PhD Course work

Ph. D. Course WorkThe course work for the Ph. D. students of this Institute starts tentatively in 2nd/3rd week of January2009. The course work comprises of two semesters. The second semester starts form July every year. Each semester comprises of 56 lectures, each of 90 minutes duration.A minimum of 80% attendance in these classes is required for all the students to appear for the exam.

Format of PhD Course Work Registration Form

Name of the student:Position (JRF/SRF/Project fellow):Funding Agency:(CSIR/UGC/DBT/DST/ICMR)Specialization in M.Sc/ M.Tech etc:Name of the supervisor:Department & Division:Date of joining:Lab. Tel. no.: Email ID:

Signature of the student:

Counter signature of the supervisor:

Dr. Keya Chaudhuri Dr.Siddhartha Majumdar Chairman Convener, Academic Affairs ________________________________________________________________________

Programme1. PhD Course Work:Registration for PhDCourse Work: 3rd & 4th week of DecemberDuration of Course work: 12 months(2 Semesters)Duration of first Semester classes: January to MayExam of first semester:1st Week of juneDuration of Second semester classes: July to NovemberExam of 2nd Semesmter:1st week of December

Summer Training:Application period: 2nd week of September to 2nd week of November Duration of Training: March to August

Announcement of result (1st List):2nd week of JanuaryAnnouncement of result (2nd List): Last week of February

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Courses

The fist semester of IICB PhD course work comprise of four subjects. There are three compulsory subjects (computer applications, statistics and instrumental analysis techniques) required for students of all disciplines, and one basic Biology / chemistry course (chemistry for biologists and biology for chemists) required for students of specific disciplines i.e. biology or chemistry.

The second semester is devoted to advanced courses i.e. advanced biology and advanced chemistry.The advanced PhD course work for the year 2009 is modules based, each .module consisting of 6 classes.

Advanced Biology consists of four modules i.e. 1) Molecular and Cellular Imaging (including Cryo & AFM)

2) Cell Signaling 3) Immune response 4) Gene Regulation.

Advanced Chemistry consists of three modules i.e. 1) Chemical Biology 2) Chemistry of Natural Products & Structural Elucidation using Modern Tools 3) Synthetic Chemistry.

The interdisciplinary topic, which is common to both Chemistry and Biology students consists of three modules i.e.

1) Systems Biology 2) Synthetic Biology 3) Cell and Tissue engineering.

The mode of examination is in the form of Two Term Papers (One on Advanced Biology or Advanced Chemistry and another on interdisciplinary Subject) and one seminar of 20 minutes._______________________________________________________________________

Teachers

Teachers of IICB PhD course work

1. Dr. C. Chowdhury

2. Dr. S. Mukhopadhyay3. Dr. P. Chattopadhyay4. Dr. A. Bhattacharya(Emeritus Sct)5. Dr. S. B. Mondal6. Dr. A. Banerjee7. Dr. Krishnananda Chattopadhyay8. Dr. Saumen Dutta 9. Dr. Rupak Bhadra10. Dr. Mrinal K. Ghosh11. Dr. Syamal Roy12. Dr. Nahid Ali13. Dr. Chitra Mondal14. Dr. Subrata Adak15. Dr. D. Bhattacharjya16. Dr. S. Bandyopadhyay17. Dr. S. Roychowdhury18. Prof.Siddhartha Roy19. Dr. Sibsankar Roy20. Dr. Rukshna Chowdhury21. Dr.Tuli Biswas22. Dr.K.P.Mohana Kumar23. Dr.Tushar Chakraborty24. Dr.Arun Bandopadhyay25. Dr. G. Suresh Kumar26. Dr. Ashis K. Sen (Jr.)27. Dr. M. C. Bagchi28. Dr. Basudeb Acharya(Emeritus Sct)29. Dr.C.Dutta30. Dr. Asoke Dasgupta31. Dr. Nanada Ghoshal32. Dr.Shyamal Dana33. Dr.P.Jaisankar34. Dr.Biswadip Banerjee35. Dr. Suvendra Bhattacharya

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Notices

i. NOTICE

Dated: 12th August’2009

Sub: Classes of Advanced Biology and Advance Chemistry of PhD course work-2009 Please note that the classes of ‘Advanced Course Work-2009, i.e. Advanced Biology and Advanced Chemistry is scheduled to start from 17th August, Monday at 4:30 pm. Advanced Chemistry class will start from 4:30 pm, and Advanced Biology class will start from 5:30 pm.

