Friday, September 14, 2012

CELL DISRUPTION


CELL DISRUPTION
Introduction
Biological products synthesized by fermentation or cell culture are either intracellular or extracellular. Intracellular products either occur in a soluble form in the cytoplasm or are produced as inclusion bodies (fine particles deposited within the cells). Examples of intracellular products include recombinant insulin and recombinant growth factors. A large number of recombinant products are found as inclusion bodies in order to accumulate in larger quantities within the cells. In order to obtain intracellular products the cells first have to be disrupted to release these into a liquid medium before further separation can be carried out. Certain biological products have to be extracted from tissues, an example being porcine insulin which is obtained from pig pancreas. In order to obtain such a tissue­ derived substance, the source tissue first needs to be homogenized or ground into a cellular suspension and the cells are then subjected to cell disruption to release the product into a solution. In the manufacturing process for intracellular products, the cells are usually first separated from the culture liquid medium. This is done in order to reduce the amount of impurity: particularly secreted extracellular substances and unutilized media components. In many cases the cell suspensions are thickened or concentrated by microfiltration or centrifugation in order to reduce the process volume.
Several factors must be considered.

Volume or sample size of cells to be disrupted

If only a few microliters of sample are available, care must be taken to minimize loss and to avoid cross-contamination.
Disruption of cells, when hundreds or even thousands of liters of material are being processed in a production environment, presents a different challenge. Throughput, efficiency, and reproducibility are key factors.

How many different samples need to be disrupted at one time?

Frequently when sample sizes are small, there are many samples. As sample sizes increase, fewer samples are usually processed. Issues are sample cross contamination, speed of processing, and equipment cleaning.

How easily are the cells disrupted?

As the difficulty of disruption increases (e.g. E. coli), more force is required to efficiently disrupt the cells. For even more difficult samples (e.g. yeast), there is a parallel increase in the processor power and cost. The most difficult samples (e.g. spores) require mechanical forces combined with chemical or enzymatic efforts, often with limited disruption efficiency.

What efficiency of disruption is required?

Over-disruption may impact the desired product. For example, if subcellular fractionation studies are undertaken, it is often more important to have intact subcellular components, while sacrificing disruption efficiency.
For production scale processes, the time to disrupt the cells and the reproducibility of the method become more important factors.

How stable is the molecule(s) or component that needs to be isolated?

In general, the cell disruption method is closely matched with the material that is desired from the cell studies. It is usually necessary to establish the minimum force of the disruption method that will yield the best product. Additionally, once the cells are disrupted, it is often essential to protect the desired product from normal biological processes (e.g. proteases) and from oxidation or other chemical events.

What purification methods will be used following cell disruption?

It is rare that a cell disruption process produces a directly usable material; in almost all cases, subsequent purification events are necessary. Thus, when the cells are disrupted, it is important to consider what components are present in the disruption media so that efficient purification is not impeded.

Is the sample being subjected to the method biohazardous?

