GS-â2012 - National Centre for Biological Sciences

GS-‐2012 

Handbook for Interviews 

Photo courtesy, Durafshan Sakeena, PhD Scholar 

Na9onal Centre for Biological Sciences, TIFR, Bangalore 

May-‐June 2012

May 2012 

Dear Students, 

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

sent separately, invi9ng you to par9cipate in the interviews carries details on the 

dates, reimbursements and travel to NCBS. This handbook is provided in an aLempt to help 

you in your experience with the selec9on process. There are sec9ons which should 

familiarize you with the actual interview process as well as those more helpful to students 

eventually joining the program. We also include a sec9on where the Faculty at NCBS 

provides an overview of their research programs. We encourage you all to read this sec9on 

before your visit and meet with members of the laboratories that you find par9cularly 

interes9ng. Addi9onal informa9on on all laboratories and the programs on offer are 

available on the NCBS website. 

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

seeing you in May. 

With best wishes 

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 mo9vated to pursue a career in research. 

The Integrated Biology (iBio) and Theore9cal Studies programs at NCBS provide a s9mula9ng 

environment for students with backgrounds in physics, chemistry and mathema9cs 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 applica9on procedure. 

In all aforemen9oned programs, students register for a PhD at the TIFR Deemed University typically 

1.5-‐2 years from the date of joining, a[er mee9ng course requirements and qualifying a 

comprehensive examina9on. 

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

selec9on interview may be appointed to this program with salary support on PI grants. 

The MSc in Wildlife & Conserva9on program is offered only at NCBS and selec9ons are made based on a 

separate test and interview process. The next selec9ons for this program will be in 2014

2. Selec9on Process 

GS-‐2012 Interviews 

Candidates are invited to apply in response to adver9sements appearing in na9onal 

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 evalua9on 

are interviewed for admission. NCBS sends out an applica9on package to students who 

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

test, together with the informa9on requested in the applica9on package is used to short-list 

candidates for interviews at Bangalore in May 2012. 

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 members of the faculty at NCBS. 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 ques9oned on their basic understanding of 

Biology, Chemistry or Physics as well as quan9ta9ve 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 some9mes 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 members and again some commiLees will have 

greater representa9on of faculty with core exper9se 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 applica9on package is used as a basis of ques9oning. However, 

candidates have to be prepared for ques9ons that have been taught at a more advanced level 

in special papers or via projects etc. In previous years, ques9ons have also been based on 

original research ar9cles that were distributed to all candidates prior to the interviews. 

Candidates uncomfortable or unable to handle ques:ons in a par:cular area must indicate this 

to the commi

The final list of selected candidates, drawn up in consulta9on with Chairpersons of the 

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

late a[ernoon/ evening of the fourth 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. 

Alterna9vely, a student on the wait-‐list may also join the graduate program with salary support 

from the Principal Inves9gator’s [PI] grant. Admission and con9nua9on on the graduate 

program in both situa9ons is con9ngent on associa9on with the PIs laboratory. 

This op9on is not available to students short-‐listed on the Integrated PhD program. Faculty at 

NCBS will post informa9on 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.

GS-‐2012 Overseas Applica9ons 

NCBS invites applica9ons from students who enrolled in Colleges and University outside 

the Indian Subcon9nent 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 Ac9vi9es before 

November each year. 

The academic office will assist you with the submission of an applica9on package and the 

subsequent steps in the selec9on process. In some instances we offer the op9on 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 na9onals 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.

Informa9on related to Interviews 

4. Accommoda9on and Meals during the Interviews 

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

as NCBS does not provide accommoda9on. Informa9on regarding short-‐term 

leased accommoda9on 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 9mes. If staying on for dinner, please inform the 

canteen management at lunch 9me 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 invi9ng them to the 

interview; proof of ID in the form of a University/Ins9tute ID card/ PAN Card may be 

required and should be available if needed. 

• A copy of your 9cket 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 9ckets 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 9cket; TA/DA form which can be downloaded from our website


6. Hotels & Commercial Guest Houses near NCBS-‐ par9al 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 & Conven9on 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 accommoda9on during the interviews

Orienta9on 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. Accommoda9on for graduate students 

NCBS offers accommoda9on 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 comple9ng administra9ve formali9es in August. 

9. Orienta9on and Rota9ons for incoming graduate students 

New students join NCBS on Wednesday August 1 st 2012. All new students must par9cipate in 

the Orienta9on Program. During the program, sessions are arranged with faculty members 

to discuss work ongoing in their laboratories. The program also includes sessions with 

individuals who manage Research, Technical and Administra9ve Services at NCBS. In the 

course of the Orienta9on Program, students are guided through procedures such as the 

comple9on of the mandatory medical test and administra9ve formali9es towards joining in 

the course of this program. Administra9ve staff will assist you in this. Addi9onal 

informa9on on rota9ons, courses etc. will be provided during the Orienta9on Program 

Laboratory allotments for graduate studies are ONLY made a[er the comple9on of laboratory 

rota9ons. No student in the graduate program is exempt from laboratory rota9ons.

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 coordina9on with the 

Administra9ve 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 selec9on and joining the 

program at NCBS. Do not call unless there is an 

emergency. Please do not contact our faculty for 

informa9on 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 jus9fied requests for 

rescheduling within the assigned dura9ons of the 

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

the subject line Name_GS2012_date change.

esearch opportuniKes for 

graduate studies 

Please visit our webpage h

The InsKtute of Stem Cell Biology & RegeneraKve Medicine 

New Ini9a9ves: inStem Labs 

Jyotsna Dhawan 

S Ramaswamy 

The Ins9tute for Stem Cell Biology and Regenera9ve Medicine (inStem) is a new ini9a9ve 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 inves9gators. InStem aims to 

complement this approach by developing teams to researchers to address important ques9ons in 

biomedical sciences and human biology. InStem’s research is currently structured into four teams with 

two others coming by soon. 

inStem teams are composed of senior, intermediate and early career scien9sts and the 

scien9sts 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 inves9gator in a team at inStem. If they would like to work for their PhD in a team 

project at inStem are expected to have a principal NCBS mentor. 

Current inStem teams along with the names of some members, who can outline research 

in their teams are given below. The teams are dynamic, both in their composi9on and science, so do be 

in touch with Jyotsna Dhawan (jdhawan@ncbs.res.in) and Apurva Sarin (sarina@ncbs.res.in) for updates 

and for introduc9ons to the contacts listed below. 

Understanding Pluripotency, Development and Regenera9on: This team aims to use 

induced pluripotent stem-‐cells (iPS cells), embryonic stem (ES) cells and model organisms (mouse, fly, 

fish, planarian and hydra) to decipher developmental and regenera9on principles. Contact: Jyotsna 

Dhawan 

Cardiac and Vascular biology. This team studies human cardiomyopathy across scale, from 

molecular, cellular to 9ssue levels. They study how mutant actomyosin motors can lead to disease, how 

these are organized and func9on in cardiac cells and how these cells func9on in the heart. Vascular 

biology and ques9ons in blood development and angiogenesis are another theme. Contact: John Mercer 

Epithelial Biology and Skin Differen9a9on. This team, star9ng in August 2012, will uses 

accessible stem cell niches in skin to understand the biology of 9ssue-‐renewal in diseases such as 

diabetes and eczemas. Human and mouse models will be used. Contact: Colin Jamora 

Chemical Biology of Cancer: This project will combine cell-‐biology, imaging technologies, 

small-‐molecule screens and structural biology to expand and define the ‘drug-‐able’ space in specific 

cancer. In addi9on, several collabora9ons across the campus on the more general theme of cancer 

biology are being embarked. 

Contact: Ashok Venkitaraman 

Two new teams, one in the Neurobiology of Au9sm Spectrum Disorders and another in 

Physical Biology are likely to evolve in the coming year.

New Ini9a9ves: The Theory Program 

What is the theory program? 

NCBS is pleased to announce new PhD and IntPhD opportuni9es in the physical and mathema9cal study of biological systems. 

Biology, all the way from molecules, through cells, 9ssues, networks in the brain, to ecosystems holds great promise today for 

bright young theorists. Exci9ng 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 mathema9cal and computa9onal study of living systems. 

Faculty members with strong bonds to theory are Aswin Seshasayee (computa9onal and func9onal genomics of bacterial gene 

regula9on), Madan Rao (physics of ac9ve, evolving systems), Madhusudhan Venkadesan (morphology and control in animals and 

machines), Mukund ThaLai (computa9onal cell biology and evolu9on), Sandeep Krishna (decisions, feedback and games in 

biological systems), Sanjay Sane (the physics and neurobiology of insect flight), Shachi Gosavi (computa9onal protein dynamics, 

folding and func9on), R. Sowdhamini (computa9onal approaches to protein science) and Upinder Bhalla (computa9onal 

neuroscience and systems biology of olfac9on and memory). Several others colleagues collaborate with theorists and with those 

who model biological systems. 

What is unusual about this program? 

Crea9ng and finding new problems is an essen9al part of all scien9fic 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 conjunc9on with faculty of the theory group. Educa9on extends beyond 

the classroom and good theory and prac9ce are intertwined. We encourage students to try their hand at designing small 

experiments -‐-‐ biological, electromechanical and computa9onal -‐-‐ 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. Each student can choose to spend 6 months in a research group outside NCBS, or in industry, to give a broader 

perspec9ve on ways of prac9sing science and to help inform their future career choices. 

What is the curriculum? 