Students of specific disciplines are advised to attend classes accordingly as per schedule.Course work calendar will be notified in due course.

ii. NOTICE

Schedule for Ph.D. Course Work Examination-2009

PhD Course work examination (compulsory) is scheduled to be held on 2nd and 4th June’09.The nature of question will be of multiple choice/fill up the blank/short question type.

Date Time Subject Marks 02.06.09(Tuesday)

2.00 p.m. to4.00 p.m.

(i) Statistics

(ii)Computer

50

50

04.06.09(Thursday)

2.00 p.m. to 4.00 p.m

(i) Instrumentation

(ii) Basic Biology

OR Basic Chemistry

50

50

Venue: Ist Floor & 2nd floor seminar rooms

iii. NOTICE

INDIAN INSTITUTE OF CHEMICAL BIOLOGY

Please note that the certificates presentation programme date for IICB PhD course work-2008 is 26th May 2009, Tuesday at 4-30 pm. Concerned students are hereby requested to present in 1st

floor seminar room as per revised schedule. Director, IICB has kindly agreed to hand over the certificates. 

 Siddhartha Majumdar, Head, Human Resource Group & Convener, Academic Affairs

Notice Board

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Important dates

Registration for PhD Course Work: 3rd /4th week of DecemberDuration of Course work: 12 months (2 Semesters)Duration of first Semester classes: January to MayExam of first semester: 1st Week of JuneDuration of Second semester classes: July to NovemberExam of 2nd Semester: 1st week of December__________________________________________________________________

Model Questions

ComputerTrue / false.

1. Operating system is a part of the computer hardware.

2. The function of the RAM is to store information permanently.

3. Disk operating system (DOS) contains external and internal commands.

4. To delete the directory from hard disk the command is delete *.*

5. Microprocessor consists of millions of transistor.

6. GUI is used both LINUX and window system.

7. The difference between ROM and RAM depends on its a) functional basis b) hardware basis c) storage basis d) none of these

8. The main function of the CPU is to a) control the arithmetic and logical unit. b) control the visual display c) control the hard disk d) control the printer.

9. MSDOS is the unit ofa) Dos familyb) Unix family

c) Irix family d) None of these

10. Spreadsheet is the combination of a) Cells onlyb) Rows only.c) Columns onlyd) rows and columns.

11. Spreadsheet Cell is called intersection ofa) rows and columns.b) rows onlyc) columns onlyd) cell only

12. Auto sum can be applied to

a) rows onlyb) columns onlyc) none of thesed) rows and columns wise

13. The count function is applied fora) counting of numbers of rowsb) counting of rows and columnsc) counting of columnsd) counting of total numbers of cells

14. To write a formula in the function address box put = signa) before the formulab) after the formulac) middle of the formulad) none of these

15. Max or min function can be applied only fora) row wiseb) column wisec) row and column wised) cell wise.

16. In molecular modeling, energy optimization by molecular mechanics can not guarantee a) global minimum b) local minimum c) none of the above

17. In Molecular modeling which of the following is the fastest method for energy optimization: a) Ab-initio or Gausian b) Molecular Mechanics c) Semi-emperical

Answer any one of the following two groups

(True/False) During energy optimization of a molecule:

1. Semi-empirical calculation takes more time than molecular mechanics calculation.

2. Molecular mechanics calculation takes more time than Semi-empirical calculation.

3. Molecular mechanics calculation takes more time than Ab-initio calculation.

4. Semi-empirical calculation takes more time than Ab-initio calculation.

(True/False)The display style in small molecular modeling does not include: 1. Stick2. Ball and stick3. Space filling4. Ribbon

Each Question carries one mark1) Ramachabdran’s Plot is plot of omega () and Psi () angles of protein backbone

True False

2) Alpha () helix and beta () sheet are the secondary structures of protein backbone

3) Right handed Alpha () helix is more common in proteins True False

4) Homology modeling is more successful technique than threading method for the prediction of the 3-D structure of a protein True False

