Brochure - National Centre for Biological Sciences

GS-‐2013 Handbook for Interviews 

Na#onal Centre for Biological Sciences, TIFR, Bangalore 

May 2013

May 2013 

Dear Students, 

I write to extend a warm welcome on behalf of the community at NCBS. The call-‐leLer, sent 

separately, invi#ng you to par#cipate in the interviews carries details on the dates, 

reimbursements and travel to NCBS. This handbook is an aLempt to assist you with the 

experience of the selec#on process. The ini#al sec#ons should familiarize you with the 

actual interview process and would also be meaningful to students eventually joining the 

program. We also include a sec#on where the Faculty at NCBS provide an overview of their 

research programs. We encourage you all to read this sec#on before you arrive on the 

campus for the interviews. Addi#onal informa#on on all laboratories and the programs on 

offer are available on the NCBS website www.ncbs.res.in 

We hope that the NCBS experience will be enriching for you and look forward to 

seeing you later in May. 

With best wishes 

Apurva Sarin 

Head Academics 

national centre for biological sciences 

tata institute of fundamental research

1. PhD & Int-‐PhD programs 

GRADUATE STUDIES AT NCBS 

NCBS offers a graduate program leading to the award of a PhD degree to students who hold a Masters 

degree in a Basic Science or a Bachelors degree in an Applied Science such as Medicine, Engineering 

etc. The Integrated PhD program seeks students with an excellent academic record at the B.Sc. 

level, strongly mo#vated to pursue a career in research. 

The Integrated Biology (iBio) and Theore#cal Studies programs at NCBS provides a s#mula#ng 

environment for students with backgrounds in physics, chemistry and mathema#cs to apply their 

knowledge to understanding concepts in biology. Students who are interested in iBio research 

projects must first be accepted into the PhD or integrated-‐PhD program at NCBS through the 

standard applica#on procedure. 

In all aforemen#oned programs, students register for a PhD at the TIFR Deemed University typically 

1.5-‐2 years from the date of joining, a[er mee#ng course requirements and qualifying a 

comprehensive examina#on. 

M. Sc by Research: A very small number of students featuring on the wait list of the Integrated PhD 

selec#on interview may be appointed to this program with salary support on PI grants. 

The MSc in Wildlife & Conserva#on program is offered only at NCBS and selec#ons are made based on a 

separate test and interview process. The next selec#ons for this program will be in 2014

2. Selec#on Process 

GS-‐2013 Interviews 

Candidates are invited to apply in response to adver#sements appearing in na#onal 

newspapers and magazines in August/September every year. Candidates short-‐listed on 

the basis of their performance in a wriLen test, academic record and leLers of evalua#on 

are interviewed for admission. NCBS sends out an applica#on package to students who 

qualify the TIFR entrance test for Biology, Physics or Chemistry. Performance in the wriLen 

test, together with the informa#on requested in the applica#on package is used to short-list 

candidates for interviews at Bangalore. 

Interviews for the PhD/Int-‐PhD programs at NCBS typically comprise two rounds. There is some 

overlap in the list of candidates invited to interview at DBS or NCBS and it is possible that 

some candidates are offered admission in both centres. Candidates are however expected 

to accept the offer at only one centre.


3. Interviews 

In the first round, interview panels will typically comprise 3-‐4 members of the faculty. Some 

commiLees include a minimum of one or two specialists in the areas of Physics or Chemistry. In 

this round all candidates should expect to be ques#oned on their basic understanding of 

Biology, Chemistry or Physics as well as quan#ta#ve and reasoning skills. The commiLee will 

probe your understanding of concepts taught in high school and at the undergraduate level. 

Please do not prepare for the interviews by memorizing material! All students are interviewed 

in this round, which is typically completed in one day and may some#mes extend into the 

morning of the second day. Based on performance in the first round, students are short-‐listed 

for the second round of the interview process. This list of candidates short-‐listed for the second 

round will be posted by 12 noon on the second day or earlier. Lists are drawn up only a[er all 

first round interviews are completed. 

In the second round, interview panels comprise 4-‐5 members and again some commiLees will have 

greater representa#on of faculty with core exper#se in areas of Chemistry or Physics. This 

interview may typically extend from 30-‐45 minutes and tests for more in-‐depth understanding 

and the ability to apply the knowledge of an area of special interest to the candidate. Typically 

the statement of purpose in the applica#on package is used as a basis of ques#oning. However, 

candidates have to be prepared for ques#ons that have been taught at a more advanced level 

in special papers or via projects etc. In previous years, ques#ons have also been based on 

original research ar#cles that were distributed to all candidates prior to the interviews. 

Candidates uncomfortable or unable to handle ques4ons in a par4cular area must indicate this 

to the commi6ee immediately. Marks are not deducted for such requests and there is enough 

diversity in the panels to allow another member to ini4ate a new line of ques4ons.

The final list of selected candidates, drawn up in consulta#on with Chairpersons of the 

commiLees and based on the performance in both rounds of interviews, will be announced 

late in the evening of the third day. 


Waitlisted candidates: Students on the wait-‐list if supported by external funding from the 

CSIR, ICMR or DBT can join the PhD program if sponsored by a laboratory at NCBS. 

Alterna#vely, a student on the wait-‐list may also join the graduate program with salary support 

from the Principal Inves#gator’s [PI] grant. Admission and con#nua#on on the graduate 

program in both situa#ons is con#ngent on associa#on with the PIs laboratory. 

This op#on is not available to students short-‐listed on the Integrated PhD program. Faculty at 

NCBS will post informa#on regarding the availability of grants on the days of the PhD 

Interviews. 

Note: 

Please report at NCBS by 8.30AM on the first day of the interviews. There is a short session 

on the morning of the first day to orient you to the selecKon process and assign students to 

various panels. NCBS student volunteers who guide you through the interviews will be also 

be assigned in this session.

Overseas Applica#ons 

NCBS invites applica#ons from students who enrolled in Colleges and University outside 

the Indian Subcon#nent for their undergraduate studies. The entrance test is waived 

for overseas applicants. However students who would like to be considered for the 

graduate program at NCBS are encouraged to write Head Academic Ac#vi#es before 

November each year. 

The academic office will assist you with the submission of an applica#on package and the 

subsequent steps in the selec#on process. In some instances we offer the op#on to 

interview students via skype/video conference if short-‐listed for the interviews. If 

selected to the program students are expected to join on August 1 st or at the earliest 

possible date therea[er. 

There are specific requirements for travel and visa documents for foreign na#onals which 

have to be completed prior to arrival at NCBS. The academic office coordinates with 

the establishment office at NCBS to assist students through this process.

Informa#on related to Interviews 

4. Accommoda#on and Meals during the Interviews 

Candidates are expected to make their own arrangements for stay during interviews 

as NCBS does not provide accommoda#on. Informa#on regarding short-‐term 

leased accommoda#on and hotels close to our campus availed by students in 

previous years is provided in the brochure. NCBS will not act as an intermediary 

in these arrangements. 

Meals -‐ Breakfast, Lunch and Tea -‐ are served to candidates Wed-‐Fri on Interview 

dates. Breakfast and lunch will be served on Saturday. Meals are free. 

Accompanying persons may purchase food at the cafeteria and canteen on the 

Campus, which operate at set #mes. If staying on for dinner, please inform the 

canteen management at lunch #me as dinner service is limited on campus. 

Please do not forward requests for Guest House accommodaKon via members of 

the Staff – academic, administraKve or technical – at NCBS during the period of 

the Interviews.


5. Material you should bring to the Interviews 

• Candidates are expected to bring a printed copy of the leLer invi#ng them to the 

interview; proof of ID in the form of a University/Ins#tute ID card/ PAN Card may be 

required and should be available if needed. 

• A copy of your #cket is required to process reimbursement, which will be given to 

you on the second day of the Interviews. 

• Air travel is reimbursed to the extent indicated in the leLer from NCBS. The 

incoming boarding pass has to be submiLed to process reimbursement. 

• Students traveling by bus are required to present Xerox copies of #ckets or proof of 

the inward journey. 

• The TA/DA form should be submiLed on the day of arrival. This is applicable only to 

candidates living outside Bangalore. 

Please carry: 

Call leLer; proof of ID; copy of #cket; TA/DA form which can be downloaded from our website


6. Hotels & Commercial Guest Houses near NCBS-‐ par#al list 

Stayafford Service Apartment, No. 1629, C Block, Sahakar Nagar, Bangalore 92 

Contact Mr. Santosh 9880194240 

Satya Comforts Service Apartments, B -‐ 31, Chitrakut Century, Behind North Side Hospital, 

Sahakar Nagar, Bangalore Contact Ms. Annapurna -‐ Tel: 9980101881, Tel: 

08042031881/32951881 fax: 080-‐42031881 Email: satyacomforts@hotmail.com 

The Royale Senate, No 24, Bellary Road, Hebbal, Bangalore – 24, Ph: 91 80 23439860, Fax: 91 80 

2343 1759 info@theroyalesenate.com 

Chairman's Resort, #14/1, Kodigehalli Main Road, Sahakarnagar, Bangalore -‐ 560 092 Tel: 

+91-‐80-‐40703703, 23546162 Contact:+91-‐9980269978 

Narayana Comforts, No. 9/9, Kendriya Vihar Apts, Bb Rd, Yelahanka, Bangalore 560064, Tel: 

080-‐28462752/51/53, 22792780 Contact: Subhash Chandra Mobile 9886217208 

Shreyas Residency 9/8 N.H 7 B.B Road, Amanikere, Yelahanka, Bangalore. Contact Subhas 

9886217208 

Royal Orchid Resort & Conven#on Centre (Previously Doddi’s Resort) Allalasandra, Bellary 

Road, Yelahanka, Near Jakkur Flying Club, Bangalore 560 065, india Tel +91 80 2856 0668 

Fax +91 80 2856 0671 Email rooms@royalorchidhotels.com 

Please note: NCBS will not act as an intermediary in arranging accommoda#on during the interviews

Orienta#on Program for new students 

7. Acceptance of the offer from NCBS 

A formal offer to join the program will reach you within a period of 10-‐15 days from the date of the 

interview. You are expected to inform NCBS about your acceptance of the offer or otherwise by the date 

specified in the leLer. 

8. Accommoda#on for graduate students 

NCBS offers accommoda#on to all students selected on the graduate program. Students on the main lists of 

the PhD and Int-‐PhD have priority, followed by PhD students on grants and the M. Sc students. Rooms 

are alloLed only a[er students arrive on campus and cannot be reserved. Rooms are alloLed only a[er 

the submission of a joining report and comple#ng administra#ve formali#es in August. 