We provide core courses to establish a rigorous founda9on in mathema9cal and numerical analysis, and cover topics including 

sta9s9cal mechanics and so[ maLer physics, molecular dynamics, stochas9c processes, nonlinear dynamics, control and 

op9miza9on, informa9on theory, and so on. Bridging courses in both basic biology and basic mathema9cs will ensure that the core 

courses are accessible to all. Based on students' needs we also offer advanced courses on mul9disciplinary topics like non-equilibrium 

sta9s9cal mechanics, complex networks, evolu9onary dynamics, biorobo9cs and func9onal genomics. Bangalore has 

an excellent diverse environment for theory: Students can complement NCBS courses with those from surrounding ins9tutes such 

as the Indian Ins9tute of Science, Raman Research Ins9tute and the Jawaharlal Nehru Centre for Advanced Scien9fic Research, all 

of with whom we have ac9ve interac9ons.

Deepa Agashe 

Selected Publica9ons 

Falk JJ, Parent CEP, Agashe D and Bolnick DI 

(2012). Asymmetrical reproduc9ve isola9on 

due to maladapta9on during an 

experimentally induced niche shi[ in 

laboratory popula9ons of Tribolium 

castaneum. In press, EvoluKonary Ecology 

Research 

Agashe D and Bolnick DI (2012). Dietary niche 

and popula9on dynamic feedbacks in a novel 

habitat. Oikos 121(3): 347-‐356. 

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

of founding gene9c varia9on on adapta9on to 

a novel resource. EvoluKon 65(9): 2481-‐2491 

Agashe D and Bolnick DI (2010). Intraspecific 

gene9c varia9on and compe99on interact to 

facilitate niche expansion. Proceedings of the 

Royal Society of London, series B. 277(1696): 

2915-‐2924 

Agashe D (2009). The stabilizing effect of 

intraspecific gene9c varia9on on popula9on 

dynamics in novel and ancestral habitats. 

American Naturalist 174(2): 255-‐267. 

EvoluKonary ecology of adaptaKon and genome evoluKon 

new labs at NCBS 

My research is largely focused on understanding the evolu9onary and ecological processes 

underlying adap9ve evolu9on. Adapta9on to various ecological factors has been an important 

force in the evolu9on of the amazing array of species on earth. However, we are only beginning 

to address some key ques9ons about adapta9on. How do ecological condi9ons (e.g. resource 

availability) and gene9c factors (e.g. gene9c diversity) determine the basis and dynamics of 

adapta9on? At the molecular level, what is the nature of selec9on on genome structure (e.g. 

arrangement of genes on chromosomes) and composi9on (e.g. GC%)? Conversely, how do 

these genomic characteris9cs affect adapta9on? My favourite approach to address these 

ques9ons has been experimental evolu9on in the lab. For instance, previously I tested how 

gene9c diversity in Tribolium beetle popula9ons affected compe99on, popula9on size, 

ex9nc9on, and adapta9on to new habitats. In later work, I tested how synonymous muta9ons 

in enzyme-‐coding genes affect bacterial fitness, and determined the gene9c basis of 

subsequent adapta9on in these mutants with genome re-‐sequencing. 

Looking ahead, I am star9ng two major projects at our new lab at NCBS. First, I 

want to determine the ecological and gene9c factors that determine a species’ range, which 

remains poorly understood for most species. We will analyze dispersal, adap9ve poten9al, 

resource availability, and gene9c popula9on structure in Tribolium castaneum popula9ons 

across India as a comprehensive example of the processes that shape an organism’s 

distribu9on. Second, we don’t quite understand the forces responsible for the evolu9on of 

major genomic features such as GC content and codon usage, and their impact on adapta9on. 

To address this, we will manipulate these genomic features in gene9cally tractable bacteria 

(e.g. Escherichia coli), and using bioinforma9c and phylogene9c methods to test the generality 

of our experimental results. 

To summarize, we would like to 9nker with gene9c and ecological features of 

organisms so that as we watch evolu9on in ac9on, we can beLer understand how it works.

Krushnamegh Kunte 

EvoluKon and organizaKon of biological diversity 

new labs at NCBS 

Research in my lab is aimed at understanding the evolu9on and organiza9on of biological diversity on 

earth. As a lab, we study biodiversity in an interdisciplinary manner, with our scien9fic ques9ons 

spanning the fields from community and popula9on ecology to evolu9onary gene9cs, and methods 

ranging from behavioral experiments to phylogene9c inference, theore9cal modeling, and molecular and 

developmental gene9c experiments. Our work addesses aspects of the origin of species, morphological 

diversifica9on, and ecological and molecular gene9c bases of sex-‐limited and polymorphic traits. We try 

to integrate the fields of popula9on biology, natural selec9on theory and molecular gene9cs, which 

serves to conceptually unify the biological sciences. 

Recent Publica9ons 

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 specia9on among 

9ger swallowtail buLerflies. PLoS 

Gene)cs, 7:e1002274. 

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

Kunte. 2009. Popula9on dynamics and 

seasonal polyphenism of Chilades 

pandava buLerfly (Lycaenidae) in 

central India. Current Science, 

97:1774-‐1779. 

Kunte, K. 2009. Female-‐limited mime9c 

polymorphism: A review of theories and 

a cri9que of sexual selec9on as 

balancing selec9on. Animal Behaviour, 

78:1029–1036. 

Kunte, K. 2009. The diversity and 

evolu9on of Batesian mimicry in Papilio 

swallowtail buLerflies. Evolu)on, 

63:2707–2716. 

Kunte, K. 2008. Mime9c 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 

protec9on from predators by mimicking toxic or otherwise protected species (called “models”). 

Predators learn to avoid models based on prior experience, and subsequently avoid ea9ng mimics due to 

misiden9fica9on. Hundreds of mime9c buLerfly species are known from tropical forests. There is 

tremendous varia9on 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 selec9ve 

pressures that favor such varia9on in mimicry, and uncover the gene9c basis of color paLern varia9on. 

We mainly use phylogene9c methods, ecological observa9ons and molecular gene9c tools in this part of 

our research. 

Our second system is Indian buLerflies, which offer many opportuni9es to study 

biogeography, community ecology, popula9on biology and conserva9on issues. Indian buLerflies are 

excellent to study various interes9ng phenomena, including large-‐scale migra9ons and seasonal 

polyphenism. Due to their considerable diversity and endmism in the Indian Subcon9nent, 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 excep9on. The problems of a very large human popula9on in a developing country, 

combined with a serious administra9ve commitment to conserva9on and strong na9onal conserva9on 

legisla9on, makes India a unique country to understand scien9fic and social issues related to the 

preserva9on of biodiversity. 

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

morphological diversifica9on, 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 interac9on between control and morphology in animals 

and machines. We combine biological, mechanical, and mathema9cal methods to 

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

Selected Publica9ons: 

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

Effects of neuromuscular lags on 

controlling contact transi9ons. Philos 

Trans R Soc London, Ser A, 367(1891): 

1163–1179, 2009. 

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

Neural control of mo9on-‐to-‐force 

transi9ons with the finger9p. Journal of 

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

M. Venkadesan, J. Guckenheimer, and F.J. 

Valero-‐Cuevas. Manipula9ng the edge of 

instability. Journal of Biomechanics, 

40(8):1653–1661, 2007. 

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. 

Humans and other animals exhibit astoundingly versa9le and robust 

motor behaviour. Nevertheless, there are limits to their capabili9es like when an 

experienced runner loses balance and falls, or even mild neuromuscular diseases 

have surprisingly severe effects. How are these limits of performance affected by 

disease, age, training, or ontogeny? Do animals outperform their robo9c 

counterparts because of or despite the nonlineari9es and `sloppiness' inherent to 

biology? Have animals finely-‐tuned their sloppiness through evolu9on in order to 

achieve the robustness one associates with biology? Can we, and how do we extract 

design and control principles for understanding biomechanical func9on and also for 

improving the state of modern robo9cs? Such ques9ons about animals and 

machines, ranging in scale from collec9ons of muscle fibres to the whole organism, 

are at the heart of our research. 

We study the dynamics and control of the hand, arm and leg, on scales 

ranging from collec9ons of muscle fibres to the whole animal. Biomechanical 

experiments with muscle recordings, kinema9cs and kine9cs are complemented by 

theore9cal approaches stemming from nonlinear dynamical systems, probability 

theory, op9miza9on theory, and numerical analysis. In parallel, bio-‐inspired 

mechanical designs test our mathema9cal theories of motor control. Our efforts are 

aimed at gaining fundamental insights about how biology deals with compe9ng 

demands on motor behaviour. We hope that this understanding will shed light on 

how diseases impair our func9oning, and thus help improve treatments, surgical 

techniques, design of prosthe9cs, rehabilita9on regimens, and also the design of 

robots.

Aswin Sai Narain Seshasayee 

ComputaKonal and funcKonal genomics of bacterial gene 

regulaKon and adaptaKon 

Lab retreat at Wynaad 

Recent Publica9ons 

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

Benes V, Fraser GM, Luscombe NM*, Seshasayee ASN*. 

Genomics of DNA cytosine methyla9on in Escherichia coli 

reveals its role in sta9onary phase transcrip9on. Nature 

CommunicaKons 2012. In Press. 

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

conserva9on of DNA methyltransferases in bacteria. 

Nucleic Acids Research 2012. In Press. 

Mar9ncorena I*, Seshasayee ASN, Luscombe NM*. 