5) Gauche (+) conformation is energetically more favorable than the trans conformation of a sidechain True False

6) All proteins have their own quaternary structures in the native state. (True/false)

Biological databases are collection of life sciences information from

(a) scientific experiments (b) published literature(c) high-throughput experiment technology(d) computational analysis(e) all of the above

The International Nucleotide Sequence Database (INSD) consists of the following databases(a) DDBJ,EMBL Nucleotide DB and GenBank(b) Entrez, Eugene and Gene Cards(c) Ensembl, ERIC nd Flybase(d) PIR, SwissProt and UniProt

Suppose you have determined the nucleotide sequence of a novel gene you have cloned. You need to submit the sequence to get an accession no. before sending it to the journal of choice. Your supervisor advised you to submit it to GenBank,NCBI. Which tool will you use for submission?

Sequin or Bankit

miRBase is a database of(a) miRNA sequences,annotations and predicted targets(b) all regulatory gene sequences(c) human miRNA sequences(d) RNA secondary structures

The 3-D (3-dimensional) structures of proteins determined by X-ray crystallography are available at(a) Prosite(b) ProDom(c) Protein Data Bank(d) PIR

Small molecule crystal structures are available at(a) CSD-Cambridge Structural Database(b) Biomodels Database(c) BioGRID(d) ArrayExpress

ChemDB is a database of(a) Small molecule crystal structures(b) Only chemical reactions(c) Commercially available compounds (d) None of the above

Suppose you are working with some infectious disease. The genome sequence of the causative organism is available. You want to know the information about virulence factors and their mechanism of action. To get an overview what database will you consult?(a) Gene Expression omnibus or GEO(b) SWISS-MODEL(c) KEGG or Kyoto Encyclopedia of Genes & Genomes(d) None of the above

Statistics

1. A frequency distribution is defined whenever i) the values which the variate takes are given only ii) the number of times each variate value is taken are specified only iii) both (i) & (ii) are specified

2. A negative skew curve i) can be folded along a vertical line so that the two halves of the figure coincide ii) has a long tail in the positive side iii) has a long tail in the negative side

3. If n non-zero and positive variate values X1, X2………..,Xn occurs f1, f2,………..fn times respectively then the geometric mean is given by

ii) [ x1f1. x2

f2…….Xnfn ]1/N

4. Quartiles are those variate values which divide the total frequency into f i X i i) four equal parts ii) ten equal parts iii) one hundred equal parts

5. The modal value of the distribution is that value of the variate for which i) the frequency is maximum. ii) the frequency is minimum. iii) the frequency is neither maximum nor minimum.

6. The value of the range of a group of observations depends on i) the two extreme observations in the group ii) all observations except two extreme observations in the group iii) no observations in the group

7. The inter quartile range of a group of observations is i) the difference between maximum and minimum values in the group ii) interval between the value of the upper quartile and lower quartile for that group iii) none of the above.

8. The standard deviation of a group of observations is 7.The variance will be

i) 25 ii) 81 iii) 49 iv) 50 9. When all variate values are equal, standard deviation is

i) 0 ii) 10 iii) 0.1

10. The coefficient of variation is given by

11. The probability p is always i) less than 0 ii) greater than 1 iii) lies between 0 and 1

12. The probability of a certain event to happen is i) 0 ii) 1 iii) 0.5

13. The probability of an event which will not happen is

i) 0 ii) 1 iii) 0.5

14. What is the probability of getting 2 in tossing a die?

i) 1/3 ii) 1/2 iii) 1/6 iv) 0

15. How many parameters are there in a binomial distribution?

i) 1 ii) 2 iii) 3

16. How many parameters are there in a Poisson distribution?

i) 1 ii) 2 iii) 3

17. We have to find the probability that atmost 5 defective fuses will be found in a box of 200 fuses if experience shows that 2 per cent of such fuses are defective. The problem can be solved by using:

i) Binomial distribution ii) Poisson distribution iii) Normal Distribution

18. The frequency curve of a distribution is symmetrical about the middle and exhibit a shape like a bell, with a peak in the middle and gradual falling of frequency in the two tails. This is an example of

i) Binomial distribution ii) Normal Distribution iii) Poisson distribution

19. For any given µ, how many normal curves are possible each with a different standard deviation σ i) A finite no. of curves ii) An infinite no. of curves iii) None

