010, Environmental Anaerobic Technology-Applications and

new Developments. World Scientific Books.ISBN 978-1-84816-543-4 (ebook).

MIC-713 TISSUE CULTURE TECHNOLOGY (THEORY) 3(2-1)

Learning Objectives:

On completion of this course, students should be able to:

1. Understand the layout and use of cell culture facilities.

2. Develop experience in basic cell culture techniques.

3. Develop an understanding of cell culture, its uses and applications.

4. Understand the importance of tissue culture in the field of virology and vaccine

development.

Unit 1: Introduction & general considerations, History of cell / tissue culture technology,

morphology & biology of cells in culture, primary explants, primary cell culture,

secondary & tertiary culture, cell lines, continuous cell lines, cell strains. Methods for the

study and use of tissue culture, methods for morphological study of cells in culture,

special techniques for the study of physiology & pathology of cells in culture.

31

Unit 2: Applications and uses of tissue culture technology in biological research: tissue

culture in virology, tissue culture in bacteriology, tissue culture in the study of snake and

arthropods poisons, tissue culture in the production of vaccines and other biological

substances.

MIC-713 TISSUE CULTURE TECHNOLOGY (PRACTICAL) 3(2-1)

Design & layout of typical tissue culture laboratory, special instruments for tissue culture

work, preparation of glassware, media & reagents for tissue culture, removal of organs

for tissue culture & preparation of cell lines, cytopathic effects of some viruses in tissue

culture & their quantification.

Recommended Books

1. Smith, R., 2000. Plant Tissue Culture. Academic Press.

2. Freshney, II., .2000. Culture of animal cells: A manual of basic techniques Wiley, John

and Sons

3. Masters, J. R., 2000. Animal cell culture. Oxford University Press.

4. Lanza, R. P., Lanza, B., Atala, A., 2001. Methods of tissue engineering Academic

Press Inc.

5. Doyle, A., Griffiths, J. B., 1998. Cells and tissue culture: Laboratory procedures in

biotechnology. Wiley, John and Sons.

6. Barnum, S., 2004. Biotechnology: An Introduction (with Infotrac) Brooks /Cole.

7. Halford, N., 2006. Plant Biotechnology: Current and Future Applications of

Genetically Modified Crops .John Wiley and Sons Limited.

MIC-714 MICROBIOLOGICAL TECHNIQUES (THEORY) 3(1-2)

Learning Objectives:

On completion of this course, students should be able to:

1. Understand how key microbiological methods work.

2. Work independently in microbiology research setups, pharmaceutical and

food industry.

3. A practical command over molecular diagnostics technique used in clinical

setups is integral part of this module.

Introduction to equipments, sterilization methods, cultivation of bacteria; culture media,

growth of bacteria and their characteristics, counting of bacteria, morphological

32

examination of bacteria, bacteriological examination of sputum, pus, faeces, urine, tissue,

blood, food, water, milk, air etc., biochemical characterization of bacteria,

standardization of disinfectants, antimicrobial susceptibility tests.

MIC-714 MICROBIOLOGICAL TECHNIQUES (PRACTICAL) 3(1-2)

Use of autoclave and hot air oven, preparation of common laboratory media, preparation

and use of common reagents, isolation and identification of bacteria from sputum, pus,

faeces, urine, tissue, blood, food, water, milk, air etc., examination of bacterial colonies

and description of their characteristics, staining of bacteria with common bacteriological

stains, determination of phenol coefficient, antibiotic sensitivity tests (Disc diffusion,

agar well diffusion, broth dilution, E-test).

Recommended Books

1. Tortora, Case, Funke. Microbiology: An Introduction. 11th

Edition. Addison Wesley

Longman, Int. California.

2. Cappuccino, Sherman, Microbiology: A Laboratory Manual. 7th

edition 2004. Pearson

Education Inc.

3. Breed R.S. et al. (2002). Bergey’s Manual of Determinative Bacteriology. The

Wiliams and Wilkins Co. Baltimore.

4. Hawkey, P and Lewis, D., 2004. Medical Bacteriology: A Practical Approach. 2nd

Edition .Oxford University Press;

MIC-715 MOLECULAR BIOLOGY TECHNIQUES (THEORY) 3(1-2)

Learning Objectives:

On completion of this course, students should be able to:

1. Understand how key microbiological methods work.

2. Work independently in microbiology research setups, pharmaceutical and

food industry.

