Year: Second Year Semester: III Course: Developmental ......Molecular analysis using UV/visible, fluorescence, circular dichroism, NMR and ESR spectroscopy Molecular structure determination

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School of Science

M.Sc. Life Science

Year: Second Year Semester: III

Course: Developmental Biology Course Code: PLSI301

Teaching

Scheme

(Hrs/Week)

Continuous Internal Assessment (CIA) End Semester

Examination Total

L T P C CIA-1 CIA-2 CIA-3 CIA-4 Lab Theory Lab

4 0 - 4 10 20 10 10 - 50 - 100

Max. Time, End Semester Exam (Theory) - 3Hrs.

Prerequisite Students should have the basic knowledge of developmental biology

Objectives

1 To study the basis of development

2 To study the fertilization and early development

3 To study the morphogenesis and organogenesis in animal

4 To study the morphogenesis and organogenesis in plant

5 Programmed cell death in plant and animal

Unit

Number Details Hours

1

Basic concepts of development : Potency, commitment, specification,

induction, competence, determination and differentiation; morphogenetic

gradients; cell fate and cell lineages; stem cells; genomic equivalence and the

cytoplasmic determinants; imprinting; mutants and transgenics in analysis of

development

12 L

2

Gametogenesis, fertilization and early development: Production of gametes,

cell surface molecules in sperm-egg recognition in animals; embryo sac

development and double fertilization in plants; zygote formation, cleavage,

blastula formation, embryonic fields, gastrulation and formation of germ layers

in animals; embryogenesis, establishment of symmetry in plants; seed

formation and germination

14 L

3

Morphogenesis and organogenesis in animals : Cell aggregation and

differentiation in Dictyostelium; axes and pattern formation in Drosophila,

amphibia and chick; organogenesis – vulva formation in Caenorhabditis

elegans, eye lens induction, limb development and regeneration in vertebrates;

differentiation of neurons, post embryonic development- larval formation,

metamorphosis; environmental regulation of normal development; sex

determination.

14 L

4

Morphogenesis and organogenesis in plants: Organization of shoot and root

apical meristem; shoot and root development; leaf development and phyllotaxy;

transition to flowering, floral meristems and floral development in Arabidopsis

and Antirrhinum

12 L

5 Programmed cell death: aging and senescence, apoptosis versus necrosis,

mechanisms of programmed cell death, and regulators of apoptosis. 8 L

Total 60 L

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Course Outcome

Students should able to

CO1 Basic concepts of plant and animal development

CO2 Process of fertilization and early development in animal

CO3 morphogenesis and organogenesis in animal

CO4 morphogenesis and organogenesis in plant

CO5 The basis of programmed cell death

Resources

Recommended

Books

1) Essential Developmental Biology, by Jonathan M. W. Slack, Wiley-

Blackwell.

2) Endosperm: Developmental and Molecular Biology, Author(s): R. C.

Brown, B. E. Lemmon (auth.), Odd-Arne Olsen (eds.)

3) Current Topics in Developmental Biology, Vol. 44, Roger A. Pedersen,

Gerald P. Schatten

Reference

Book

1. Taiz L. & Zeiger E. 2002 Plant Physiology Sinauer Associates, Inc.

2. Mary S. Tyler. Developmental Biology A Guide For Experimental Study

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School of Science

M.Sc. Microbiology


Course: Bioinformatics Course Code: PLS302

Teaching

Scheme

(Hrs/Week)


Examination Total


4 0 - 4 10 20 10 10 - 50 - 100


Prerequisite Students should have the basic knowledge of genomics and proteomics data

and its analysis for the disease diagnosis and drug development

Objectives

1 To study the development and scope of bioinformatics

2 To study the various biological databases and its importance

3 To study the basis of proteomics

4 To study the genomics and phylogenetics analysis

5 To study the basic concepts of molecular modelling

Unit


1

Introduction to Bioinformatics:

History, development, scope, importance and application of Bioinformatics,

introduction of computer, internet and related programs for file/data sharing e.g.

WWW, HTML, HTTP, telnet, ftp etc., Internet resources of biological data; Pubmed,

Entrez, NCBI, NLM, NIH, EMBnet, Genomnet, DBGet, EMBL, database retrieval.

Concept of database, various types of biological databases.

12 L

2

Biological sequence and structure databases: Protein and DNA sequencing, cDNA

libraries, submission of sequence to databases, sequence formats, protein primary,

composite, secondary sequence databases. DNA sequence databases: Human genome

project, European molecular Biology laboratory (EMBL), DNA Databank of Japan

(DDBJ), GenBank, websites for protein sequence databases. Structural databases:

Three-dimensional structure prediction, X-ray, NMR and Cryo-EM techniques, protein

folding classes, structure classification databases, Protein Data bank (PDB), Nucleic

Acid Data Bank (NDB), Molecular modeling Data Bank (MMDB).

