U.O.No. 5080/2013/CU Dated, Calicut University.P.O, 26.10.2013

Anuja Balakrishnan

Assistant Registrar

File Ref.No.4794/GA - IV - J1/2012/CU

UNIVERSITY OF CALICUT

AbstractScheme and Syllabus of MSc programme in Aquaculture and Fishery Microbiology under Credit Semester

System (CUCSS-PG-2010) for affiliated colleges - Revised and implemented with effect from 2013 admission

- orders issued.

UNIVERSITY OF CALICUT (G & A - IV - J)

Read:-1. U.O.No.GAIV/J1/1373/08 dated 23.07.2010.

2. U.O.No.GAIV/J1/4660/2010 dated 24.09.2010.

3. U.O.No.GAIV/J1/4660/2010 dated 01.04.2011.

4. Item No:1 of the minutes of the meeting of the Board of Studies in Aquaculture Dtd:

26/06/2013

5. Remarks of the Dean, Faculty of Science dated 29/8/13

6. Orders of Vice-Chancellor in the file of even number on 27/9/2013 .

ORDER

Credit Semester System (CUCSS-PG-2010) has been introduced for the PG programmes of all affiliated

colleges of this University with effect from 2010 admissions vide paper read as (1) above. The Board of

Studies in Aquaculture restructured the syllabus of M.Sc Aquaculture and Fishery Microbiology in tune with

the Credit Semester System 2010 and the syllabus for the same was implemented vide University Order read

as 2 & 3 above.

Vide paper read as (4) above, the Board of Studies in Aquaculture has approved the revised syllabus of

MSc Aquaculture and Fishery Microbiology programme under Calicut University Credit Semester System PG

2010 and forwarded the revised Syllabus. And as per paper read as 5 above the Dean, Faculty of Science

has recommeded to approve the syllabus.

Vide Paper read as 6 above the Vice-Chancellor ,in view of exigency, approved the syllabus

for implementation subject to ratification by the Academic Council. Sanction has therefore been accorded for

implementing the scheme and syllabus of M.Sc Aquaculture and Fishery Microbiology programme under

Calicut University Credit Semester System -PG –2010 for affiliated colleges with effect from 2013 admission.

Orders are issued accordingly. Scheme and Syllabus of M.Sc Aquaculture and Fishery

Microbiology programme appended. The same is also available in the University website.

To

1) The Principals of all affiliated Colleges offering M.Sc. programme in Aquaculture and Fishery

Microbiology.

Forwarded / By Order

Section Officer

Microbiology.

2) Self financing centres of the University of Calicut offering M.Sc programme in Aquaculture and

Fishery Microbiology.

3) CE/Enquiry

4) Information centres/DR III (Exams)/EG-I/ DR PG/Tabulation section/GAI ‘F’ ‘G’ sections/

5) Digital wing (with a request to upload in University website/GAII/GAIII/SF/FC

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UNIVERSITY OF CALICUT

Regulations, Eligibility, Scheme and Syllabus For M. Sc. Aquaculture and Fishery Microbiology (CSS)

(Effective from 2013 Admission onwards)

All the general rules and regulations laid down by the University of Calicut for PG (CSS) Curriculum 2013 for affiliated colleges shall be applicable.

I. ELIGIBILITY CRITERIA. Those students who possess B.Sc. Degree in Zoology, Aquaculture and Industrial Fish and Fisheries as Core/Main subject with Zoology/ Botany/ chemistry/ Biochemistry/ Computer Sciences/ as Complementary/subsidiaries are eligible for admission to this Programme.

II. PROGRAMME AND SCHEME OF EXAMINATIONS

1. M.Sc. Aquaculture and Fishery Microbiology, programme shall have 4 core courses and 2 core practical course each in 1st and 2nd semesters, 2 core course, 2 core practical course and 2 elective courses each in 3rd and 4th semester. Viva-voce, evaluation of project work/ dissertation and evaluation of study tour and specimen collection will be conducted at the end of 4th semester.

2. There shall be external university examination of 3 hour duration for each theory courses at the end of the each semester, to be conducted after the completion of 80 working days.

3. Each theory and practical course shall have 4 credits.4. Practical examinations shall be conducted by the university at the end of each semester5. Each practical examination is of 3 hour duration and shall carry 1 credit each.6. Project / dissertation evaluation and viva-voce shall be conducted at the end of the

programme only. Practical examination, project / dissertation evaluation and viva voce shall be conducted by two external examiners.

7. Project / dissertation, combined field mapping and viva voce shall carry 4 credits each. Combined field studies and study tours may be carried out at any time during the entire period of the programme.

8. Each theory question paper may contain 14 short answer types, of weightage 1, 7 short essays out of 10 questions of weightage 2. Two long essays out of 4 questions of weightage 4.

III. EVALUATION AND GRADING The evaluation scheme for each course shall contain two parts (a) Internal evaluation and (b) external evaluation. 25% weightage shall be given to internal evaluation and the remaining 75% to external evaluation therefore the ratio and weightage between internal and external is 1: 3. Both internal and external evaluation shall be carried out using direct grading system.

Internal evaluation: The internal evaluation shall be based on predetermined transparent system involving periodic written tests, assignments, seminars and attendance. In respect of theory courses and based on written tests, lab skill/records/viva and attendance in respect of practical courses. The weight age assigned to various components for internal evaluation is a follows.

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Components of Internal Evaluation

Component Weightage

A Assignment 1B Seminar 1C Attendance 1D Test paper 2

To ensure transparency of the evaluation process, the internal assessment grade awarded to the students in each course in a semester shall be published on the notice board at least one week before the commencement of external examination. There shall not be any chance for improvement for internal grade.The course teacher shall maintain the academic record of each student registered for the course, which shall be forwarded to the University, through the college Principal. External evaluation: The external Examination in theory courses is to be conducted by the University with question papers set by external experts. The evaluation of the answer scripts shall be done by examiners based on a well-defined scheme of valuation. The external evaluation shall be done immediately after the examination preferably in a Centralized Valuation Camp. Photocopies of the answer scripts of the external examination shall be made available to the students for scrutiny on request and revaluation/scrutiny of answer scripts shall be done as per the existing rules prevailing in the University. Awarding of a higher grade after revaluation may be given only after a second revaluation. Direct Grading System

1. Direct Grading System based on a 5 - point scale is used to evaluate the performance (External and Internal Examination of students)

Direct Grading SystemLetter Grade Performance Grade

PointGrade Range

A Excellent 4 3.50 to 4.00B Very good 3 2.50 to 3.49C Good 2 1.50 to 2.49D Average 1 0.50 to 1.49E Poor 0 0.00 to 0.49

2. Each course is evaluated by assigning a letter grade (A,B,C,D or E) to that course by the method of direct grading. The internal (weightage =1) and external weightage =3) components of a course are separately graded and then combined to get the grade of the course after taking into account of their weightage.

3. An aggregate of C-grade (when external and internal put together) is required in each course for a pass and also for awarding the degree.

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4. A student who fails to secure a minimum grade for a pass in a course will be permitted to write the examination along with the next batch.

1V. Grievance Redress Mechanism for internal evaluation

There is provision for grievance redresses at four levels- first at the level of teacher concerned; second, at the level of Department committee consisting of the Head of the Department, Departmental Coordinator and the teacher concerned; third, at the level of the College committee consisting of the Principal, HOD and member of the College council nominated buy the Principal each year, and also a student member of that class nominated by the HOD. And fourth, at University level committee consisting of the Pro-vice chancellor, chairman-PG board of studies of subject expert nominated by the Vice-Chancellor, Controller of the Examination and the Convener of the Examination standing Committee.

College or Department Level complaints will be filed within one week of the publication of the results and the decision taken within the next two weeks. Appeals, if any, on such decision shall be filed in the University level committee within a period of one week and decision taken within one month for the date of the submission of complaints. The time schedule in regard to the grievance redresses will be announced by the colleges concerned and the University in advance.

For university level complaints, a fee, as fixed by the Syndicate from time to time, will be levied from the students.

Normalization of continuous internal evaluation may be done by the university when there is inflation of grades in internal evaluation. The grades will be scaled down proportionately if the variation between the internal and external evaluation exceeds 40%.

V. Evaluation of Project Report/ Dissertation

Dissertation will be valued by two examiners who conduct the practical examination (external) at the time of 4th semester. Distribution of 10 weightage allotted for dissertation will be as follows

Methodology 2 WeightageContent 4 WeightagePresentation 1 WeightageAnswering question 1 WeightageOriginality or overall outlook 2 Weightage Total 10 Weightage

VI. Specimen Collection All the students need to collect specimens based on the assignment given to them and neatly displayed with a short description after proper preservation and identification. The specimen collection will be valued externally with following criteria.