Evidence of non-‐random muta9on rates suggests an 

evolu9onary risk management strategy. Nature 2012. In 

Press.[PMID: 22522932] 

Prieto AI, Kahramanoglou C, Ali RM, Fraser GM*, 

Seshasayee ASN*, Luscombe NM*. Genomic analysis of 

DNA bingind and gene regula9on by homologous 

nucleoid-‐associated proteins IHF and HU in Escherichia 

coli. Nucleic Acids Research 2012. In Press. [PMID: 

22180530] 

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. [PMID: 

21097887] 

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 gene9c material and / or altera9ons in the nature and amounts 

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

bacterial biology using a combina9on of molecular and 'genomic' 

experiments and computa9onal analysis. In par9cular, we study the 

following: 

the role of global transcrip9onal regulators in influencing growth 

physiology of E. coli 

gene9c and transcrip9onal adapta9on of E. coli popula9ons to 

chemical and nutrient stresses 

computa9onal analysis of molecular mechanisms influencing-‐ and 

consequences of horizontal gene transfer 

We expect an incoming PhD student to be competent in computa9on 

and sta9s9cs and be able to develop an independent research plan 

within the ambit of our group's interests. 

*corresponding author(s) 

#joint first author

Sandeep Krishna 

InformaKon, Decisions and Feedback in Biological Systems 

I'm interested in how biological organisms acquire and process informa9on, and integrate 

different pieces of informa9on to make decisions. I use computa9onal modeling and 

theore9cal analyses to understand the role of feedback mechanisms in regulatory networks 

that process informa9on. 


Pedersen, L, Jensen, M. H. & 

Krishna, S (2011), PLoS One 6, 

e25550. 

Hunziker, A., Tuboly, C., 

Horvath, P., Krishna, S. & 

Semsey, S. (2010), Proc. Natl. 

Acad. Sci. (USA) 107, 12998– 

13003 

Avlund, M., Dodd, I., Sneppen, 

K. & Krishna, S. (2009) J. Mol. 

Biol. 394, 681–693. 

Avlund, M., Dodd, I., Semsey, 

S., Sneppen, K. & Krishna, S. 

(2009) J. Virol. 83, 11416– 

11420. 

Krishna, S., Semsey, S. & 

Jensen, M. H. (2009) Phys. Biol. 

6, 036009. 

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

organisms that could be said to make a developmental decision. Upon infec9ng a bacterium, 

temperate phage enter either the ly9c 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 informa9on such as the number of 

infec9ng 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 posi9ve one 

regula9ng transport and a nega9ve one regula9ng metabolism. In contrast, iron metabolism in 

several bacteria has at its core two nega9ve feedback loops. I’m interes9ng in understanding 

the dynamics of mul9ple entangled loops by inves9ga9ng compara9ve models of metabolic 

regula9on in E. coli, H. pylori and Y. pes9s, and mapping the transi9on to sta9onary 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 combina9ons of feedback loops. 

3. Oscillatory control in signaling systems. Periodic behaviour in cells covers a wide range of 

9mescales, from circadian rhythms (24 hours) to calcium oscilla9ons (seconds). Oscilla9ons of 

1-‐5 hour 9me periods have been observed in NF-‐kB, p53 and Wnt signaling, which are, 

respec9vely, crucial regulators of immune response, cell growth/death and embryo 

development. Yet, the precise role of oscilla9ons is unclear. I use theore9cal models to explore 

whether informa9on about the s9muli that trigger NF-‐kB, p53 and Wnt can be encoded in 

characteris9cs of oscilla9ons, e.g. their frequency.

Vatsala Thirumalai 


Marder E and Thirumalai V (2002) 

Cellular, synap9c and network 

effects of neuromodula9on. Neural 

Networks 15(4-‐6):479-‐93. 

Thirumalai V, Prinz AA, Johnson, CD 

and Marder E (2006) Red Pigment 

Concentra9ng Hormone Strongly 

Enhances the Strength of the 

Feedback to the Pyloric Rhythm 

Oscillator but Has LiLle Effect on 

Pyloric Rhythm Period. J. 

Neurophysiol., 95(3):1762-‐70. 

Thirumalai V and Cline HT (2008) A 

commanding control of behavior. 

(2008) Nat Neurosci. 11(3):246-‐8. 

Thirumalai V and Cline HT (2008) 

Endogenous dopamine suppresses 

ini9a9on of swimming in pre-‐feeding 

zebrafish larvae. J. Neurophysiol. 

100(3):1635-‐48. 

Neural control of movement during development and in adulthood 

For most animal species, survival depends cri9cally on the ability to move-‐ be it for 

feeding, escaping predators or selec9ng a suitable mate. To generate movement, 

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

control the spa9al and temporal paLern of skeletal muscle contrac9ons. Our lab is 

interested in understanding the hierarchy, mechanisms and development of neural 

circuits that generate movement. 

In vertebrates, the circuits that control movement are found in the spinal 

cord and in the brain. The spinal circuits controlling the genera9on of locomo9on are 

referred to as ‘central paLern generators’ as the output from these circuits is 

paLerned and rhythmic electrical ac9vity sent to the muscles. These central paLern 

generators are in turn controlled by sensory drive and by commands from the 

locomotory centers of the brain. My lab focuses on the development of central paLern 

generators and the development of descending motor control from the brain. We also 

seek to understand the mechanisms by which brain locomotor circuits control 

movement in mature organisms. 

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 observa9on of developing internal organs including the brain. 

We employ a suite of techniques to tease out the circuitry responsible for genera9ng 

swimming in developing and more mature zebrafish. We record electrical ac9vity from 

individual spinal and brain neurons using extracellular and whole-‐cell patch clamp 

techniques. We record ac9vity from popula9ons of neurons simultaneously using 

calcium imaging. We generate transgenic zebrafish to express proteins of interest in 

par9cular neurons. This allows us to selec9vely ablate and also to electrically ac9vate/ 

inac9vate specific popula9ons at will. Using these cu ng edge tools and technologies, 

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

locomo9on.

Shachi Gosavi 

Selected Publications: 

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

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

triggers route-‐switching on the 

func9onal landscape of interleukin-‐1β.” 

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

1490-‐1493, 2012. 

P. C. Whiƒord, J. K. Noel, S. Gosavi, A. 

Schug, K. Y. Sanbonmatsu and J. N. 

Onuchic, “An All-‐atom Structure-‐Based 

Poten9al for Proteins: Bridging Minimal 

Models with All-‐atom Empirical 

Forcefields.” Proteins, 75, 430-‐441, 

2009. 

S. Gosavi, P. C. Whiƒord, P. A. Jennings 

and J. N. Onuchic, “Extrac9ng func9on 

from a b-‐trefoil folding mo9f.” Proc. 

Natl. Acad. Sci. USA, 105, 10384-‐10389, 

2008. 

L. L. Chavez, S. Gosavi, P. A. Jennings and 

J. N. Onuchic, “Mul9ple routes lead to 

the na9ve state in the energy landscape 

of the b-‐trefoil family.” Proc. Natl. Acad. 

Sci. USA, 103, 10254-‐10258, 2006. 

S. Gosavi, L. L. Chavez, P. A. Jennings and 

J. N. Onuchic, “Topological Frustra9on 

and the folding of Interleukin-‐1b.” J. 

Mol. Biol., 357, 986-‐996, 2006. 

ComputaKonal folding and funcKonal dynamics of proteins 

Proteins are the workers of the cell. It is important to be able to both predict and engineer 

their func9on. The na9ve or folded shape of a protein, (as seen in the crystal or NMR 

structure) is essen9al for this func9on. Also, proteins are constantly moving and jiggling 

and these dynamics aid binding and conforma9onal change. So, protein mo9on, both 

large-‐scale folding as well as small scale local vibra9ons, facilitates protein func9on. 

The same amino acid sequence helps the protein both fold efficiently and a[er 

folding, work accurately. So, protein folding and protein func9on are interconnected. For 

example, one can’t engineer func9on without aLen9on to folding because this can 

destabilize the protein, and one can’t increase folding rates by changing func9onal 

residues. I am interested in understanding this tradeoff between folding and func9on using 

computa9onal methods. 

Computa9onal molecular dynamics (MD) provides a detailed descrip9on of 

protein mo9on not easily accessible to experimental methods. Protein dynamics occur on 

diverse 9mescales but o[en it is only the low frequency (long 9mescale) mo9on that is 

func9onally relevant. Including all atoms of the protein in a model restricts the maximum 

allowed simula9on 9mescale and gives an incomplete descrip9on of the func9onal mo9on. 

One solu9on to the 9mescale problem is the simplifica9on of the interac9on between 

atoms and I use a class of models called the structure-‐based models to perform my MD 

simula9ons. 

I intend to use two families of proteins as a test bed for my studies. One of 

them is the β-‐trefoil family of proteins. Proteins from this family are interes9ng because 

they all have the same core structure but they perform different binding func9ons in 

different organisms. They also fold very slowly. The main ques9on is whether their slow 

folding can be related to their func9on. 

The second set of proteins that I intend to work on is a family of protease 

inhibitors called the serpins. These are big proteins (350+ residues), which require a large 

shape change before they can func9on. I want to understand the interplay between the 

shape change and the folding of these proteins.

Raghu Padinjat 

Selected publica9ons 

Raghu, P., Yadav, S and Mallampa9, 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 

sensi9ve to phospha9dic acid levels. Journal of 

Cell Biology 185 129-‐145 

Raghu P, Hardie RC. 2009 Regula9on 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 phospha9dylinositol turnover during 

Drosophila phototransduc9on. Neuron. 29:4, 

533-‐546. 