3. A practical command over molecular diagnostics technique used in clinical

setups is integral part of this module.

33

Introduction to molecular biology, history and basic concepts, molecular nature of gene

& gene function, nucleic acids-physical and chemical structures of DNA-forms of DNA

helix-size, denaturation- renaturation, circular and super helical DNA, DNA replication-

repair-mutagenesis, mutations and mutants, transcription in prokaryotes-transcription

apparatus-operons: time control major shifts in prokaryotic transcription, DNA-protein

interactions, transcription in eukaryotes-RNA polymerases- promoters-transcription

factors-transcription activators, chromatin structure and its effects on transcription, post

transcriptional events-splicing, capping & polyadenylation and other events, translation-

initiation- elongation and termination, ribosomes and transfer RNA.

MIC-715 MOLECULAR BIOLOGY TECHNIQUES (PRACTICAL) 3(1-2)

DNA Manipulation and analysis: Genomic & Plasmid DNA isolation, DNA quantitation,

restriction enzyme digestion of DNA, agarose gel electrophoresis of DNA, purification of

DNA from an agarose gel, ligation of DNA E. coli transformation – chemical and

electroporation. Polymerase Chain Reaction (PCR), Southern Blotting, tour of DNA

sequencing facility.

Protein analysis: Inducible expression of fusion protein in E. coli, SDS-PAGE, Protein

quantitation by densitometry and dye binding, Western blot analysis.

RNA analysis: RNA isolation from E. coli and animal tissue, RNA quantitation, RT-PCR,

Northern blotting.

Recommended Books

1. Snustad, D.P. and Simmons, M. J., 2005. Principles of Genetics, 4th Edition. John-

Wiley and Son Limited.

2. Kornberg, A., and Baker, T.A., 2005. DNA Replication, 2d

edition, University science

books, Sausalito, California,

3. Jack.J.P., 2005. An Introduction to Human Molecular Genetics, 2nd

edition New Jersey

Wiley.

4. Howe, H., 2007. Gene Cloning and Manipulation CMICROridge University Press.

5. L. Snyder, L. and W. Champness, W., 2007. Molecular Genetics of Bacteria, 3rd edn

American Society for Microbiology.

34

6. Watson, J. D., Caudy, A. A., Myers, R. M. and Witkowski, J. A., 2007. Recombinant

DNA Genes and Genomes - A Short Course Palgrave Macmillan Ltd.

7. Dennis Lo, Y. M., Chiu, R. W. K. and Chan, K. C., 2006. Clinical Applications of

PCR, 2nd edn. Humana Press.

8. Franks, L.M., and Teich, N.M., 1997. and Introduction to the Cellular and Molecular

Biology of Cancer, 1997, Oxford University Press.

MIC-716 RECOMBINANT DNA TECHNOLOGY (THEORY) 3(2-1)

Learning Objectives:

On completion of this course, students should be able to:

1. Understand basic Recombinant DNA techniques

2. Work independently in biotechnology lab to manipulate DNA &RNA.

Unit 1: Introduction to Recombinant DNA Technology, Techniques and enzymes used in

genetic recombination: restriction endonucleases, type I, II, III, recognition sequences,

properties, nomenclature, classification of type II endonucleases, their activity. DNA

ligase: properties and specificity, S1 nuclease, BAL 31 nuclease, DNA polymerase,

polynucleotide kinase, phosphatase, reverse transcriptase its activity and mode of action.

Chemical synthesis of DNA. Restriction digestion, ligation and transformation.

Unit 2: Cloning Vectors: Plasmids; properties, incompatibility, isolation and purification

techniques, PBR 322, its construction and derivatives, single stranded plasmids, promoter

probe vectors, runaway plasmid vectors. Bacteriophage lMICROda (l) as a vector:

Essential features, organization of l genome, general structure, rationale for vector

construction, improved l vectors, l gt series, l EMBL vectors, in vitro packaging,

cosmids, phasmids, filamentous phage vectors, l zap, l blue print vectors.

Unit 3: Specialized cloning strategies, Expression vectors, promoter probe vectors,

vectors for library construction, genomic DNA libraries, chromosome walking and

jumping, cDNA libraries, short gun cloning, directed cloning, phage display.