Diversity 2 WeightageIdentification 4 WeightageDisplay 2 WeightageDescription 2 Weightage Total 10 Weightage

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University of CalicutM. Sc. Aquaculture and Fishery Microbiology - Course Structure, Scheme &

Syllabus(Credit Semester System – 2013 Admission onwards)

I Semester

CourseCourse Code Course Title L P

Exam Duratio

n

Internal (%)

External (%)

Credits

Core AFM 1 C01 Fish Biology & Fisheries

5 3 hrs 25 75 4Core AFM 1 C02 Aquatic Ecology 5 3 hrs 25 75 4Core AFM 1 C03 General Microbiology 5 3 hrs 25 75 4Core AFM 1 C04 Seed Production &

Hatchery Management5 3 hrs 25 75 4

*Practical

AFM 1 C05P

Fish Taxonomy & Biology

3 3 hrs 25 75 1*Practica

l AFM 1 C06P

Instrumentation 2 3 hrs 25 75 1 Total

Credits18

II Semester

CourseCourse Code Course Title L P

Exam Duratio

n

Internal (%)

External (%)

Credits

Core AFM 2 C07 Fishery Microbiology 5 3 hrs 25 75 4Core AFM 2 C08 Introduction to

Sustainable Aquaculture5 3 hrs 25 75 4

Core AFM 2 C09 Fish Biochemistry & Genetics

5 3 hrs 25 75 4

Core AFM 2 C10 Research Methodology 5 3 hrs 25 75 4*Practical AFM 2

C11PGeneral & Fishery

Microbiology3 3 hrs 25 75 1

*Practical AFM 2 C12P

Biocomputing and Bioinformatics

2 3 hrs 25 75 1

Total Credits

18

III Semester

CourseCourse Code Course Title L P

Exam Duratio

n

Internal (%)

External (%)

Credits

Core AFM 3 C13 Fish Physiology 5 3 hrs 25 75 4

Core AFM 3 C14 Seafood Processing Technology

5 3 hrs 25 75 4

Elective AFM 3 E01 Aquaculture Production Systems

5 3 hrs 25 75

Choose one 4

credits

Elective AFM 3 E02 Aquaculture Engineering

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Elective AFM 3 E03 Aquaculture Economics and Extension

Elective AFM 3 E04 Quality Control, Inspection &

Certification in Seafood 5 3 hrs 25 75

Choose one 4

credits

Elective AFM 3 E05 Industrial MicrobiologyElective AFM 3 E06 Fishery by-products and

Value addition*Practical AFM 3

C15PSoil and Water Quality

Assessment3 3 hrs 25 75 1

*Practical AFM 3 C16P

Biochemistry 2 3 hrs 25 75 1

Total Credits

18

IV Semester

CourseCourse Code

Course Title L PExam

Duration

Internal (%)

External (%)

Credits

Core AFM 4 C17 Biotechnology & Molecular Biology

5 3 hrs 25 75 4

Core AFM 4 C18 Disease Diagnosis & Aquatic Health Management

5 3 hrs 25 75 4

Elective AFM 4 E07 Live Feed Culture

5 3 hrs 25 75

Choose one 4

credits

Elective AFM 4 E08 Ornamental Fish Breeding & Rearing

Elective AFM 4 E09 Fish Nutrition & Feed Technology

Elective AFM 4 E10 Immunology

5 3 hrs 25 75

Choose one 4

credits

Elective AFM 4 E11 Developmental Biology

Elective AFM 4 E12 Aquatic Pollution & Toxicology

*Practical

AFM 4 C19P Fish Processing & Quality Control

3 3 hrs 25 75 1

*Practical

AFM 1 C20P Physiology, Cytology & Molecular Biology

2 3 hrs 25 75 1

AFM 4 C21Pr Dissertation 2 25 75 2AFM 4 C22Pr Field Work & Specimen

Collection** 25 75 2

AFM 4 C23V Viva-Voce 25 75 2 Total Credits 24 Total Credits for the whole Programme 78

L – Lecture hours; P – Practical Hours (Hour distribution in a week)* Examination will be conducted at the end of each semester.

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** Field work & specimen collection may be carried out anytime during the entire period of the

programme

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THEORY

AFM 1 C01 - FISH BIOLOGY & FISHERIES

Unit I

Morphology and Sexual dimorphism in fishes and crustaceans. Maturation and spawning in fishes. Maturity stages, Gonado-somatic index, Fecundity, ova diameter studies, breeding cycles. Life history of economically important fish species. Age and growth in fish. Methods employed for age determination. Length-weight relationships. Migration in fishes and crustaceans.

Unit II

Structure of digestive system in fishes, Digestive glands and enzymes. Food and feeding habits of fishes. Food analysis indices. Respiration-Structure of gills, branchial glands, respiratory pigments, mechanism of gas exchange. Accessory respiratory organs in fishes and its significance. Endocrine system,-Pituitary gland in fishes. Endocrine control of reproduction in crustaceans and molluscs.

Unit III

Fisheries resources of India, potential and trends in fish production. Marine capture fisheries, PFZ, EEZ and FAO’s code of conduct of responsible fisheries, fishery of commercially important pelagic and demersal fishes, crustaceans, molluscs and seaweeds. Oceanic and deep sea fisheries resources. Principles of fish population dynamics. Fish stock assessment models.

Unit IV

Inland capture fishery resources and production in India. Fisheries in major riverine systems, estuaries, reservoirs and lakes of India. Exploitation of freshwater and marine ornamental fish resources of India. Types of crafts and gears used in present day fishing . Selectivity of fishing gears and by-catch reduction devices. Use of modern techniques and equipments for fish finding and capturing. Fisheries Extension.

Suggested reading

1. Jhingran V.G. Fish and Fisheries of India2. Jhingran V.G. and Talwar S.K. Fisheries of India (Vol 1 & 2)3. Bal J and Rao S.R. Fishes of India4. Hameed M.S & Bhoopendranath M.R. Modern Fishing Gear Technology5. Santhanam S. Fisheries Science6. Bensam K. Development of marine Fisheries Science in India7. Moyle and Cech Fishes and Introduction of Ichthyology8. Matty Fish Endocrinology9. Hoar and Randall Fish Physiology10. Tandon K.L. Age and Growth in Indian freshwater fishes11. Yadav Y.R. Fish and Fisheries12. Cushing D.H Marine Ecology and Fisheries13. Devaraj,M. Fish Population Dynamics Course Manual

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14. Nelson J.S. Fishes of the World.15. Royce W.F. Introduction to Fishery Sciences,16. Bliss D.E. Biology of Crustacean17. Samuel,C.T. Marine Fisheries in India.18. Sreekrishna, Y. & Shenoy L. Fishing Gear and Craft Technology.19. Talwar.P.K. & Kacker,R.K. Commercial Sea Fishes of India.20. Pitcher T.U. Behavior of Teleost Fishes

Supplementary & Advanced Reading

1. Nikolsky Ecology of fishes2. Wooran R.J. Fish Ecology3. CMFRI. The Commercial Molluscs of India.4. Wootton, R.J. Fish Ecology.5. Prosser C.L. Comparative Animal Physiology.6. FAO Fisheries management. FAO Technical Guidelines for Responsible

Fisheries. 7. ICAR Handbook of Fisheries and Aquaculture, ICAR New Delhi: 756 p.8. CMFRI Tuna Fisheries of the Exclusive Economic Zone of India.9. CMFRI. Cephalopod Resources of the EEZ of India.10. CMFRI. Shell Fish Resources and Farming.

AFM1CO2: AQUATIC ECOLOGY

Unit 1 Introduction to Ecology

Definition, principle and scope of ecology, Classification of aquatic ecology, freshwater, marine and estuarine. Community concept, types of community, succession process, competition and Coexistence, types of interactions: predation, parasitism, antibiosis, commensalism, cooperation and mutualism, population growth. Characteristics of eco system, structure of ecosystem and function of an ecosystem, population.

Unit 2 Organization of Ecological systems

Ecosystem components, Producers, consumers and decomposer, Food chains, food web and ecological pyramids, Biotic and abiotic components, Ecological pyramids, Bioaccumulation and biomagnifications, mass and energy transfer in successive trophical level. Energy and Ecological succession: Flow and energy fixation, construction of ecological pyramids.

Unit 3 Aquatic Ecology

Major physical and chemical factors (light, temperature, gases, nutrients). Ecological stratification of freshwater ecosystem, Aquatic biota: phytoplankton, zooplankton, benthos, periphyton, macrophytes, fish and other animals. Production in lakes, rivers, estuaries and wetlands. Nutrient dynamics in lakes, rivers, estuaries and wetlands. Eutrophication and water pollution: monitoring and control conservation and management of lakes, rivers and wetlands.

Unit 4 Marine Ecology

The division of the marine environment – benthic, pelagic, bathyal, littoral. Ocean waters as a biological environment. Distribution and population of plants and animals. Marine ecology and fisheries potential.

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Effects of pollution on marine life. Dynamics, Carrying capacity. Abiotic and Biotic environment, limiting factors, adaptation, Habitat and niche, nature of environment. Littoral Zones: Fauna of intertidal zones, their distribution and adaptations, ecological importance of mangrove vegetation.

Unit 5 Functions of EcologyEcology and Productivity: Biota in different types of zones, its diversity-plankton, nekton, benthos, their adaptations and productivity, Indian marine territory, Exclusive Economic Zones (EEZ). Biogeochemical cycles: Hydrological cycles, carbon cycle, oxygen cycle, nitrogen cycle, sulfur cycle, phosphorus cycle-its importance and applications. Interaction of biotic and abiotic ecological factors. Biodiversity and diversity indices.