The architecture of phosphoinosiKde signalling in vivo 

Our long term scien9fic interest is the analysis of signalling mediated by lipid 

molecules generated during phosphoinosi9de metabolism. Phosphoinosi9de signals 

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

remodelling, cytoskeletal func9on, transcrip9on and transla9on. 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 op9mal physiological outputs. We use the fruit fly Drosophila as our model 

system; the goal is to discover key principles of signal transduc9on that are likely to 

be conserved during evolu9on but are experimentally more tractable in Drosophila. 

Phospha9dylinositol 4,5 bisphosphate [PI(4,5)P2] is a phosphoinosi9de 

with mul9ple, key cellular func9ons. Despite the widespread use of PI(4,5)P2 as a 

signalling substrate, its levels in animal cells are stable and demonstrable changes 

during normal cell signalling are at best minimal. In order to 9ghtly regulate 

PI(4,5)P2 levels, it is essen9al 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 

consump9on by signalling reac9ons. We are studying the mechanisms by which 

PI(4,5)P2 levels are regulated in the context of Drosophila phototransduc9on, a 

process that depends cri9cally on PI(4,5)P2 hydrolysis and during which the 

turnover of this lipid is 9ghtly regulated (Hardie and Raghu, 2001). 

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

larval development. We have recently iden9fied a novel phosphoinosi9de kinase 

that appears essen9al for larval growth and works thorough the evolu9onarily 

conserved growth regulator TOR. Several exci9ng projects are available in both the 

above areas. They involve a mixture of modern Drosophila molecular gene9cs, lipid 

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

organism.

Deepak T. Nair 

Molecular determinants of genomic integrity and plasKcity 

Recent Publica9ons: 

Amit Sharma, Vidya Subramanian and Deepak T. Nair. 

The PAD region in the mycobacterial dinB homolog 

MsPolIV exhibits posi9onal heterogeneity Acta 

Crystallogr D Biol Crystallogr. 2012 (in press). 

Amit Sharma and Deepak T. Nair, “MsDpo4—a DinB 

Homolog from Mycobacterium smegma9s—Is an Error-‐ 

Prone DNA Polymerase That Can Promote G:T and T:G 

Mismatches,” Journal of Nucleic Acids, vol. 2012, 

Ar9cle ID 285481, 2012. 

Amit Sharma and Deepak T. Nair. Cloning, expression, 

purifica9on, crystalliza9on and preliminary 

crystallographic analysis of MsDpo4: a Y-‐family DNA 

polymerase from Mycobacterium smegma9s. Acta 

Crystallogr Sect F Struct Biol Cryst Commun. 2011 Jul 

1;67(Pt 7):812-‐6. 

Sivakumar Namadurai*, Deep9 Jain*, Dhananjay S. 

Kulkarni*, Chaitanya R. Tabib, Peter Friedhoff, Desirazu 

N Rao and Deepak T Nair. The C-‐terminal domain of the 

MutL homolog from Neisseria gonorrhoeae forms an 

inverted homodimer. PLoS One. 2010 Oct 

28;5(10):e13726. (* equal contribu9on) 

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

acid metabolizing enzymes play cri9cal roles in ensuring proper 

informa9on transfer from the genome for synthesis of effector 

molecules. Members of this broad group of enzymes are also 

instrumental in the maintenance of the genome. Perturba9on in the 

func9on of these enzymes due to muta9ons or inhibitors has an adverse 

effect on the survival of the organism. A chemical and topological 

descrip9on of enzymes in their func9onal state – in the form of three-dimensional 

structures-‐ has always provided important insights into the 

mechanism of their ac9on and the molecular basis of related diseases. 

In my laboratory we are using this approach to study three 

processes involving the ac9on of nucleic acid metabolizing enzymes on 

the genome. These processes are (a) DNA Mismatch repair (b) DNA 

damage tolerance and (c) Japanese Encephali9s Virus Replica9on. Using 

X-‐ray crystallography as the primary tool in conjunc9on with relevant 

biochemical methods and allied biophysical techniques, we aim to 

provide structural insight into the mechanism of ac9on of enzymes/ 

enzyme complexes that are cri9cal in each of these processes. Through 

ongoing and new collabora9ve efforts, we aim to shed more light on the 

rela9on between biochemical and structural proper9es of these enzymes 

and their observed and predicted roles in physiology.

Sanjay P. Sane 


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

P.* (2011). The biomechanics of fast 

prey capture by aqua9c bladderworts. 

Biology Lecers, 7, 547-‐550. 

Sane S.P.*, Srygley R.B., Dudley R. 

(2010) Antennal regula9on of 

migratory flight in the neotropical moth 

Urania fulgens, Biology Lecers 6: 

406-‐409 

Sane SP* and McHenry MJ (2009) The 

biomechanics of sensory organs, 

IntegraKve and ComparaKve 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. 

Sane, S. P. (2003). The aerodynamics of 

insect flight. Journal of Experimental 

Biology, 206, 4191-‐4208. 

Neural and physical basis of insect flight 

The spectacular evolu9onary success of insects owes much to the evolu9on 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 informa9on at similar rates. How do the nervous 

systems of insects tackle the extraordinary challenges of acquiring, integra9ng and 

processing mul9modal sensory informa9on and genera9ng 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 ques9on. 

Broadly speaking, our approach involves the iden9fica9on and 

measurement of interes9ng flight behaviours in diverse insect taxa (Diptera, 

Hymenoptera, Lepidoptera), and the dissec9on 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 mo9on to understand how flapping wings 

generate and modulate aerodynamic flight forces to determine their aerial 

trajectories. On the neurobiological front, we are inves9ga9ng the combined role of 

vision and mechanosensa9on in flight control in insects, including the neural 

pathways that integrate and process these mul9-‐sensory inputs. More recently, we 

have also begun specific inves9ga9ons on insect flight in their natural context. These 

include specific projects on insect-‐plant interac9ons, as well as inves9ga9ons of 

longer-‐scale flight phenomena such as long distance migra9on and dispersal. 

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

from neurons and physiology to ecology. In addi9on 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 

Selected Publica9ons : 

Higgins, S.I., Scheiter, S. & Sankaran, M. 

(2010). The stability of African savannas: 

insights from the indirect es9ma9on of the 

parameters of a dynamic model. Ecology. 

91(6):1682-‐92 

Sankaran, M. (2009). Diversity paLerns in 

savanna grassland communi9es: implica9ons 

for conserva9on strategies in a biodiversity 

hotspot. Biodiversity & ConservaKon 18: 

1099-‐1115. 

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

R. C & Zamba9s, N. (2008). Nutrient 

resorp9on paLerns of plant func9onal groups 

in a tropical savanna: varia9on and func9onal 

significance. Oecologia 157 (1): 141 – 151 (doi: 

10.1007/s00442-‐008-‐1047-‐5). 

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. 

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

interac9ons and biodiversity-‐ecosystem func9on rela9onships. 

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

• How interac9ons and feedbacks between climate, biogeochemistry, fires 

and herbivory influence the structure, composi9on and stability of ecosystems and 

the cycling and sequestra9on of nutrients. 

• The role of species diversity in regula9ng ecosystem func9on 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 deposi9on and rising CO2 will impact ecosystem func9on, stability and 

services. 

Our current and planned future work will address the above ques9ons 

across the gamut of natural ecosystem types of the Indian sub-‐con9nent, with the 

goal of bringing a comprehensive understanding of biome-‐scale vegeta9on and 

nutrient dynamics in the sub-‐con9nent. Most of our research thus far has been 

carried out in savanna ecosystems in Africa. Besides being economically important 

biomes, savannas are also perfect model systems for the kinds of research ques9ons 

that we are interested in. We are now extending this work to savanna ecosystems in 

India, but also expanding to encompass a wider range of ecosystem types including 

rainforests and grasslands. Addi9onally, recognizing that much of the terrestrial sub-con9nent 

is 9ed up in agricultural ecosystems, the dynamics of which will play a 

cri9cal role in our ability to cope with changes in climate regimes and provide food 

security in the coming decades, we are now also expanding into this area.

Dominik Schwudke 

Linking biological phenotypes to their chemical basis 


Entchev, E.V., Schwudke, D., Zagoriy, V., Matyash, V., 

Bogdanova, A., Habermann, B., Zhu, L., Shevchenko, A. 

and Kurzchalia (2008). TV. LET-‐767 is required for the 

produc9on of branched chain and long chain faLy acids in 

C. elegans. Journal of Biochemistry, 283, 17550-‐17560. 

Matyash, V., Liebisch, G., Kurzchalia, T.V., Shevchenko, A. 

and Schwudke, D. (2008), Lipid extrac9on by methyl-‐tert-butyl 

ether for high-‐throughput lipidomics. Journal of 

Lipid Research 49, 1137-‐1146. 

Graessler J #, Schwudke D #, Schwarz PE, Herzog R, 

Shevchenko A, and Bornstein SR. Top-‐down lipidomics 

reveals ether lipid deficiency in blood plasma of 

hypertensive pa9ents. PLoS One. 2009 Jul 15;4(7):e6261. 

Carvalho, M.; Schwudke, D.; Sampaio, J. L.; Palm, W.; 

Riezman, I.; Dey, G.; Gupta, G. D.; Mayor, S.; Riezman, H.; 

Shevchenko, A.; Kurzchalia, T. V.; Eaton, S., Survival 

strategies of a sterol auxotroph. Development 2010, 137 

(21), 3675-‐3685. 