Recombinant DNA technology with reference to cloning and production of interferon and

insulin. Miscellaneous applications of genetically engineered micro organisms (GEMS) /

genetically modified organisms (GMO’s).

35

Unit 4: PCR methods and Applications, DNA sequencing methods, dideoxy and

chemical method, sequence assembly, automated sequencing. Molecular mapping of

genome: molecular markers in genome analysis: RFLP, RAPD and AFLP analysis,

molecular markers linked to disease resistance genes.

MIC-716 RECOMBINANT DNA TECHNOLOGY (PRACTICAL) 3(2-1)

Isolation of genomic DNA and its confirmation by Southern blotting, Isolation of plasmid

DNA and its restriction digestion, DNA sequencing by Sanger’s method, DNA cloning

using plasmid vectors and expression vectors, RFLP analysis, amplification of DNA by

PCR and RNA by RT-PCR.

Recommended Books

1. Principles of Gene Manipulations 1994 by Old and Primrose Blackwell Scientific

Publications.

2. DNA Cloning: A Practical Approach by D.M. Glower and B.D. Hames, IRL Press,

Oxford. 1995.

3. Molecular Biotechnology 2nd Edition by S.B. Primrose. Blackwell Scientific

Publishers, Oxford. 1994.

4. Genetic Engineering and Introduction to Gene Analysis and Exploitation in Eukaryotes

by S.M. Kingsman and A.J. Kingsman, Blackwell Scientific Publications, Oxford 1998.

5. PCR Technology - Principles and Applications for DNA Amplification by Henry A.

Erlich (Ed.) Stockton Press. 1989.

6. Recombinant DNA and Biotechnology: Guide for Teachers. 2nd Edition by Helen

Kreuz.

MIC-717 DNA DAMAGE, REPAIR AND CARCINOGENESIS 3(3-0)

Learning Objectives:

On completion of this course, students should be able to:

1. Understand DNA damage and repair mechanisms.

2. Knowledge of mutation, its types and carcinogenesis

Unit-1: Introduction, Radiation (ionizing and non-ionizing) as damage inducing agents.

DNA, the critical site for damage and interaction, Biological consequences of damage.

Inactivation of biological systems: bacterial cells and bacteriophages by UV radiations.

36

Post-irradiation macromolecular system. Chemical as damage inflicting agents.

Exogeneously and endogeneously induced base modifications and their biological

consequences.

Unit-2: Restoration of DNA damages: photo-enzymatic restoration and dealkylation.

Environmental and physiological factors influencing recovery phenomenon viz. Liquid

holding recovery, thermal and UV reactivation. Repair of DNA damages: excision repair

processes, mismatch repair, tolerance mechanism, conditioned repair phenomenon

(phenomenology and genetic control of SOS functions, adaptive responses to DNA

alkylation and oxidative stress.

Unit-3: Relevance of inducible repair to carcinogenesis. Somatic theory of cancer.

Chemistry of carcinogenesis, cellular transformation. Anticarcinogenesis: role of repair

processes in tumor progression. Molecular genetics of human cancer: diagnostic and

therapeutic indices. Repair and spontaneous mutagenesis, plasmid gene mediated repair,

genetic control of repair phenomenon, Enzymology of DNA repair, Cancer and gene

therapy.

Recommended Books:

1. Snustad, D.P. and Simmons, M. J., 2005. Principles of Genetics, 4th Edition. John-

Wiley and Son Limited.

2. Kornberg, A., and Baker, T.A., 2005. DNA Replication, 2d

edition, University science

books, Sausalito, California,

3. Jack. J.P., 2005. An Introduction to Human Molecular Genetics, 2nd

edition New

Jersey Wiley.

4. Brooker, R. J., 2005. Genetics. McGraw-Hill Science.

5. Leland, H., Leroy, H., Michael, G.L., Silver, L., Lee M. Veres, R. C. and Ann. R.,

2004. Genetics. McGraw-Hill Science.

6. Howe, H., 2007. Gene Cloning and Manipulation CMICROridge University Press.

MIC-718 VACCINOLOGY (THEORY) 3(2-1)

Learning Objectives:

On completion of this course, students should be able to:

1. Get insights into manipulation of immune system for vaccine development.

37

2. Exploit natural disease resistance as a tool to find out vaccine targets.

3. Obtain detailed knowledge of different types of vaccines, characteristics of

successful vaccines and their mode of protection.