Preparation of cell-free extracts of pathogens presents unique difficulties. Mechanical disruption techniques are not always applicable owing to potential biohazard problems associated with contamination of equipment and generation of aerosols.
Cells
Different types of cell need to be disrupted in the bio­industry:
·         Gram positive bacterial cells
·         Gram negative bacterial cells
·         Yeast cell
·         Mould cells
·         Cultured mammalian cells
·         Cultured plant cells
·         Ground tissue
Bacterial cells: The cell wall of Gram positive bacteria is thick and mainly composed of thick layer of peptidoglycan layer. While the plasma or cell membrane which is made up of phospholipids and proteins is relatively fragile. In certain cases polysaccharide capsules may be present outside the cell wall. The cell wall of gram positive bacteria is particularly susceptible to lysis by the antibacterial enzyme, lysozyme. Unlike gram positive bacteria, gram negative bacteria do not have distinct cell walls but instead have multi­layered envelops. The peptidoglycan layer is significantly thinner than in gram positive bacteria. An external layer composed of lipopolysaccharides and proteins is usually present. Another difference with gram positive bacteria is the presence of the periplasm layers which are two liquid filled gaps, one between the plasma membrane and the peptidoglycan layer and the other between the peptidoglycan layer and the external lipopolysaccharides. Periplasmic layers also exits in gram positive bacteria but these are significantly thinner than those in gram negative bacteria. The periplasm is important in bioprocessing since a large number of proteins, particularly recombinant proteins are secreted into it. An elegant way to recover the periplasmic proteins is by the use of osmotic shock. This technique is discussed below.
Yeast/Mould cells: Yeasts which are unicellular have thick cell walls, typically 0.1 to 0.2 microns in thickness. These are mainly composed of polysaccharides such as glucans, mannans and chitins. The plasma membrane in a yeast cell is composed of phospholipids and lipoproteins. Mould cells are largely similar to yeast cells in terms of cell wall and plasma membrane composition but are multicellular and filamentous.
Mammalian cells: Mammalian cells do not possess the cell wall and are hence quite fragile i.e. easy to disrupt.
Plant cells: Plant cells on the other hand have very thick cell walls mainly composed of cellulose and other polysaccharides. Cell wall wherever present is the main barrier which needs to be disrupted to recover intracellular products. A range of mechanical methods can be used to disrupt the cell wall. Chemical methods when used for cell disruption are based on specific targeting of key cell wall components. For instance, lysozyme is used to disrupt the cell wall of gram positive bacteria since it degrades peptidoglycan which is a key cell wall constituent. In gram negative bacteria, the peptidoglycan layer is less susceptible to lysis by lysozyme since it is shielded by a layer composed of lipopolysaccharides and proteins.
Cell membranes: Cell membranes or plasma membranes are composed of phospholipids arranged in the form of a bi­layer with the hydrophilic groups of the phospholipids molecules facing outside (Figure below). The hydrophobic residues remain inside the cell membrane where they are shielded from the aqueous environment present both within and outside the cell. The plasma membrane can be easily destabilized by detergents, acid, alkali and organic solvents. The plasma membrane is also quite fragile when compared to the cell wall and can easily be disrupted using osmotic shock i.e. by suddenly changing the osmotic pressure across the membrane. This can be achieved simply by transferring the cell from isotonic medium to distilled water.
Figure 1: Plasma membrane
Cell disruption methods can be classified into two categories: Mechanical methods and Non-mechanical methods.
A. Mechanical Methods of Cell Disruption:  uses mechanical forces to disintegrate the cells like soli shearing, liquid shearing, pressure etc. Some methods are:
1.                  Disruption in bead mill
2.                  Disruption using a rotor­ stator mill
3.                  Homogenization
4.                  Disruption using French press
5.                  Disruption using ultrasonic vibrations
B. Non-mechanical Methods of Cell Disruption: includes physical, chemical and biological treatment of cells to disrupt the cells.
1.      Physical methods
a.       Disruption using osmotic shock
b.      Freeze-thaw method
2.      Chemical methods
a.       Detergents
b.      Solvents
c.       Acid and alkali methods
3.      Biological methods
a.       Enzymes e.g. lysozyme
b.      Phage
c.       Autolysis

The mechanical methods are targeted more towards cell wall disruption while the non-mechanical methods are mainly used for destabilizing the cell membrane.
A. Mechanical methods for cell disruption
1. Cell disruption using bead mill
Bead mill equipment consists of a tubular vessel made of metal or thick glass within which the cell suspension is placed along with small metal or glass beads. The tubular vessel is then rotated about its axis and as a result of this the beads start rolling away from the direction of the vessel rotation. At higher rotation speeds, some the beads move up along with the curved wall of the vessel and then cascade back on the mass of beads and cells below. The cell disruption takes place due to the grinding action of the rolling beads as well as the impact resulting from the cascading beads.
Figure 2: Cell disruption by Bead Milling
Bead milling can generate enormous amounts of heat. While processing thermolabile material, the milling can be carried out at low temperatures, i.e. by adding a little liquid nitrogen into the vessel. This is referred to as cryogenic bead milling. An alternative approach is to use glycol cooled equipment. A bead mill can be operated in a batch mode or in a continuous mode and is commonly used for disrupting yeast cells and for grinding animal tissue. Using a small scale unit operated in a continuous mode, a few kilograms of yeast cells can be disrupted per hour. Larger unit can handle hundreds of kilograms of cells per hour.
Disadvantages:
  • Occasional problems with foaming and sample heating, especially for larger samples.
  • Tough tissue samples such as skin or seeds are difficult to disrupt unless the sample is very small or has been pre-chopped into small pieces.