Herzog R#, Schwudke D# , Schuhmann K, Sampaio JL, 

Bornstein SR, Schroeder M and Shevchenko A. A novel 

informa9cs concept for high-‐throughput shotgun 

lipidomics based on the molecular fragmenta9on query 

language Genome Biol. 2011 Jan 19;12(1):R8. [Epub 

ahead of print] # These authors contributed equally to 

this work. 

Interdisciplinary inves9ga9ons at the interface of biology and 

analy9cal chemistry are my personal interest, which focused on 

development and applica9on of mass spectrometric methods for 

biological research. 

In par9cular, I will inves9gate cell and 9ssue 

differen9a9on during development of D. melanogaster with 

lipidomics and proteomics approaches. In all higher organism cells 

take diverse func9onal responsibili9es. In that regard it can be 

observed that cells, forming specialized 9ssues, contain specific 

lipidomes. Interes9ngly, func9ons and specific lipid composi9ons are 

assigned during embryogenesis and we do not fully understand how 

this is happening. From this perspec9ve we want to learn how, when 

and where specific lipidomes are established in the course of 9ssue 

differen9a9on.

Mukund ThaLai 

ComputaKonal and evoluKonary cell biology 


Rai N, Anand R, Ramkumar K, 

Sreenivasan V, Dabholkar S, Venkatesh 

KV, ThaLai M (2012) Predic9on by 

promoter logic in bacterial quorum 

sensing. PLoS Comput. Biol. 8: 

e1002361. 

Anand R, Rai N, ThaLai M (2011) 

Promoter reliability in modular 

transcrip9onal networks. Methods 

Enzymol. 497: 31. 

Ramadas R, ThaLai M (2010) Flipping 

DNA to generate and regulate microbial 

consor9a. GeneKcs 184: 285. 

Callahan B, ThaLai M, Shraiman BI 

(2009) Emergent gene order in a model 

of modular polyke9de synthases. Proc. 

Natl. Acad. Sci. USA 106: 19410. 

Though cells are the basic units of all living things, we know remarkably 

liLle about their ac9vity and evolu9on. At the same 9me, new experiments 

are genera9ng a torrent of data about the structure and interac9ons of the 

bio-‐molecules from which cells are made up. We seek to bridge the gap: 

going from molecules to cellular phenotypes. What makes this enterprise 

exci9ng is that a complex system can have proper9es different from those 

of its cons9tuent parts. We study the molecular basis of the emergent 

proper9es of two cellular systems: the network of factors that turn gene 

transcrip9on on and off; and the complex trafficking of materials between 

the mul9tude of intracellular compartments. 

Our work involves a close interplay between simple 

mathema9cal models and quan9ta9ve experiments: we use techniques 

borrowed from control theory and electrical engineering to design and 

experimentally test synthe9c transcrip9onal networks built from well-understood 

molecular components in bacterial cells; and we use 

biophysical models to explore how organelles and traffic arise from basic 

molecular interac9ons in eukaryo9c cells. Ul9mately, cells are products of 

basic evolu9onary forces: muta9on and recombina9on which act on 

molecules; selec9on and dri[ which act on phenotypes and popula9ons. 

Studying the emergence of phenotype from molecular interac9ons will be 

essen9al if we are to understand the deep evolu9onary origins of modern 

cells.

Yamuna Krishnan 

Structure and dynamics of Nucleic acids 


Chakraborty, S., Mehtab, S., Patwardhan, A.R., Krishnan, Y.* 

(2012) Pri-‐miR-‐17-‐92a Transcript folds into a ter9ary 

structure and autoregulates its processing. RNA 18, 

1014-‐1028. 

Saha, S., Chakraborty, K. and Krishnan, Y*. (2012) Tunable, 

colorimetric DNA based pH sensors mediated by A-‐mo9f 

forma9on. Chem. Commun. 48, 2513. 

Bha9a, D., Sharma, S. and Krishnan, Y*. (2011) Synthe9c, 

biofunc9onal nucleic acid-‐based molecular devices. Curr 

Opin Biotechnol, 22, 475-‐484. 

Modi, S. and Krishnan, Y.* (2011) A method to map 

spa9otemporal pH changes insde living cells using a pH 

triggered DNA nanoswitch. Methods Mol. Biol. 749, 61-‐77. 

Surana, S., Bhat, J.M., Koushika, S.P. and Krishnan, Y.* (2011) 

An autonomous DNA nanomachine maps spa9otemporal pH 

changes in a mul9cellular living organism. Nature 

CommunicaKons, 2, 340. 

Bha9a, D., Surana, S., Chakraborty, S., Koushika, S.P. and 

Krishnan, Y.* (2011) A synthe9c, icosahedral DNA-‐based 

host-‐cargo complex for func9onal in vivo imaging. Nature 

CommunicaKons, 2, 339. 

Krishnan, Y and Simmel, F. C. (2011) Nucleic Acid Based 

Molecular Devices. Angew. Chem. Int. Ed. 50, 3124-‐3156. 

Bionanotechnology aims to learn from nature -‐ to understand the 

structure and func9on of biological devices and to u9lise nature's 

solu9ons in advancing science and engineering. Evolu9on has 

produced an overwhelming number and variety of biological devices 

that func9on 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 exploi9ng the knowledge gained 

for applica9ons 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 oligonucleo9des with 

unique and predictable recogni9on capabili9es. This makes DNA an 

ideal nanoscale construc9on material. Understanding and thereby 

controlling structure and dynamics in designed DNA assemblies is key 

to realizing DNA’s poten9al as a nanoscale building block. 

We make DNA based molecular assemblies for 

applica9ons as fluorescent sensors of second messengers in-‐cellulo 

and in-‐vivo. Another area of interest involves understanding naturally 

occurring RNA structural mo9fs and how they impact RNA processing.

Uma Ramakrishnan 

Natural environments around us are changing at unprecedented rates. As wildlands 

shrink, human popula9ons increase and the temperature escalates, we scramble to 

understand how the species around us will respond. We hope that such understanding 

will aid in stewarding species survival in the future. Integral to this stewardship are the 

fields of ecology and evolu9on, and I focus on this research interface. I study the 

processes governing the response of species to environmental history, clima9c 

perturba9on and human history in the context of species ecologies, and hence gain a 

beLer understanding of their evolu9on. 


ChaLopadhyay, B, Garg, KM, Vinoth Kumar, AK, 

Swami Doss, DP, Ramakrishnan, U & Kandula, S. 

Sibling species in the south Indian popula9ons of 

Rufous horse-‐shoe bat, Rhinolophus rouxii (in press, 

ConservaKon GeneKcs) 

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. 

O’Keefe, K, Ramakrishnan, U, van Tuinen, M & Hadly, 

EA. Source-‐sink dynamics in a common montane 

mammal (2009) Molecular Ecology, 18(23): 

4775-‐4789. 

Mondol, S, et al (2009a) Evalua9on of non-‐invasive 

gene9c sampling methods for es9ma9ng 9ger 

popula9on size. Biological ConservaKon, 

142:2350-‐2360. 

Mondol, S, Karanth, KU, Ramakrishnan, U (2009b) 

Why the Indian subcon9nent holds the key to global 

9ger recovery. PLoS GeneKcs, 5(8):e1000603. 

In prac9cal terms, my research focuses on revealing the processes that 

drive paLerns of mammalian gene9c varia9on (in the present and the past). I use field-collected 

samples, assemble molecular gene9c data and analyze these data with 

phylogene9c, phylochronologic, phylogeographic and popula9on gene9c inferences. Much 

of my research over the last few years has focused on the Indian subcon9nent because of 

(1) its geographic se ng, represen9ng the intersec9on of three major biogeographic 

realms (Palearc9c, Africotropical, Indomalayan); (2) its geologically drama9c history, 

driven by plate tectonics, volcanism and clima9c change; (3) its ecologically diverse habitat 

types from the highest mountains on earth to very dry deserts and tropical forests, 

including biodiversity hotspots; (4) the presence of Homonins in India for perhaps one 

million years, and modern humans in rela9vely high (and ever increasing) densi9es for 

about 70,000 years impac9ng the Indian biota; and finally the fact that (5) virtually 

nothing is known about paLerns of gene9c varia9on in na9ve Indian species, and even 

less is known about the impact of climate on species in this region in par9cular. 

Broadly, the research in my laboratory can be divided into three types of 

ques9ons: (1) What drives paLerns of diversity in the Indian subcon9nent? (2) What are 

the impacts of climate on temporal changes in diversity? (3) What is the cryp9c 

biodiversity of India and how can we safeguard its future?

R. Sowdhamini 

ComputaKonal approaches to protein science 


Pugalenthi, G., Bhaduri, A. and 

Sowdhamini, R. (2005). genDiS: 

Genomic distribu9on of protein 

structural superfamilies. Nucleic Acid 

Research, 33, D252-‐255. 

Chakrabar9, S. and Sowdhamini, R. 

(2004). Regions of minimal structural 

varia9on among members of protein 

domain superfamilies: Applica9on to 

remote homology detec9on and 

modelling using distant rela9onships 

FEBS Lecers, 569, 31-‐36. 

Innis, C.A., Anand, OP.A. and 

Sowdhamini, R. (2004). Predic9on of 

Func9onal Sites in Proteins using 

Conserved Func9onal Group Analysis. 