4. Prepare vaccine at industry level and implement vaccination program.

Unit 1: Introduction, immunity & its types, immunization: passive and active

immunization, vaccines: introduction & types of vaccines with their merits & demerits,

Whole cell live attenuated & killed bacterial & viral vaccines, purified macromolecules

as vaccines, toxoids and antitoxins, attenuation, vaccine production methods, different

routes of vaccine administration, current vaccination practices.

Unit 2: EPI vaccines: production and testing of tetanus toxoids, diphtheria toxoids,

pertussis vaccine, BCG vaccines; preparation of Hepatitis B vaccine, tissue culture

derived rabies vaccine and AIDS vaccine. Adjuvants: classification and properties;

carriers- types and functions; vehicles: types, functions and mode of action;

biodegradable polymers- microspheres, liposomes and ISCOMs.

UNIT 3: Recombinant vaccines: polynucleotide as vaccines; vector vaccines; naked

DNA vaccines; biosynthetic and chemically synthesized vaccines; subunit vaccine; anti

idiotype vaccines; fussion vaccines; mixed particle vaccines; human mucosal vaccines;

combination vaccines; edible vaccines produced in transgenic plants and

microencapsulation, multivalent subunit vaccines, recent research and development of

AIDS vaccines.

MIC-718 VACCINOLOGY (PRACTICAL) 3(2-1)

Purification of antibody, preparation of different bacterial and viral antigens, raising of

hyperimmune sera, seed cultivation, purification & quantification of important bacteria

and viruses for vaccine production, use of cell culture in attenuation of pathogenic

microorganisms and vaccine production, use of adjuvants, study of immunogenicity of

prepared vaccines in experimental animals.

Recommended Books

1. Janis Kuby, Immunology. 5th

Edition. W H Freeman and company New York.

38

2. Gregory G. et al; 1995 Vaccines; new generation immunological adjuvants. Series A:

Life Sciences; Volume: 282.

3. Heing K. and T. L. Philip: 1986 Vaccines: New concepts and developments-

proceedings of the 10th international convocation on immunology; July 14 – 17 buffalo,

New York. Longman scientific and technical 1998; New York.

4. Gregory G., C.A. Anthony and P. George; 1990. Vaccines: recent trends and progress.

Series A: Life sciences: vol; 215 plenum press, New York

5. David male, Jonathan Brostoff, David B Roth, Ivan Roitt “Immunology”7th

edition

2006, Mosby, Europe Ltd, London.

MIC-719 INDUSTRIAL & PHARMACEUTICAL MICROBIOLOGY (THEORY) 3(2-1)

Learning Objectives:

At the end of the course students should be able to

Explain the kinetics of microbial death.

Explain the concepts associated with sterilization.

Describe the methods and equipment used to sterilize pharmaceuticals

Define pyrogens and describe the methods to test for pyrogens

Define GMP

Describe the potential sources of microbial contamination in the pharmaceutical

industry

Describe the method to control microbial contamination in industry

Design clean rooms and microbiology quality control lab

Define and explain fermentation

Describe fermentation methods to produce antibiotics

Unit 1: History and chronological development of industrial microbiology. Industrially

important strains: isolation and preservation. Inoculum development for various

fermentation processes. Strain development: mutation, recombinant DNA technology and

plasmid fusion. Types of fermentation: submerged and solid state fermentation.

Components of CSTR, types of fermentors (tower, cylindroconical and airlift) – batch

39

fermentation, continuous fermentation. Downstream process, intracellular and

extracellular product, separation; liquid extraction, precipitation and floatation,

fermentation methods to produce antibiotics (penicillins, cephalosporins, gentamicin,

erythromycin, tetracyclines, rifamycin, griseofulvin).

Unit 2: Introduction to chemotherapy and selective toxicity, anti-microbial agents, their

sources and mechanism of actions, anti-microbial resistance and mechanisms of

resistance (genetic and acquired), anti-microbial susceptibility testing, hospital antibiotic

policies, anti-viral chemotherapy and problems in anti-viral chemotherapy.

Unit 3: Introduction to sterilization, disinfection and antisepsis, methods of sterilization

and sterility testing, pyrogens and pyrogens testing, factory and hospital hygiene and

Good Manufacturing Practices, sources and control of microbial contamination during

manufacturing, manufacture of sterile products, design clean rooms and microbiology

quality control lab.