9. Orienta#on and Rota#ons for incoming graduate students 

New students join NCBS on Thursday August 1 st 2013. All new students must par#cipate in 

the Orienta#on Program. During the program, sessions are arranged with faculty members 

who review work ongoing in their laboratories. The program also includes sessions with 

individuals who manage Research, Technical and Administra#ve Services at NCBS. In the 

course of the Orienta#on Program, students are guided through procedures such as the 

comple#on of the mandatory medical test and administra#ve formali#es towards joining in 

the course of this program. Administra#ve staff will assist you in this. Addi#onal 

informa#on on rota#ons, courses etc. will be provided during the Orienta#on Program 

Laboratory allotments for graduate studies are ONLY made a[er the comple#on of laboratory 

rota#ons. No student in the graduate program is exempt from laboratory rota#ons.

Your contact: phd@ncbs.res.in 

Academic Office 

Academic Office 

K.S. Vishalakshi 

MaLers related to Student Affairs are managed by the 

Academic Office, in coordina#on with the 

Administra#ve Office. The academic office is managed 

by Ms NN Shantha and Ms KS Vishalakshi. 

Ms KS Vishlakshi is the primary contact for all 

correspondence related to selec#on and joining the 

program at NCBS. Do not call unless there is an 

emergency. Please do not contact our faculty for 

informa#on regarding the interviews. 

All queries related to the interviews should be directed 

to phd@ncbs.res.in. 

In case of medical emergencies or clashes with exams 

or other interviews, suitably jus#fied requests for 

rescheduling within the assigned dura#ons of the 

Interviews may be submiLed to phd@ncbs.res.in with 

the subject line Name_GS2013_date change.

Please visit our webpage h6p://www.ncbs.res.in for more informa4on on research programs

Padubidri Shivaprasad 

Plant gene silencing and epigeneKcs 

new labs at NCBS 

Selected Publica#ons 

Padubidri Shivaprasad, Ho-‐Ming, Kanu Patel, 

Donna Bond, and David Baulcombe (2012). 

A micro RNA superfamily regulates disease 

resistance via effects on NBS-‐LRR mRNAs 

and secondary siRNAs. Plant Cell 24: 

859-‐874. 

Padubidri Shivaprasad, R. Dunn, B. Santos, 

A. BasseL, and D.C. Baulcombe (2012). 

Extraordinary transgressive phenotypes of 

hybrids are influenced by epigene#cs and 

small silencing RNAs. EMBO J. 31:257-‐266. 

Padubidri V. Shivaprasad, R. Rajeswaran, T. 

Blevins, J. Schoelz, F. Meins, Jr, T. Hohn and 

M. M. Pooggin (2008). The CaMV 

transac#vator/viroplasmin interferes with 

RDR6-‐dependent trans-‐ac#ng and 

secondary siRNA pathways in Arabidopsis. 

Nucleic Acids Res. 36: 5896-‐5909. 

Research in our laboratory deals with molecules called small RNAs. Small RNAs 

are the key molecules resul#ng from RNA silencing pathways and they regulate 

both transcrip#on and transla#on with the help of their protein partners. Small 

RNAs are also important factors in ini#a#ng and maintaining heritable changes in 

gene expression without changes in DNA sequence (called ‘epigene#cs’). Small 

RNAs and epigenome modifica#ons impact every aspect of eukaryo#c 

development and disease. Contribu#on of individual small RNAs and epigene#c 

varia#ons in phenotypes of plants are well documented but we really do not 

know how they work. We are interested in understanding the pathways that 

generate small RNAs and epigenome modifica#ons to be able to use them 

effec#vely in plants. Our laboratory uses various biochemical, gene#c, 

bioinforma#c and whole-‐genome approaches in a wide variety of plants. 

We use cauliflower and wheatgerm to isolate na#ve protein complexes that 

generate small RNAs to iden#fy partner proteins to help us understand how they 

bring about changes in transcrip#on and transla#on. We also use rice and its wild 

rela#ves to profile RNAs and look for varia#ons in epigenome (such as DNA 

methyla#on and histone modifica#ons) using whole-‐genome techniques. The 

idea is not only to generate fine map of genomic regions that show epigene#c 

and small RNA varia#ons, but also to understand what contribu#on they have 

towards plant phenotypes and to understand how they are inherited. Once the 

role of a small RNA/epigenome modifica#on for a given phenotype is iden#fied, 

they can be introduced to plants through transcrip#onal gene silencing 

technology that relies on viruses to alter the epigenome. Our approach should 

facilitate us to generate crop plants with specific, useful and predictable 

phenotypes.

Axel Brockmann 

Honeybees and the mechanism of behavior 

new labs at NCBS 

I am interested in the mechanisms of animal behavior. Honeybees provide the opportunity to 

study mechanisms of behavior at the level of the individual and the level of the social 

organiza#on. Moreover, honeybees are one of the few animal model systems to study the 

interac#on between individual behavior and social organiza#on. We are able to manipulate the 

social structure and analyze its effects on the individual’s behavior, brain physiology, and brain 

gene regula#on. 


Streinzer M, Brockmann A, Nagaraja N, 

Spaethe J. 2013. Sex and caste-‐specific 

varia#on in compound eye morphology of five 

honeybee species. PLoS One. 8(2):e57702. doi: 

10.1371/journal.pone.0057702. 

Barron AB, Brockmann A, Sen Sarma M & 

Robinson GE. 2012. Molecular dissec#on of 

honey bee dance behaviour. 2012. In 

“Honeybee neurobiology and behaviour – a 

tribute for Randolf Menzel”. Eds.: Eisenhardt 

D et al., Springer Verlag, Berlin Heidelberg 

New York. 

Brockmann A, Annangudi SP, Richmond TA, 

Ament SA, Xie F, Southey BR, Rodriguez-‐Zas 

SR, Robinson GE, Sweedler JV. 2009. 

Quan#ta#ve pep#domics reveal brain pep#de 

signatures of behavior. Proc Natl Acad Sci U S 

A. 106(7):2383-‐8. doi: 10.1073/pnas. 

0813021106. . 

So far, most behavioral and neurobiological research on honeybees focused on the European-‐ 

African species Apis mellifera, unfortunately neglec#ng the variability in social organiza#on and 

individual behavior among honeybee species. Honeybee species par#cularly vary in colony 

organiza#on, worker ac#vity and longevity, pheromone communica#on and dance language 

communica#on. A special focus of my lab will be research on Asian honeybee species na#ve to 

India: Apis florea (the red dwarf honeybee), Apis dorsata (the giant honeybee), and Apis cerana 

(one of the Asian cavity nes#ng honeybees). The genomes of all three species are currently 

sequenced which will open the possibility to analyze the molecular underpinnings of behavioral 

differences and the evolu#on of these behaviors. 

In addi#on to studies on honeybee behavior, I plan to expand my research on Drosophila. 

Currently, I am developing lab assays that can be performed with honeybees and flies. The 

neurogene#c tools available for Drosophila allow iden#fying neural circuitries involved in 

specific behaviors, and the hope is that Drosophila can help to iden#fy neural circuits involved 

in honeybee behavior. 

Specific Research Projects: (a) Social organiza#on and behavioral matura#on in Apis florea, (b) 

Neuromodula#on and organiza#on of daily foraging ac#vity, (c) Molecular and neural 

mechanisms of dance language communica#on, (d) Circadian regula#on of ma#ng behavior 

and sex-‐pheromone communica#on, (e) Behavioral and neural mechanisms of seasonal 

migra#on.

Deepa Agashe 


Agashe D, Mar#nez-‐Gomez NC, 

Drummond DA and Marx CJ (2013). Good 

codons, bad transcript: large reduc#ons in 

gene expression and fitness arising from 

synonymous muta#ons in a key enzyme. 

Molecular Biology and Evolu#on 30(3): 

549-‐560. 

Falk JJ, Parent CEP, Agashe D and Bolnick 

DI (2012). Dri[ and selec#on entwined: 

Asymmetric reproduc#ve isola#on in an 

experimental niche shi[. Evolu#onary 

Ecology Research 14: 403-‐423. 

Agashe D, Falk JJ and Bolnick DI (2011). 

Effects of founding gene#c varia#on on 

adapta#on to a novel resource. Evolu#on 

65(9): 2481-‐2491 

. 

EvoluKonary ecology of adaptaKon 

Adapta#on to various ecological factors has been an important force in the 

evolu#on of the amazing array of species on earth. However, we are only 

beginning to address some key ques#ons about adapta#on. How do ecological 

condi#ons and gene#c factors determine the basis and dynamics of 

adapta#on? At the molecular level, what is the nature of selec#on ac#ng on 

genome structure and composi#on and how do these genomic characteris#cs 

affect adapta#on in turn? In previous work, I’ve shown that the gene#c 

diversity of laboratory beetle popula#ons can profoundly alter compe##on, 

popula#on size and stability, and adapta#on to new habitats. In later work, I 

found that synonymous muta#ons in enzyme-‐coding genes could have 

surprisingly large effects on bacterial fitness, although the bacteria quickly 

recover fitness via small muta#ons of large effect. 

In our new lab at NCBS we aim to integrate concepts in molecular evolu#on, 

ecology, and macroevolu#on using insect and bacterial systems. For instance, 

we are analyzing the gene#c popula#on structure and varia#on in fitness 

components of Tribolium beetle popula#ons across India to understand the 

links between genotype and phenotype in a generalist species. In another 

project, we are manipula#ng genomic features such as tRNA gene content and 

codon usage in bacteria to test their impact on bacterial fitness. For various 

other projects we use phylogene#c compara#ve and bioinforma#cs methods 

to test signals of long-‐term selec#on on bacterial genomes. Together, these 

analyses will help us understand how ecological and gene#c characteris#cs 

interact to influence adapta#on and evolu#on.

Krushnamegh Kunte 

EvoluKon and organizaKon of biological diversity 

Research in my lab is aimed at understanding the evolu#on and organiza#on of biological diversity on 

earth. As a lab, we study biodiversity in an interdisciplinary manner, with our scien#fic ques#ons 

spanning the fields from community and popula#on ecology to evolu#onary gene#cs, and methods 

ranging from behavioral experiments to phylogene#c inference, theore#cal modeling, and molecular and 

developmental gene#c experiments. Our work addesses aspects of the origin of species, morphological 

diversifica#on, and ecological and molecular gene#c bases of sex-‐limited and polymorphic traits. We try 

to integrate the fields of popula#on biology, natural selec#on theory and molecular gene#cs, which 

serves to conceptually unify the biological sciences. 

Recent Publica#ons 

Kunte, K., C. Shea, M. L. Aardema, J. M. 

Scriber, T. E. Juenger, L. E. Gilbert, and 

M. R. Kronforst. 2011. Sex chromosome 

mosaicism and hybrid specia#on among 

#ger swallowtail buLerflies. PLoS 

Gene4cs, 7:e1002274. 