Texts/References:1) E. P. Odum Fundamentals of Ecology, Nataraj Publisher, Dehra Dun.2) K.M.M. Dakshini Principle and Practices in Plant Ecology, CRC, Boston.3) M.C. Dash Fundamentals of Ecology, Tata McGraw Hill, New Delhi.4) M.C. Molles Jr. Ecology- Concepts and Application, McGraw Hill, New Delhi.5) V. Ingegnoli Landscape Ecology: a widening foundation, Springer, Bonn.6) E.J. Kormondi Concepts of Ecology, Prentice Hall of India, New Delhi.7) Chapman, J.L. & Reiss M.J. Ecology Principles and Applications, Cambridge University Press,

London.8) E.P. Odum &G. W. Barrett Fundamentals of Ecology, Thomson Asia Pvt. Ltd., Singapore.9) S.V.S. Rana (2005) Essentials of Ecology and Environmental Sciences, Prentice Hall of

India, New Delhi.10) R.Rajagopalan Environment And Ecology- EAS105/EAS 205-11) R.Rajagopalan Environmental Studies From Crisis To Cure-2nd Edition-12) Alan Scragg Environmental Biotechnology-, Oxford University Press.

AFM1C03: GENERAL MICROBIOLOGY

Unit I- General Introduction

Scope and importance of Microbiology, Modern concept in Microbiology, Classification of Microorganisms. Nutritional requirements of microorganisms–general growth media. Microbial communities in the aquatic environment, kinetics of microbial population, biofilms, Biofouling and biocorrosion. Microbial interactions– symbiosis, antagonism, commensalism. Routine tests for identification of microorganisms- morphological, cultural, biochemical and serological.

Unit II- Bacteria

Morphology and ultrastructure, Nutritional types of bacteria, Culture of bacteria- Pure culture.MPN estimation-isolation and identification of faecal coliforms. Salmonella-Isolation and identification. Vibrio- Isolation and identification. Streptococcus- Isolation and identification. Listeria spp isolation and identification. Pseudomonas aeroginosa, General understanding about different microbiological methods. Quantitative measurement of bacterial growth, isolation, enumeration, preservation and maintenance of cultures, biochemical characterization, regulation of bacterial growth, Bacterial enzymes, antibacterial agents.

Unit III- Fungus

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Fungal classifications, biology of fungi, slime, mould, protist fungi, true fungi, imperfect fungi. Morphology and ultrastructure of molds, cultivation of molds, some molds of microbiological interest. Mycotoxins. Techniques for isolation and identification of yeasts and molds.

Unit IV- Virus

Viral morphology and taxonomy, mode of viral entry, virus replication strategies, viral interference, cytopathic effect, Antiviral agents, viral immunity. Laboratory diagnosis of viral diseases- Isolation of viruses using cell culture; Purification and characterization of viruses.

Unit V- Instrumentation

Basic methods in water analysis and Microbiology. Light and electron microscopy. Spectrophotometry- UV-visible, Flame Photometry and Atomic Absorption Spectrophotometry.. Laminar Flow. Ultracentrifuge. Autoclave. PCR Machine. Electrophoresis. Chromatography and HPLC. ELISA- Blotting techniques - Southern and Northern blotting. Handling of instruments and precautions. Databases in biology: Protein, Nucleotide, Literature- Primary, Secondary. Databases of NCBI, EMBL, DDBJ, KEGG. Protein and DNA Sequence analysis using common software- Phylo-genetic analysis using Phylip and similar software.

Suggested reading

1. Sali A.J. Fundamental Principles of Bacteriology2. Schlegel General Microbiology3. Maat A.G. and Wiley A Microbial Physiology4. Pelezar Read and Chan Microbiology5. Collins C.H. and Lyns P.M. Microbiological Methods6. Lengeler Biology of Prokaryotes7. Subbarao Soil Microbiology 8. Rheinheimer Aquatic Microbiology 9. ZoBell Marine Microbiology 10. Pawar and Diganawala General Microbiology 11. Frobisher et al. Fundamentals of Microbiology 12. Harry W. Seeley, et al. Microbes in Action: A Laboratory Manual of

Microbiology.13. Hawkey P M & Lewis D A Medical Bacteriology: A Practical Approach14. Barrow G I & Feltham R K A. Manual for the Identification of Medical Bacteria15. Kimberley A.Whitman Finfish and shellfish bacteriology manual-Techniques

and procedures 16. Kathleen P.T. and Arther T. Foundation in Microbiology 17. Ingraham, J.I. et al. Introduction to Microbiology

AFM 1 C04 -Seed Production & Hatchery Management

Unit I

Induced breeding in fishes. Seed production technology of carps and tilapia. Management of hatchery, nursery and rearing ponds. Chinese circular hatchery and its modifications. Hatchery layout and designing. Recirculating hatchery systems.

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Unit II

Reproductive biology and life cycle in crustaceans. Induced breeding in prawns and shrimps. Hatchery production techniques of shrimp. Larval disease. Hatchery production techniques of Macrobrachium rosenbergii.

Unit III

Natural breeding and seed resources of cultivable crabs, lobsters and molluscs. Seed production technique of mud crab. Hatchery technology for lobsters. Methods for spat collection. Induced maturation, spawning and hatchery rearing of mussels, edible oysters and pearl oysters.

Unit IV

Marine and brakishwater fish seed production in India. Marine fish hatchery-general considerations. Seed production techniques of Sea Bass, Cobia and Groupers.

Unit V

Live feed culture techniques. Mass production of algae for hatcheries. Artemia production techniques. Culture of zooplanktons for larviculture. Artificial feeds in larviculture.

Suggested Readings1 Jhingran VG Fish and Fisheries of India 2 Chonder S.L Hypophysation of Indian major carps 3 Pillay . T.V.R Advances in aquaculture 4 Bardach, Rhyther & McLarney Aquaculture 5 V.G Jhingran & Saigal Cold water fisheries of India 6 Anon, Hatchery production of penaeid prawn seed 7 Anon A Guide to prawn farming in India8 Peteri, S. Nandi & SN. Chowdhury Manual on Seed Production of Carps. FAO 9 Anon FISH Seed Production And Distribution In

India - FAO10 PC Thomas, et al Breeding and Seed Production of Finfish and Shell Fish11 P C Thomas Shrimp Seed Production And Farming

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Theory

II Semester

AFM 2 C07 - FISHERY MICROBIOLOGY

Unit I

Introduction-Microbiological standards fixed for fish. Encapsulation-Formation of cell aggregates. Lactics-Acetics-Butrics-Propionics. Proteolytic and putrefactive bacteria-Lipolytic and saccharolytic bacteria. Mesophiles-Thermophiles and Psychrophiles-Halophiles.

Unit II

Source of micro organism to fish-Sanitary measures adopted to reduce microbial load in fish. Microbiology of fish and some fishery products. Intrinsic and extrinsic parameters that affect microbial growth. Micro flora associated with the habitat, body surface and internal organs of fish and shell fish.

Unit III

Total plate count Coliforms-concept- indicator organism-MPN estimation-isolation and identification of faecal coliforms. Salmonella-Isolation and identification. Vibrio- Isolation and identification. Streptococcus- Isolation and identification. Listeria spp isolation and identification. Pseudomonas aeroginosa, General understanding about different microbiological methods. (FDA, CFIA, FSIS, AOAC).

Unit IV

Food borne diseases-Food infection and food intoxication. Botulism. Typhoid and Paratyphoid, Clostridium perfringens, Listeriosis Sources and transmission of bacteria in foods:from human, animal, and environmental reservoirs; cross-contamination; food associations.

Suggested Readings:1. Chincheste, C.O and Graham, H.D. Microbial Safety of Fishery products,2. Frasier, W.C and Westhoff,D.C Food Microbiology 3. Jay, J.M. Van Nostrand.D. Modern Food Microbiology4. Amerine,M.A, pangborm,R.M Principles of sensory evaluation of food5. Connell.J.J Control of fish Quality, 6. Sali A.J. Fundamental Principles of Bacteriology7. Schlegel General Microbiology 8. Maat A.G. and Wiley A Microbial Physiology 9. Pelezar Read and Chan Microbiology 10. Collins C.H. and Lyns P.M. Microbiological Methods 11. Lengeler Biology of Prokaryotes

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AFM 2 C08- INTRODUCTION TO SUSTAINABLE AQUACULTURE

Unit I Present scenario and problems: Trends in global and Indian aquaculture; different farming systems; intensive systems and constraints - environmental degradation and disease outbreaks. Sustainability and development, Role of aquatic resources in food and nutrition; Aquatic resource and livelihood systems.

Unit II Environmental issues: Exotic species introduction; escapement; contamination of indigenous gene pool; salinization of soil and water; environmental impact; over exploitation of wild stocks; mangrove deforestation. Socio-economic issues: Conflicts over water and land use; conflicts of interest between aqua farmers and fishermen; resistance from local public; anti-dumping duties.

Unit III Biological constraints in aquaculture, the availability of juveniles, supply of essential nutrients, control of pathogens and diseases. Guiding principles to sustainable aquaculture development. Open and closed systems and the principles of water system design. Coastal Aquaculture Guidelines Source Book, FAO Code of Conduct for Responsible Fisheries; Guidelines for Sustainable Aquaculture.