12 L

3

Proteomics study: Protein sequence and structure information, physicochemical

properties of protein based on sequence, secondary structure analysis, sequence

comparison, pair-wise and multiple sequence alignment, gaps, gap-penalties, scoring

matrices, ClustalW. Secondary structure prediction from sequence, Homology

modeling; 3D protein structure prediction from sequence, validation of protein model,

Ramachandran plot, significance of 310 helix and loops, proteomics analysis using

internet tools, protein folding classes.

12 L

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4

Genomics study: Goals of the Human Genome Project, structural and functional

aspects of DNA and RNA, Central dogma, recombinant DNA technology, next

generation sequencing (NGS), designing primer for DNA sequencing, Genome

Mapping, Genome information and special features, Nucleotide sequence analysis,

Expressed sequence tag, DNA Microarray and analysis, Gene identification: masking

repetitive DNA, DNA database search, codon-bias detection, identification of

functional sites in the DNA. Internet resources for gene identification. Phylogenetic

analysis: Evolution, elements of phylogeny, methods of phylogenetic analysis,

phylogenetic tree of life, phylogenetic analysis online tools.

12 L

5

Molecular Modelling: Introduction of molecular modeling approach, co-ordinate

system; bond distance, bond angle, torsion angle, Van der Waals and electrostatic

interactions, Introduction of quantum mechanics, force field, energy calculations,

energy minimization and geometry optimization, conformational search, Molecular

docking and virtual screening, post docking analysis, Computer aided drug design,

ligand and structure based approach. Introduction to molecular dynamics simulation,

theory and applications of MD simulations.

12 L

Total 60 L

Course Outcome


CO1 Understand the history and development of Bioinformatics

CO2 Understand the use of biological databases and its use

CO3 Understand the proteomics data and how to analyze

CO4 Analyze the genomics data

CO5 Understand the basis of molecular modeling and molecular dynamics simulations

Resources

Recommended

Books

1. Introduction to computational biochemistry, by C.Stan Tsai, A John

WILEY & SONS, Inc., Publication.

2. Essential Bioinformatics by Jin xiong

3. Introduction to Bioinformatics by Attwood and Parry-Smith

Reference Books 1. Molecular modeling of proteins by Andreas Kukol, Humana press

2. Bioinformatics, Sequence and Genome analysis by David Mount.

3. Molecular modeling of proteins by Andreas Kukol, Humana press.

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School of Science

M.Sc. Life Science


Course: Research Methodology and Biostatistics Course Code: PLS303

Teaching

Scheme

(Hrs/Week)


Examination Total


4 0 - 4 10 20 10 10 - 50 - 100


Prerequisite Students should understand the basics of analysing and writing the

biological data scientifically

Objectives

1 Introduce the objectives of research and set the motivation in research

2 To identify various sources of information for literature review and understanding the

framework of research process

3 To understand the available techniques for qualitative data analysis

4 Appreciate the components of scholarly writing and evaluate its quality

5 Using computer-intensive methods for data analysis

Unit


1 Introduction to Research: Meaning of Research; Objectives of Research;

Motivation in Research; Types of Research; Research Approaches;

Significance of Research; Research Methods versus Methodology; Research

Process; Criteria of Good Research.

12 L

2

Research formulation: Defining and formulating the research problem,

selecting the problem, necessity of defining the problem, importance of

literature review in defining a problem, Literature review - primary and

secondary sources, reviews, monographs, patents, research databases, web as

a source, searching the web, critical literature review, identifying gap areas

from literature review and research databases, writing a research proposal.

12 L

3

Statistics in Research: Data Collection: Types of Data, Primary and

Secondary Data - Definition, Sources, Characteristics, Questionnaire

Construction, Statistics Fundamentals, Sampling Distribution.

Data Analysis: Data Preparation – Univariate analysis (frequency tables,

barcharts, pie charts, percentages), Bivariate analysis – Cross tabulations and

Chi-square test, Least square method, Correlation Regression, Testing of

hypothesis, Analysis of Variance.

12 L

4 Documentation and scientific writing: Preparation of manuscript for

Publication of Research paper, Presenting a paper in scientific seminar, Thesis

writing. Structure and Components of Research Report, Bibliography.

Research Ethics: Ethical issues, ethical principles that govern research,

12 L

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ethically valid information sources, regulatory compliance, plagiarism,

Introduction to IPR and Patent registration.

5

Computer applications for Research: Utilisation of word processing, spread

sheet, database software and Microsoft Power Point or similar tools. Plotting

of graphs. Internet and its application, Mathematical and statistical analysis

using software tools like MAT Lab, SPSS, PsiLAB or free ware tools.