Journal of Molecular biology, 337, 

1053-‐1068 

The knowledge-‐based approach to protein structure-‐and-‐func9on 

predic9on exploits the property of evolu9onary convergence where it is 

es9mated that there is a limited number of protein folds in the en9re 

universe (Chothia, 1992, Nature, 357, 543-‐544) shared by protein 

superfamilies. Computa9onal approaches on protein structure and 

func9on predic9on from mere sequence informa9on should be of value to 

address the vast amount of data emerging from genome projects and for 

the ra9onal design of high-‐throughput experiments. Sowdhamini and her 

group have contributed to the following major areas: 

(i) development and maintenance of rela9onal and sub-‐derived databases 

(ii) development of algorithms and approaches for the sensi9ve detec9on 

of puta9ve members of protein families and superfamilies 

(iii) development of equipment and so[ware for genome-‐wide surveys of 

protein families, cross-‐genome surveys and calcula9on of diversity 

measures 

(iv) construc9on of protein func9onal templates useful for func9on 

predic9on 

(v) development of improved homology modeling during distant 

rela9onship with structural homologues.

Sumantra (Shona) ChaLarji 

SynapKc plasKcity in the amygdala: implicaKons for stress & 

auKsm spectrum disorders 


Roozendaal, B.l, McEwen, B.S., & ChaLarji, S. (2009) 

Stress, Memory and the amygdala. Nature Reviews 

Neuroscience 10: 423-‐433. 

Suvrathan, A., Hoeffer, C. A., Wong, H., Klann, E., 

and ChaLarji, S. (2010) Characteriza9on and reversal 

of synap9c defects in the amygdala in a mouse 

model of fragile X syndrome. Proc. Natl. Acad. Sci. 

USA 107 (25): 11591-‐11596. 

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

Syndrome and the Amygdala. Current Opinion in 

Neurobiology, 21 (3): 509-‐515. 

Malik, R. and ChaLarji, S. (2012) Enhanced intrinsic 

excitability and EPSP-‐spike coupling accompany 

enriched environment induced facilita9on of LTP in 

hippocampal CA1 pyramidal neurons. Journal of 

Neurophysiology, 107 (5): 1366-‐1378. 

Rao, R.P., Anilkumar, S., McEwen, B.S., and 

ChaLarji, S. (2012) Glucocor9coids protect against 

the delayed behavioral and cellular effects of acute 

stress on the amygdala. Biological Psychiatry (in 

press). 

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

Emo9onally significant experiences tend to be well remembered, and the 

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

encoding of emo9onal memories can become maladap9ve — severe stress 

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

mechanisms underlying these powerful emo9onal symptoms? To answer 

this ques9on, we have been using a range of behavioral, morphometric, in 

vitro and in vivo electrophysiological tools to iden9fy neural correlates of 

stress-‐induced modula9on of amygdala structure and func9on — from 

cellular and synap9c mechanisms to their behavioural consequences in 

rodents. Our findings point to unique features of stress-‐induced plas9city 

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 affec9ve disorders. 

In addi9on to behavioral experience, the genes we inherit can 

also cause cogni9ve and emo9onal dysfunc9on. Strikingly, individuals 

afflicted with certain types of au9sm spectrum disorder o[en exhibit 

impaired cogni9ve func9on alongside high anxiety and mood lability. 

Hence, we are extending our analyses to gene9cally engineered mice to 

iden9fy cellular and molecular targets that can be used to correct 

symptoms of Fragile X Syndrome, the leading gene9c cause of au9sm.

Apurva Sarin 

RegulaKng cell number in mulK-‐cellular organisms 


Perumalsamy LR et al., (2009) A hierarchical cascade 

ac9vated by non-‐canonical Notch signaling and the 

mTOR -‐ Rictor complex regulates neglect-‐induced 

death in mammalian cells. Cell Death & 

DifferenKaKon 16:879-‐889 

Purushothanam D & Sarin A (2009) Cytokine-dependent 

regula9on of NADPH oxidase ac9vity and 

the consequences for ac9vated T cell homeostasis 

Journal of Experimental Medicine 206:1515-‐23 

Perumalsamy LR et al., (2010) A Notch ac9vated 

signaling cascade interacts with mitochondrial 

remodeling proteins to regulate cell survival Proc. 

Natl. Acad. Sc USA. 107:6882-‐6887. 

Perumalsamy LR et al.,(2012) Dis9nct spa9al and 

molecular features of Notch pathway assembly in 

Regulatory T-‐cells. Science Signaling (accepted) 

Garg M et al., -‐Linker Histone H1.2 triggers apopto9c 

cascades integrated by the mitochondrion (submi

Upinder S. Bhalla 

Memory, smell, and networks 


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

track odour trails accurately using a mul9-‐ 

layered strategy with near-‐op9mal sampling. 

Nature CommunicaKons. 3(703), doi: 

10.1038/ncomms1712, 2012. 

Ramakrishnan, N., Bhalla, U.S., Tyson, J.J. 

Compu9ng with proteins. Computer 42(1): 

47-‐56, doi:10.1109/MC.2009.12 

Bhalla, U.S. How to Record a Million 

Synap9c Weights in a Hippocampal Slice. 

Public Library of Science: ComputaKonal 

Biology. 4(6): e1000098, 2008. 

Khan, A.G., ThaLai, M., and Bhalla, U.S. 

Odor Representa9ons in the Rat Olfactory 

Bulb Change Smoothly with Morphing 

S9muli. Neuron. 57(4):571-‐85, 2008. 

! 

If we could take a picture of a memory, what would it look like? How do you store 

the memory of a fragrance, or of how to ride a bicycle? We are working on the idea 

that memories are stored in the paLern of connec9ons between brain cells. To 

store memories in this manner, the brain must convert informa9on into ac9vity 

paLerns, modify connec9ons, and stably retain these modifica9ons. Our research 

covers each of these topics. 

First, we monitor cellular ac9vity in the hippocampus of mice as they 

learn to associate a sound or other sensory s9mulus with a subsequent puff or air. 

We do these recordings in the rat hippocampus, a region of the brain involved in 

memory. This lets us get a picture of how the ac9vity and connec9ons change in 

real 9me, as the animal learns. 

Second, by systema9cally s9mula9ng input cells and monitoring which 

cells they influence, we can build up connec9on diagrams that define what 

memories have already been encoded. Building on advances in microscopy, we can 

monitor ac9vity of hundreds of cells using chemical sensors whose light emission 

changes when a cell is ac9ve. We use electrical and op9cal triggers to carry out the 

s9mulus, again poten9ally scaling to hundreds of inputs. 

Third, the connec9ons need to be stable to store informa9on for a long 

9me. This is very hard to do, because each connec9on, or synapse, is so small that a 

rela9vely small number of individual molecules must do all the work and withstand 

thermal noise, turnover, and chemical insults. We probe events at these 9ny scales 

using both experiments and computer models. We are developing powerful 

so[ware tools to model how these events are orchestrated. This so[ware, MOOSE, 

runs on laptops as well as giant Unix-‐based supercomputers. 

Overall, our work falls into the domains of systems biology and 

computa9onal neuroscience, with a lively mix of experiments and computer 

modeling. Our lab includes people from physics, chemistry, mathema9cs, biology, 

computer science and other branches of engineering.

Satyajit Mayor 

! 


Gowrishankar, K, et al, (2012). Ac9ve 

remodeling of cor9cal ac9n regulates 

spa9otemporalorganiza9on of cell 

surface molecules. Cell in press. 

Howes, M., Mayor, S. and Parton, R. 

(2010). Molecules, mechanisms, and 

cellular roles of clathrin-‐independent 

endocytosis. Curr Opin Cell Biol ;22(4): 

519-‐27. 

Vyas, N., et al., (2008). Nanoscale 

organiza9on of hedgehog is essen9al 

for long-‐range signaling. Cell, 133(7), 

1214-‐27. 

Goswami, D., et al., (2008). 

Nanoclusters of GPI-‐anchored proteins 

are formed by cor9cal ac9n-‐driven 

ac9vity. Cell. 135(6), 1085-‐97. 

Kumari, S., et al. (2008). Nico9nic 

acetylcholine receptor is internalized 

via a Rac-‐dependent, dynamin-independent 

endocy9c pathway. J Cell 

Biol 181, 1179-‐1193. 

Mechanisms of membrane organizaKon and traffic 

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

organiza9on of its cell surface cons9tuents. This will help in understanding how a eukaryo9c cell 

constructs signaling complexes (composi9on) and also how it may engage in deforming its membrane 

(endocytosis) in a regulated fashion. To study phenomena at the cellular scale, principles from the 

physical sciences provide a powerful paradigm in framing ques9ons about the mechanisms of movement 

of molecules and organelles inside cells. Consequently, in my laboratory we have taken a mul9-‐ 

disciplinary approach, combining biology with physics and chemistry to address the main theme of our 

research. 

We have developed new microscopy technologies to study nanometer scale organiza9on 

of cellular components, and explored the organiza9on and dynamics of fluorescently-‐tagged molecules in 

a variety of living cells, including stem cells; from the nanometer scale in specialized domains in cell 

membranes to the micron scale prevalent in mapping endocy9c pathways. We also study sor9ng 

proper9es and endocy9c 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 ac9ve 

composite of the lipid bilayer and a dynamic cor9cal ac9n layer beneath, wherein, dynamic ac9n 

filaments help in controlling the local composi9on of membranes. 