2. Cell disruption using rotor­-stator mill
A rotor­-stator mill device consists of a stationary block with a tapered cavity called the stator and a truncated cone shaped rotating object called the rotor. Typical rotation speeds are in the 10,000 to 50,000 rpm range. The cell suspension is fed into the tiny gap between the rotating rotor and the fixed stator. The feed is drawn in due to the rotation and expelled through the outlet due to centrifugal action. The high rate of shear generated in the space between the rotor and the stator as well as the turbulence thus generated are responsible for cell disruption. These mills are more commonly used for disruption of plant and animal tissues based material and are operated in the multi­pass mode, i.e. the disrupted material is sent back into the device for more complete disruption. The cell disruption caused within the rotor­-stator mill can be described using the equations discussed for a bead mill.
Figure 3: Cell disruption using rotor-stator mill
3. Homogenization
Liquid based homogenization is the most widely used cell disruption technique for small volumes and cultured cells. Cells are lysed by forcing the cell or tissue suspension through a narrow space known as clearance space (0.001 mm- 0.006 mm), thereby shearing the cell membranes. Three different types of homogenizers are in common use. A Dounce homogenizer consists of a round glass pestle that is manually driven into a glass tube. A Potter-Elvehjem homogenizer consists of a manually or mechanically driven Teflon pestle shaped to fit a rounded or conical vessel. The number of strokes and the speed at which the strokes are administered influences the effectiveness of Dounce and Potter-Elvehjem homogenization methods. Both homogenizers can be obtained in a variety of sizes to accommodate a range of volumes.
Figure 4: Cell disruption using homogenizer
4. Cell disruption using French press
A French press is a device commonly used for small ­scale recovery of intracellular proteins and DNA from bacterial and plant cells. The device consists of a cylinder fitted with a plunger which is connected to a hydraulic press. The cell suspension is placed within the cylinder and pressurized using the plunger. The cylinder is provided with an orifice through which the suspension emerges at very high velocity in the form of a fine jet. The cell disruption takes place primarily due to the high shear rates and differential pressure. The internal FRENCH Pressure Cell pressure increases as the pressure developed by the Laboratory Press increases. The intracellular pressure increases as well. As the sample is dispensed through the sample outlet tube, the external pressure on the cell wall drops rapidly toward atmospheric pressure. The pressure within the cell drops as well but not as quickly as the pressure external to the cell. This pressure differential causes the cell wall membrane to burst, releasing the intra-cellular contents. A French press is frequently provided with an impact plate, where the jet impinges causing further cell disruption. Typical volumes handled by such devices range from a few milliliters to a few hundred milliliters. Typical operating pressure ranges from 10,000 to 50,000 psi.
Advantages:
  This technique results in more uniform and complete disruption
  Cells do not require pre-treating.
  Easy to use

Figure 5: Cell disruption using French press
5. Cell disruption using ultrasonic vibrations
Ultrasonic vibrations (i.e. having frequency greater than 18 kHz) can be used to disrupt cells. The cells are subjected to ultrasonic vibrations by introducing an ultrasonic vibration emitting tip into the cell suspension (Figure below). Ultrasound emitting tips of various sizes are available and these are selected based on the volume of sample being processed. The ultrasonic vibration could be emitted continuously or in the form of short pulses. A frequency of 25 kHz is commonly used for cell disruption. The duration of ultrasound needed depends on the cell type, the sample size and the cell concentration. These high frequency vibrations cause cavitations, i.e. the formation of tiny bubbles within the liquid medium. When these bubbles reach resonance size, they collapse releasing mechanical energy in the form of shock waves equivalent to several thousand atmospheres of pressure. The shock waves disrupt cells present in suspension. For bacterial cells such as E. coli, 30 to 60 seconds may be sufficient for small samples. For yeast cells, this duration could be anything from 2 to 10 minutes.
Ultrasonic vibration is frequently used in conjunction with chemical cell disruption methods. In such cases the barriers around the cells are first weakened by exposing them to small amounts of enzymes or detergents. Using this approach, the amount of energy needed for cell disruption is significantly reduced.
Disadvantages:
  • Heat generated by the ultrasound process must be dissipated.
  • High noise levels (most systems require hearing protection and sonic enclosures)
  • Yield variability
  • Free radicals are generated that can react with other molecules.