12 L

Total 60 L

Course Outcome


CO1 The objectives of research and set the motivation in research

CO2 Identify the sources of information for literature review

CO3 Understand the available techniques for qualitative data analysis

CO4 Understand the how to write the manuscript and other related scientific documents

CO5 Use the various computer-intensive methods for data analysis

Resources

Recommended

Books

1. Research Methodology: Methods and Techniques C.R. Kothari

2. Essentials of Research Design and Methodology

Author(s): Geoffrey R. Marczyk

Reference Books

1. Biostatistics: A foundation for Analysis in the Health Sciences 7/E

Wayne W. Daniel, Wiley Series in Probability and Statistics.

2. Introductory Statistics. Fifth Edition. (2004) Prem S. Mann. John Wiley

and Sons (ASIA) Pte Ltd.

3. Basic Statistics-Aprimer for Biomedical Sciences- (Olive Jean Dunn).

4. Biostatistics-An introductory text - (Auram Gold Stein).

5. Statistics : An Introductory Analysis (Taro Yamane) Harper and Row

Publisher 1964,67,73

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School of Science

M.Sc. Life Science


Course: Instrumentation Course Code: PLS304

Teaching

Scheme

(Hrs/Week)


Examination Total


4 0 - 4 10 20 10 10 - 50 - 100


Prerequisite Students should understand the basic principles and applications of

instruments used in biological science

Objectives

1 To study the basic tools and techniques of life science

2 To study the chromatography and centrifugation methods

3 To study electrophoresis and tracer techniques and its application in biology

4 To study the analysis of molecules using different spectroscopy methods

5 To study the basic microscopy and electrophysiology techniques

Unit

Number Details

Hour

s

1

Tools and techniques in life science: General scheme for purification of bio-

components, methods for studying cells and organelles, sub-cellular

fractionation and marker enzymes, methods for lysis of plant, animal and

microbial cell, ultrafiltration, freeze drying and fractional precipitation. Use of

detergents in isolation of membrane proteins.

12 L

2 Chromatography: Basic principles and applications of ion-exchange, gel

filtration, partition, affinity, HPLC and reverse phase chromatography, gas

chromatography, TLC, Paper chromatography.

Centrifugation: Ultracentrifugation-velocity and buoyant density determination

Density gradient centrifugation, molecular weight determination.

12 L

3

Electrophresis Techniques: Basic techniques, poly acrylamide/ starch/

agarose gel electrophoresis, use of SDS/urea, isoelectric focusing, capillary

electrophoresis. Pulse field gel electrophoresis.

Tracer techniques: Principles and applications of tracer techniques in

biology, Measurement of alpha, beta and gamma radiations. Radiation

dosimetry, Radioactive isotopes and half life of isotopes, Autoradiography,

Cerenkov radiation, Liquid Scintillation spectrometry.

12 L

4

Molecular analysis using UV/visible, fluorescence, circular dichroism, NMR

and ESR spectroscopy Molecular structure determination using X-ray

diffraction and NMR, Molecular analysis using light scattering, different

types of mass spectrometry and surface plasma resonance methods.

12 L

5

Microscopy: Visualization of cells and sub-cellular components by light

microscopy, resolving powers of different microscopes, microscopy of living

12 L

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cells, scanning and transmission microscopes, different fixation and staining

techniques for EM, freeze-etch and freeze fracture methods for EM, image

processing methods in microscopy.

Electrophysiological methods: Single neuron recording, patch-clamp

recording, ECG, Brain activity recording, lesion and stimulation of brain,

pharmacological testing, PET, MRI, fMRI, CAT.

Total 60

Course Outcome


CO1 Cell purification and characterization

CO2 How to perform the chromatography and centrifugation for isolation of biomolecules

CO3 electrophoresis and tracer techniques in biology

CO4 Study the different spectroscopy methods

CO5 Understand the basic microscopy and electrophysiology techniques

Resources

Recommended

Books

1.Practical Biochemistry, V th edition, Keth, Wilson and Walker.

2.Tools in Biochemistry David Cooper

Reference Books

1) Protein Purification by Robert Scopes, Springer Verlag Publication, 1982

2) Methods of Protein and Nucleic acid Research, Osterman Vol I – III

3) Centrifugation D. Rickwood

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School of Science

M.Sc. Life Science


Course: Developmental Biology and Bioinformatics Laboratory Course Code: PLS311

Teaching

Scheme

(Hrs/Week)


Examination Total


o 0 4 4 - - - - 50 - 50 100


Objectives

1 To study various stages of development in animals and plants

2 To understand queering and analyzing the proteomics and genomics data, and its use in the

finding the cause of disease and in the drug development

Sr.

No. Description

1 Introduction to scientific literature database at National Centre for Biotechnology

Information (NCBI) and querying the PUBMED literature database.

2 Getting the primary sequences of protein or DNA from protein database and querying the

protein/DNA sequence database.