Unit IVStrategies for sustainability: Sustainability concept; food security; biosecurity; organic farming; integrated farming; responsible aquaculture; rotational aquaculture; bioremediation; role of biotechnology, traceability. Application of renewable energy in aquaculture - solar energy, wind, and tidal energy, Economic viability: export vs. domestic marketing, value addition.

Suggested Reading 1. Beets, W.C. Raising and Sustaining Productivity of Small-Holder Farming Systems in

the Tropics. 2. Edwards, P & H. Demaine Rural Aquaculture: Overview and Framework for Country 3. Edwards, P., D.C. Little & H. Demaine Rural Aquaculture. 4. J. E. Bardach: Sustainable Aquaculture 5. James P& Mc Vey Handbook of Mariculture Vol. I. Crustacean Aquaculture. 6. Takeo Imai Aquaculture in shallow seas. Sea culture 7. Bardach, Rhyther, & Mc. Larney. Aquaculture. Farming & Husbandry of freshwater &

Marine Organisms 8. Pillay, T.V.R. & Dill, W.M.A. Advances in Aquaculture. 9. Pillay. T.V.R. & M.N. Kutty Aquaculture – Principles and Practices. 10. Takeo Imai Aquaculture in shallow seas.

AFM 2 C09 FISH BIOCHEMISTRY &GENETICS

Unit I

Biochemical constituents of fish, crustaceans and molluscs. Biochemistry of fish proteins, structure of fish muscles, effect of processing on proteins. Non-protein nitrogenous compounds in fishes. Classification. Sarcoplasmic proteins, Myofibrillar proteins and Stroma proteins . Post

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mortem biochemical changes, rigor mortis, K-value, TMAO and its decomposition products, demethylase. Non-protein nitrogenous compounds: Free amino acids, peptides, nucleotides, guanidins, urea, quarternary ammonium compounds etc.

Unit IIFunctional properties of seafood proteins: Solubility, emulsification, viscosity, water holding, stability, gelation, texture profile analysis. Changes in proteins during processing: Denaturation- At high and low temperatures and kinetics, dissociation / aggregation / coagulation, reversibility, significance to processing and quality. Hydrolysis and hydrolysates: Process and applications, proteinases.

Unit IIISeafood lipids: Composition and nutritive value, lipid types and their variations, lipid fractionation, estimation of lipid fractions, triglycerides, phospholipids, nonsaponifiables including sterols and vitamins. Fatty acid composition of fish liver and body oils, auto-oxidation of fatty acids, rancidity, lipasas and phospholipases, pro- and anti-oxidants, oxidation indices, lipid-protein interactions, oxidized lipids-protein interactions and their impact on quality.

Unit IV Definition, classification and biological significance of carbohydrates; Chemical reactions; stereoisomerisms and mutarotation, structure and properties of monosaccharides, disaccharides, polysaccharides and mucopolysaccharides

Unit V Principles of fish Genetics-, cytogenetics, biochemical genetics, quantitative genetics, population genetics. Genetic Selection-Mass selection and genotypic selection. Genotypic selection-types Family selection, sib selection, progeny testing and combined selection. Breeding principles and Methods-Selective hybridization, interspecific and intraspecific hybridization, hybrid vigour, inbreeding and cross breeding. Gene manipulation in fish, transgenic fish production, chromosome manipulation in fishes and shell fishes, triploidy, gynogenesis and interspecific hybridization. Monosex production, super male and super female fish production techniques.

Suggested readings1. Lehninger, A.L. Principal of Biochemistry.2. Michael Eskin N. A. Biochemistry of foods. 3. Owen, R. F. Food chemistry.4. Pare J.R.J. & Belanger J.M.R. Instrumental Methods in Food Analysis. 5. Ranganatha Rao Textbook of Biochemistry.6. Regenstein, J. M. & Regenstein C. E. Food Protein Chemistry. 7. Roy, E.M., Geroge, J.F. & Donn, R.W. Chemistry and Biochemistry of marine food8. Smith, E.L., et al. The principles of Biochemistry9. Stewart K.K. Modern Methods of Food Analysis. 10. Whitaker, J.R. & Tannenbaum. Food Proteins, AVI Publishing Company11. Glick B.R. Molecular biotechnology12. Singleton Elementary Genetics13. Gjedrem, T. Genetics in Aquaculture 14. Purdom,C.E Genetics and Fish breeding15. Alberts,B and others Molecular Biology of the cell 1994

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16. Peter Proksch Frontiers in Marine Biotechnology17. Le Gal Marine Biotechnology 18. Thieman WJ Introduction to Biotechnology

AFM 2 C10 RESEARCH METHODOLOGYUnit I

Definition, need, process. Research objectives, Research approaches and Research process. Types of Research: Pure, Applied and Action Research. Kinds of Research: Diagnostic, Descriptive, Exploratory, Explanatory. Research Ethics – Animal ethics; Human ethics. Biosafety in research

Unit II

Types of Literature search – use of library, books & journals – Medlines, internet. Review of Literature. Formulation of Hypothesis. Identification and selection of research problems, preparation of research proposal. Synopsis.

Unit III

Need for research design. Important concepts relating to design. Features of good design. Research designs. Basic principles of experimental design. Pre-experimental, CRD and Quasi-Experimental designs. Types of research design: Historical design, Descriptive design, case control, cohort, cross sectional, longitudinal

Unit IV

Data for Research. Collection of Data : Primary Data, Secondary data, Data Collection methods, Sampling Technique Data Analysis, , tabulations, classifications, Interpretations. Common softwares for data analysis. Statistics in Research: Specific applications of measures of Central tendency and Dispersion, Measures of Relationship. Hypothesis Testing and estimation. Measurement in Research

Unit V

Scientific documents: Research Journal: online journals, Impact factor. Research paper, reviews, thesis, conference papers and project reports. Publication – role of author, guide, co-authors. Components of a research articles. Citation styles: Footnotes, abbreviations, Referencing. Structure of Thesis and Content. Preparing Abstracts. Publishing: submission of manuscript, Evaluation of research articles, reprints. Report writing. Types of reports and Oral presentation. Steps in drafting reports. Layout of the Research project. Preparation and submission of research project proposals to funding agencies.

Recommended Books: 1. RA. Day & Barbara Gastel How to Write and Publish a Scientific Paper. 2. C.R. Kothari Research Methodology Methods and Techniques 3. Santosh Gupta Research Methodology Methods and Statistical Techniques

17

Theory

III Semester

AFM 3 C13 FISH PHYSIOLOGY

Unit-IDigestion: Alimentary Canal and associated digestive glands (liver, pancreas and gall bladder), Mechanism of digestion Respiration: Structure and function of gills, Mechanism of respiration, Haemoglobin - Oxygen Uptake and Dissociation, accessory respiratory organs

Unit-II Circulation: Blood and its components. Structure of heart and functionExcretion: Structure and function of kidney, nitrogenous end products and pattern of their excretion. Osmoregulation: Introduction, Osmoregulation in fresh water, marine water and estuarine fish

Unit-IIIReproduction: Structure and function of Gonads, Reproduction and fecundityDevelopment: Fertilization, Incubation, Hatching, Larvae and Metamorphosis

Unit-IV Endocrinology: Fish Endocrine system (structure and functions of pineal, thyroid, pituitary gland) in fish Hormonal control of Reproduction (oogenesis, spermatogenesis, oocyte maturation) Pancreatic hormone in fish Gonadotropin releasing hormone Pheromone communication in fishes Endocrinology of ecdysis in crustaceans

References:Evans, Devid H. (1998): Physiology of Fishes. Hoar, W. S., Randal, D. J. and Farrell, A. P. (1992): Cardiovascular system, Vol. 12, Part 2 Prosser, C. L. (1973): Comparative Animal Physiology, Khanna S.S. and Singh, H.R. (2003): A text book of fish biology and fisheries. Pandey A.K. and Sandhu G.S. (1992): Encyclopedia of fishes and fisheries of India Smith, L.S. (1982): Introduction of fish physiology. Yadav, B.N. (1995): Fish endocrinologyHoar, W. S. and Randal, D. J. (1993): Fish endocrinology Vol. I to VII. Yadav, B. N. (2006): Fish & Fisheries, Khanna S.S. (1989): An Introduction to Fishes.

AFM 3 C14 FISH PROCESSING TECHNOLOGY Unit IFish as raw material for processing. Handling of fish onboard fishing vessels. Structural and chemical changes associated with postmortem. Factors affecting quality of fresh fish. Chill storage of fish. Discolouration in aquatic products, Depuration of bivalves. Live fish/shell fish Transportation to local markets and processing centers.

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Unit IIGeneral Principles of food preservation. High temperature, low temperature, drying, radiation and chemicals. Microbial growth in food: intrinsic and extrinsic parameters and means of control (food formulations, cooking, preservatives, pH. aW)

Unit IIISimple mechanical refrigeration systems. Ice plants, chilling, supper chilling, refrigerated and chilled seawater. Freezing, slow freezing, quick freezing, types of freezers, freezing time, freezing of fish and shell fish. Technological aspects of freezing: Methods of freezing, comparison of various freezing

Unit IVPreparation of salted fishes, dried fish and smoked fish. Accelerated freeze drying. Canning: Principles of thermal processing Mechanism of heat transfer, canning in oil and brine. Filleting, breading etc. utilisation of fishery wastes such as prawn shell, fish offal, fish meal, chitin, chitosan. Fish silage.