Tiple, A., D. Agashe, A. M. Khurad and K. 

Kunte. 2009. Popula#on dynamics and 

seasonal polyphenism of Chilades 

pandava buLerfly (Lycaenidae) in 

central India. Current Science, 

97:1774-‐1779. 

Kunte, K. 2009. Female-‐limited mime#c 

polymorphism: A review of theories and 

a cri#que of sexual selec#on as 

balancing selec#on. Animal Behaviour, 

78:1029–1036. 

Kunte, K. 2009. The diversity and 

evolu#on of Batesian mimicry in Papilio 

swallowtail buLerflies. Evolu4on, 

63:2707–2716. 

Kunte, K. 2008. Mime#c buLerflies 

support Wallace's model of sexual 

dimorphism. Proceedings of the Royal 

Society, B, 275:1617-‐1624. 

We primarily use two systems as microcosms to study biodiversity. The first system is 

Batesian mimicry, which is a phenomenon whereby unprotected prey species (called “mimics”) gain 

protec#on from predators by mimicking toxic or otherwise protected species (called “models”). 

Predators learn to avoid models based on prior experience, and subsequently avoid ea#ng mimics due to 

misiden#fica#on. Hundreds of mime#c buLerfly species are known from tropical forests. There is 

tremendous varia#on in the nature of Batesian mimicry: mimicry can be sexually monomorphic, 

polymorphic or sex-‐limited within and across species. Our work aims to understand the selec#ve 

pressures that favor such varia#on in mimicry, and uncover the gene#c basis of color paLern varia#on. 

We mainly use phylogene#c methods, ecological observa#ons and molecular gene#c tools in this part of 

our research. 

Our second system is Indian buLerflies, which offer many opportuni#es to study 

biogeography, community ecology, popula#on biology and conserva#on issues. Indian buLerflies are 

excellent to study various interes#ng phenomena, including large-‐scale migra#ons and seasonal 

polyphenism. Due to their considerable diversity and endmism in the Indian Subcon#nent, they are also 

outstanding subjects to study origins of species, and biogeography and phylogeography in the Oriental 

Region. Finally, due to increasing human pressures, the persistence of biodiversity is under threat, and 

buLerflies are no excep#on. The problems of a very large human popula#on in a developing country, 

combined with a serious administra#ve commitment to conserva#on and strong na#onal conserva#on 

legisla#on, makes India a unique country to understand scien#fic and social issues related to the 

preserva#on of biodiversity. 

Thus, the long-‐term goal of our “Biodiversity Lab” is to study mechanisms that facilitate 

morphological diversifica#on, processes that shape the origins and dispersion of species, and the means 

to preserve biodiversity. You can find out more about the lab at hLp://biodiversitylab.org.

Madhusudhan Venkadesan 

Control and Morphology Lab 

Our lab is interested in the interac#on between control and morphology in animals 

and machines. We combine biological, mechanical, and mathema#cal methods to 

study how animals control their limbs and body to interact with the surrounding. 

Selected Publica#ons: 

N.T. Roach, M. Venkadesan, M. 

Rainbow, D.E. Lieberman. Elas#c 

energy storage in the shoulder and the 

evolu#on of high-‐speed throwing in 

Homo. Nature, In press. 

D.E. Lieberman, M. Venkadesan, W.A. 

Werbel, A.I. Daoud, S. D’Andrea, I.S. 

Davis, R.O. Mang’eni, I. Pitsiladis. Foot 

strike paLerns and collision forces in 

habitually barefoot versus shod 

runners. Nature, 463(7280):531–5, 

2010. 

M. Venkadesan and F.J. Valero-‐Cuevas. 

Neural control of mo#on-‐to-‐force 

transi#ons with the finger#p. Journal of 

Neuroscience, 28(6):1366-‐1373, 2008. 

! 

My lab studies the interac#on between control and morphology in animals and 

machines. Why do animals o[en outperform their robo#c counterparts in terms of 

robustness and versa#lity of motor behaviour? Have animals finely-‐tuned their 

morphology through evolu#on in order to achieve the robustness one associates 

with biology? How do we extract design and control principles for understanding 

biomechanical func#on, the diagnosis and treatment of disease and also for 

improving the state of robo#cs and prosthe#cs? Theore#cal efforts drive the 

design of our experiments and our experimental outcomes o[en call for new 

theore#cal approaches to analyze and interpret the results. 

Current projects in the lab span several aspects of human motor behaviour, 

including locomo#on, throwing and grasping. What is the role of the foot and the 

leg in maintaining stability when people run on uneven terrains? Which 

morphological features of the human body, different from other primates, allow 

us to throw at accurately very high speeds? Our work on how humans use their 

finger#ps in fine manipula#on seeks to understand how the anatomical layout and 

physiological proper#es of muscles and tendons help in dexterous manipula#on. In 

all of these projects, we seek to understand how evolu#on has shaped our 

morphology and in turn, how that affects the choice of motor control strategies 

that our nervous system uses.

Aswin Sai Narain Seshasayee 

ComputaKonal and funcKonal genomics of bacterial gene 

regulaKon and adaptaKon 

Recent Publica#ons 

Kahramanoglou C, Prieto AI, Khedkar S, Haase B, 

Gupta A, Benes V, Fraser GM, Luscombe NM, 

Seshasayee ASN. Genomics of DNA cytosine 

methyla#on in Escherichia coli reveals its role in 

sta#onary phase transcrip#on. Nature 

Communica#ons 2012. 3: 886. 

Seshasayee ASN, Singh P, Krishna A. Context-dependent 

conserva#on of DNA 

methyltransferases in bacteria. Nucleic Acids 

Research 2012. 40: 7066-‐73. 

Bacteria are the most numerous among free-‐living life on earth. They 

adapt to their environment, including a variety of stresses, by changes 

to their gene#c material and / or altera#ons in the nature and amounts 

of proteins produced. Our lab is interested in studying these aspects of 

bacterial biology using a combina#on of molecular and 'genomic' 

experiments and computa#onal analysis. In par#cular, we study the 

following: 

1. the role of global transcrip#onal regulators in influencing 

growth physiology of E. coli 

2. gene#c and transcrip#onal adapta#on of E. coli 

popula#ons to chemical and nutrient stresses 

3. mechanisms regula#ng horizontal gene transfer 

Kahramanoglou C, Seshasayee ASN, Prieto AI, 

Ibberson D, Schmidt S, Zimmermann J, Benes V, 

Fraser GM, Luscombe NM. Direct and indirect 

effects of H-‐NS and Fis on global gene expression 

control in Escherichia coli. Nucleic Acids Research 

2011. 39: 2073-‐2091.

Sandeep Krishna 

Life and death decisions in biological systems 

I'm interested in how biological cells, organisms and popula#ons acquire and 

process informa#on, and integrate different pieces of informa#on to make 

decisions. I use computa#onal modeling and theore#cal analyses to understand 

the role of feedback mechanisms in regulatory networks that process informa#on. 


Semsey, S & Krishna, S. (2013) 

Combining theory and experiments 

to understandd sugar regula#on in 

bacteria, Curr. Chem. Biol. in press. 

Heilmann, S., Sneppen, K. & 

Krishna, S. (2012) A life on the 

edge: Coexistence of virulent 

phage and bacteria on the 

boundary of self-‐organized refuges, 

Proc. Natl. Acad. Sci. (USA) 109, 

12828–12833. 

Seshasayee, A. S. N., Singh, P. & 

Krishna, S. (2012) Context-dependent 

conserva#on of dna 

methyltransferases in bacteria, 

Nucl. Acids. Res. 40, 7066–7073. 

1. Bacteriophage lysis-‐lysogeny decision. Temperate bacteriophage are amongst 

the simplest organisms that could be said to make a developmental decision. Upon 

infec#ng a bacterium, temperate phage enter either the ly#c pathway, where they 

replicate rapidly and eventually lyse the host, or the lysogenic pathway, where 

they insert their DNA into the genome of the cell and lay dormant. I’m interested 

in understanding how informa#on such as the number of infec#ng phage, bacterial 

growth rate, bacterial density, etc., is used to bias the lysis-‐lysogeny decision. 

2. Metabolism in prokaryotes. Sugar uptake and metabolism networks in bacteria 

are ideal systems to study feedback. Typically, they have two entangled feedback 

loops, a posi#ve one regula#ng transport and a nega#ve one regula#ng 

metabolism. In contrast, iron metabolism in several bacteria has at its core two 

nega#ve feedback loops. I’m interes#ng in understanding the dynamics of mul#ple 

entangled loops by inves#ga#ng compara#ve models of metabolic regula#on in E. 

coli, H. pylori and Y. pes#s, and mapping the transi#on to sta#onary phase in 

bacteria growing on single carbon sources. More generally, I would like to uncover 

principles that can be used to predict the behaviour of combina#ons of feedback 

loops.

Vatsala Thirumalai 

Neural control of movement during development and in adulthood 


Thirumalai V (2012) Assembling 

neural circuits for genera#ng 

movement. J. Ind. Inst. Sci., 92(4), 

411-‐426. 

Thirumalai V and Cline HT (2008) 

Endogenous dopamine suppresses 

ini#a#on of swimming in pre-‐feeding 

zebrafish larvae. J. Neurophysiol. Sep; 

100(3):1635-‐48. 

Thirumalai V and Cline HT (2008) A 

commanding control of behavior. Nat 

Neurosci. 2008 Mar;11(3):246-‐8. 

For most animal species, survival depends cri#cally on the ability to move-‐ be it for 

feeding, escaping predators or selec#ng a suitable mate. To generate movement, 

skeletal muscles need to be contracted in precisely coordinated paLerns. Neural 

circuits control the spa#al and temporal paLern of skeletal muscle contrac#ons. 

Our lab is interested in understanding the hierarchy, mechanisms and development 

of neural circuits that generate movement. 

We use zebrafish, a small fresh water tropical fish endemic to the Ganges, as our 

model system. The embryonic and larval stages of these fish are transparent 

allowing for direct visual observa#on of developing internal organs including the 

brain. We employ a suite of techniques to tease out the circuitry responsible for 

genera#ng swimming in developing and more mature zebrafish. These include 

whole-‐cell patch clamping, calcium imaging, high-‐speed videography and confocal 

and two-‐photon microscopy. Using these cung edge tools and technologies, we 

hope to throw light on the development of neural circuits and the neural basis of 

locomo#on.

Shachi Gosavi 

ComputaKonal folding and funcKonal dynamics of proteins 


D. T. Capraro, M. Roy, J. N. Onuchic, S. 

Gosavi, and P. A. Jennings,“ β-‐Bulge 

triggers route-‐switching on the func#onal 

landscape of interleukin-‐1β.” Proc. Natl. 