20. For which distribution, mean, mode and median are the same?

i) Normal Distribution ii) Poisson distribution iii) Binomial distribution

21. When sample size is large,‘t’ distribution closely approximates to

i) Poisson distribution ii) Binomial distribution iii) Normal Distribution

22. For solving problems in ‘t’ distribution, if |t| > the critical value, what should we do

i) Accept Ho ii) Reject Ho iii) No decision can be taken

23. The correlation coefficient ‘r’ is always

i) greater than 1 ii) less than -1 iii) lies between -1 to +1

24. Complete absence of correlation is represented by

i) 0 ii) 1 iii) -1

25. How many regression line can be computed for every set of data?

i) 1 regression line ii) 2 regression lines iii) 3 regression linesInstrumental Analysis

1. Name the seven crystal systems.

2. Write Bragg’s Law.

3. Write name of the two metals we commonly use as anode in home X-ray source. 4. How many primers are required during PCR based DNA sequencing using Sanger’s method?a. Oneb. Zeroc. Twod. Four

5. During the manual method of DNA sequencing the primer is labelled by:a. Adding all four dNTPs in regular amount and DNA polymeraseb. Adding all four dNTPs in regular amount of which one is radioactively labelled

and DNA polymerasec. Adding all four dNTPs in limiting amount of which one is radioactively labelled

and DNA polymerased. Adding all four dNTPs in limiting amount and DNA polymerase

6. High throughput DNA sequencing using Sanger’s method was possible due to improvement in the:a. Labelling and detection methodb. Fragment separation techniquec. DNA polymerase used and resulting strategies for generation of fragmentsd. All of the above

7. In the ABI Prism 310 machine the capillary is filled with:a. Polyacrylamide gel solutionb. A liquid polymerc. Agarose gel solutiond. Sephadex beads

8. The novelties of the Solexa method of DNA sequencing are:a. Generation of millions of clusters of different DNA templates on a tiny solid

surfaceb. Use of reversibly 3’ blocked deoxynucleotidesc. Use of fluorescence labelled dideoxynucleotidesd. a and b both

9. Which of the following of the DNA polymerising reaction product is detected during pyrosequencing method of DNA sequencing?

a. the growing DNA chainb. ATP

c. PPid. none of the above

10. A cation-exchanger chromatography column can be done at any pH?

True False

11. At a constant pH, all unabsorbed fractions of a cation-exchanger will bind to an anion-exchanger.

True False

12. Re-chromatography always yields better purification. True False

13. A gel filtration chromatography followed by a cation or anion-exchanger chromatography is a better sequence for purification of a protein than the reverse order.

True False

14. Resolution power of a gel filtration column is significant near or within its Void volume Fractionation range Desalting zone

15. Can a lectin (carbohydrate binding protein) be separated using a Sephadex matrix (cross inked dextran) based on its molecular weight?

Yes No16. Antigen-antibody binding is used in:

Cation exchange chromat. Anion exchange chromat. Affinity chromat Adsorption chromat.

17.Binding of a material to hydroxyapatite column involves: Adsorption phenomenon Absorption phenomenon Non-specific binding Specific binding.

18. In reverse-phase HPLC, the column matrix is: positively charged negatively charged Hydrophobic Hydrophilic.

19. Is there any restriction on the volume of sample to be applied to a cation or anion exchanger column? Yes No

20. Define Precision frequency. What is the relationship between Precision frequency and Static Magnetic Field strength (B0)?

21. Using arbitrary chemical shift scale draw 1H NMR spectra of the following compounds explaining the observed peak patterns:i) Butan-2-ol (CH3CH2CHOHCH3)

ii) Propan-1-ene (CH3CH=CH2)

22. Discuss the significance of the relative positions and relative intensities of signals obtained in an NMR spectrum.

23. What is Scalar coupling? Explain its effect on the observed NMR spectrum. 24. Circular dichroism is the difference in the absorption(a) of incident and diffracted light(b) of incident and absorbed light(c) left and right circularly polarized light(d) incident and scattered light

25. Circular dichroic spectral pattern is generally expressed in terms of (a) wavelength versus optical density(b) wavelength versus molar ellipticity(c) wavelength versus refractive index(d) wavelength versus absorbance