Figure 6: Cell disruption by sonication

6. Mortar and Pestle
It is a manual grinding method, most commonly used to disrupt plant cells. In this method, tissue is frozen in liquid nitrogen and then crushed using a mortar and pestle. Because of tensile strength of the cellulose and other polysaccharides comprising the cell wall, this method is the fastest and most efficient way to access plant protein and DNA.

Thursday, September 6, 2012

M.Sc. Microbiology First Year Course Syllabus


Syllabus for M. Sc. Microbiology

Master of Science in Microbiology
(M. Sc. Microbiology)

Revised Curriculum



Effective from 2009



Office of the Dean
Institute of Science and Technology
Tribhuvan University
Kathmandu, Nepal




Introduction
The M.Sc. Microbiology program was started in Nepal for the first time by Tribhuban University in 1990 at the Central Department of Microbiology, Tribhuvan University, Kirtipur. The course structure of the initial programme was entirely changed in 1999. However, no revisions were made in the curriculum for many years. Therefore, the present revision on existing course that was introduced in 1999 is targeted to make the program more competitive and research oriented. The main objective the present revision is to upgrade and update the existing curriculum of M.Sc. Microbiology of Tribhuvan University to the level of top class international Universities offering similar courses in microbiology.

Objectives
The objective of the revised curriculum is to produce quality microbiologists as per national and international demand. It is expected that after completion of the course:
1.      The Master’s degree holders will be qualified to get admission in Ph.D. in medical and molecular virology, microbiology, immunology, microbial biochemistry and related programs offered by top class universities of the world.
2.      The Master’s degree holders will be able to work as highly specialized microbiologist and research scientist in monitoring, identifying and helping to control infectious diseases.
3.      The Master’s degree holders will be able to use skills of modern molecular biology techniques to develop and test new, bioactive compounds, biomolecules and medicines required to treat emerging infectious diseases and they will be able to study and discover the measures to control drug resistant problems in microorganisms, will be eligible to work as qualified scientist for investigating the potential uses of microorganisms to produce antibiotics, antibodies, steroids, vaccines, hormones and other produce of microbial origin.
4.      The Master’s degree holders will be eligible to work as qualified researchers and scientists in the institutions related to food production, crop protection and soil fertility.
5.      The Master’s degree holders will be eligible to be the lectures of microbiology in universities or teaching hospitals for teaching, monitoring and supervising bachelors and masters level microbiology students.

Course Structure
Entire course is divided into two academic years. The first year course covers disciplines of General microbiology, Immunology, Microbial biochemistry, Epidemiology, Microbial biotechnology, Pharmaceutical microbiology and Practical on this course. In the second year, there are four different optional courses each carrying 450 marks. Though there are four different optional groups to choose, subject committee can offer at least two groups or more in a year depending upon the facilities available at the campus/department.

M. Sc. First Year
Course No.
Course Title
Full Marks
Pass Marks
MB 511
Microbiology Structure Physiology and Genetics
100
40
MB 512
Immunology
100
40
MB 513
Biochemistry and Instrumentation
100
40
MB 514
Microbial Biotechnology and Pharmaceutical Microbiology
100
40
MB 515
Epidemiology, Research methods and Biostatistics
100
40
MB 516
Practical Course on ((MB 511+ MB 512)
50
20
MB 517
Practical Course on ((MB 513+ MB 514)
50
20
Total
550

M. Sc. II Year
Course No.
Course Title
Full marks
Pass Marks
Optional Course I: Environmental and Public Health Microbiology
MB 611
Applied Environmental Microbiology
100
40
MB 612
Public Health Microbiology
100
40
MB 613
Systematic Microbiology
50
20
MB 614
Practical Course on MB 611, MB 612 and MB 613
100
40
MB 615
dissertation
100
40
Total
450

Course No.
Course Title
Full marks
Pass Marks
Optional Course II: Medical Microbiology
MB 621
Bacteriology
100
40
MB 622
Virology, Mycology and Parasitology
100
40
MB 623
Human Anatomy and Physiology
50
20
MB 624
Practical Course on MB 621, MB 622 and MB 623
100
40
MB 625
Dissertation
100
40
Total
450

Course No.
Course Title
Full marks
Pass Marks
Optional Course III: Food Microbiology
MB 631
General Food Microbiology
100
40
MB 632
Applied Food Microbiology and Biotechnology
100
40
MB 633
Food Sanitation and Quality Control
50
20
MB 634
Practical Course on MB 631, MB 632and  MB 633
100
40
MB 635
Dissertation
100
40
Total
450