References:Desrosier N.W. & Treasler D.K Fundamentals of Food FreezingGovindan T.K. Fish Processing TechnologyMoorjani M.N. Fish Processing in IndiaBrody J. Fishery Byproduct TechnologyChicheste C.O. & Graham H.D. Microbial Safety of fishery ProductsAmerien M.A. et.al. Principles of sensory evaluation of FoodConnel J.J. Control of Fish QualityAnthony T. Tu. Handbook of Natural toxins. Gopakumar K. Text Book of Fish Processing Technology. Hall, G.M. Fish Processing Technology.Huss, H. H. et al. Quality assurance in the fish industry.John, D. E. V. Food safety and toxicity Krenzer, R. Fish inspection and quality control.

AFM 3 E01 AQUACULTURE PRODUCTION SYSTEMS

Unit ITrends and status of world aquaculture production. Aquaculture practices in different parts of the world. Criteria for selection of organisms for aquaculture. Criteria for selection of sites for aquaculture, farms, hatcheries, nurseries. grow outs. Aquaculture systems: Pond culture, cage culture, pen culture. Recirculating Aquaculture Systems. Traditional, extensive, semi intensive and intensive aquaculture systems.

Unit IIPreparation and stocking of grow-out ponds and water and soil quality maintenance. Natural and supplementary feeding. Feed management in Aquaculture. Health management. Integration of aquaculture with agriculture and animal husbandry, organic aquaculture.

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Unit III Aquaculture practices for freshwater fish (Carps, Catfish, Snakeheads). Coldwater Aquaculture (Salmon, Mahseer, Trouts). Culture of tilapia- GIFT. Marine fish culture (sea bass, cobia).

Unit IVCulture of freshwater prawn (Macrobrachium rosenbergii). Shrimp culture (Penaeus monodon, Feneropenaeus indicus and Litopenaeus vannamei). Culture of molluscs (mussels, oysters, pearl oysters, clams). Culture of crabs and Lobsters. Culture of aquatic weeds including seaweeds. Unit VDiseases in Aquaculture: Viral, bacterial, protozoan and fungal. Probiotics in aquaculture. Good manufacturing practice (GMP), Responsible Aquaculture, Sanitary and phytosanitary (SPS) agreement. Harvest and post harvest technology in aquaculture Aquaranching.

Suggested readings1 Jhingran VG Fish and Fisheries of India 2 Chonder S.L Hypophysation of Indian major carps3 Pillay . T.V.R Advances in aquaculture 4 Bardach et al Aquaculture 5 V.G Jhingran & Saigal Cold water fisheries of India 6 Anon A Guide to prawn farming in India . 7 New M.B & Singholka, K. Farming of freshwater prawns FAO Technical Paper 4288 P C Thomas, et al Breeding and Seed Production of Fin Fish and Shell Fish9 P C Thomas Shrimp Seed Production And Farming

AFM 3 E02 AQUACULTURE ENGINEERING

Unit IIntroduction to technical components of farm designing, future trends in aquaculture engineering. Aquaculture facilities: planning process, site selection and evaluation, design, components and construction of tanks, ponds, cages and hatcheries.

Unit IIWater intake and outlet systems- pipe line, water flow and head loss, pumps. Water treatment: Equipment used for water treatment, filters, ultraviolet light, ozone, heating and cooling and other processes of disinfection

Unit IIIAeration and oxygenation: design and fabrication of aerators, oxygen injection system. Recirculation and water use system: definition, components and design. Instrumentation and monitoring: instruments for measuring water quality.

Unit IVFeeding systems: different types of feeding equipment, feed control systems, dynamic feeding systems. Adjustment of pH, removal of particles, Ammonia removal, Disinfection, heating and cooling equipments in hatcheries.

Unit V

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Preparation of aquaculture projects, estimation of efficiency, management of pond and hatchery machineries. New technologies in aquaculture engineering. Tank basins and other closed production unit.

Suggested Readings1. Thomas B Lawson Fundamentals of Aquacultural Engineering2. Wheaton, F.W. Aquacultural Engineering3. Santhosh Kumar Garg Water supply Engineering 4. Bose et. al. Coastal Aquacultural Engineering 5. Odd-Ivar Lekang Aquaculture Engineering6. Pillay, TVR and Kutty MN Aquaculture: Principles and Practices7. Michael BT and Thomas L Aquaculture water reuse systems

AFM3 EO3 AQUACULTURE ECONOMICS & EXTENSION

Unit IProduction economics- nature and scope, approaches terms and concepts Different production relationship – factor- product, factor - factor, product-product Farm Management. Risk and Uncertainty, Productions and Cost Concept. Decision making with no risk, with risk, Technology, Input use and factor share, Farm business analysis.

Unit IIEconomic aspects of different aquaculture production systems in India and abroad. Mathematical analysis of production relationship – concept of production function, different types, characteristics, Economics Implications, Economic optimum and Physical Optimum, Decision make with multiple variables. Economic efficiency in fish production, Yield gap, Yield penalties and Yield declines.

Unit IIIOverview of fisheries and aquaculture sector in India and world; Special characteristics of fisheries sector and its stakeholders; Understanding extension education, research, and service; Overview of fisheries research, development and extension systems in India; Scope and importance of fisheries and aquaculture extension.

Unit IVAquaculture extension system - review of extension approach as practiced by DoF, FFDA, and BFDA; Market led extension approaches; Importance of Information and Communication Technology (ICT) in aquaculture extension system. Critical review of philosophy, principles, concepts, and practices of fisheries extension systems and approaches; Teaching, learning and co-learning.

Unit VFisheries extension – advantages and limitations of present welfare and subsidy oriented extension systems; Development and extension approaches as practiced by public agencies like Department of Fisheries, KVKs, Agricultural Technology Management Agency (ATMA), NGOs, FAO, Bay of Bengal Programme (BOBP-IGO), and by the private sector; participatory fisheries extension approaches.

Suggested Readings

21

1. Andrew, P. Fish business management: strategy, marketing2. Rao, P.S. Fisheries economics and management in India. 3. Shaug, Y.C. Aquaculture economics : Basic concepts and methods of analysis4. FAO, Fisheries technical paper, 351. Economic engineering 5. Paul, A.S. Economics6. Seijo, J.C. et al. FAO Fisheries technical paper 368. Fisheries bioeconomics7. Rao, T. V. Readings in human resource development. 8. Ray, G. L. Extension communication and management.9. Supe, S. V. An introduction to Extension Education

AFM 3 E04 – QUALITY CONTROL, INSPECTION & CERTIFICATION IN SEAFOOD

Unit IIntroduction to quality control in food processing. Necessity of quality control. Food laws in India, integrated food law. Quality management, total quality concept and application in fish trade. Quality assessment of fish and fishery products - physical, chemical, organoleptic and microbiological quality standards. - sensory evaluation of quality, general testing conditions, different sensory tests.

Unit IIFish spoilage- Stages of fish spoilage- rigor mortis- Microbial evaluation of quality. Different aspects of seafood quality, quality control in fish as a raw material, intrinsic and extrinsic quality defects. Process water quality, water treatment. Fish plant sanitation, disinfectants, detergents, Quaternary Ammonium Compounds, cleaning schedule.

Unit IIIPublic health aspects in seafood- microbial and chemical. Verification of plant sanitation and personal hygiene (swab tests and ATP monitoring). Factory sanitation and hygiene: National and international requirements, SSOP, Sanitary and Phytosanitary measures. An overview of fish inspection in India. Export Inspection Agency- National standards, sanitation and hygiene control in seafood establishments as required by the regulating agencies

Unit IVInternational scenario in seafood inspection and quality control- IQPC, MIQPC, HACCP and Good manufacturing practices. HACCP principles, practical aspects of planning and implementation, verification, validation and audit. HACCP based quality control systems in India. Hazard analysis, preparation of HACCP plan, implementation of HACCP based quality control systems.

Unit VNational and International standards: ISO 9000: 2000 series of quality assurance system, Codex alimentarius, USFDA and EU regulations for fish export trade, IDP and SAT formations in certification of export worthiness of fish processing units, regulations for fishing vessels, pre-processing and processing plants, EU regulations. ISO 22000:2006. Microbial quality standards for major importing countries like USA, Japan, EEC.

Unit VI

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Packing of marine products. Nutritional labelling and education act. The US/ International labelling requirements (Codex/Indian standards for labelling). Food grade packaging materials. Seafood Export from India- Group-wise, product-wise and country-wise export. Domestic and export marketing of fish and fishery products, trends, channels, mechanisms, trade and non-trade barriers.