MIC-719 INDUSTRIAL & PHARMACEUTICAL MICROBIOLOGY (PRACTICAL) 3(2-1)

Methods of sterilization, sterilization of different pharmaceutical products. Sampling of

pharmaceuticals for microbial contamination and load (syrups, suspensions, creams and

ointments, ophthalmic preparations). Bioassay for antibiotics & vitamins. Pyrogens

testing through LAL test. Determination of antimicrobial activity of a chemical

compound (phenol, resorcinol, thymol, formaldehyde) to that of phenol under

standardized experimental conditions. Atimicrobial susceptibility testing and

determination of MIC & MBC.

Recommended Books

1. Hugo and Russell, Pharmaceutical microbiology. 7th

edition 2004. Blackwell Science

Ltd London.

2. Michael J Waites. 2007 “Industrial microbiology”, Blackwell publishing.UK

3. Mansi, EMT. and C.F.A. Bryce. 2002. “Fermentation Microbiology and

Biotechnology”. Taylor and Francis, New York

4. Shuler, M.L. and F. Kargi. 2005 “Bioprocess engineering basic concepts”. Pearson

Education, New Delhi.

40

MIC-720 FOOD & DAIRY MICROBIOLOGY (THEORY) 3(2-1)

Learning objectives:

On completion of this course, students should be able to:

1. To analyze and differentiate the interrelationships of microorganisms with dairy

animals and environment and their role in milk processing, milk product

manufacture, milk spoilage, and milk safety.

2. To predict the impact of milk processes and milk handling on the microbiology of

milk and milk products.

3. To develop advanced success skills including critical thinking, professionalism,

and life-long learning.

Unit 1: Introduction to food & dairy industry, Industrial food fermentations; starter

cultures & their biochemical activities, production and preservation of the following

fermented foods (a) Soy sauce fermentation by moulds (b) Fermented vegetables-

Sauerkraut (c) Fermented meat-sausages (d) Production and application of bakers yeast

(e) Application of microbial enzymes in food industry

Unit 2: Quality assurances in foods: Food borne infections and intoxications; bacteria

with examples of infective and toxic types; Clostridium, Salmonella, Shigella,

Staphylococcus, Campylobacter, Listeria. Mycotoxins in food with reference to

Aspergillus species. Quality assurance: Microbiological quality standards of food.

Government regulatory practices and policies; FDA, EPA, HACCP, ISI.

Unit 3: Food preservation methods: Radiations- UV, gamma and microwave,

temperature, chemical and naturally occurring antimicrobials. Biosensors in food

industry. Microbiology of cheese and beverage fermentation, microbiology of fermented

milk products (acidophilus milk, yoghurt). Role of microorganisms in beverages - tea and

coffee fermentations, vinegar fermentation. Genetically modified foods. Utilization and

disposal of dairy by-product; whey.

MIC-720 FOOD & DAIRY MICROBIOLOGY (PRACTICAL) 3(2-1)

Production and estimation of lactic acid by Lactobacillus Spp. or Streptococcus Spp.,

Sauerkraut fermentation, Isolation of food poisoning bacteria from contaminated foods &

dairy products, Extraction and detection of aflatoxins from infected foods, Production of

41

fermented milk by Lactobacillus acidophilus, rapid analytical techniques in food quality

control using microbial biosensors.

Recommended Books

1. Food Microbiology. 2nd Edition by Adams

2. Basic Food Microbiology by Banwart George J.

3. Food Microbiology: Fundamentals and Frontiers by Dolle

4. Biotechnology: Food Fermentation Microbiology, Biochemistry and Technology.

Volume 2 by Joshi.

5. Fundamentals of Dairy Microbiology by Prajapati.

6. Essentials of Food Microbiology. Edited by John Garbult. Arnold International

Students Edition.

7. Microbiology of Fermented Foods. Volume II and I. By Brian J. Wood. Elsiever

Applied Science Publication.