Acad. Sci. USA, 109, 1490-‐1493, 2012. 

D. T. Capraro, S. Gosavi, M. Roy, J. N. 

Onuchic, and P. A. Jennings, “Folding 

circular permutants of IL-‐1β: route 

selec#on driven by func#onal frustra#on.” 

PLoS ONE, 7, e38512, 2012. doi:10.1371/ 

journal.pone.0038512 

S. Gosavi, “Understanding the Folding-‐ 

Func#on Tradeoff in Proteins.” PLoS ONE, 

8, e61222, 2013. doi:10.1371/ 

journal.pone.0061222 

Molecular dynamics (MD) simula#ons provide a detailed descrip#on of protein 

mo#on not easily accessible to experimental methods. My group is interested in 

the long #mescale mo#ons of proteins, in par#cular, large-‐scale conforma#onal 

transi#ons and folding. We use models based solely on the folded structure of 

the protein to access such long #mescales. 

We use structural (e.g. the β-‐trefoil fold) families of proteins, to understand how 

protein func#on affects protein folding. In this context, we have begun 

computa#onal and experimental protein design of func#on-‐less proteins. 

We study several large proteins (e.g. adenylate kinase, serpins) in order to 

understand how the constraints of folding and func#on mold the design of 

mul#-‐domain proteins. 

In addi#on, my group inves#gates several folding related phenomena such as 

folding coopera#vity, domain swapping, etc. We develop and adopt new 

computa#onal methods to understand protein structure and folding, as 

required.

Raghu Padinjat 

The architecture of phosphoinosiKde signalling in vivo 

Selected publica#ons 

Raghu, P., Yadav, S and Mallampa#, N. (2012) 

Lipid signalling in Drosophila photoreceptors. 

Biochimica et Biophysica Acta -‐ Molecular and 

Cell Biology of Lipids. Vesicular Transport. (in 

press) 

Georgiev, P., et.al (2010). TRPM channels 

mediate zinc homeostasis and cellular growth 

during Drosophila larval development. Cell 

Metabolism. 12, 386–397 

Raghu, P, et.al (2009) Rhabdomere biogenesis 

in Drosophila photoreceptors is acutely 

sensi#ve to phospha#dic acid levels. Journal of 

Cell Biology 185 129-‐145 

Raghu P, Hardie RC. 2009 Regula#on of 

Drosophila TRPC channels by lipid messengers. 

Cell Calcium. 45(6):566-‐73. 

Garcia-‐Murillas I, et.al (2006) Iazaro encodes a 

lipid phosphate phosphohydrolase that 

regulates phospha#dylinositol turnover during 

Drosophila phototransduc#on. Neuron. 29:4, 

533-‐546. 

Our long term scien#fic interest is the analysis of signalling mediated by lipid 

molecules generated during phosphoinosi#de metabolism. Phosphoinosi#de signals 

provide molecular control for key sub-‐cellular processes such as membrane 

remodelling, cytoskeletal func#on, transcrip#on and transla#on. Through these 

processes, this signalling pathway orchestrates basic cellular behaviours such as cell 

division, shape changes, polarized movement and cell death. The overall goal of our 

work is to understand how the architecture this signalling cascade is designed to 

deliver op#mal physiological outputs. We use the fruit fly Drosophila as our model 

system; the goal is to discover key principles of signal transduc#on that are likely to 

be conserved during evolu#on but are experimentally more tractable in Drosophila. 

Phospha#dylinositol 4,5 bisphosphate [PI(4,5)P2] is a phosphoinosi#de 

with mul#ple, key cellular func#ons. In order to #ghtly regulate PI(4,5)P2 levels, it is 

essen#al for cells to closely monitor PI(4,5)P2 levels at the plasma membrane and 

to closely match the rate of PI(4,5)P2 resynthesis with its consump#on by signalling 

reac#ons. We are studying the mechanisms by which PI(4,5)P2 levels are regulated 

in the context of Drosophila phototransduc#on. 

A second area of research is the analysis of cellular growth during 

larval development. We have recently iden#fied a novel phosphoinosi#de kinase 

that appears essen#al for larval growth and works thorough the evolu#onarily 

conserved growth regulator TOR. Several exci#ng projects are available in both the 

above areas. They involve a mixture of Drosophila molecular gene#cs, lipid 

biochemistry, cell biology and live imaging both in cells and in the intact organism.

Deepak T. Nair 

Nucleic Acid RecogniKon and Metabolism 

Selected Recent Publica#ons: 

Sharma A., KoLur, J., Narayanan, N. and Nair, 

D. T.§ (2013) A strategically located serine 

residue is cri#cal for the mutator ac#vity of 

DNA Polymerase IV from Escherichia coli. 

Nucleic Acids Research (in press) 

Jain, D. and Nair, D. T.§ (2013) Spacing 

between core recogni#on mo#fs determines 

rela#ve orienta#on of AraR monomers on 

bipar#te operators. Nucleic Acids Research 

41:639 

Sharma, A., Subramanian, V. and Nair, D. T.§ 

(2012) The PAD region in the mycobacterial 

dinB homolog MsPolIV exhibits posi#onal 

heterogeneity. Acta Crystallogr D Biol 

Crystallogr. 68:960 

The blueprint of life for each organism is resident in its genome. Nucleic acid 

metabolizing enzymes ensure proper informa#on transfer from the genome 

for synthesis of appropriate effector molecules. Members of this broad 

group of enzymes are also instrumental in the replica#on and maintenance 

of the genome. Perturba#on in the func#on of these enzymes due to 

muta#ons or inhibitors has an adverse effect on the survival of the 

organism. In my laboratory we study four processes involving the ac#on of 

nucleic acid metabolizing enzymes on the genome. These processes are (a) 

DNA Mismatch repair (b) Translesion DNA synthesis (c) Adap#ve 

mutagenesis and (d) Replica#on of the Japanese Encephali#s Virus genome. 

Using X-‐ray crystallography in conjunc#on with relevant biochemical 

methods, biophysical techniques and func#onal assays, we aim to provide 

structural insight into the mechanism of ac#on of enzymes/enzyme 

complexes involved in each of these processes. 

Generally, for all cellular processes to func#on op#mally, the integrity of the 

genome has to be maintained. However, the crea#on and reten#on of error 

in DNA allows for the evolu#on of the genome in order to relieve selec#on 

pressure imposed by an adverse environment. These two conflic#ng 

requirements have led to the presence of molecules and molecular 

mechanisms that either prevent (e.g. DNA mismatch repair) or facilitate (e.g. 

error-‐prone DNA Polymerases) the appearance of muta#ons. My laboratory 

aims to unearth the structural mechanisms employed by these molecular 

determinants of genomic integrity and plas#city to achieve func#on and 

modulate the rate of evolu#on.

Sanjay P. Sane 


Singh, A.K, Prabhakar, S and Sane, S. P.* 

(2011). The biomechanics of fast prey 

capture by aqua#c bladderworts. Biology 

LeLers, 7, 547-‐550. 

Sane S.P.*, Srygley R.B., Dudley R. (2010) 

Antennal regula#on of migratory flight in 

the neotropical moth Urania fulgens, 

Biology LeLers 6: 406-‐409 

Sane SP* and McHenry MJ (2009) The 

biomechanics of sensory organs, 

Integra#ve and Compara#ve Biology, 

49(6):i8-‐i23; 

Sane, S.P.*, Dieudonne, A., Willis, M. A. 

and Daniel, T. L. (2007). Antennal 

mechanosensors mediate flight control in 

moths. Science 315, 863-‐866. 

Neural and physical basis of insect flight 

The spectacular evolu#onary success of insects owes much to the evolu#on of 

flight. Insect flight is characterized by speed, control and manoeuvrability. Their 

wings flap at very rapid rates (typically on the order of 10-‐100 Hz) and hence their 

sensory system must acquire and process informa#on at similar rates. How do the 

nervous systems of insects tackle the extraordinary challenges of acquiring, 

integra#ng and processing mul#modal sensory informa#on and genera#ng of 

rapid behavioural responses to ensure stable flight? Our laboratory combines 

inputs from diverse disciplines such as physics, biomechanics, neurobiology and 

behaviour to address this ques#on. 

Broadly speaking, our approach involves the iden#fica#on and measurement of 

interes#ng flight behaviours in diverse insect taxa (Diptera, Hymenoptera, 

Lepidoptera), and the dissec#on of their physical and sensorimotor machinery to 

understand the mechanisms underlying these behaviours. On the physical front, 

we combine aerodynamic studies on flapping wings with high-‐speed videographic 

measurements of wing mo#on to understand how flapping wings generate and 

modulate aerodynamic flight forces to determine their aerial trajectories. On the 

neurobiological front, we are inves#ga#ng the combined role of vision and 

mechanosensa#on in flight control in insects, including the neural pathways that 

integrate and process these mul#-‐sensory inputs. More recently, we have also 

begun specific inves#ga#ons on insect flight in their natural context. These include 

specific projects on insect-‐plant interac#ons, as well as inves#ga#ons of longer-scale 

flight phenomena such as long distance migra#on and dispersal. Together, 

these studies are aimed to provide a broader level picture of insect flight from 

neurons and physiology to ecology. In addi#on to the above, we are also beginning 

new projects to study the physics and biology of termite mound architecture in the 

coming years.

Mahesh Sankaran 

Community and Ecosystems Ecology 

My research interests span two broad areas of ecology: plant-‐herbivore-‐soil 

interac#ons and biodiversity-‐ecosystem func#on rela#onships. 

Selected Publica#ons : 

Ratnam, J., Bond, W. J., Fensham, R. J., 

Hoffmann, W. A., Archibald, S., Lehmann, 

C. E. R., Andersen, M. T., Higgins, S. I. & 

Sankaran, M. (2011). When is a forest a 

savanna and why does it maLer? Global 

Ecology & Biogeography 20: 653 – 660 

Sankaran, M., Ratnam, J & Hanan, N. P. 

2008. Woody cover in African savannas: 

the role of resources, fire and herbivory. 

Global Ecology & Biogoegraphy. 17: 236 -‐ 

245. 

Sankaran, M., et al. 2005. Determinants 

of woody cover in African savannas. 

Nature 438: 846 -‐ 849 

Current research in the lab is grouped around three themes that examine 

• How interac#ons and feedbacks between climate, 

biogeochemistry, fires and herbivory influence the structure, composi#on and 

stability of ecosystems and the cycling and sequestra#on of nutrients. 

• The role of species diversity in regula#ng ecosystem func#on and 

provisioning of ecosystem services to humans. 

• How projected changes in climate such as increasing variability of 

rainfall, increased frequency of droughts, increasing aridity in the tropics, 

nitrogen and phosphorus deposi#on and rising CO2 will impact ecosystem 

func#on, stability and services. 