Suggested Readings

1. Balachandran K.K. Post Harvest Technology of Fish and Fishery Products2. Desrosier N.W. & Treasler D.K Fundamentals of Food Freezing3. Govindan T.K. Fish Processing Technology4. Moorjani M.N. Fish Processing in India5. Brody J. Fishery Byproduct Technology6. Chicheste C.O. & Graham H.D. Microbial Safety of fishery Products7. Amerien M.A. et.al. Principles of sensory evaluation of Food8. Connel J.J. Control of Fish Quality9. Anthony T. Tu. Handbook of Natural toxins. 10. Gopakumar K. Text Book of Fish Processing Technology. 11. Hall, G.M. Fish Processing Technology.12. Huss, H. H. et al. Quality assurance in the fish industry.13. John, D. E. V. Food safety and toxicity 16. Krenzer, R. Fish inspection and quality control. 17. Sen D. P. Advances in Fish Processing Technology. 18. Vincent K. et al. Principles of Total Quality. 13. Hui,Y.Het al. Food borne Disease

AFM 3 E05 INDUSTRIAL MICROBIOLOGY

Unit IAn introduction to fermentation processes - the range of fermentation processes. Microorganisms used in industrial microbiological processes - the isolation, preservation and strain improvement of industrially important microorganisms, screening methods, isolation of autotrophic mutants. Media and materials required for industrial microbiological processes - sources, formulation, antifoams and optimization.

Unit IIMicrobial growth kinetics, batch culture, continuous culture, fed-batch culture, applications and examples, scale up of fermentation processes. Sterilization of media, fermentor and feeds, Inoculum development for large scale bioprocesses.

Unit IIIDesign of a Fermentor: Functions, construction, and maintenance of aseptic conditions. Control of various parameters, types of fermentors, computer applications in fermentation technology. Aeration and agitation (Non-newdonian fermentations). Recovery and purification of fermentation products. Fermentation economics.

Unit IVIndustrial products produced by microorganisms - Enzymes (amylase, proteases), organic acids (lactic acid, citric acid, vinegar), amino acids (L-lysine, L-glutamic acid), food supplement

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and hormones. Production of important antibiotics - penicillin, streptomycin, erythromycin, bacitracin and tetracyclines. Production of Vitamins B12 & Ethyl alcohol, beer & wine. Baker's yeast production. Microbial transformation of Steroids.

Unit VEnzyme probes- bio sensors, biochips, biofilms and biosurfactants. Petroleum microbiology - microbiology and microbial leaching - role of microorganisms in the recovery of minerals (uranium, copper) from ores. Deterioration of' materials - paper, textiles, painted surfaces, prevention of microbial deterioration. Biotransformation, biodegradation. Analytical Microbiology - microbiological assays of Vitamins (riboflavin, B12), amino acids (lysine, tryptophan) and antibiotics (penicillin and streptomycin).

Suggested readings: 1. Casida. LE Industrial Microbiology2. Prescott & Dunns Industrial Microbiology. 3. A.H. Patel Industrial Microbiology. 4. P.F. Stanbury, et al Principles of Fermentation Technology 5. W. Crueger et al A text book of Industrial Microbiology

AFM 3 E06 FISHERY BY-PRODUCTS AND VALUE ADDITION

Unit INutritional importance of fish meal and quality requirements -Raw material quality and changes during processing and storage. Production of fish meal - dry and wet process, machinery, control of quality of products, specifications, packaging and storage.

Unit IIFish body and liver oils. Nutritional importance of fish oil and methods to impart stability to fish oils on storage, Unsaponifiables in fish liver oils. Enzyme hydrolysis of fish, fish hydrolysates, fish peptones, hydrolysates enriched food beverages.

Unit III Shrimp waste, crab shell and squilla utilisation: Resources and composition, conventional uses, feeds and manure, conversion to useful materials like chitin, chitosan, glucosamine hydrochloride, shrimp extract, commercial production, production and use of protein isolates from squilla and shrimp waste.

Unit IV Fish protein concentrate: Different methods of production, functional properties, different types of FPC, texturised products and comparison of FPC to fish meal. Production of fish flour, quality standards and applications

Unit V Fish silage: Acid silage and fermented silage, advantages over fish meal, nutritional value of silage. Fish hydrolysates: Production and utilisation, biochemical composition and importance in food and nutrition.

Unit VI

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Miscellaneous by-products: Fish maws, shark liver oil, squalene, ambergris, shark skin, shark cartilage, isinglass, pearl essence, fertilizer, beche-demer, fish glue, agar agar, alginic acid, carrageenan. Extraction of collagen from fish processing wastes, properties and application. Preparation of biological membranes using collagen and chitosan for biomedical applications.

Unit VIIValue Added Products: Present market trends, scope of value addition, Types of value addition, Important value added products. Coated products – Principles and type of coating, Coating functions, in gradients, Batter classification, Mechanical properties of batter, Bread crumbs, Flavorings, Seasonings and Hydrocolloids in coatings, Fat and oils in coated food, Application of batters and breading to seafood.

Suggested readings

1. Balachandran, K.K. Post Harvest Technology of fish and fish products.2. Gopakumar K. Text Book of Fish Processing Technology. 3. Hall, G.M. Fish Processing Technology.4. Hui,Y.H., M.D. Pierson & J.R. Gorham Food borne Disease5. Sen D. P. Advances in Fish Processing Technology. 6. Wheaton & Lawson Processing Aquatic Food Products.

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Theory

IV SEMESTER

AFM 4 C17 BIOTECHNOLOGY & MOLECULAR BIOLOGY

Unit I

Nucleic acid : Structural aspects – Components of DNA and RNA, Nucleosides & Nucleotides. Double helical structure of DNA (Watson - Crick Model). DNA Replication –The Basic Rule for Replication of all Nucleic acids. The Geometry of DNA. Replication, Enzymology of DNA replication, Discontinuous Replication, Events in the Replication Fork, Initiation of Synthesis of the Leading Strand, Bidirectional Replication, Termination of Replication, Methylation of DNA and Mismatch Repair, Replication of Eukaryotic Chromosomes. Mutation – Occurrence, kinds of Mutation, spontaneous & induced Mutation, Mutagens, detection of Mutation, Lethal Mutations, Biochemical Mutations, Phenotypic effects of Mutation, Molecular basis of Mutation, Significance & Practical applications of Mutation

Unit II

Transcription: Enzymatic Synthesis of RNA Basic features of RNA synthesis, E.coli RNA polymerase, Classes of RNA molecules, processing of tRNA and rRNA in E.coli, Transcription in Eukaryotes, Eukaryotic rRNA genes, formation of eukaryotic tRNA molecules, RNA Polymerases of eukaryotes, RNA polymerase II Promoters, Eukaryotic Promoters for RNA polymerase III, Hypersensitive sites, Upstream activation sites and enhancers, Splicing mechanisms, Splicing of tRNA precursors, Splicing of rRNA precursors, Splicing without a protein enzyme. Translation: Outline of Translation, The Genetic Code, The Decoding System, Codon Anticodon interaction, The special properties of the prokaryotic Initiator tRNA, Transfer RNA genes, suppressors, Ribosomes, Protein Synthesis, Complex Translation units, , Inhibitors and Modifiers of protein synthesis, Protein Synthesis in Eukaryotes.

Unit III

Regulation of activity of Genes and Gene products in Prokaryotes: General aspects of Regulation, The lactose system and the operon model, The Galactose operon, The Arabinose operon, The Tryptophan Operon, Relative positions of Promoters and Operators, Regulation of Translation, Regulation of the synthesis of Ribosomes.

Unit IV

Regulation in Eukaryotes: Regulatory strategies in Eukaryotes, Gene alteration (Gene loss, Gene amplification, Gene rearrangement: the joining of coding sequences in the immune system) Transcriptional Control by hormones, Regulation mediated through Transcription factors, Regulation of enhancer activity, Methylation, Regulation of processing, Translational control. Unit V

Introduction to recombinant DNA technology, gene cloning, tissue culture ,organ culture, cell line and its applications, cloning of animals, transgenic animals ,plants, and fishes, stem cells and its application, application of microbial technology in culture ponds; bioaugmentation,

26

bioremediation, biofertilizers, and probiotics Present status of marine biotechnology, marine natural products, bioactive compounds from marine organisms,, single cell protein ,bio-sensors, marine biofilms and biofouling

Suggested reading1. Lehninger, A.L. Principal of Biochemistry.2. Smith, E.L., et al. The principles of Biochemistry3. Glick B.R. Molecular biotechnology4. Singleton Elementary Genetics5. Gjedrem, T. Genetics in Aquaculture 6. Purdom,C.E Genetics and Fish breeding7. Alberts,B and others Molecular Biology of the cell 19948. Peter Proksch Frontiers in Marine Biotechnology

9. Le Gal Marine Biotechnology

AFM 4 C18- DISEASE DIAGNOSIS AND AQUATIC HEALTH MANAGEMENT

Unit I

Basics of fish and shellfish health management: Host-pathogen-environment relationship, Management of culture systems, Environmental stress. Defence system in fish and shellfish: Defence systems in fish, innate and acquired immunity, inflammation response to diseases. Antibody and cell mediated immunity in fish and shellfish.

Unit II

Infectious bacterial and viral diseases: General characteristics, Epizootiology, Diagnosis, Prevention and treatment. Aetiology, pathogenesis, epidemiology, treatment and control of viral diseases of finfishes such as EHN, IHN, VER, SVC etc. Major pathogens of commercially important cultured crustaceans with special reference to shrimp and freshwater prawn such as WSSV, YHV, TSV, IHHNV, MBV, HPV, BP etc.

Unit III Parasitic and mycotic diseases: General characteristics, Epizootiology, Diagnosis, Life cycle, Prevention and treatment. Non-infectious Diseases: Nutritional diseases, water, soil, environmental parameters and their effects on fish health. Disease in hatcheries and grow-out systems.