We are now involved in several specific lines of inquiry. These include; i) theore9cal and 

experimental studies on the basis for the forma9on of membrane ra[s in living cells (in collabora9on 

with Madan Rao, NCBS, RRI); ii) exploring the dynamics of such membrane complexes during signaling 

and templated differen9a9on in mul9ple cell systems, including stem cells; ii) understanding the ac9ve 

organiza9on of many cell surface proteins including the Acetylcholine receptor modula9on (in 

collabora9on with Prof. Francisco Barrantes, INIBIB, Bahia Blanca, Argen9na), the T-‐ Cell Receptor (in 

collabora9on with Ron Vale, UC at San Francisco, USA), and integrins; iii) scales of organiza9on in the 

func9oning of cholesterol-‐tethered Hedgehog in paLerning 9ssues in situ, in collabora9on with RS. 

Sowdhamini, NCBS; iii) molecular mechanism of dynamin-‐independent endocytosis using cell-‐based 

assays at the individual gene scale, and genome wide-‐RNAi screening methods (in collabora9on with 

Mukund ThaLai, NCBS); iv) understanding the roles of different endocy9c pathways in paLerning 9ssues 

in the animal, in collabora9on with Prof. KS Krishnan, NCBS, and K. Vijayraghavan, NCBS; 

The trajectory of this work has led us to explore the fine structure of the plasma 

membrane, providing for the first 9me an in vivo picture of lipidic assemblies challenging exis9ng no9ons 

of membrane ra[s, an understanding of the role of specialized endocy9c mechanisms for the 

establishment of developmental gradients, and a genome-‐wide analysis of endocy9c pathways.

Sudhir Krishna 

Notch signalling in human epithelial cancers and leukemias: 

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

College 


Maliekal TT, Bajaj J, Giri V, Subramanyam D, Krishna S. 

(2008).The role of Notch signaling in human cervical cancer: 

implica9ons for solid tumors. Oncogene; 27(38):5110-‐4. 

Srivastava S, Ramdass B, Nagarajan S, Rehman M, 

Mukherjee G, Krishna S.(2010). Notch1 regulates the 

func9onal contribu9on of RhoC to cervical carcinoma 

progression. Br J Cancer. 102(1):196-‐20 

Rangarajan A, Talora C, Okuyama R, Nicolas M, Mammucari 

C, Oh H, Aster JC, Krishna S, Metzger D, Chambon P, Miele 

L, Aguet M, Radtke F, DoLo GP. (2001). Notch signaling is a 

direct determinant of kera9nocyte growth arrest and entry 

into differen9a9on. EMBO J. 20(13):3427-‐36. 

Rangarajan A, Syal R, Selvarajah S, Chakrabar9 O, Sarin A, 

Krishna S. (2001). Ac9vated Notch1 signaling cooperates 

with papillomavirus oncogenes in transforma9on and 

generates resistance to apoptosis on matrix withdrawal 

through PKB/Akt. Virology. 286(1):23-‐30. 

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. 

Our lab has for some 9me now been interested in the role of Notch 

signalling in human epithelial cancers. We have focussed our analysis on 

human cervical cancer-‐ a tumour ini9ated and sustained by oncogenically 

high risk Human Papillomaviruses. Our recent work has led to the 

iden9fica9on of a 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 collabora9ve hospital in this programe so far 

has been the Kidwai Memorial Ins9tute of Oncology. 

Department of Biotechnology Glue grant inita)ve: 

We have been awarded a major 5 year grant to co-‐develop laboratory 

facili9es at St. John’s Medical College. In addi9on to the exis9ng research 

infrastructure in St. John’s Medical College, we are developing molecular 

biology and 9ssue culture labs along with a flow cytometry and imaging 

facility. From NCBS, Drs. Sweta Srivastava and H. Krishnamurty are some 

of the key scien9sts 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.

Mitradas M. Panicker 


Raote, I., BhaLacharya, A. and Panicker, M.M. (2007). 

Serotonin 2A (5-‐HT2A) Receptor Func9on: Ligand-‐ 

Dependent Mechanisms and Pathways. In Serotonin 

Receptors in Neurobiology. FronKers in Neuroscience 

Vol 35 Edited by A. ChaLopadhyay (Taylor and Francis, 

CRC Press). 105-‐132. 

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

Mai9, S., and Panicker, M.M. (2008). Serotonin in pre-implanta9on 

mouse embryos is localized to the 

mitochondria and can modulate mitochondrial 

poten9al. ReproducKon. 135: 657-‐659. 

Karuppiah Kanagarajadurai, Manoharan Malini, 

BhaLacharya Adi9, Mitradas M. Panicker and 

Ramanathan Sowdhamini. (2009). Molecular Modeling 

and docking studies of human 5-‐hydroxytryptamine 2A 

(5-‐HT2A) receptor for the iden9fica9on of hotspots for 

ligand binding. Molecular Biosystems 5: 1877-‐1888. 

Adi9 BhaLacharya, Shobhana Sankar and Mitradas M. 

Panicker (2009). Differences in the C-‐terminal tail 

contribute to the varia9on in trafficking between the 

Rat and Human 5-‐HT2A receptor isoforms: 

Iden9fica9on of a primate-‐specific tripep9de ASK mo9f 

that confers GRK-‐2 and β2-‐Arres9n interac9on. J. 

Neurochem. 112: 723-‐32. 

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

The major interests of my laboratory are the cellular and molecular 

regulatory mechanisms ac9vated by serotonin, a molecule widely 

recognized as an important neurotransmiLer. Interes9ngly most of the 

serotonin is expressed outside the nervous system and seems to be involved 

in normal physiology in a number of ways including early development in 

mammals for e.g. stem cells. Most of the interac9ons of serotonin take 

place through its receptors i.e. protein molecules 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 

stress and in schizophrenia. So serotonin plays an important role in 

communica9on between neurons and also governs development, behavior 

and physiology, in fact, all aspects of an organism’s life. 

Our studies have primarily focused on the regula9on 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 an9psycho9cs. Using modified 5-‐HT2A 

receptors, which can be visually localized within cells, we have made 

significant observa9ons regarding the behavior of the receptor in the 

presence of serotonin and an9psycho9cs. These studies have helped us 

dissect the details of how these receptors are regulated by endogenous and 

exogenous ligands. 

Our recent results using pre-‐implanta9on mouse embryos and 

mammalian embryonic stem cells also suggest that serotonin receptors and 

serotonin may play an important role in early differen9a9on. Serotonin has 

been localized to the mitochondria and affects mitochondrial poten9al. This 

has important implica9ons for development and cell survival.

Gai9 Hasan 


Agrawal, N, Padmanabhan, N and Hasan G. (2009) Inositol 

1,4,5 -‐ trisphosphate Receptor Func9on in Drosophila Insulin 

Producing Cells. PLOS One, 4(8): e6652 

Venkiteswaran, G and Hasan, G (2009). Intracellular calcium 

signaling and store operated Ca 2+ entry are required in 

Drosophila neurons for flight. Proc. Natl. Acad. Sci. USA, 

106, 10326-‐10331. 

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

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

receptor and dSTIM func9on 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 InsP 3 receptor mutant larvae reveal 

a role for InsP 3 signaling in carbohydrate and energy 

metabolism. PLoS One, 6(8): e24105. doi:10.1371/ 

journal.pone.0024105 

Chorna, T and Hasan, G. (2011). The gene9cs of calcium 

signaling in Drosophila melanogaster. Biochem Biophys Acta 

doi:10.1016/j.bbagen.2011.11.002. 

Chakraborty S. and Hasan G. (2012). IP 3 Receptor, Store-‐ 

Operated Calcium Entry and neuronal calcium homeostasis in 

Drosophila. Biochemical Society Transac)ons 40, 279-‐281. 

! 

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

systemic physiology 

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 func9on of a receptor for InsP3 and a channel for 

calcium release. We address InsP3 receptor func9on in the model 

organism Drosophila using gene9c, molecular, cellular, 

electrophysiological and behavioral methods. 

Our recent work has demonstrated that reducing InsP3R 

func9on in Drosophila neurons affects feeding and growth in larvae 

and mul9ple aspects of flight circuit development and func9on in 

pupae and adults. These studies have shown that restoring InsP3R 

func9on in neurons which either synthesize monoamines (like 

dopamine) or insulin-‐like pep9des (ILPs) rescues InsP3R mutant 

defects. More recently, projects to understand how InsP3R mutants 

respond to changes in regula9on of intracellular store Ca2+ and to 

stress condi9ons (S. Manivannan, S.K. Metya, submiLed) have been 

ini9ated. Work from my group has demonstrated for the first 9me in 

a physiological context the requirement for store-‐operated calcium 

entry downstream of InsP3 signaling in neurons. Results from these 

studies suggest that gene9c and pharmacological methods could be 

used for controlling intracellular Ca2+ homeostasis as a possible 

therapeu9c strategy in certain neurodegenera9ve and metabolic 

diseases. Drosophila model and human studies in the context of such 

diseases are in progress.

Mathew K Mathew 


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 

func9ons 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 

Pannaga Krishnamurthy, Kosala Ranathunge, 

Shraddha Nayak, Lukas Schreiber & M.K.Mathew 

(2011) Root barriers block Na+ traffic to shoots in 

rice (Oryza sa9va L.) J Exp Botany 62, 4215 – 4228 

Godbole A, Mitra R, Dubey AK, Reddy PS & 

Mathew MK (2011) Bacterial Expression, 

Purifica9on and Characteriza9on of a Rice Voltage 

Dependent Anion-‐Selec9ve Channel Isoform, 

OsVDAC4 J Membrane Biol 244, 67–80 

Kavitha PG, Miller T, Mathew MK & Maathuis FJM 

(2012) Rice cul9vars with differing salt tolerance 

contain similar ca9on channels in their root cells. J 

Exp Botany in press doi:10.1093/jxb/ers052 

Crossing Barriers: Studies of Membrane Transport 

Biological membranes pose a significant barrier to the movement of ions and polar 

molecules, requiring the ac9vity of transmembrane proteins to cross these barriers. 