Course No.
Course Title
Full marks
Pass Marks
Optional Course IV: Agricultural Microbiology
MB 641
Soil Microbiology
100
40
MB 642
Plant Microbiology
100
40
MB 643
Soil Fertility and Fertilizers
50
20
MB644
Practical Course on MB 641, MB 642 and MB 643
100
40
MB 645
Dissertation
100
40
Total
450

Eligibility and Admission Procedures
Candidates having a Bachelor’s Degree in Microbiology form Tribhunan University or equivalent degree recognized by Tribhuvan University are eligible to apply for M. Sc. Microbiology program. Each applicant should appear and pass entrance examination conducted by the Central Department of Microbiology. The enrollment will be based on merit. The candidates failed to get minimum qualifying marks/pass marks in the entrance examination will not be enrolled in the program.
Hours of Instruction
a)      Working days: 180 days in a academic year
b)      Class hour:
a.       Theory: One Theory paper of 100 marks should have 4 hours of lecture per week.
b.      Practical: The practical course for MB 516 should have 4 hours per day, (3 days a week) and for MB 517 should have 4 hours per day, (3 days a week).
c)      Attendance: 70 percent attendance in the class is compulsory
d)     Language of Instruction: English

Examination and Evaluation
The students should appear in final examination of four hours for each theoretical course carrying 100 full marks and two hours examination for the course each carrying 50 full marks. Twelve hour long practical examination (2days -6+6 hrs) will be conducted for 100 marks practical course and 8 hours (2 days-4+4 hrs) practical examination will be conducted for 50 marks practical course.
The students will have to pass each level and each course numbers separately. The minimum pass marks is 40 percent, both for theory and practical.
A student having passed his/her two years of study will be graded on the basis of the two-year’s aggregate marks as follows:
75 percent and above      Distinction
60 percent and above      First Division
50 percent and above      Second Division
40 percent and above      Third Division

             
 For 1st Year

Microbial Structure, Physiology and Genetics
Course Title: Microbial Structure, Physiology and Genetics
Course No. MB 511
Nature of Course: Theory
Full Marks: 100
Pass Marks: 40
Year: 1
Objectives
Upon the completion of the course students will have advanced knowledge on
·                     Bacterial and viral taxonomy
·                     The microbial genetics and application
·                     Structure and physiology of bacteria, virus and fungi
·                     Growth and recovery of bacteria and bacteriophage.
Microbial Structure and Physiology
Bacterial Classification
History, Fundamental and new approaches to bacterial taxonomy and nomenclature, Bacterial phylogeny, Characteristic of major families of bacteria ( Gram positive, Gram negative, Mycobacteria, Actinomyctes, Rickettsia, Chlamydia, Mycoplasma)                                                                                                                   14 hrs
Molecular Structure and Composition of Bacterial Cell
Structure, physiology and function of bacterial Cell wall, Cell membrane, Capsule, Spore, Flagella, pili, Ribosome and other cellular structures                                                                10 hrs
BacterialGrowth                                                                                                                              Growth in individual cell, Batch and Continuous growth, Kinetics of bacterial growth, growth curve, Synchronization Procedures, Measurement of bacterial growth                                                                                                                               6 hrs
 Bacterial Metabolism 
Transport mechanism of nutrients, Respiration and fermentation, Major energy yielding pathways and their significance, Electron transport chain, Oxidative and substrate level phosphorylation, Different types of fermentative pathways                                                                                                                               12hrs                                                                           
Fungi: Structure and Physiology
Classification, Morphological and growth characteristics, Reproduction and life cycle of Yeast and Mold                                                                                                                                       8 hrs
Viruses: Structure, Classification and Replication
Structure of viruses, Classification schemes of bactriophages and virus, Replication, Enumeration, Culture and recovery of Viruses                                                                 10 hrs