Our work addresses the above ques#ons across the gamut of natural 

ecosystem types of the Indian sub-‐con#nent, with the goal of bringing a 

comprehensive understanding of biome-‐scale vegeta#on and nutrient 

dynamics in the sub-‐con#nent.

Mukund ThaLai 

Retracing the evoluKon of complex cells 

Recent Publica#ons: 

Ramadas R, ThaLai M (2013) New 

organelles by gene duplica#on in a 

biophysical model of eukaryote 

evolu#on. In press, Biophys. J. 

ThaLai M (2013) Using topology to tame 

the complex biochemistry of gene#c 

networks. Phil. Trans. Roy. Soc. A 371: 

20110548. 

Brodsky F, ThaLai M, Mayor S (2012) 

Evolu#onary cell biology: Lessons from 

diversity. Nature Cell Biol. 14: 651. 

We are interested in the ancient origins of the eukaryo#c 

compartmentalized cell plan. Surprisingly liLle is known about this key 

phase of the evolu#on of life: eukaryotes began to diverge from bacteria 

during the global oxygena#on event 2.5 billion years ago, but all living 

eukaryotes share a more recent common ancestor da#ng from about 1.5 

billion years ago. Data from modern eukaryo#c genomes might allow us to 

reconstruct the intervening billion-‐year period during which quintessen#al 

eukaryo#c features emerged: the nucleus, mitochondria, 

compartmentalized organelles, the cytoskeletal machinery, and vesicle 

traffic. 

In par#cular, we are pursuing two complementary research direc#ons. 

Forward in #me: we analyze poten#al origin scenarios using biophysical 

and evolu#onary simula#ons, to uncover general principles about the 

evolu#on of compartmentalized cells. Backward in #me: we study the 

evolu#on of the molecular machinery underlying compartmentaliza#on 

using sequence data and phylogene#c techniques; we especially 

concentrate on molecules that underwent eukaryote-‐ specific gene family 

expansions, including Rabs, coat proteins, and SNAREs. The popula#on-‐ 

gene#c mechanisms that generated the earliest compartmentalized cells 

con#nue to drive the diversifica#on of eukaryotes. Our evolu#onary 

perspec#ve might therefore shed light both on ancient events as well as on 

modern lineage-‐specific and #ssue-‐specific elabora#ons of traffic systems.

Yamuna Krishnan 

Structure and dynamics of Nucleic acids 


Modi, S., Surana, S., Halder, S., Nizak, C., Krishnan, Y.* 

(2013) Mul#plexing DNA nanomachines to map pH 

changes on intersec#ng endocy#c pathways. Nature 

Nanotechnology accepted. 

Bha#a, D., Chakraborty, S. and Krishnan, Y.* (2012) 

Designer DNA give RNAi more spine. Nature 

Nanotechnology, 7, 344-‐346. 

Chakraborty, S., Mehtab, S., Patwardhan, A.R., 

Krishnan, Y.* (2012) Pri-‐miR-‐17-‐92a Transcript folds 

into a ter#ary structure and autoregulates its 

processing. RNA 18, 1014-‐1028. 

Surana, S., Bhat, J.M., Koushika, S.P.*, Krishnan, Y*. 

(2011) An autonomous DNA nanomachine maps 

spa#otemporal pH changes in a mul#cellular living 

organism. Nature Communica#ons, 2, 340. 

Bha#a, D., Surana, S., Chakraborty, S., Koushika, S.P. 

and Krishnan, Y*. (2011) A synthe#c, icosahedral DNA-based 

host-‐cargo complex for func#onal in vivo 

imaging. Nature Communica#ons, 2, 339. 

Bionanotechnology aims to learn from nature -‐ to understand the 

structure and func#on of biological devices and to u#lise nature's 

solu#ons in advancing science and engineering. Evolu#on has 

produced an overwhelming number and variety of biological devices 

that func#on at the nanoscale or molecular level and whose 

performance is unsurpassed by man-‐made technologies. My lab uses 

chemical and biophysical tools to explore structure and dynamics in 

nucleic acid assemblies with a view to exploi#ng the knowledge gained 

for applica#ons in biology. 

With a diameter of 2 nm and a helical periodicity of 3.5 nm, the DNA 

double helix is inherently a nanoscale object. The specificity of Watson-‐ 

Crick base pairing endows oligonucleo#des with unique and 

predictable recogni#on capabili#es. This makes DNA an ideal 

nanoscale construc#on material. Understanding and thereby 

controlling structure and dynamics in designed DNA assemblies is key 

to realizing DNA’s poten#al as a nanoscale building block. 

We make DNA based molecular assemblies for applica#ons as 

fluorescent sensors of second messengers in-‐cellulo and in-‐vivo. 

Another area of interest involves understanding naturally occurring 

RNA structural mo#fs and how they impact RNA processing.

Uma Ramakrishnan 

Ecology details interac#ons between organisms and their environment, 

while evolu#on quan#fies their change through #me. I study the 

response of species to environmental history, clima#c perturba#on and 

human history in the context of species ecologies, and hence gain a 

beLer understanding of their evolu#on. 


Srinivasan, U, Tamma, K & Ramakrishnan, U 

(accepted) Past climate and species ecology 

drive nested species richness paLerns along 

an east-‐west axis in the Himalaya. Global 

Ecology and Biogeography 

Garg, KM, ChaLopadhyay, B, Doss, DPS, 

Vinoth Kumar, AK, Kandula, S & 

Ramakrishnan, U (2012), Promiscuous ma#ng 

in the harem-‐roos#ng fruit bat, Cynopterus 

sphinx. Molecular Ecology, 21: 4093–4105. 

doi: 10.1111/j.1365-‐294X.2012.05665.x 

Robin VV, Sinha A & Ramakrishnan, U (2010) 

Ancient Geographical Gaps and Paleo-‐climate 

Shape the Phylogeography of an Endemic Bird 

in the Sky Islands of Southern India. PLoS ONE 

5(10): e13321. doi:10.1371/journal.pone. 

0013321. 

Focusing on mammals and birds, we use field-‐collected samples, 

assemble molecular gene#c data and analyze these data with 

phylogene#c, phylogeographic and popula#on gene#c inferences. So 

far, I have focused on the Indian subcon#nent because of its 

geologically drama#c history, driven by plate tectonics, volcanism and 

clima#c change and its ecologically diverse habitat types from the 

highest mountains on earth to deserts and tropical forests, including 

biodiversity hotspots. Addi#onally, very liLle is known about paLerns of 

gene#c varia#on in na#ve Indian species, and even less is known about 

the impact of climate on species in this region in par#cular. 

We address four types of ques#ons: (1) What drives paLerns of 

diversity in the Indian subcon#nent? (2) What are the impacts of 

climate on changes in diversity? (3) What can we learn about adapta#on 

and behavior in mammal popula#ons using popula#on gene#c and 

genomic methods?(4) What is the cryp#c biodiversity of India and how 

can we safeguard its future?

R. Sowdhamini 

ComputaKonal approaches to protein science 


1. Sony Malhotra and R. Sowdhamini 

(2012) Re-‐visi#ng protein-‐centric two-‐ 

#er classifica#on of exis#ng DNA-‐protein 

complexes. BMC Bioinforma#cs, 13:165. 

2. Swa# Kaushik and R. Sowdhamini. 

(2011) Structural analysis of prolyl 

oligopep#dases using molecular docking 

and molecular dynamics: insights into 

conforma#onal changes and ligand 

binding. PLoS One, 6(11):e26251. 

3. Karuppiah Kanagarajadurai, Manoharan 

Malini, Adi# BhaLacharya, Mitradas M. 

Panicker and Ramanathan Sowdhamini 

(2009) Molecular Modeling and docking 

studies of human 5-‐ 

hydroxytryptamine2A (5-‐HT2A) receptor 

for the iden#fica#on of hotspots for 

ligand binding. Molecular Bio Systems, 

5:1877. 

Just as few alphabets give rise to large number of words, nature uses 

20 amino acids to produce large number of proteins in the living cell. 

The type and order in which amino acids are arranged in a protein 

completely dictate the structure and func#on of a protein. Huge 

amounts of amino acid sequence data are generated from whole-genome 

sequencing projects. We employ computer algorithms which 

try to match new protein sequences to mathema#cal profiles or 

Hidden Markov Models of previously characterized protein families, 

see for example (1). 

Structure implies func#on, but proteins could undergo structural 

changes that are relevant to func#on. We employ molecular dynamics 

simula#ons to reveal structural changes of proteins, for example (2). 

Proteins are seldom isolated in a biological cell. Protein-‐protein and 

protein-‐small molecule interac#ons drive specificity in biological 

pathways. We examine and model these interac#ons by docking, for 

example (3).

Sumantra (Shona) ChaLarji 

SynapKc plasKcity in the amygdala: implicaKons for stress & 

auKsm spectrum disorders 


Roozendaal, B., McEwen, B.S., & ChaLarji, S. 

(2009) Stress, Memory and the amygdala. 

Nature Reviews Neuroscience 10: 423-‐433. 

Suvrathan, A. and ChaLarji, S. (2011) Fragile X 

Syndrome and the Amygdala. Current Opinion 

in Neurobiology, 21 (3): 509-‐515. 

Ghosh, S., Rao, L.T., and ChaLarji, S. (2013) 

Func#onal Connec#vity from the Amygdala to 

the Hippocampus Grows Stronger a[er Stress. 

Journal of Neuroscience (in press) 

Memories come in many different flavors, some more potent than others. 

Emo#onally significant experiences tend to be well remembered, and the 

amygdala has a pivotal role in this process. But the rapid and efficient 

encoding of emo#onal memories can become maladap#ve — severe stress 

o[en turns them into a source of chronic anxiety. What are the cellular 

mechanisms underlying these powerful emo#onal symptoms? To answer 

this ques#on, we have been using a range of behavioral, morphometric, in 

vitro and in vivo electrophysiological tools to iden#fy neural correlates of 

stress-‐induced modula#on of amygdala structure and func#on — from 

cellular and synap#c mechanisms to their behavioural consequences in 

rodents. Our findings point to unique features of stress-‐induced plas#city 

in the amygdala, which are in striking contrast to those seen in the 

hippocampus and cortex, and could have long-‐term consequences for 

pathological fear and anxiety exhibited in people with affec#ve disorders. 

In addi#on to behavioral experience, the genes we inherit can also cause 

cogni#ve and emo#onal dysfunc#on. Strikingly, individuals afflicted with 

certain types of au#sm spectrum disorder o[en exhibit impaired cogni#ve 

func#on alongside high anxiety and mood lability. Hence, we are extending 

our analyses to gene#cally engineered mice to iden#fy cellular and 

molecular targets that can be used to correct symptoms of Fragile X 

Syndrome, the leading gene#c cause of au#sm. 