My laboratory studies several such proteins, called transporters, 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 ac9vity contributes to the overall physiology of the cell or organism. 

The voltage-‐gated K+ channel is involved in genera9ng Ac9on Poten9als 

in neurons. It senses transmembrane electric fields and opens and closes in response 

to changes in membrane poten9al. Star9ng with a crystal structure, we have 

combined computer modeling with mutagenesis and electrophysiology to come up 

with a detailed mechanism of how voltage drives channel opening and closing. 

Plants use a variety of strategies to survive in salty soil. We have shown 

earlier that controlling the amount of Na+ that reaches the shoot is cri9cal, as are 

cellular mechanisms for maintaining low Na+ levels in the cytoplasm. 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. The principal route 

for Na+ entry to the rice shoot appears to be by bypassing these barriers. Our data 

indicates that barriers are beLer developed in salt-‐tolerant varie9es than in sensi9ve 

varie9es and we are inves9ga9ng the mechanisms underlying their deposi9on. 

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

from tolerant varie9es are much less permeable to Na+ than those from sensi9ve 

varie9es. Tolerant varie9es also accumulate a significant amount of Na+ in their 

vacuoles. We are using a combina9on of molecular biology, microscopy and 

electrophysiology to inves9gate the basis of these differences. A study of vesicle 

trafficking in plant cells shows that endocytosis is drama9cally affected by salinity 

and suggests a plausible mechanism for maintaining a steady state in the vacuole 

despite “dumping” so much Na+ into it.

Jayant Udgaonkar 

How do proteins fold, unfold and misfold? 


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

demonstra9on 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) Kine9c 

studies of the folding of heterodimeric 

monellin: evidence for switching between 

alterna9ve parallel pathways J. Mol. Biol. (In 

press) 

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

pathway of worm-‐like amyloid fibril forma9on 

by the mouse prion protein by delinea9on of 

the produc9ve and unproduc9ve 

oligomeriza9on reac9ons. Biochemistry 50, 

1153-‐1161. 

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

Evidence for the existence of a secondary 

pathway for fibril growth during the 

aggrega9on of tau. J. Mol. Biol. (In Press). 

The polypep9de 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 func9on 

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 solu9on has obvious biotechnological as well as medical implica9ons. In par9cular, 

the improper folding of some proteins, and their consequent aggrega9on into amyloid 

fibrils, are characteris9c features of several neuro-‐degenera9ve 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 func9onal 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 op9cal spectroscopic 

methods such as 9me-‐resolved fluorescence methods, as well as nuclear magne9c 

resonance spectroscopy and mass spectrometry methods. Our kine9c measurements span 

the 9me domain of 100 microseconds to 10 hours. 

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

demonstra9on that a dry molten globule forms ini9ally during unfolding; (2) the 

demonstra9on that the PI3 kinase SH3 domain folds and unfolds via mul9ple intermediates; 

and (3) the demonstra9on of switching between mul9ple folding pathways during the 

folding of monellin. Highlights of our recent work on protein misfolding and aggrega9on 

include (1) the demonstra9on that amyloid protofibrils may have different morphologies 

when formed on different pathways, and that a single muta9on in the protein sequence or 

a change in aggrega9on condi9ons can lead to switching between alterna9ve available 

pathways; (2) the demonstra9on that tau can u9lize a secondary pathway for amyloid 

fibril forma9on; and (3) the iden9fica9on 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 

Mukherjee, P., Gildor, B., Shilo, B., VijayRaghavan, K., & Schejter, E. D. 

(2011). The ac9n 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). Iden9fica9on and analysis of a 

glutamatergic local interneuron lineage in the adult Drosophila 

olfactory system. Neural Systems & Circuits 1, 4. 

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 func9onal proper9es of these circuits are put in place. 

The segmental organiza9on of the brain in the fly is 

remarkably similar to that of vertebrates and points to a 

common-‐, rather than an independent-‐ origin during 

evolu9on. This, and the conserved nature of many molecular 

and cellular aspects, holds out the promise of a general 

relevance to the understanding of how func9onal neural 

circuits underlying behavior are assembled during 

development. 

DuLa, D., Umashankar, M., Lewis, E. B., Rodrigues, V., VijayRaghavan, 

K. (2010). Hox genes regulate muscle founder cell paLern 

autonomously and regulate morphogenesis through motor neurons 

Journal of NeurogeneKcs, 24(3), 95-‐108.

K. S. Krishnan 

Reent Publica9ons: 

Gupta K, Kumar M, Chandrashekara K, Krishnan 

KS, Balaram P. (2012) Combined electron 

transfer dissocia9on-‐collision-‐induced 

dissocia9on fragmenta9on in the mass 

spectrometric dis9nc9on of leucine, isoleucine, 

and hydroxyproline residues in Pep9de natural 

products. J Proteome Res. 11(2):515-‐22. 

Swetha MG, Sriram V, Krishnan KS, Oorschot 

VM, ten Brink C, Klumperman J, Mayor S. ( 2011) 

Lysosomal membrane protein composi9on, 

acidic pH and sterol content are regulated via a 

light-‐dependent pathway in metazoan cells. 

Traffic. 12(8):1037-‐55. 

Majumder R, Krishnan KS. ( 2012) Synap9c 

vesicle recycling: gene9c and cell biological 

studies. J Neurogenet. 24(3):146-‐57. 

! 

Research Themes 

A major interest in my lab is to iden9fy and characterize new neuro-‐ac9ve 

compounds from a variety of organisms. These include venoms of Marine 

cone snails, frog skin secre9ons and wasp venoms. The highly toxic cono-pep9des 

from Conus, once characterized, could be exploited as 

pharmacological tools in neuroscience, cell biology and in search for drugs 

to treat many debilita9ng diseases. We have isolated many novel pep9des 

from a few cone snail species collected off the shores of South Eastern 

India and TIFR. Mass spectrometry-‐based de novo sequencing of venom 

components combined with deep sequencing RNA from the venom glands 

and valida9on by chemical synthesis is our main thrust. We have started 

iden9fying and characterizing pep9des of therapeu9c value from wasp 

venoms and frog skin secre9ons. We are developing several assays mainly 

u9lizing the power of Drosphila gene9cs, Oocyte expression of specific 

channel proteins and cell biology to establish protocols for ac9vity 

dependent purifica9on of pep9des that could be drug leads. 

These studies are done in collabora9on mainly with Prof. 

Balaram at IISc. I also ac9vely collaborate with colleagues at IISc (S Sarma, 

Hanumae Gowd), colleagues at NCBS (MK Mathew, S. Mayor), GKVK 

( Chandrasekhar Krishnappa) Annamali Univeristy (Olivia and Anthony 

Fernando) Andhra University( Y. P. Rao) and North Orissa ( Sushil DuLa).

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 incarna9ons the fly’s olfactory behavior 

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

to dis9nguish between innate and acquired behavior. This is a difficult and, in 

several respects, an unseLled issue. Understanding adap9ve 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 

condi9oning 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. 

Chakraborty TS, Siddiqi O. (2011). Odor 

recep9on in antenna and antennal lobe of 

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

2011 Jan 1. 

Some years ago we began to inves9gate imaginal condi9oning, a 

process by which, in the first few days a[er eclosion, the fly learns to dis9nguish 

between aLractants and repellents. It develops aLrac9on 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 condi9oning. Tuhin Chakraborty and 

Sunil Prabhakar have found that imaginal condi9oning 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-‐induc9on is our first aLempt to develop psychophysics of odor percep9on 

with Drosophila.

Direc:ons to the campus 

From City Railway Station : NCBS is to the North of Bangalore about 

15kms from Majestic city railway station, 9kms from Mekhri Circle and 

4kms form Hebbal Blyover (besides the Blyover is the hebbal lake). Each o 

these is a well-‐known landmark. Mekhri circle is a major trafBic junction 

From Mekhri circle take the Bellary Highway (leading to Yelahanka), go 

over the Hebbal Blyover and after about 4kms you reach the L&T factory on 

left. Next to L&T Factory is the GKVK main gate. Enter the gate and you wil 

see NCBS signages. Please follow the sign boards and you reach NCBS. 

From Airport : From the International Airport at Devanahalli, NCBS is 

~25kms. It takes ~45 minutes – one hour to reach NCBS from the Airport 

The post-‐paid taxi facility is available on meter charges @ Rs.15/-‐ per km 

(subject to Govt. regulation). Once you exit from the airport it is a long 

straight road for about 18kms till you reach the trafBic light near Kendriya 

Vihar Apartments. This is a “y” Junction. Take the straight road which is the 

Yelahanks bypass high way. Stay on this road. You will pass the Jakkur 

Flying club and at the next TrafBic Junction (Amruthahalli) take a “U” turn 

Drive down to a short distance and you will spot the L&T Komatsu Factory 

on ypur left. Adjoining this is the GKVK Campus (Gandhi Krishi Vigyan 

Kendra). Enter the campus and follow the signage to reach NCBS.

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GS-â2012 - National Centre for Biological Sciences