Microbial Genetics
Overview
Molecular Structure and Function of DNA and RNA of Prokaryotic and Eukaryotic Cells                                                                                                                                         2 hrs
DNA Transfer in Prokaryote
Types and Function of Plasmids, Recombination (Homologous and Non-homologous), Transformation, Transduction (Generalized and Specialized), Conjugations, Genetic mapping                                                                                                                                            8 hrs
DNA Replication
Molecular mechanism of DNA Replication in prokaryotic and eukaryotic cells, Enzymes involved in DNA replication: Topoisomerases, Helicases, DNA polymerases; Proofreading, post-replicational modification of DNA                                                                                       8 hrs
Transcription
Role of RNA in transcription, Mechanism of RNA Synthesis, Initiation and Termination of Transcription, Post transcription modification of RNA                                                    5hrs  
Protein Biosynthesis
Role of RNA in protein biosynthesis, Translation of the genetic code, Steps involve in translation (Initiation, Elongation and Termination)                                                                                      8 hrs
Regulation of the Gene Expression
Mechanism of Lac-operon and trp Operon: Gene expression in Eukaryotic cells                 6hrs 
 Mutations
Types of Mutation, Mutagenic agents: Physical, Chemical and Biological, Detection of Mutants                                                                                                                                   8 hrs 
Recombinant DNA Technology
Principle, procedures and mechanism of gene cloning, Formation of the Recombinant DNA, Cloning vectors, Expression vectors, Detection of the recombinant DNA, Cloning of eukaryotic genes in bacteria                                                                                                                            8 hrs 
Molecular techniques
Extrication and purification of plasmid and chromosomal DNA and RNA, Principle, procedures and applications of PCR based techniques and blotting techniques in microbiology: Plasmid Profiling, PCR, Real time PCR, RFLP, DNA Finger Printing, Western blotting, Southern blotting and Northern blotting, Gene Sequence.                                                                        7 hrs

Textbooks
1.      Madigan MT, Martinko JM and Parker j. Brock’s Biology of Microorganisms, 10th Edition, Prentice-Hall International (2004).
2.      Prescott LM, Haley JP and Klein DAMicrobiology, 7th Edition (International Edition) McGraw Hill (2005).
3.      Lewin B. Genes IX, Oxford University Press and Cell Press (2007)
4.      Sambrook J and Russell DW. Molecular Cloning: A laboratory Manual, (Vol I, II & III) 3rd Edition, Could Spring Harbor laboratory Press (2001).
5.      Bergey’s Manual of Systematic Bacteriology, Volume I (2001), Volume 2 (2005), Volume 3 (2009), Volume 4 (2009), Volume 5 (2009)




Immunology
Course title: Immunology
Course No.: MB 512
Nature of Course: Theory
Full Marks: 100
Pass Marking: 40
Year: I
Objectives
Upon completion of the course, students will be able to
·                     Understand basic immunology
·                     Understand current immunological techniques and assays
·                     Be familiar with immunopathology of viral, bacterial, parasite, autoimmune, tumor and fungal diseases
·                     Be able to search, study, comprehend and apply information gathered in current immunological journals/publications
Overview of Immunology                                                                                                       2 hrs
Introduction to Immunology and Serology                                          
Cells and Tissues of the Immune System; Primary & Secondary Lymph Organs                  12 hrs 
Innate immunity
Development and function, Non-specific Defense against the Microbial Infections. Physical and Anatomical Barriers, Cells and Secretary Molecular serum component, Phagocytosis                                                                                                                           5 hrs
Complements
Mechanism and significance of classical and alternative pathways of complement system                                                                                                                                     5 hrs
Antigens
Types and properties; Conditions of the antigenicity                                                             2 hrs
Antibodies and immunoglobulins
Molecular structure, Classes, Subclasses, Types, Subtypes, Genetic Basis of the Diversity                                                                                                                                 10 hrs
Antigen-antibody Reactions
Principle of Antigen-Antibody reactions in vitro
Precipitation: Types, principle, procedures and applications
Agglutination: Types, principle, procedures and applications
Immunochemical methods: Antibodies Labeling Methods
Immunofluorescence assay, ELISA
Radioimmuno assay
Immunoelecrophoresis and Immuno Blotting Methods                                                         20 hrs
Cells and Tissues of Adaptive Immunity
Types, development and function, MHC, antigen processing, presentation and receptors                                                                                                                                  5 hrs
Cell Mediated Immunity
T cell development, activation, effectors mechanisms; B cell activation, Antibody production, immunological tolerance, Assays used to measure CMI                                                         15 hrs