.

Apurva Sarin 

SpaKal organizaKon and assembly of signaling networks 

regulaKng cell survival 


Perumalsamy LR, Marcel N, Kulkarni K, Radtke F 

and Sarin A [2012] Dis#nct spa#al and molecular 

features of Notch pathway assembly in Regulatory 

T-‐cells Science Signaling 5 (234), ra53. [DOI: 

10.1126/scisignal.2002859] 

Gupta S*, Marcel N*, Talwar S*, Garg M, Indulaxmi 

R, Perumalsamy L, Sarin A and Shivashankar GV 

[2012] Developmental heterogeneity in DNA 

packaging paLerns influences T-‐cell ac#va#on and 

transmigra#on. PLOS One, 10.1371/journal.pone. 

0043718 

Purushothaman D*, Marcel N*, Garg M*, 

Venkataraman R, and Sarin A [2013] Apopto#c 

programs are determined during lineage 

commitment of CD4+ T-‐effectors: Selec#ve 

regula#on of T-‐effector-‐memory apoptosis by 

iNOS. J. Immunol. 190 (1):97-‐105. 

We study signal transduc#on pathways that underlie cellular decision-making. 

Specifically, we are interested in mechanisms underlying the 

dele#on of damaged or redundant cells while sparing healthy cells in 

mul#cellular organisms. Current research in the laboratory focuses mainly 

[but not exclusively], on understanding interac#ons between cell death and 

survival cues in the control of T-‐cell number in the mammalian immune 

system. Although nomadic and distributed in different #ssues, T-‐cell 

numbers show minimal changes during life-‐span and are conserved across 

individuals, indica#ve of cell-‐autonomous programs of death and survival. 

Like many other cell types, T-‐cells depend on extrinsic cues from growth 

factors to regulate nutrient uptake for their metabolic needs. However, the 

integra#on of signals received from cytokine receptors at the cell membrane 

with processes occurring within cells and necessary for survival remain to 

be understood. 

In an effort to understand these we study cellular responses ini#ated in 

response to nutrient depriva#on as well as mechanisms that prevail in cells 

that survive this stress. We have shown that spa#al regula#on of molecular 

intermediates and resultant crosstalk with other pathways has significant 

bearing on signaling outputs regula#ng cell survival. In this context, Notch 

signaling and the consequences to nutrient sensing and calcium 

homeostasis is an emerging area of interest in my laboratory. 

*equal contribu#on

Upinder S. Bhalla 

Shining light on brain computaKon 

What would you do if you could watch brain cells as they compute, and 

control their ac#vity by shining light on them, and model all this on a 

computer? Neuroscience is being transformed by techniques that make all this 

real. We use these methods to understand how the brain computes, and 

specifically, to ask how we learn. 


Khan, A.G., Sarangi, M., Bhalla, U.S. Rats 

track odour trails accurately using a mul#-‐ 

layered strategy with near-‐op#mal sampling. 

Nature Communica#ons. 3(703), doi: 

10.1038/ncomms1712, 2012. 

Bhalla, U.S. Mul#scale interac#ons between 

chemical and electric signaling in LTP 

induc#on, LTP reversal and dendri#c 

excitability. Neural Netw. 2011 Nov;24(9): 

943-‐9. doi: 10.1016/j.neunet.2011.05.001. 

Dhawale, A.K., Hagiwara, A., Bhalla, U.S., 

Murthy, V.N., Albeanu, D.F. Non-‐redundant 

odor coding by sister mitral cells revealed by 

light addressable glomeruli in the mouse. 

Nat Neurosci. 2010(11):1404-‐12 

! 

First, we use 2-‐photon microscopy to monitor cellular ac#vity in the brain of 

mice as they learn to associate a sound or other sensory s#mulus with a 

reward or a subsequent puff or air. This lets us get a picture of how the 

ac#vity and connec#ons change in real #me, as the animal learns. 

Second we use electrical and op#cal s#mulus methods to turn brain cells on 

and off under computer control. This lets us build up connec#on diagrams 

(although s#ll very incomplete) of circuits that compute the meaning of 

sensory informa#on. It also lets us probe in detail how these connec#ons 

change during learning. 

Third we model these computa#ons and learning events. Because the brain 

computes both with chemical and electrical signals, we build models that 

represent all these processes: protein synthesis, molecular signaling, electrical 

ac#vity, and the growth of new connec#ons between cells. We #e these 

models closely to our own experiments, and work done by collaborators and 

labs around the world. 

Together, these models and experiments build towards a deeper 

understanding of brain computa#on in percep#on, learning, and disease.

Satyajit Mayor 


Ac#ve remodeling of cor#cal ac#n 

regulates spa#otemporal organiza#on of 

cell surface molecules. Gowrishankar K, 

Ghosh S, Saha S, S.Rumamol, C., Mayor S, 

Rao M. Cell. 2012 Jun 8;149(6):1353-‐67. 

Spa#otemporal regula#on of chemical 

reac#ons by ac#ve cytoskeletal 

remodeling. Chaudhuri A, BhaLacharya 

B, Gowrishankar K, Mayor S, Rao M. Proc 

Natl Acad Sci U S A. 2011 Sep 6;108(36): 

14825-‐30. 

Molecules, mechanisms, and cellular 

roles of clathrin-‐ i n d e p e n d e n t 

endocytosis. Howes MT, Mayor S, Parton 

RG. Curr Opin Cell Biol. 2010 Aug;22(4): 

519-‐27. 

! 

Mechanisms of membrane organizaKon and endocytosis in metazoan 

cells 

The broad aim of my laboratory is to develop an understanding of how a cell 

regulates the local organiza#on of its cell surface cons#tuents how it may engage in 

deforming its membrane in a regulated fashion. This will help in understanding how 

a eukaryo#c cell constructs signaling complexes (local composi#on) and engages in 

membrane traffic, in par#cular during endocytosis. To study phenomena at the 

cellular scale, we u#lize principles from the physical sciences to frame ques#ons 

about movement of molecules and organelles inside cells. We have also have 

developed numerous microscopy tools to study organiza#on of cellular 

components, from the nanometer scale in specialized domains in cell membranes 

to the micron scale prevalent in mapping endocy#c pathways. We also study 

sor#ng proper#es and endocy#c pathways of a variety of molecules, including 

membrane proteins, lipids and lipid-‐tethered proteins in vivo. Our studies provide a 

new picture of the cell membrane as an ac#ve composite of the lipid bilayer and a 

dynamic cor#cal ac#n layer beneath, wherein, dynamic ac#n filaments help in 

controlling the local composi#on of membranes. 

We are now involved in several specific lines of inquiry. These include; i) theore#cal 

and experimental studies on the basis for the forma#on of membrane domains in 

living cells and in vitro; ii) exploring the dynamics of such membrane complexes 

during signaling and templated differen#a#on in mul#ple cell systems, including 

stem cells; iii) iii) understanding the role(s) of scales of organiza#on in the 

func#oning of lipid-‐tethered morphogens in paLerning #ssues in situ, iv) 

uncovering molecular mechanism of dynamin-‐independent endocytosis using cell-based 

assays at the individual gene scale, and genome wide-‐RNAi screening 

methods to study its regula#on and evolu#on.

Sudhir Krishna 

Notch signalling in human epithelial cancers and leukemias: 

A research program based in both NCBS and St. John’s Medical 

College 

Our lab has for some #me now been interested in the role of Notch signalling in human 

epithelial cancers. We have focussed our analysis on human cervical cancer-‐ a tumour 

ini#ated and sustained by oncogenically high risk Human Papillomaviruses. Our recent 

work has led to the iden#fica#on of a CD66+ sub-‐set of cells (Bajaj, Maliekal et al., Cancer 

Research 2011) that has features of cancer stem like cells and is dependent on Notch 

signaling. Our major collabora#ve hospital in this programe so far has been the Kidwai 

Memorial Ins#tute of Oncology. 

Department of Biotechnology Glue grant inita6ve: 


Bajaj, J., Maliekal., TT., Vivien, E., PaLabiraman, 

C., Srivastava, S., Krishnamurty, H., Giri, V., 

Subramanyam, D & Krishna, S (2011). Notch 

signaling in CD66+ cells drives the progression of 

human cervical cancers. Cancer Research, 71, 

4888-‐97. 

We have been awarded a major 5 year grant to co-‐develop laboratory facili#es at St. 

John’s Medical College. In addi#on to the exis#ng research infrastructure in St. John’s 

Medical College, we are developing molecular biology and #ssue culture labs along with 

a flow cytometry and imaging facility. From NCBS, Drs. Sweta Srivastava, H. Krishnamurty 

and Srinag are some of the key scien#sts involved in this program 

The St. John’s Medical college program has led to a second cancer that we 

are studying ie: Chronic Myeloid Leukemia (CML). Our focus is on CML stem cells and our 

key collaborator is Cecil Ross, a senior hematologist. 

Key features in the crea#on of collobora#ve clinical-‐basic hemato-‐oncology working 

group 

-‐ 

Dual loca#on laboratories at the campuses of NCBS and St. John’s medical 

colleage 

-‐ 

Teamwork driven projects that includes clinicians, bio-‐informa#cs/ 

structual biologists, experimental biologists etc 

-‐ 

Combining research, training and also enabling beLer diagnos#cs 

-‐ 

Leveraging technologies such as genomics in public health efforts: 

currently evalua#ng the possibility of a NGS based na#onal HLA registry for translants, 

research in vaccines etc.

Mitradas M. Panicker 

The roles of serotonin in neural and non-‐neural systems 

! 


Basu, B., Desai, R., Balaji, J., Chaerkady,R., 

Sriram, V., Mai#, S., and Panicker, M.M. 

(2008). Serotonin in pre-‐implanta#on mouse 

embryos is localized to the mitochondria and 

can modulate mitochondrial poten#al. 

Reproduc#on. 135: 657-‐659. 

Adi# BhaLacharya, Shobhana Sankar and 

Mitradas M. Panicker (2009). Differences in 

the C-‐terminal tail contribute to the varia#on 

in trafficking between the Rat and Human 5-‐ 

HT2A receptor isoforms: Iden#fica#on of a 

primate-‐specific tripep#de ASK mo#f that 

confers GRK-‐2 and β2-‐Arres#n interac#on. J. 

Neurochem. 112: 723-‐32. 

Raote I, BhaLacharyya S, Panicker M.M. 

(2013). Func#onal selec#vity in serotonin 

receptor 2A (5-‐HT2A) endocytosis, recycling, 

and phosphoryla#on. Mol Pharmacol. 83: 

42-‐50. 

The major interests of my laboratory are the cellular mechanisms ac#vated by 

serotonin, a molecule widely recognized as an important neurotransmiLer. 