26. The CD spectrum of a DNA polynucleotide has a long wavelength negative band (in the 280-300 nm) followed by positive band around 250 nm. The structure can be most likely

(a) alpha helix(b) left handed Z-form(c) beta sheet(d) right handed B-form

27. An alpha helical conformation of a protein is characterized in CD by the (a)double minima at 222 and 208 bands

(b)negative and an equally positive band at 222 nm(c)positive CD bands in the 200-230 nm region

(d)a negative band at 205 nm

28. An induced circular dichroism is obtained for a (a) CD active or inactive compound due to asymmetric environment (b) CD inactive compounds only (b) CD active compounds only(c) none of the above

29. In fluorescence spectroscopy external energy is supplied to the sample by means of

(a) UV/V is light(b) Radio active decay(c) Fluorescent light(d) None of the above

30. In fluorescence spectroscopy the detector is placed at 90o to the incident light to get better signal-to-noise ratio, when compared to the 180° geometry

(a) avoid external light(b) to avoid reflection (c) to avoid interference from diffracted light(d) to avoid transmitted excitation light and stray light

31. Fluorescence polarization (anisotropy) gives information about (a) shape, size and flexibility of the molecules(b) molecular weight of the molecules(c) location of the molecule(d) concentration of the molecules in the solution

32. Fluorescence Resonance Energy Transfer only occurs when the two fluorophores are more or less within about

(a) anywhere beyond 1000 Ǻ (>0.1μm)(b) 200-1000 Ǻ (0.02-0.1μm)(c) 500-1000 Ǻ (0.05-0.1μm)(d) 20-100Ǻ (0.002-0.01μm) of each other

33. The strongest fluorescent amino acid is(a) tyrosine(b) tryptophan(c) phenylalanine(d) glutamic acid

34. The fluorescence spectrum of a protein has an emission maximum at 348 nm when excited at 280 nm. The fluorescence may be most likely from the

(a) phenylalanines (b) tyrosines (c) tryptophans (d) none of the above Key:

1.c 2.b 3.b 4.a 5.b6.a 7.d 8.a 9.d 10.b11.c

35. Intracellular Ca2+ using Confocal Microscope can be measured by loading cells

with which of the following dyes?

(a) Fluo 3AM

(b) Fluo 3

(c) Rhodamine

(d) Alexa Fluor 488

36. The amount of “out of focus light rays” into the detector of a confocal

microscope will be increased if

(a) Pinhole is decreased

(b) Pinhole is increased

(c) the wavelength of the excitation beam is increased

(d) None of the above

37. The primary benefit of the confocal microscope over the conventional

wide field microscope is

(a) The ability to control the depth of the field by confocal microscope

(b) Image is more clear in confocal microscope.

(c) The digitization is more easier by confocal microscope

(d) None of the above.

38. Which one of the following is the correct excitation maximum of GFP?

(a) 340 nm

(b) 630 nm

(c) 488 nm

(d) 588 nm

39. Name the suitable dye (s) for staining nucleus.

(a) Alexa Fluor 633

(b) DAPI

(c) Propidium iodide

(d) Both b and c

40. Confocal eliminates “out of focus information” by using which one of the

following devices?

(a) Beam splitter

(b) Pinhole

(c) Mirror

(d) Objective

41. The primary limiting factor for resolution in a light microscope is the:

a) quality of the lenses

b) index of refraction

c) wavelength of light

42.Which of the following is NOT true of electron microscopy (EM):

a) EM can be used to examine the movement of flagella

b) EM uses heavy metals as stains

c) Electrons replace light in the electron microscope

43. When biologists wish to study the internal ultra-structure of cells, they most likely would use:

a) a transmission electronic microscopeb) a light microscopec) a scanning electron microscope

44. In its optical design, the transmission electron microscope is most like a(n):

a) atomic force microscopeb) compound light microscopec) scanning electron microscope

45. Which instrument gives the most "3-dimensional-like" image?

a) Compound light microscopeb) Transmission electron microscopec) Scanning electron microscope

46. How does the scanning electron microscope differ from the transmission electron microscope? It:

a) uses electromagnetic lensesb) operates with a vacuumc) maps images rather than optically projecting them

47. Define the role of isotype-matched control antibody in immunofluorescence staining.

48. Explain the principle of annexin V-FITC staining for measurement of apoptosis.

49. How can you distinguish apoptosis from necrosis in flow cytometry?

50. Design the protocol for intracellular staining of IFN-gamma in CD4+ T cells after

incubation of human peripheral blood mononuclear cells with phytohaemagglutinin.