Unit IV

Techniques in health management: Microbiological, haematological, histopathological, immunological and molecular techniques. Disease surveillance and reporting. Disease control and management: Environment management, chemotherapeutic agents, host management, prophylaxis- vaccines, adjuvants, immunostimulants and probiotics. Use and abuse of antibiotics and chemicals in health management. Fish health and quarantine systems. Seed certification, SPF and SPR stocks - development and applications.

1. Aline, W. Fish diseases.

27

2. Schaperclaus, W. Fish diseases (Vol. I & II).. 3. Wedmeyer, Meyer & Smith Environmental Stress and Fish Diseases\4. Ronald J. Roberts Fish Pathology. 2nd Edition. 5. Carl, J. Sindermann Principal diseases of Marine Fish and Shelfish. Vol. I & II,

6.Iwama G. and Nakanishi T. Fish Immune system – Organism, Pathogen & Environment.

7. Austin, B. and Austin, D.A. Bacterial Fish Pathogens (Diseases in Farm and Wild). 8. Valerie Inglis et al., Bacterial Diseases of Fish. 9. Chris Andrews et al., The Manual of Fish Health. 10. Felix et al., Fish Disease Diagnosis and Health Management. 11. Shankar. K.M. & Mohan. C.V Fish and Shellfish Health Management, 12. Andrews, Excell & Carrington The manual of fish health. Salamander

AFM 4 EO7 LIVE FEED CULTURE TECHNIQUES

Unit INatural food and its importance in aquaculture. Nutritional quality of commonly used fish food organisms. Enrichment and preservation of live feeds. Use of periphyton in aquaculture. Unit II Microalgal Culture: Uses of microalgae in aquaculture. Major classes and genera of cultured algal species. Algal production; physical and chemical conditions; growth dynamics; isolation and maintenance of stock cultures. Culture media. Algal mass culture techniques. Algal production in outdoor ponds. Quantifying algal biomass. Harvesting and preservation of microalgae. Nutritional value of microalgae. Bacterioplankton as live feed.

Unit III Zooplankton culture: Morphology, biology, life cycle and general culture conditions of live feed organisms; rotifers, cladocerans and copepods. Zooplankton mass culture techniques. Nutritional value of cultured zooplanktons. Zooplankton Production and use of resting eggs of rotifers and cladocerans. Culture of nematods. Mesocosm systems for live feed production.

Unit IVArtemia: Morphology, strains, biology, life cycle and ecology of artemia. Use of cysts; disinfection procedure, decapsulation; hatching. Nauplii and meta nauplii: morphology, harvesting, nutritional quality, enrichment and preservation. Production and use of grown artemia; pond production; harvesting and processing techniques.

Suggested Reading

CIFE Publn. Training manual on culture of live food organisms for Aqua hatcheries,

28

MPEDA Publn. Hand book on Aqua farming – Live feed. Micro algal culture Lavens P.and Sorgelose P. Manual on the production and use of live food for aquaculture. Sorgelos, P. & Pandian, S. Culture of live food organisms with special reference to Artemia

culture Tonapi, G.T. Freshwater animals of India, Hagiwara, A., et al. Live food in aquaculture

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AFM 4 EO8 ORNAMENTAL FISH BREEDING & REARING

Unit I

Ornamental fish breeding and rearing-overview. Species for aquarium trade- freshwater and marine. Status of world trade of ornamental fish. Concept of quality and varieties in aquarium trade. Farming of ornamental fishes.

Unit II

Biology, sexing, courtship, breeding, larval rearing and mass production of freshwater ornamental fishes- Live bearers, Goldfish, Barbs, Gouramy and Angelfishes. Breeding of Koi Carps. Indigenous freshwater ornamental fishes of India.

Unit III

Marine ornamental fishes in aquarium trade. Status of marine ornamental fish breeding. Breeding of Anemone fish and damsels. Methods of collection and rearing of marine ornamental fishes from natural habitats. Impact of marine ornamental fish collection and hatcheries on reef ecosystem.

Unit IV

Ornamental invertebrates in aquarium trade. Marine invertebrate rearing systems. Culture and maintenance of corals. Keeping of echinoderms and ornamental crustacenas in aquariums. Sponges and opisthobranchs in aquariums. Marine aquarium management. Biological and chemical processes in aquariums. Setting up of aquariums.

Unit V

Brood stock management of ornamental fishes. Common diseases and their control. Conditioning, packing, transport and quarantine methods. Common aquarium plants. Agencies involved in popularisation and extension of ornamental fish culture in India. Economics of ornamental fish farms.

Suggested Reading:1. Biswas. S.P., et al Ornamental fishes of North East India : An Atlas 2. Ramachandran.A, Breeding, Farming and Management of Fishes,3. Madhusoodana kurup et al Ornamental Fish - Breeding, Farming and Trade4. Jhingran,V.G. Fish and Fisheries of India.5. Bijukumar,A. Rearing of Aquarium Fishes.6. Rath,A.K. Freshwater Aquaculture,7. Santhanam, et.al. AManual of Freshwater Aquaculture8. Murthi.V.S. Marine ornamental Fishes of Lakshadweep 9. Butting.B., et al. Marine Aquarium Industry and conservation.10. Oliver, K Marine Ornamental species; collection and Conservation

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AFM 4 EO9 FISH NUTRITION & FEED TECHNOLOGY

Unit I

Food and feeding behaviour of fishes and prawns. Digestive system and digestive physiology of fishes and crustaceans. Nutritional evaluation of live feeds.

Unit II

Nutritional requirements of cultivable species and their sources. Bioenergetics in fishes. Dietary components in aquaculture feeds. Protein nutrition, Lipid nutrition, Carbohydrate nutrition, Vitamin nutrition and Minerals nutrition. Larval nutrition, Brood stock nutrition and Feed additives

Unit III

Proximate principles in feeds. Classification of feed ingredients: energy source & protein source, Evaluations of ingredients quality. General principle of feed formulation. Different steps of feed formulation, Methods of feed Formulation. Feeding methods in aquaculture. Feeds for aquarium fishes.

Unit IV

Type of feeds-Compounded feeds, pellets, crumbles and live feed. micro-encapsulated, micro-bound and microcoated feeds. Additives in feeds. Live feeds. Shrimp feeds-Starter, grower and finisher feeds, storage of feeds, exogenous toxins in feeds, aflatoxins nutritional diseases. Feed manufacturing units and processes: Hydro-stability of feed and their storage and prevention of spoilage from rancidity, fungus formation and associated toxins. Fish disease vectors in feed and quality control; Feed value in relation to processing;

Unit V

Methods used in studies of nutrition, digestibility studies and nutritional deficiency studies. Chemical evaluation of aquaculture feeds. Evaluation criteria: FCR, PER, NPU, EAAI, chemical score, biological value. Aqua feed industries in India. Economics of aquaculture feed manufacturing.

Suggested Reading:1. Halver J.E. 1989. Fish Nutrition, Academic Press, San Diego, CA2. Hepper, B. 1988. Nutrition of pond fishes.3. Lovell, T., 1988. Nutrition and Feeding of Fish. Kluwer Academic

Publishers.4. Halver, J & Hardy, RW. Fish nutrition. Academic press, London. 8245. S.S.De Silva & TA Anderson Fish Nutrition in Aquaculture6. Lovell, R.T. Nutrition and Feeding of Fishes

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AFM 4 E10 IMMUNOLOGY

Unit 1Basic principles of immune system in fishes and shell fish Organs and cells involved in immunity, passive immunity, Active immunity, Herd Immunity, Innate immunity Types of immune response ,Cell mediated Immunity, Humeral immunity, Structure and types of immunoglobulins, Functions of immunoglobulins, Monoclonal Antibodies, Production and Applications of Immunoglobulins, Invertebrate immune response

Unit IIImmuno-stimulant, immunomodulation. fatty acid, levanisole, nucleotide, alginates, bovine lactoferine, etc. on fish/ shellfish immunity and mechanism of their action. Principles of stress resistance, stress tolerance. Challenge study.

Unit IIIDefense mechanisms in fishes. Innate and adaptive/acquired immunity, Cellular and humoral basis of immunity. Cytokines & Antagonists , antimicrobial and antitumor substances. Immune responses to infection, inflammation. Compliment System-components & functions. Compliment activation and regulations. Inflammation & hypersensitivity. Immune system in relation to parasitic infections.

Unit IVCells of the immune system. Cell mediated immunity. T-cells, T-cell receptors, T-cell maturation, activation, differentiation. Antigens and Antibodies: Structure and functions of Immunoglobulin, Antibody diversity. Immunodeficiency, Vaccines, methods of vaccination in fish. Factors influencing immunogenicity.

Suggested Readings : 1. Kindt TJ Immunology2. Paul WP Fundamental of Immunology3. Goldsby R A Immunology 4. A. K Abbas and A. H Lichtman Cellular and Molecular Immunity5. Carpenter. Immunology and Serology6. Das Gupta Modern Immunology

AFM 3 E11 DEVELOPMENTAL BIOLOGY

Unit IHistory of Embryology - Types of egg based on the amount of yolk, distribution, development . egg membranes gametogenesis : Growth of oocytes - Synthesis and storageof macromolecules in the oocytes - Nuclear activities during oocytes growth. Hormonal and nervous control of ovulation.

