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Cytogenetics

By Prof. Mahammad Niamat Ali   |   Centre of Research for Development (CORD), University of Kashmir
Learners enrolled: 499

Students embark on an exciting journey through the course Cytogenetics, a core paper for B.Sc. Medical Sciences under the Choice Based Credit System (CBCS). This course opens the gateway to understanding the intricate architecture of life at the cellular and chromosomal level. It takes learners from the historical foundations of cell theory to the modern frontiers of molecular cytogenetics, exploring how cells, genes, and chromosomes shape living organisms. Students will discover the organization of prokaryotic and eukaryotic cells, the structure of viruses and phages, and the unique roles of immune organs and cells. Key topics include mitosis, meiosis, linkage, crossing over, gene mapping, sex determination, chromosomal mutations, and cytogenetic techniques such as microscopy, flow cytometry, and FISH. The course also highlights the structural and functional organization of cell organelles, the dynamics of biomembranes, and cell signaling mechanisms that coordinate life processes. Learners will delve into chromatin organization, nuclear functions, and genome architecture, gaining insight into how genetic abnormalities lead to cancer, mitochondrial disorders, and developmental defects. Integrating classical cytogenetics with modern molecular biology, the course nurtures analytical thinking, laboratory competence, and scientific curiosity. By the end of this course, students are prepared to explore advanced studies and research in genetics, biotechnology, and biomedical sciences, contributing to a deeper understanding of life itself.

Indicative Program Alignments :
B.Sc.
Summary
Course Status : Upcoming
Course Type : Core
Language for course content : English
Duration : 12 weeks
Category :
  • Microbiology
Credit Points : 4
Level : Undergraduate
Start Date : 05 Jan 2026
End Date : 30 Apr 2026
Enrollment Ends : 28 Feb 2026
Exam Date :
Translation Languages : English
NCrF Level   : 5.0

Page Visits



Course layout

WEEK - I
1. Historical perspective of cells, cell theory and exceptions to cell theory 
2. A detail classification of cell types within an organism; cell, tissue, organ and organisms as different levels of organization.
3. Overview of prokaryotic and eukaryotic (plants and aimals) cells
4. Structure of viruses - general structure, properties of viral envelopes and enzymes (principles of virus taxonomy)

WEEK - II
5. General Characteristics and Biological Roles of Phages, Viroids, Mycoplasma, and Escherichia coli"
6. Structural and Functional Aspects of Immune Organs and Cells: Focus on Hematopoiesis, Adaptive and Innate Immune Components
7. Structural Features, Characteristics, and Functional Roles of Immune Cells and Organs: A Focus on Neutrophils, Eosinophils, Basophils, Mast Cells, and Dendritic Cells
8. Structure, properties and functions of the immune cells & organs - thymus and bone marrow; lymph nodes, spleen, MALT, GALT and SALT

WEEK - III
9. Chromosomal Dynamics and the Cytogenetic Basis of Mitosis and Meiosis
10. Principles of Linkage, Crossing Over, and Chromosomal Gene Mapping
11. Understanding Crossing Over: Cytological Basis and Gene Mapping Approaches
12. Chromosomal mechanisms and environmental factors determining sex (Barr bodies, dosage compensation)

WEEK - IV
13. Gametogenesis and fertilization: structure and production of gametes, zygote formation
14. Functional organization of the cell nucleus: chromatin movements, nuclear bodies and its significance.
15. Structural and Numerical Chromosomal Mutations: An Overview of Deletion, Duplication, Inversion, Translocation, Aneuploidy, and Polyploidy
16. Microscopy and its types: principles of light microscopy, phase contrast, confocal microscopy. Electron microscopy (EM) - scanning EM and scanning transmission EM (STEM), fluorescence microscopy