51. How can you quantitate apoptotic cells by DNA cell cycle analysis?

52. You would like to amplify a 1kb fragment using the Polymerase Chain Reaction. What is the expected number of copies of the fragment at the end of 20 cycles if (i) two primers are used ____________________ (ii) one primer is used in the PCR _______________ 53. Specificity of a PCR can be increased using the technique ______________PCR

54. Increasing Mg concentration decreases specificity of a PCR due to (1)

a. increased stability of the DNA Polymerase b. increased activity of the DNA Polymerase c. increased stability of double stranded DNA d. increased stability of single stranded DNA e. none of the above

55. Advantage of Sybr Green over ethidium bromide in real time PCR id due to one or more of the followinga. Sybr Green and not ethidium bromide intercalates into double stranded DNA

b. Sybr Green fluoresces with higher intensity than ethidium bromide when bound to double stranded DNAc. Sybr Green fluoresces with higher intensity than ethidium bromide when bound to single stranded DNA d. Sybr Green fluoresces with higher intensity than ethidium bromide when bound to double stranded and single stranded DNA

(1)

Students

Qualified Students of IICB PhD Course Work 2008

Students of IICB PhD Course Work 2009

Name of the studentsAmrita Das Subhra PradhanSandip Koley Sujoy DasSunny Sharma Gunjan SharmaJune Ghosh Dipto BhattacharyyaManish Goyal Debratna SahaNilanjana Banerjee Sajal SamantaPrasenjit Chakraborty Indranil PaulG.Kiran Kr. Naidu Anirban MannaTapashi Mondal Srinjana GhoshSukanta Jash Amit Kr. BaidyaUdayan Bhattacharya Tanaya DasVivek Chander Sudarshan BhattacharjeeMoumita Ghosh Epshita chatterjeeRanendu Ghosh Poornima ChandranWritoban Basu Ball Biswajit KhatuaAnirban Datta Nabendu BiswasSupriya Srivastava Sumana BhattacharjyaSrinivasarao Repudi Kalpataru HalderSatyabrata Bag Debalina MukherjeeRajan Guha Deepak VermaRanjan Dhar J. B. KharlyngdohPoulami Karmoker Mumu ChakrabortySupratim Dey Bimalendu AdhikariShyam Sundar Nandi Jayanta NandaAmit Kr. Dey Nirmal Das AdhikariSumanta Dey Koushik RoyMonoj Kr. Singh Chinmay Pal

Name of the studentsIshita Saha Atreyee SahaSubhendu Naskar Seemana BhattacharyaShyamal Mondal Moumita BoseRupankar Paira Rudra Narayan MundaPritam Saha Shinjinee SenguptaPiyali Deb Barman Subhadip ChakrabortyMadhumita Mandal Maitreyee MondalTulika Mukherjee Sashwata MukherjeeKaushik Brahma Piyali SahaSubhashish Haldar Kunal Kumar BasuAbhijit Ghorai Moitri BasuAvirup Chakraborty Debdut NaskarSamir Mandal Mithun MajiBornita Das Ragini SinhaJyoirmoy Mitra Joy ChakrabortySamrat Dutta Debashmita TripathySwarbhanu Sarkar Thoppuvalappil Ambili

AppukuttanSourav Chakraborty Samir MondalGitashri Naiya Subir KarmakarAnirban Basu RaghavanAtanu Das Amartya MishraSoumyanil Bhaumik Shantanabha DasSouvik Ghosh Sumit Sen SantraAranyak Goswami Rupkatha MukhopadhyayDeborshi Sengupta Sharmistha SinhaAbhi Das Samik BinduAnup Mazumder Sayan ChowdhurySupratim Mukherjee Ayantika PalSupratim Mandal Debrup SenGeorge Maity Anirban ChatterjeeDebashree Chatterjee Arindam MaityPallashri Saha Rajiv Karmakar