Humeral Immune Responses
Effectors Mechanisms; Cell Signaling: Intra & Extra- cellular mediators and pathways, Cytokines; TLR                                                                                                                 10 hrs
Immune Disorder
Hypersensitivity, Autoimmunity & Allergy; congenital & Acquired Immunodeficiencies                                                                                                                8 hrs
Diagnostic Immunology
Concept of Immunopathology and Immunodiagnostic tests, their development and use in diagnosis of infectious and non-infectious disease (Cover at least one example from each group: Bacterial, Viral, Fungal, Parasitic, Tumor and Allergy)                                                                                                                            15 hrs
Vaccines
History of vaccine and vaccination, Types of vaccines-killed organism as a vaccine, attenuated vaccine, methods of attenuation, experimental; vaccines, Overview of vaccine production techniques, Quality and Efficacy, Adverse events following immunization, Recent Developments and Prospects                                                                                                                      15 hrs
 Textbooks
1.      Roitt IM and Delves PJ. Roitt’s Essential immunology, 10th Edition, ELBS, Blackwell Scientific Publication (2001)
2.      Kindt TJ, Goldsby RA, Osborne  BA. Kuby Immunology, 6th Edition, W.H. Freeman (2006).
3.      Abbas AK, Lichtman AH, and Pillai S. Cellular and MolecularImmunology, 6th Edition, Elsevier (2007)
4.      Abbas AK and Lichtman AH. Basic Immunology: Functions andDisorders of the Immune System, 3rd Edition, WB Saunders Co (2008)


  
Biochemistry and Instrumentation
Course Title: Biochemistry and Instrumentation
Course No: MB 513
Nature of Course: Theory
Full Marks: 100
Pass Marks: 40
Year: I
Objectives
Upon completion of the course, students will have
·                     Advanced knowledge on general and microbial biochemistry
·                     Advanced knowledge on principle and procedures of various biochemical techniques and instrumentation required for conducting analysis and research.
Overview of Principles of Biochemistry, Bio-molecules                                                       2 hrs
Carbohydrates
Classification, Structures and Biological functions of Carbohydrates and Glycoprotein                                                                                                                           6 hrs
Amino Acids and Proteins
Classification, Structure and Biological function: Amino acids, Protein, Peptides and Polypeptides, Methods for characteristization and Purification of Proteins                                                                                                                                   3 hrs
Lipids and Fatty Acids
Biological role of lipids. General properties, distribution, classification and nomenclature of lipids, Structure and properties of neutral fats and phospholipids, Glycolipids, steroid, Structure components of lipids: Hydrophilic components, Fatty acids with even and odd number of carbon atoms saturated and unsaturated fatty acids, Fatty alcohols , glycerol, diols, inositol, carbohydrate component, amino alcohol / sphingozine / amino acids / phosphates, sulfates. Neutral lipids, Ethers, Steroid derivatives, Fatty acids and their role in lipid metabolism                                                                                                                              6 hrs
Enzymes: Kinetics and Regulation
Nomenclature and principle of enzyme classification, Henri equation, Michaelis-Menten equation; kinetics of enzymatic reaction involving two substrates, Factors affecting enzymatic activity and kinetics, Mechanisms of enzymes catalysis; Structure and mechanisms of lysozyme; serine proteases and glutathione redcutase, immobilized enzymes. Allosteric regulation, rate limiting enzymes, Isozymes and their role, Enzymes of microbial origin and their applications                                                                                                                             8 hrs
Biological Membrane
Biological function, Structure and properties of membrane lipids, Formation of artificial membrane and their applications. Dynamic properties of membrane lipids. Classification, characteristics and distribution of membrane proteins, extraction and isolation of membrane proteins, movements of main proteins and lipids, Asymmetry of membrane, Factors influencing on membrane fluidity                                                                                                                       3 hrs  
                                                                                                                                     
                                                      
Vitamins and Coenzymes
Role of vitamins, metals and other cofactors in enzyme functions. Types, properties and classification of Vitamins: Water-soluble vitamins and their coenzymes, Lipid-soluble vitamins, Iron containing coenzymes and metal cofactors.                                                                                                                                8 hrs
Nucleic Acids
Structure of nucleic acids, Purines and Pyridines base, Carbohydrate components, Mononucleotides, Nucleoside: mono, di-and tri-phosphates, DNA and RNA, their localization in cell                                                                                                                                                    2 hrs
Metabolism of carbohydrates
Interconversion of carbohydrates. Coenzymatic functions of nucleotides (eg. UTP, UDP). Anaerobic and aerobic degradation of carbohydrates. Differenent types of fermentation. Glycolysis. Oxidative phosphorylation in the level of substrate, Glyconeogenesis Oxidative decarboxylation  of pyruvic acid, Pyruvate dehydrogenase complex, Cycle of di-and tri-carbonic acids and their biological role, Terminal processes of oxidation. Electron transport system, Energetic significance of cascade process of electron transport from substrate to oxygen. Oxidative phosphorylation of respiratory chain, concept of conjugated oxidation and phosphorylation in respiratory chain, transmembrane potential of hydrogen ions, energetic effect of glycolysis and respiration. Gluconeogenesis: substrates of gluconeogenesis (lactate, pyruvate and other c3 compounds, acetate, glyoxylate)                                                                            6 hrs 
                                                                                                             