8. Microbiology of Foods by John C. Ayres. J. Orwin Mundt. William E. Sandinee. W.

H. Freeman and Co.

9. Dairy Microbiology by Robinson. Volume II and I.

MIC-721 ENVIRONMENTAL MICROBIOLOGY (THEORY) 3(2-1)

Learning objectives:

On completion of this course, students should be able to:

1. Understand the scope and concepts of Environmental Microbiology

2. Understand the methods to study environmental samples and environmental diseases.

3. Apply this information for diseases control and eradication.

Unit 1: Environment and Ecosystems: definitions, biotic and abiotic environment,

environmental segments, composition and structure of environment, concept of

biosphere, communities and ecosystems, ecosystem characteristics, structure and

function, food chains, food webs and trophic structures, ecological pyramids.

Water pollution and its control: Need for water management, sources of water pollution.

Measurement of water pollution, Eutrophication: definition, causes of eutrophication, and

microbial changes in eutrophic bodies of water induced by various inorganic pollutants.

42

Unit 2: Effluent treatment techniques: Microbiology of wastewater and solid waste

treatment, waste-types-solid and liquid waste characterization, physical, chemical,

biological, aerobic, anaerobic, primary, secondary and tertiary treatments. Anaerobic

processes: Anaerobic digestion, anaerobic filters, and up flow anaerobic sludge.

Treatment schemes for effluents of dairy, distillery, tannery, sugar and antibiotic

industries (types, microbes used, types of Effluent Treatment Plants). Bioconversion of

Solid Waste and utilization as fertilizer. Bioaccumulation of heavy metal ions from

industrial effluents.

Unit 3: Bioremediation of Xenobiotics: Microbiology of degradation of xenobiotics in

the environment, ecological considerations, decay behavior, biomagnification and

degredative plasmids, hydrocarbons, substituted hydrocarbons, oil pollution, surfactants

and pesticides. Genetically Modified Organisms released and its environmental impact

assessment and ethical issues. Global environmental problems: Ozone depletion, UV-B,

green house effect and acid rain, their impact and biotechnological approaches for

management. Containment of acid mine drainage applying biomining with reference to

copper extraction from low grade ores.

Unit-4: Biofilms, bacterial biofilms, mechanism of formation of biofilms of pathogenic

bacteria, Quorum sensing, how to avoid biofilm formation?

MIC-721 ENVIRONMENTAL MICROBIOLOGY (PRACTICAL) 3(2-1)

Physical analysis of sewage/industrial effluent by measuring total solids, total dissolved

solids and total suspended solids. Determination of indices of pollution by measuring

BOD/COD of different effluents. Bacterial reduction of nitrate from ground waters.

Isolation and purification of degradative plasmid of microbes growing in polluted

environments. Utilization of microbial consortium for the treatment of solid waste.

Reduction of distillery spent wash (or any other industrial effluent) BOD by bacterial

cultures. Microbial dye decolourization /adsorption.

Recommended Books

1. Bioremediation by Baker K.H. And Herson D.S. 1994. McGraw Hill Inc. N.Y.

2. Waste Water Engineering - Treatment, Disposal and Re-use by Metcalf and Eddy, Inc.,

Tata McGraw Hill, New Delhi.

43

3. Pollution: Ecology and Biotreatment by Ec Eldowney, S. Hardman D.J. and Waite S.

1993. - Longman Scientific Technical.

4. Environmental Microbiology edited by Ralph Mitchell. A John Wiley and Sons. Inc.

5. Waste Water Microbiology 2nd Edition by Bitton.

6. Chemistry and Ecotoxicology of pollution. Edited by Des. W. Connell, G.J. Miller.

Wiley Interscience Publications.

7. Environmental Biotechnology. Edited by C. F. Forster and D.A., John Wase. Ellis

Horwood Ltd. Publication.

MIC-722 BIOINFORMATICS, GENOMICS & PROTEOMICS (THEORY) 3(2-1)

Learning Objectives:

On completion of this course, students should be able to:

1. Understand the tools and softwares of bioinformatics and their application if

Microbiology

2. Understand the methods to study genomics and proteomics

3. Apply these tools for diseases diagnosis and control.

Unit 1: Bioinformatics and its applications: Databases, types, pair wise and multiple

alignments. Structure-function relationship. Sequence assembling using computers.

Computer applications in molecular biology, protein domains and human genome

analysis program (BLAST, FASTA, GCC etc.) Search and retrieval of biological

information and databases sequence, databank. (PDB and gene bank), accessing

information (Network expasy, EMB Net, ICGEB Net).