WEEK - V
17. Cytoochemical techniques: spectrophotometery: mass spectrometery, X-ray diffraction analysis. Flow cytometery: flurochromes, fluorescent probe and working principle
18. Principles and techniques of sub-cellular fractionation: Differential and Density Gradient Centrifugation
19. Cell fixation and staining: freeze-drying and free-substitution, microtomes  and embedding, chemical basis of staining, metachromasia
20. Human Karyotype Analysis: Banding Patterns, Nomenclature, and Genetic Syndromes from Chromosomal Number and Structure Variations

WEEK - VI
21. Human cytogenetics technique: Fluorescence In Situ Hybridization (FISH)
22. Chromatography: paper, TLC, gel-filtration 
23. Basic Principles and Characteristics of Cell Differentiation
24. Molecular Regulation of Cell Differentiation

WEEK - VII
25. Biomembranes: Composition and Properties of Components, the Fluid Mosaic Model, and Membrane Asymmetry
26. Selective permeability of the membranes, membrane transport, liposomes, freeze-etching and freeze fracture technique for membrane study.
27. Cell wall, extracellular matrix and cell interactions; Bacterial and eukaryotic cell wall; the extracellular matrix and cell matrix interactions; cell-cell interactions.
28. Membrane Permeability and Transport Mechanisms: Active Transport, Passive Transport, and Proton Pumps (Na⁺/K⁺, Ca²⁺-Calmodulin

WEEK - VIII
29. Phagocytosis, pinocytosis, exocytosis.
30. Nuclear structure and functions
31. Nuclear lamina, transport across nuclear envelope, Chromatin: molecular organization 
32. Nucleolus and rRNA processing.

WEEK - IX
33. Genome sequence and chromosome diversity, chromosome duplication and segregation, the nucleosome. 
34. Chromatin structure: euchroamtin, heterochromatin-constitutive and facultative heterochromatin
35. Regulation of Chromatin Dynamics, Nucleosome Assembly, and Chromosomal Organization
36. Human chromosomal abnormalities: aneuploidy, reciprocal translocations, sex chromosomal abnormalities and autosomal abnormalities.

WEEK - X
37. Structural organization, function and marker enzymes of mitochondria, mitochondrial biogenesis, protein import in mitochondria. Semiautonomous nature of mitochondria and chloroplast, chloroplast DNA, peroxisomes assembly.
38. Structure and functions of endoplasmic reticulum, Golgi apparatus, Mechanism of vesicular transport  and lysosomes
39. Mitochondria and chloroplast DNA (endosymbiotic hypothesis for the origin of mitochondria and chloroplasts)
40. Extra-chromosonal inheritance: chloroplast mutation/ variegation in four o’ clock plant and Chlymodonas.

WEEK - XI
41. Mitochondrial mutations, maternal effects and  ineffective heredity
42. Cytoskelton and cell movement
(Structure and organisation of actin filaments, actin, myosin and cell movement)
43. Structure and organization of intermediate filaments, microtubules and their role
44. Cell Signaling: Signaling Molecules, Receptors, and Functions of Cell Surface Receptors
45. Overview of the Eukaryotic Cell Cycle, Its Regulation, and Key Events in Mitosis, Meiosis, and Fertilization

WEEK - XII
46. Cancer Cell Characteristics and the Stages of Carcinogenesis: Initiation, Promotion, Progression, and Termination
47. Common chromosome abnormalities in cancer
48. Molecular Perspectives on the Development, Causes, and Treatment of Cancer
49. Maintenance of Adult Tissues by Stem Cells; Applications of Embryonic Stem Cells and Therapeutic Cloning
50. Cell Injury: Pathways of Reversible and Irreversible Damage, Necrosis, and Apoptosis

Books and references

Name of recommended books for Cytogenetics

 

1.          Cytogenomics by Thomas Liehr, Academic Press (Elsevier), 1st edition, 2021

2.          An Essential Guide to Cytogenetics by J. A. Tompkins and A. J. M. M. van den Oetelaar (Editors), Nova Science Publishers,1st edition, 2018

3.          Recent Trends in Cytogenetic Studies: Methodologies and Applications by Padma Tirunilai (Editor), Intech Open,1st edition, 2018

4.          Cytogenetics Past, Present and Further Perspectives by Marcelo L. Larramendy (Editor), Intech Open,1st edition, 2018