Metabolism of Amino acids and Proteins
Enzymatic hydrolysis of proteins, proteolytic enzymes. Degradation of amino acids, Transamination and its mechanism, various types of deamination, urea cycle, Link between urea cycle and Krebs’s cycle. Metabolism of Ammonia. Deamination and carboxylation of amino acids, amines and their physiological role, Proteineous nitrogenous substances: biosynthesis, degradation and biological function                                                                                                                                   6 hrs
Metabolism of Lipids
Enzymatic degradation of triglycerols and absorption by cell membrane. Oxidation of fatty acids, b-oxidation mechanism of fatty acids, biosynthesis of neutral fats, phospholipids and cholesterol                                                                                                                               8 hrs
Nucleic Acids Metabolism
Mechanism of biosynthesis of nucleosides and degradation of nucleotides                          4 hrs 
United system of Process of Metabolism
Integrated system of metabolism of proteins, carbohydrates and lipids                                2hrs
Hormones
General Characteristics, Classification, Mechanism of action                                                4 hrs

Instrumentation
Biochemical Techniques
General principle and approaches to biochemical investigations, In Vivo / in vitro studies physiological solutions, Tissues homogenization and separation                                              3 hrs
Cell disruption
Methods of tissues and cells, Protein purification: Background factors, protein extraction, preliminary fractionation procedures, chromatographic and electrophoretic techniques, monitoring the purification process                                                                                      4 hrs
Working Principle, Instrumentation and Application of –Phase contrast and Electron Microscopy, Gel-Doc system                                                                                                 3 hrs   
Principle, types and uses of- Centrifugation techniques, Gel filtration, Electrophoretic techniques: Starch gel, Agarose gel. Cellulose Acetate, Polyacrylamide gel, Electrophoresis, Isoelectirc focusing, Two-dimensional Electrophoresis, Blotting technique                                                                                                                            10 hrs 
Principles, types and uses of Chromatographic Techniques
Basic concepts and instrumentation- Ion exchange chromatography, Affinity Chromatography, Partition chromatography, Paper and Thin layer Chromatography, Gel permeation chromatography, GAS chromatography, High performance Liquid Chromatography (HPLC)                                                                                                                                     10 hrs
Instrumentation, Working Principle and Application of – Atomic absorption spectroscopy, Atomic emission Spectroscopy-Flame photometry, Plasma emission Spectroscopy, Fluorimetry and spectrofluorimetry                                                                                                                      10 hrs
Principle, Instrumentation and Application of –Ultra-violet and visible spectrometry, Infra-red spectroscopy, Molecular luminescence spectrometry, Nuclear Magnetic resonance spectroscopy, Mass Spectroscopy                                                                                                                  10 hrs

Textbooks
1.      Nelson DL and cox MM. Lehninger Principle of Biochemistry, 5thEdition, Freeman (2004)
2.      Wilson k and Walker J (Eds). Principles and Techniques ofBiochemistry and Molecular Biology, 6th Edition, Cambridge University Press (2005).
3.      Voet D and Voer J. Biochemistry. 3rd Edition, Wiley International Edition(2004)
4.      Stryer L. Biochemistry, 4 th Edition, W.H. Freeman Company, New York (1995)
5.      Plummer DT. An introduction to Practical Biochemistry, 3rd Edition, Tata McGraw Hill (1988)
6.      Skoog DA , Holler FJ and Nieman TA. Principle of InstrumentalAnalysis, 5th Edition, Thomson Books/Cole (2005)
7.      Mendham j, Denny RC, Barnes JD and Thomas M. Vogel’s Text Book of Quantitative Chemical Analysis, 6th Edition, Pearson Education (2008)


Bacteria in Photos

Bacteria in Photos