Interes#ngly, most of the serotonin is present outside the nervous system and 

seems to be involved in normal physiology in a variety of ways including early 

development in mammals. Most of the interac#ons of serotonin take place 

through its receptors expressed on the cell surface. Among the many receptors 

that it interacts with, two of these i.e. the 5-‐HT1A and 5-‐HT2A receptors have 

also been strongly implicated in psychiatric condi#ons. Therefore, serotonin 

plays an important role in communica#on in the nervous system and also 

governs development and physiology. 

Our studies have primarily focused on the regula#on of 5-‐HT2A receptors in 

neuronal and non-‐neuronal cells and also on its role in early developmental 

processes. The 5-‐HT2A receptor is also an important target of many clinically 

prescribed an#psycho#cs. Using modified 5-‐HT2A receptors which can be 

visually localized within cells and ‘5-‐HT2A knockout’ mice, we have made 

significant observa#ons regarding the behavior of the receptor in the presence 

of serotonin and an#psycho#cs. 

Recent results using pre-‐implanta#on mouse embryos and mammalian 

embryonic stem cells have determined that serotonin localizes to the 

mitochondria and affects mitochondrial poten#al. This has important 

implica#ons for development and cell survival. These studies are being 

extended to human induced pluripotent stem cells and could help us determine 

the role of these receptors and their endogenous and exogenous ligands

Gai# Hasan 

Inositol 1,4,5-‐trisphosphate signalling in cellular and systemic 

physiology 


Agrawal, N, Venkiteswaran, G, Sadaf, S, Padmanabhan, 

N, Banerjee, S and Hasan, G. (2010). Inositol 1,4,5-‐ 

trisphosphate receptor and dSTIM func#on in Drosophila 

insulin producing neurons regulates systemic 

intracellular calcium homeostasis and flight. J. Neurosci, 

30, 1301-‐1313. 

Kumar, S., Dey, D and Hasan, G. (2011) PaLerns of gene 

expression in Drosophila InsP3 receptor mutant larvae 

reveal a role for InsP3 signaling in carbohydrate and 

energy metabolism. PLoS One, 6(8): e24105. doi: 

10.1371/journal.pone.0024105 

Chakraborty, S and Hasan, G. (2012). Func#onal 

complementa#on of Drosophila itpr mutants by Rat 

IP3R1. J. Neurogenet, 26: 328-‐337: DOI: 

10.3109/01677063.2012.69750. 

Subramanian, M., Metya, S.K., Sadaf, S., Kumar, S., 

Schwudke, D. And Hasan, G. (2013). Altered lipid 

homeostasis in Drosophila InsP3 receptor mutants leads 

to obesity and hyperphagia. Dis. Model. Mech in press 

doi: 10.1242/dmm.010017. 

Hasan, G. (2013). Intracellular signaling in neurons: 

unraveling specificity, compensatory mechanisms and 

essen#al gene func#on. Current Opinion in 

Neurobiology, 23:62–67 hLp://dx.doi.org/10.1016/ 

j.conb.2012.07.004. 

Research in my group addresses systemic and cellular consequences of 

changes in intracellular calcium levels in animals. We are specifically 

interested in the second messenger Inositol 1,4,5-‐trisphosphate (InsP3) 

and its receptor – the InsP3 receptor. This protein exists on the 

membranes of intracellular calcium stores and performs the dual func#on 

of a receptor for InsP3 and a channel for calcium release. We address InsP3 

receptor func#on in the model organism Drosophila using gene#c, 

molecular, cellular, electrophysiological and behavioral methods. 

Our recent work has demonstrated that reducing InsP3R func#on in 

Drosophila neurons affects feeding and growth in larvae and mul#ple 

aspects of flight circuit development and func#on in pupae and adults. 

These studies have shown that restoring InsP3R func#on in neurons which 

either synthesize monoamines (like dopamine) or insulin-‐like pep#des 

(ILPs) rescues InsP3R mutant defects. A gene#c RNAi screen in the lab has 

helped iden#fy a set of surface receptors that ini#ate IP3 signaling in flight 

circuit neurons (Agrawal, T et al., in prep). More recently, projects to 

understand how InsP3R mutants respond to changes in regula#on of 

intracellular store Ca2+ and to stress condi#ons have been ini#ated. Work 

from my group has demonstrated for the first #me in a physiological 

context the requirement for store-‐operated calcium entry downstream of 

InsP3 signaling in neurons. Results from these studies suggest that gene#c 

and pharmacological methods could be used for controlling intracellular 

Ca2+ homeostasis as a possible therapeu#c strategy in certain 

neurodegenera#ve and metabolic diseases. Drosophila model and human 

studies in the context of such diseases are in progress.

Mathew K Mathew 

Crossing Barriers: Studies of Membrane Transport 

Biological membranes are oil-‐like, and charged solutes can only cross these 

barriers with the help of transport proteins. My laboratory studies several such 

proteins, ranging from the voltage-‐gated K+ channel in neurons to transporters 

that play a rôle in the survival of plants in salty soils. Our aim is to understand 

how these proteins do their jobs and to see how their ac#vity contributes to 

the overall physiology of the cell or organism. 


Rajagopal A, Rao AU, Amigo J, Tian M, 

Upadhyay S, Hall C, Uhm S, Mathew MK, 

Fleming MD, Paw BH, Krause M & Hamza I 

(2008) Heme homeostasis is regulated by 

the conserved and concerted func#ons of 

HRG-‐1 proteins Nature 453, 1127 – 1131 

Upadhyay SK, Nagarajan P & Mathew MK 

(2009) Potassium Channel Opening: A 

Subtle Two-‐Step J Physiol 587, 3851–3868 

Kavitha PG, Miller T, Mathew MK & 

Maathuis FJM (2012) Rice cul#vars with 

differing salt tolerance contain similar 

ca#on channels in their root cells. J Exp 

Botany 63, 3289–3296 

Electrical signaling in the nervous system requires rapid movement of ions 

across the nerve cell membrane. We have studied how the proteins that 

mediate this ionic movement func#on using a combina#on of molecular 

modeling, mutagenesis and electrophysiology. 

Plants use a variety of strategies to survive in salty soil. Barriers in the root 

which prevent external fluid from directly entering the xylem contribute to the 

ability of the plants to regulate what gets sent up to the shoot. Our data 

indicates that barriers are beLer developed and func#onal in salt-‐tolerant 

varie#es of rice than in sensi#ve varie#es and we are inves#ga#ng the 

mechanisms underlying their deposi#on. 

At the cellular level, we have found that the plasma membranes of cells from 

tolerant varie#es are much less permeable to Na+ than those from sensi#ve 

varie#es. We are using a combina#on of molecular biology, microscopy and 

electrophysiology to inves#gate the basis of these differences. Finally, studies 

of membrane trafficking in plant cells are providing insights into novel 

mechanisms of handling salt.

Jayant Udgaonkar 

How do proteins fold, unfold and misfold? 


Jha, S.K. & Udgaonkar, J.B. (2009) Direct 

demonstra#on of a dry molten globule 

intermediate on the unfolding pathway of a 

small protein. Proc. Natl. Acad. Sci. USA 106, 

12289-‐12294. 

Aghera, N. & Udgaonkar, J.B. (2012) Kine#c 

studies of the folding of heterodimeric 

monellin: evidence for switching between 

alterna#ve parallel pathways J. Mol. Biol. (In 

press) 

Jain, S. & Udgaonkar, J.B. (2011) Defining the 

pathway of worm-‐like amyloid fibril forma#on 

by the mouse prion protein by delinea#on of 

the produc#ve and unproduc#ve 

oligomeriza#on reac#ons. Biochemistry 50, 

1153-‐1161. 

Ramachandran, G. & Udgaonkar J. B. (2012) 

Evidence for the existence of a secondary 

pathway for fibril growth during the 

aggrega#on of tau. J. Mol. Biol. (In Press). 

The polypep#de chain of a protein must coil, turn, bend, loop and twist itself in a very 

precise manner while folding into the unique structure that enables the protein to func#on 

in the cell. The protein folding problem is to understand how structure develops as a 

protein folds. How proteins fold has been a long-‐standing, unsolved puzzle in biology, 

whose solu#on has obvious biotechnological as well as medical implica#ons. In par#cular, 

the improper folding of some proteins, and their consequent aggrega#on into amyloid 

fibrils, are characteris#c features of several neuro-‐degenera#ve diseases as well as of the 

prion diseases. An understanding of the mechanism of protein folding will also lead to a 

beLer understanding of the other facet of the protein folding problem, which is how to 

predict the func#onal structure of a protein from the amino-‐acid sequence that specifies it. 

My laboratory uses several small proteins, including barstar, monellin, the SH3 domain of 

the PI3-‐kinase, α-‐synuclein, tau, and the mouse prion protein as archetypical model 

proteins for studying how proteins fold, unfold as well as aggregate. We also study how 

correct folding is assisted by the chaperone GroEL. We use the tools of protein engineering 

and physical biochemistry. These include diverse op#cal spectroscopic methods such as 

#me-‐resolved fluorescence methods, as well as nuclear magne#c resonance spectroscopy 

and mass spectrometry methods. Our kine#c measurements span the #me domain of 100 

microseconds to 10 hours. 

Highlights of our recent work on protein folding and unfolding include (1) the 

demonstra#on that a dry molten globule forms ini#ally during unfolding; (2) the 

demonstra#on that the PI3 kinase SH3 domain folds and unfolds via mul#ple intermediates; 

and (3) the demonstra#on of switching between mul#ple folding pathways during the 

folding of monellin. Highlights of our recent work on protein misfolding and aggrega#on 

include (1) the demonstra#on that amyloid protofibrils may have different morphologies 

when formed on different pathways, and that a single muta#on in the protein sequence or 

a change in aggrega#on condi#ons can lead to switching between alterna#ve available 

pathways; (2) the demonstra#on that tau can u#lize a secondary pathway for amyloid 

fibril forma#on; and (3) the iden#fica#on of the direct oligomeric precursor of worm-‐like 

amyloid fibrils formed by the mouse prion protein.

K VijayRaghavan 

Developmental neurobiology of olfacKon and movement 


Brierley D, Rathore K, VijayRaghavan K, Williams D. 

Developmental origins and architecture of Drosophila 

leg motoneurons. J Comp Neurol. 2011 Nov 25.doi: 

10.1002/cne.23003. [Epub ahead of print] 

Guruharsha KG, Rual JF, Zhai B, Mintseris J, Vaidya P, 

Vaidya N, Beekman C,Wong C, Rhee DY, Cenaj O, 

McKillip E, Shah S, Stapleton M, Wan KH, Yu C, Parsa B, 

Carlson JW, Chen X, Kapadia B, VijayRaghavan K, Gygi 

SP, Celniker SE, Obar RA, Artavanis-‐Tsakonas S. A 

protein complex network of Drosophila melanogaster. 