5.          Advanced Genetics by Gurbachan S. Miglani, Alpha Science International,1st edition, 2019

6.          Cytogenetics and Molecular Cytogenetics by Thomas Liehr, CRC Press (Taylor & Francis), 1st edition, 2022

7.          Cell and Molecular Biology by Gerald Karp, John Wiley and Sons, 9th edition, 2023

8.          Molecular Cell Biology by Lodish, Berk, Matsudaira, Kaiser, Kreiger, Scott, Zipursky, and DarnellW., H. Freeman (Macmillan Learning), 9th edition, 2021

9.          Cell and Molecular Biology by De Robertis and De Robertis, Wolters Kluwer (Lippincott Williams & Wilkins), 8th edition, 2010

10.        Genetics in Medicine (Strong cytogenetics coverage, especially chromosomal disorders) by Robert L. Nussbaum, Roderick R. McInnes, Huntington F. Willard Elsevier, 9th edition, 2023

 

Name of recommended Online Resources for Cytogenetics

 1.       Cytogenetics – Nature Scitable (Nature Education) Excellent introductory and advanced articles on classical and molecular cytogenetics, chromosome structure, banding, FISH, and cytogenomics:

https://www.nature.com/scitable/topicpage/cytogenetics-14/2ISCN 2020

 2.       Cytogenetics (ScienceDirect Topics) page: Useful textbook-style summary of cytogenetics including conventional methods and molecular extensions; gives quick definitions and context:

https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/cytogenetics

 3.       Molecular cytogenetics: Past, Present and Future” (review article) A good review of how classical cytogenetics has evolved with molecular methods — helpful for grasping the historical and methodological context:

https://pubmed.ncbi.nlm.nih.gov/11575843/

 4.       Cytogenetics - Encyclopaedia Britannica article: A clear, authoritative overview of cytogenetics, chromosomes, and chromosomal analysis — good for foundational understanding. Encyclopedia Britannica:

https://www.britannica.com/science/cytogenetics

 5.       Overview of Clinical Cytogenetics”-review article on PubMed         Outlines basic cytogenetic analysis, applications in prenatal/postnatal diagnosis, structural/ numerical abnormalities-important for understanding clinical relevance:

https://pubmed.ncbi.nlm.nih.gov/18428310

 6.       Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer          A comprehensive, freely accessible database linking chromosomal aberrations, gene fusions, and cancer-essential for cytogenetics + cancer genetics research:

https://pubmed.ncbi.nlm.nih.gov/27910033/

 7.       NCBI Bookshelf – Chromosome Abnormalities and Genetic Counseling (5th ed., 2019) Full textbook chapters available free (Gardner & Amor). Classic reference for constitutional cytogenetics:

https://www.ncbi.nlm.nih.gov/books/NBK115548

 8.       Coriell Institute – Cell and Molecular Biology Resources (includes cytogenetics protocols) Free protocols for karyotyping, FISH, chromosome breakage studies, and cell culture techniques used in research labs worldwide:

         https://www.coriell.org/research-services/cytogenetics

Instructor bio

Prof. Mahammad Niamat Ali

Centre of Research for Development (CORD), University of Kashmir

Prof. Mahammad Niamat Ali

Former Director: Centre of Research for Development (CORD) and Former Officer-in-charge: P. G. Programme in Microbiology, University of Kashmir, Srinagar-190006, J & K, India.