Unit 2: Whole genome analysis: Preparation of ordered cosmid libraries, bacterial

artificial chromosomal libraries, shotgun libraries and sequencing, conventional

sequencing (Sanger, Maxam and Gilbert Methods), automated sequencing. Sequence

analysis: Computational methods, homology algorithms (BLAST) for proteins and

nucleic acids, open reading frames, annotations of genes, conserved protein motifs related

structure / function (PROSITE, PFAM, Profile Scan). DNA analyses for repeats (Direct

and inverted), palindromes, folding programmes. Use of Internet, public domain

databases for nucleic acid and protein sequences (EMBL, Gene Bank), database for

protein structure (PDB).

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UNIT 3: DNA Microarray: Printing or oligonucleotides and PCR products on glass

slides, nitrocellulose paper. Whole genome analysis for Global patterns of gene

expression using fluorescent-labelled cDNA or end labelled RNA probes. Analyses of

single nucleotide polymorphism using DNA chips. Proteome analysis: Two dimensional

separation of total cellular proteins, isolation and sequence analysis of individual protein

spots by Mass Spectroscopy. Protein microarrary advantages and disadvantages of DNA

and protein microarrays.

MIC-722 BIOINFORMATICS, GENOMICS & PROTEOMICS (THEORY) 3(2-1)

Use of Internet / software for sequence analysis of nucleotides and proteins. Studies of

public domain databases for nucleic acid and protein sequences. Determination of protein

structure (PDB). Genome sequence analysis.

Recommended Books

1. Bioinformatics 2000 by Higgins and Taylor OUP.

2. Nucleic acid Research 2001. Jan. Genome database issue.

3. The Internet and the new Biology: Tools for Genomics and Molecular Research by

Peruski, Jr. and Peruske (ASM) 1997.

4. Functional Genomics. A Practical Approach Edited by Stephen P Hunt and Rick

Liveey (OUP) 2000.

5. Bioinformatics - A Practical Guide to the Analysis of Genes and Proteins. 2nd Edition

by Baxevanis.

6. Bioinformatics: Sequence, structure and Data Bank: A Practical Approach by Higgis.

7. Bioinformatics - from Genomes to drug. 2 volumes by Lenganer.

8. Proteome Research: New Frontiers in Functional Genomics: Principles and Practices.

MIC-723 RESEARCH METHODOLOGY 2(2-0)

Unit-1: Introduction to Research, Research Design & Research Methods; Scientific

Research: Science, Scientific Methods, Techniques & Pre-requisites for Scientific

Research, Critical Thinking and Developing the Research Question: Defining the

Research Problem; Selecting the Research Method; Research Proposal: its importance -

A pre-requisite for Research; Research Proposal Writing Techniques: Importance of

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Research Design, How to put things together? Introduction, Objectives, Review of

Literature, Material & Methods, Bibliography / Literature.

Unit-2: Search: Database, Search Engines; Analytical tools in research: qualitative and

quantitative methods; Sampling: the logic of sampling, concepts and terminologies,

population and sampling frames, types of sampling design/; Data Collection: Techniques

in data collection: Quantitative & Qualitative Data; Experimental Research, Case Studies,

Surveys, Interviews, Questionnaire; Data Analysis: Data Interpretation: Current data

interpretation with comparative studies (Inter-laboratory comparison), Inference based on

findings; Research Presentation Techniques – Data presentation

Recommended Books:

1. Designing and Conducting Mixed Methods Research, Creswell, J. W. & Plano Clark,

V.L. Thousand Oaks, Sage CA, USA, 2007.

2. The Craft of Research by Wayne C. Booth, 2nd Edition, Univ. of Chicago Press. USA,

2003.

3. Case Study Research: Design and Methods, Robert Yin, 3rd Edition, Sage Publishers.

USA, 2003.

4. Students project in Environmental Science, Harrad, S., Batty, H., Diamon, M. and

Arhonditsis, G, John and sons Ltd., Chichester, England, 2008.

MIC-724 SEMINAR (COMPULSORY) 1(1-0)

MIC-725 SPECIAL PROBLEM 1(0-1)

MIC-726 RESEARCH & THESIS (COMPULSORY) 6(0-6)

Prepared By

Dr. Muhammad Hidayat Rasool

Chairman

Department of Microbiology

GC University Faisalabad

Phone: +92-41-9201205; +92-301-7102378 Ext. 256

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Email: drmhrasooluaf@hotmail.com

drmhrasooluaf@gmail.com