Unit IIFertilization : polyspermy - Androgenesis - Egg activation- Electron microscopic and biochemical aspects - Fertility ofsperm and its in vitro fertilization - artificial fertilization -Chemodiffertiation. cleavage, blastulation.Unit III

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Gastrulation movements : role of egg cortex - Cellsurface in morphogenesis - Cell adhesion and cellcommunication. Chemotatic induced aggregation -. Early development stage of fish.organogenesis, growth and differentiation,

Unit IVInvertebrate Embryology, Early development - larval metamorphosis and organogenesis in Crustaceans and Molluscs.

Suggested Readings : 1. Balinsky, B.L., An introduction to embryology,.2. Karp. G. and Berrill, N.J. Development, McGraw-Hill, New York.3. Eber, J.D Interacting system in Development,4. Grant, P., Biology of developing systems, , J.W. 1982. Developmental Biology. MacmillanCo., London.6. Brachet J. Introduction to Molecular Embryology.7. Nagabhushanam . InvertebrateEmbryology. 8. Gilbert, Scott. F. . Developmental Biology..9. Tyagi, Rajiv and A.N. Shukla, Development offishes.10. Raven, P. An outline of developmental physiology,Pergamon.11. Browder, W. . Developmental Biology,

AFM 4E12 AQUATIC POLLUTION AND TOXICOLOGY

Unit IWater pollution: Types, sources and impacts Surface water, ground water pollution Domestic, Industrial, agricultural and natural sourcesWater Pollution: Assessment and control Pollution due to municipal sewage dumping, industrial effluent discharge and solid waste dumping- leachate infiltrationAssessment of the level of pollution based on BOD, COD, nitrogen, phosphate and microbiological analysis, Wastewater treatment: Primary, Secondary and tertiary

Unit IIBiological and chemical factors influencing toxicity inorganic and organic toxicants- entry into the environment, cycles and residence TimeToxicity of pesticides, insecticides heavy metals, radioactive minerals, fluriodes, chemical fertilizers etc

Unit IIIToxicants and Ecosystem Toxicants and communities in ecosystem Multilevel trophic interactions and non-trophic interactions Functional changes in the ecosystem Effect of interspecific interactions in the environment Bio-concentration, Bio-accumulation and bio-magnification and its impactsSensitivity of ecosystems and ecotones

Unit IVToxicity Testing and Indicators Principles of toxicity testingMethods of toxicity evaluation at cellular and molecular level by in vitro and in vivo methodsMonitoring approaches- indicator populations and indicator species Lacustrine communities as indicators of ecosystem stress Bacterial, algal and invertebrate microbiotests Bio-sensors and Bio-markers- Concept and approach, advantages and disadvantages Molecular marker to toxicants- metabolites as indicators, protein induction, cytochrome P450 enzymes, stress proteins and metallothioneins.

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Suggested Readings : Ballantyne B, Marris T and Turner P (ED) General and applied toxicology Cairns Jr , J and Niedrelehner B R (Ed) Ecological Toxicity testingCasarret and Doull (Ed). Toxicology- The basic science of poisons. Cockerham L G, B. S. Shane (2008) Basic Environmental Toxicology Freedman B (Ed) Environmental Ecology Landis W G, M.-H. Yu. Introduction to Environmental ToxicologyMoriarty F Ecotoxicology. Niesink J M, Dc Vries and Hollinger M R Toxicology Principles and Applications Nurenberg H W Pollutants & their eco-toxicological significance. Ramada F Ecotoxicology Richardson M Environmental toxicology assessment. Sigel A et al Organometalics in Environment and Toxicology Stina K E and Brown T M (Ed) Principles of Toxicology

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PRACTICALSAFM 1 C05P - TAXONOMY, BIOLOGY & FISHERIES

Taxonomy

• Collection and identification of commercially important freshwater and marine fishes • Collection and identification of commercially important crustaceans and molluscs.• Identification of major groups of phytoplankton and zooplankton.

Biology

• Gut content analysis of fishes of fishes with different feeding habits. • Determination of maturity stages and Gonadosomatic index of commercially important

fishes. • Estimation of Fecundity and ova diameter. • Collection and identification of eggs and larvae of economically important fishes and

crustaceans. • Determination of length weight relationship of fishes and estimation of growth

parameters.

AFM 1 C06P- INSTRUMENTATION

Micrometry- Determination of maturity of fish egg using ovadiameter method Camera Lucida- Diagrammatic representation of given microscopic sampleInstruments in field survey- pH meter, Refractometer, DO meter & Conductivity meter (Demonstration) Spectrometry- Preparation of standard graph for a biochemical compoundFlame Photometry- Determination of concentration of a given metal in the sampleDifferential centrifugation (demonstration)Chromatography- Separation of Amino acids using Paper and Thin Layer ChromatographyElectrophoresis- Separation of muscle proteins through SDS PAGE and DNA electrophoresisELISA (Demonstration)PCR- Amplification of DNA template with primer through RAPD (Demonstration)

AFM 2 C11 P: GENERAL AND FISHERY MICROBIOLOGY

• Basic microbiological techniques• Sterilisation- dry heat, moist heat, filtration, flaming, UV-irradiation• Preparation and sterilisation of media• Bacterial Handling Techniques, aseptic transfer of microbes• Estimation of bacterial population in water and fish- TPC• MPN• Isolation and maintenance of pure culture• Study of morphological characters, colony morphology, microscopic examination of micro

organisms

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• Staining of bacteria, gram stain, spore stain, capsule stain• Enrichment culture using selective media- Salmonella, vibrio.• Identification of E. coli, Staphylococcus, faecal streptococci• Growth of Fungi and yeast• Determination of mobility of bacteria• Latex agglutination for identification of bacteria• Antibiotic sensitivity tests.

AFM 2 C12P BIO COMPUTING AND BIOINFORMATICS

Pictorial representation of morpho metric data of fishesEstimation of population parameters. Usage of FiSAT and LFDA.Data analysis using SPSSBiological data acquisition from databases.Sequence analysis using software Development of phylogenetic tree using softwareBLAST and FASTAMolecular visualisation using RASMOL

AFM 3 C15P AQUAFARM AND HATCHERY MANAGEMENT

• Determination of Dissolved Oxygen• Determination of salinity• Determination of Hardness of water• Determination of soil pH and organic carbon content in Soil.• Determination of Nutrients- Nitrates and Phosphates • Determination of Ammonia• Estimation of BOD and primary productivity• Water quality analysis using various equipments. • Collection and identification of cultivable fishes, shrimps and molluscs.• Collection and Identification of predatory and weed fishes• Collection and identification of aquatic weeds and insects• Collection and biochemical evaluation of locally available feed ingredients • Assessment of growth of fish in culture system and FCR.• Aquarium keeping- setting up of home aquarium.• Induced breeding in fishes-Demonstration• Eye stalk ablation in shrimps• Breeding and rearing of common ornamental fishes• Algal culture• Zooplankton culture• Visit to hatcheries and farms to study design and operation• Visit to fish farms, hatcheries and ornamental fish breeding units • Visit to brackish water and marine farm and hatcheries• Visit to various institutes of aquaculture importance.• Design and earthwork Calculation

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• Estimation of Lime and Nutrient requirements to the aqua farms• Layout and designing of freshwater fish, prawn and shrimp hatcheries

AFM 3 C16 P BIOCHEMISTRY

1. Estimation of moisture content by hot air–oven method2. Estimation of crude fat content3. Estimation of crude protein content by Micro-Kjeldahl method4. Estimation of total ash content5. Determination of soluble protein content by Lowry method6. Estimation of DNA by diphenylamine reaction7. Determination of RNA by orcinol method8. Determination of iodine number of a fat sample9. Determination of saponification value of fats and oils10. Estimation of glucose in a given sample

AFM 4 C19P: FISH PROCESSING TECHNOLOGY & QUALITY CONTROL

• Preparation of dried, cured and fermented fish products (Demonstration), • Examination of salt, protein, moisture in dried / cured products, • Examination of spoilage of dried / cured fish products. • Preparation of fish meal, FPC, fish oils, chitin, chitosan (Demonstration). Fish maws,

isinglass, agar, alginic acid, glue, pearl essence, fish sauce.• Preparation of fish wafers, fish fingers, cutlets, pickles etc. • Organoleptic analysis of fish and shell fish, • Analysis of indole, total nitrogen, trimethyl amine (TMA).• Analysis of filth and other extraneous materials from sea food, • Estimation of percentage chlorine in hypochlorate solution, • Peroxide value of fish oil, acid value or free fatty acids of fish oil and refractive index of

fish oil.• Visit to fish processing plants

AFM 4 C20P-PHYSIOLOGY, CYTOLOGY & MOLECULAR BIOLOGY

Enumeration of total RBC, WBC and estimation of haemoglobin content in fish bloodDetermination of LC50 for any pesticide and its impact on external morphology of fish RBC Detection of amylase, protease and lipase activities alimentary canal of fishEstimation of oxygen consumption in fishesDetermination of rate of ammonia excretion in fishesHistology and Histochemistry of liver and intestineKaryotyping of fish chromosome using Giemsa stain techniqueIsolation of genomic DNA and RNA from yeastNorthern and Southern Blotting (Demonstration)