 Prof. Md. Niamat Ali is a senior academician, cytogeneticist, and molecular biologist with more than three decades of experience in teaching, research, and academic leadership. He specializes in cytogenetics, molecular biology, human genetics and toxicogenomics, and he has contributed profoundly to higher education and interdisciplinary biological research in India through 30 years of university-level teaching—7 at Aligarh Muslim University and 24 at the University of Kashmir—and 32 years of active research. He mentored 8 awarded M.Phil., 21 awarded and 2 submitted Ph. Ds, with 6 ongoing, in cytogenetics, molecular biology, toxicogenomics, insect genetics, environmental mutagenesis and DNA barcoding. His work is bolstered by administrative roles, resource person engagements, consultancy projects, and national academic responsibilities. He has earned 5500 citations, an h-index of 35, an i10-index of 120, and a cumulative impact factor over 250. Academically, he holds a B.Sc. (Hons.) and M.Sc. in Zoology with specialization in Cytogenetics and Molecular Biology from the University of Burdwan, West Bengal. He pursued M.Phil. and Ph.D. in Zoology from Aligarh Muslim University, focusing on cytogenetics and molecular biology. This foundation underpinned his expertise in genetic research, molecular diagnostics, environmental toxicology, and genomics. He has laboratory proficiency in PCR technologies, chromosomal analysis, FISH, gene expression, and molecular profiling. Currently, he leads a RUSA-funded major researchproject on morphological and molecular profiling via DNA barcoding of Coccinellidae and Syrphidae species for pest management in Kashmir. He also directs CORD consultancy for environmental impact assessments and conservation. A proponent of digital education, he coordinated MHRD-SWAYAM-MOOCs including Basic Human Genetics (2021, 2 credits, 25 modules, 2331 learners), Cytogenetics (2018, 4 credits, 50 modules, 563+ learners), and an updated Cytogenetics (July 2025, 4 credits, 1034 learners). He reviewed 35 video modules for EMMRC. Consultancy highlights include establishing the Conservation Science and Innovation Laboratory (COSI Lab) with CSIR-CCMB, AIC-CCMB, and IKP Knowledge Park via 1.85 crore REC Foundation CSR. He led a Environmental Impact Assessment for houseboat relocation at Doledem Dal Lake, showcasing aquatic toxicology and ecological risk assessment. He is honored with CSIR Pool Officer and Research Associate positions, ICAR SRF, UGC JRF, West Bengal National Merit Scholarship, and Dr. Navin Chandra Award for top B.Sc. (Hons.) marks. He attended over 20 national workshops at institutions like Tata Memorial Centre, AIIMS, NDRI, and RGCB. He gained skills in molecular biology, DNA barcoding, stem cells, microscopy, tissue culture, diagnostics, and bioinformatics. He holds a one-year Diploma in Statistics from AMU for biostatistics expertise. He delivered 10 invited talks and 15 presentations. He organized workshops, seminars, and training on DNA isolation, qPCR, microbiology, biodiversity, environmental pollution, microbiome, wildlife reproduction, and conservation in collaboration with CCMB and IKP. He published 112 peer-reviewed papers in journals like Environmental Chemistry Letters, Journal of Clinical Medicine, Chromosoma, International Immunopharmacology, Drug and Chemical Toxicology, Microbial Pathogenesis, Mutation Research, and Chemosphere (impact factors 0.5 – 20.40), plus 10 chapters and 3 books. Administratively, he served on roster, pre-BORS, and DRC committees. He was Vice-Chancellor’s nominee for selection committee and inquiries. He evaluated DST R&D projects for Jammu and Kashmir Government. He handled faculty recruitment and oversight. His expertise covers cytogenetics, molecular biology, toxicogenomics, human genomics, proteomics, stem cell biology, regenerative medicine, radiation biology, gene therapy, cell culture, biostatistics, and bioinformatics. He holds life memberships in the Indian Science Congress Association and Environmental Mutagen Society of India. His career marks enduring scholarly excellence, mentorship, and institutional advancement in biological sciences and higher education in India.

Course certificate

1. End-Term Examination:
Weightage: 70% of the final result
 Minimum Passing Criteria: 40%
2. Internal Assessment:
 Weightage: 30% of the final result
 Minimum Passing Criteria: 40%
Calculation of IA Marks:
Out of all graded weekly Assessments/Assignments, the top 50% of Assignments shall be considered for the calculation of the final Internal Assessment marks.
All students who obtain 40% marks in the internal Assessment and 40% marks in the end-term proctored exam separately will be eligible for the SWAYAM Credit Certificate.
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