Cell. 2011 Oct 28;147(3):690-‐703 

Our work is aimed at understanding how circuits are put together 

during development to generate the animal’s behaviour. We study 

the development and morphogenesis of individual neural and 

neuromuscular circuit components. We integrate these studies 

with those that examine how neurons connect to form circuits in 

the brain and also connect with muscles. This gives us a picture of 

how the ‘plumbing’ is developmentally put together. We next 

examine when and how func#onal proper#es of these circuits are 

put in place. The segmental organiza#on of the brain in the fly is 

remarkably similar to that of vertebrates and points to a common-‐, 

rather than an independent-‐ origin during evolu#on. This, and the 

conserved nature of many molecular and cellular aspects, holds 

out the promise of a general relevance to the understanding of 

how func#onal neural circuits underlying behavior are assembled 

during development. 

Mukherjee, P., Gildor, B., Shilo, B., VijayRaghavan, K., & 

Schejter, E. D. (2011). The ac#n nucleator WASp is 

required for myoblast fusion during adult Drosophila 

myogenesis Development. 138(11), 2347-‐2357. 

Das, A., Chiang, A., Davla, S., Priya, R., Reichert, H., 

VijayRaghavan, K., and Rodrigues, V. (2011). 

Iden#fica#on and analysis of a glutamatergic local 

interneuron lineage in the adult Drosophila olfactory 

system. Neural Systems & Circuits 1, 4.

K. S. Krishnan 

 

Reent Publica#ons: 

Gupta K, Kumar M, Chandrashekara K, 

Krishnan KS, Balaram P. (2012) Combined 

electron transfer dissocia#on-‐collision-induced 

dissocia#on fragmenta#on in the 

mass spectrometric dis#nc#on of leucine, 

isoleucine, and hydroxyproline residues in 

Pep#de natural products. J Proteome Res. 

11(2):515-‐22. 

Sanyal S, Krishnan K.S (2012). 

Gene#c modifiers of comatose muta#ons 

in Drosophila: insights into neuronal NSF 

(N-‐ethylmaleimide-‐sensi#ve fusion factor) 

func#ons. J Neurogenet. 26(3-‐4):348-‐59. 

! 

A major interest in my lab is isola#on and characteriza#on of pep#des of 

therapeu#c value from marine cone snails, frog skin secre#ons and wasp 

venoms. Mass spectrometry-‐based de novo sequencing of venom 

components combined with deep sequencing RNA from the venom glands 

and valida#on by chemical synthesis is our main thrust. We are 

developing several assays mainly u#lizing the power of Drosophila 

gene#cs, Oocyte expression of specific channel proteins and cell biology 

to establish protocols for ac#vity dependent purifica#on of pep#des that 

could be drug leads. These studies are done in collabora#on mainly with 

Prof. Balaram at IISc. I also ac#vely collaborate with colleagues at IISc 

(Sushil DuLa, Hanumae Gowd), colleagues at NCBS (MK Mathew, S. 

Mayor), GKVK (Chandrasekhar Krishnappa)

O. Siddiqi 

GeneKc analysis of chemosensory percepKon in Drosophila 

Drosophila, like the Brahmin, is born twice, first from the egg as a maggot, then 

from the pupa as an imago. In both of its incarna#ons the fly’s olfactory behavior 

undergoes profound changes with age and experience. An important problem is 

to dis#nguish between innate and acquired behavior. This is a difficult and, in 

several respects, an unseLled issue. Understanding adap#ve behavior and 

establishing its neural correlates is the focus of our group’s interest. As a part of 

this effort we are studying learning and memory in larva and imago. 


Chakraborty TS, Goswami SP, Siddiqi O 

(2009) Sensory correlates of imaginal 

condi#oning in Drosophila melanogaster. J 

Neurogenet.23(1-‐2):210-‐9. 

Khurana S, Abu Baker MB, Siddiqi O. 

(2009) Odour avoidance learning in the 

larva of Drosophila melanogaster. J Biosci. 

34(4):621-‐31. 

Iyengar A, Chakraborty TS, Goswami SP, 

Wu CF, Siddiqi O. (2010) Post-‐eclosion 

odor experience modifies olfactory 

receptor neuron coding in Drosophila. Proc 

Natl Acad Sci U S A. 107(21):9855-‐60. 

Epub 2010 May 6. 

Some years ago we began to inves#gate imaginal condi#oning, a process by 

which, in the first few days a[er eclosion, the fly learns to dis#nguish between 

aLractants and repellents. It develops aLrac#on towards chemicals to which it is 

exposed and an increased aversion to odors it has not experienced (these 

reports, 1999). Bilal Rashid, Farzana Anjum and Jawaid Ahsan have described 

mutants, which affect imaginal condi#oning. Tuhin Chakraborty and Sunil 

Prabhakar have found that imaginal condi#oning is correlated with an increased 

peripheral sensory response (EAG). Abu Baker and Gayatri Ranganathan have 

analyzed shock avoidance learning in the larva to separate various components of 

olfactory memory. The experiment by Annapoorna Bhat on co-‐induc#on is our 

first aLempt to develop psychophysics of odor percep#on with Drosophila. 

Chakraborty TS, Siddiqi O. (2011). Odor 

recep#on in antenna and antennal lobe of 

Drosophila. Fly (AusKn). 5(1):14-‐7. Epub 

2011 Jan 1.

The Theory Program 

What is the theory program? 

NCBS is pleased to announce PhD and IntPhD opportuni#es in the physical and mathema#cal study of 

biological systems. Biology, all the way from molecules, through cells, #ssues, networks in the brain, to 

ecosystems holds great promise today for bright young theorists. Exci#ng problems abound, a vibrant and 

connected global community of theorists is growing and the thrill of conceptual discoveries await the prepared 

and well-‐trained student. The theory program is open to students with a physics/maths/chemistry/engineering 

background and a strong curiosity in biology, as well as students with a biology background having a strong 

interest in the mathema#cal and computa#onal study of living systems. 

What is unusual about this program? 

Crea#ng and finding new problems is an essen#al part of all scien#fic research. We put developing this skill at 

the heart of our program design. Students will learn to create, select and solve research problems at the 

interface of biology and other sciences. They are encouraged to chart their own research path in conjunc#on 

with faculty of the theory group. Educa#on extends beyond the classroom and good theory and prac#ce are 

intertwined. We encourage students to try their hand at designing small experiments -‐-‐ biological, 

electromechanical and computa#onal -‐-‐ in laboratories maintained by faculty associated with the theory group. 

We have a strong visitor program with researchers from all over the world regularly spending a few days to a 

few months at the group. 

What is the curriculum? 

We provide core courses to establish a rigorous founda#on in mathema#cal and numerical analysis, and cover 

topics including sta#s#cal mechanics and so[ maLer physics, molecular dynamics, stochas#c processes, 

nonlinear dynamics, control and op#miza#on, informa#on theory, and so on. Bridging courses in both basic 

biology and basic mathema#cs will ensure that the core courses are accessible to all. Based on students' needs 

we also offer advanced courses on mul#disciplinary topics like non-‐equilibrium sta#s#cal mechanics, complex 

networks, evolu#onary dynamics, biorobo#cs and func#onal genomics. Bangalore has an excellent diverse 

environment for theory: Students can complement NCBS courses with those from surrounding ins#tutes such 

as the Indian Ins#tute of Science, Raman Research Ins#tute and the Jawaharlal Nehru Centre for Advanced 

Scien#fic Research, all of with whom we have ac#ve interac#ons.

The InsKtute of Stem Cell Biology & RegeneraKve Medicine 

New Ini#a#ves: inStem Labs 

The Ins#tute for Stem Cell Biology and Regenera#ve Medicine (inStem) is a new ini#a#ve 

growing in an expanded campus with NCBS. In the previous pages you have seen a 

diversity of research programs across the scale of the Life Sciences in the laboratories of 

principal inves#gators. InStem aims to complement this approach by developing teams of 

researchers to address important ques#ons in biomedical sciences and human biology. 

InStem’s research is structured into teams. 

inStem teams are composed of senior, intermediate and early career scien#sts and the 

scien#sts themselves are a mix of researchers, technology developers and clinicians. Team 

members are drawn from inStem, NCBS and elsewhere. Students wishing to rotate in 

these teams will be associated with an appropriate inves#gator in a team at inStem. The 

possibility of joining one of the themes at inStem for a PhD, will require a mentor at NCBS 

and will be decided in consulta#on with the Theme Coordinator and Head Academics, 

NCBS.

Route Map to NCBS [not to scale] 

X 

x. 

1. 

5 

K 

M 

s. 

NCB 

S 

Signa 

ge 

First Left Turn 

Play Ground 

Yelahanka 

GKVK 

Main Gate 

X 

A 

pp 

ro 

x. 

1. 

5 

K 

M 

s. 

NCB 

S 

Signa 

ge 

NCB 

S 

Signa 

ge 

First Left Turn 

L & T Factory 

X 

Way to NCBS 

Academic Block 

Bellary Road 

NCB 

S 

Play Ground Signa 

ge 

From Mekhri Circle proceed towards North. The L&T factory is about 8 

K.M. from Mekhri Circle after the Hebbal flyover on the left hand side of the 

road. Turn left after L&T factory into GKVK campus. After about one and 

half kilometer take left turn (the very first left turn). 

You will see a sigage board at this point and a basket ball ground on the left 

side. Proceed about 200 meters to come to the T junction. Please look for 

Hebbal 

Lake 

X 

Way to NCBS 

Academic Block 

NCBS 

HOUSING 

BLOCK 

Way to NCBS 

Guest House & 

Housing Block 

NCB 

S 

Signa 

ge 

NCBS 

ACADEMIC 

BLOCK 

From Mekhri Circle proceed towards North. The L&T factory is about 8 

K.M. from Mekhri Circle after the Hebbal flyover on the left hand side of the 

road. Turn left after L&T factory into GKVK campus. After about one and 

half kilometer take left turn (the very first left turn). 

You will see a sigage board at this point and a basket ball ground on the left 

side. Proceed about 200 meters to come to the T junction. Please look for 

signage board again at this point. If you drive about 400 yards to the left you 

signage board again at this point. If you drive about 400 yards to the left you 

are at the Academic Block. 

If you drive to the right from T junction for about 50 meters and again take a 

left turn and proceed about 100 meters you will reach NCBS guest house and 

housing accommodation. 

Ring Road 

Hebbal 

Flyover 

NCBS 

HOUSING 

BLOCK 

Way to NCBS 

Guest House & 

Housing Block 

NCBS 

ACADEMIC 

BLOCK 

Bellary Roa

Brochure - National Centre for Biological Sciences

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