3 Introduction of Basic local alignment search tool (BLAST).

4 Pairwise and multiple protein sequence analysis using the Clustal Omega.

5 Introduction of RCSB and querying, and analyzing the primary, secondary tertiary and

quaternary structure of protein using PyMol.

6 Three dimensional protein structure prediction using homology modeling technique.

7 Molecular docking of protein and ligand using AutoDock4.2 software.

8 Molecular dynamics simulation using GROMACS/AMBER.

9 Filter paper ring method for in vitro culturing of chick Embryo & observations.

10 Gross anatomy and histology of chick embryo upto 72 hrs. Brain, heart, lens, ear

development.

11 Drosophila development on live material: egg structure, egg laying and early development

in culture by phase contrast

12 Study of embryonic and post-embryonic development using frog egg as a model system.

13 Study of effect of ligature in Drosophila / House fly larva

14 Study the imaginal disc in Drosophila larva

15 Chick limb bud staining with neutral red for morphogenetic cell death

16 Study of grafting of Hensen’s node, or Regeneration of Hydra/Planaria

17 Study of anther development in angiosperms

18 Study of embryo development in angiosperms

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Term Work:

Term Work assessment shall be conducted for the Project, Tutorials and Seminar. Term work is

continuous assessment based on attendance, good laboratory practice (GPL), timely completion,

journal/record book, oral/viva, respectively. It should be assessed by course teacher of the institute. At

the end of the semester, the final grade for a term work shall be assigned based on the performance of

the student and is to be submitted to the University.

Notes

1 The regular attendance of the students during semester for practical course will be monitored and

marks will be given accordingly (10 Marks).

2 Good Laboratory Practices (10 Marks)

3 Timely Completion (10 Marks)

4 Journal / Record Book (10 Marks)

5 Oral / Viva (10 Marks)

Practical/Oral/Presentation:

Practical/Oral/Presentation shall be conducted and assessed jointly by at least a pair of examiners

appointed as internal and external examiners by the University. The examiners will prepare the

mark/grade sheet in the format as specified by the University, authenticate and seal it. Sealed envelope

shall be submitted to the head of the department or authorized person.

Notes

1 One experiment from the regular practical syllabus will be conducted (40 Marks).

2 Oral/Viva-voce (10 Marks).

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School of Science

M.Sc. Microbiology


Course: Research Methodology and Biostatistics and

Instrumentation Laboratory

Course Code: PLS312

Teaching

Scheme

(Hrs/Week)


Examination Total


0 0 4 2 - - - - 50 - 50 100

Max. Time, End Semester Exam (Theory) – 3 Hrs.

Objectives

1 To analyze the statistical data

2 To study the basic concepts of statistic and its application in data analysis

3 To get experience learning of handling of various lab instruments

4 To learn new techniques in the biology

Sr. No. Description

1 Measures of Central Tendency and Dispersion

2 Statistical Analysis using EXCEL. (Descriptive statistics and graphical presentation.

3 Sketching of pmf/pdf of Binomial, Poisson and Normal distributions.

4 Correlation and Regression Analysis

5 Simple random sampling and stratified sampling.

6 Hypotheses testing and confidence intervals.

7 Analysis of Variance.

8 Word processing.

9 UV spectrophotometer analysis

10 Centrifugation methods and its applications

11 Cell disintegration methods

12 Chromatography methods

13 Electrophoresis techniques

14 Microscopy methods and applications

15 Electrocardiograph analysis

16 Demo NMR and x-ray diffraction analysis

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Term Work:

Term Work assessment shall be conducted for the Project, Tutorials and Seminar. Term work is

continuous assessment based on Attendance, Good Laboratory Practice (GLP), Timely

Completion, Journal/Record book and Oral. It should be assessed by subject teacher of the

institute. At the end of the semester, the final grade for a Term Work shall be assigned based on

the performance of the student and is to be submitted to the University.

Notes

1 The regular attendance of the students during semester for practical course will be monitored and

marks will be given accordingly (10 Marks).

2 Good Laboratory Practices (10 Marks)

3 Timely Completion (10 Marks)

4 Journal / Record Book (10 Marks)

5 Oral / Viva (10 Marks)

Practical/Oral/Presentation:

Practical/Oral/Presentation shall be conducted and assessed jointly by at least a pair of examiners

appointed as internal and external examiners by the University. The examiners will prepare the

mark/grade sheet in the format as specified by the University, authenticate and seal it. Sealed envelope

shall be submitted to the head of the department or authorized person.

Notes

1 One experiment from the regular practical syllabus will be conducted (40 Marks).

2 Oral/Viva-voce (10 Marks).

Documents

Year: Second Year Semester: III Course: Developmental ......Molecular analysis using UV/visible, fluorescence, circular dichroism, NMR and ESR spectroscopy Molecular structure determination