Department of Biological Sciences

Department of Biological Sciences

LIFE What immortal hand or eye
dare frame thy fearful symmetry ?

- Blake

Indian Institute of Science Education
& Research (IISER) Mohali

CONTENTS 1
3
Foreword 51
Faculty Profiles 67
Departmental Details and Indices 73
Campus Life
Departmental and other Facilities

Foreword Message from the Head

The Indian Institutes of Science Education and Research (the IISERs)
are a group of institutes set up by the Ministry of Human Resource
Development (MHRD) of the Government of India (GOI), to facilitate high
quality science education and research in the country. The first two
IISERs were set up in Pune and Kolkata in 2006. The IISER at Mohali
(IISER-M) began functioning in 2007. Two more IISERs were set up at
Bhopal and Trivandrum in 2008. After functioning out of a transit campus
located in Chandigarh for several years, IISER-M moved into its own
campus fully during the summer of 2013.

In June, 2012, the institute organized itself into separate
departments to facilitate more effective functioning, given the growth of faculty numbers that had taken
place in all subject areas during previous years. However, despite this fractionation, IISER-M's original
intent of fostering inter-disciplinary teaching and research has remained unchanged. Thus, research and
teaching in the Department of Biological Sciences include all aspects of classical and modern biology, as
well as every allied science that relates either nominally, or intimately, to any biological question, or
pursuit.

In its educational aspects, IISER-M is modeled on the highly successful Indian Institutes of
Technology (the IITs). In its research-related aspects, IISER-M is modelled on the Indian Institute of
Science (the IISc), Bangalore. All five IISERs were originally set up to facilitate scientific research and
teaching in an environment conducive to (and supportive of) routine, everyday interactions between
undergraduate, or graduate, students, and researchers who are still extremely active and at the leading
edges of their individual disciplines. This particular mode of functioning is IISER-M's main leitmotif. It is
also the main leitmotif of the Department of Biological Sciences, which currently has a strength of over 20
regular faculty members, over 80 Ph.D students, and a total strength of over 250 including all students,
postdocs, staff, and project assistants. The Department participates in three academic programs: the
Integrated 5- year BS-MS program, the Integrated MS-Ph.D program, which takes 4-6 years, and the
PhD program which ideally takes a maximum of 5 years to complete. During the 5-year BS-MS program,
students spend two years learning all science subjects, before choosing to specialize. Thus, although the
Department aids in the teaching of the first two years, it becomes a real stakeholder in the BS-MS
program mainly during the final three years of specialization, which include one (final) year of research.
The Integrated MS-PhD program is offered only to select students who have completed their Bachelors’
degrees’ elsewhere. The PhD program consists of two semesters of coursework and lab exposure,
followed by about four years of research.

As you go through this brochure, we hope that you will find that the Department manages to combine
(and recombine) formidable strengths in many different areas of the biological sciences, including
microbial and eukaryotic, cellular, molecular and organismal biology, biochemistry, and biophysics. As
with everything else in this world, this department too is a piece of work that is ever under construction,
and we intend to keep it that way - dynamic, sensitive, competent, diverse, responsive, colorful, joyous,
exciting, inspiring, well-fitted-out, and populated with students and faculty who love to cooperate and
create something higher, even as each individual in the department continues to plough his, or her, own
lonely furrow.

Purnananda Guptasarma 1

An inside view of AB-1 The Academic-cum-Research Block in which the department is housed

CONTACT DETAILS
Department of Biological Sciences (DBS)
Indian Institute of Science Education and Research (IISER) Mohali
Knowledge City, Sector-81, SAS Nagar, Punjab - 140 306, India
DBS Office Email : [email protected] DBS Office Tel : +91-172-2293152
2 DBS Office Location : Room No. 3F12A, Block AB-1, IISER Campus

DBS Faculty Profiles Faculty Profiles

3

Joined Dec 2008

Samrat Mukhopadhyay

Associate Professor

M.S., Indian Institute of Science, Bangalore, 2000.
Ph.D., Indian Institute of Science, Bangalore, 2005.
Postdoc, Scripps Research Institute, 2005-2008.
Samrat Mukhopadhyay has guided 1 Ph.D. thesis and 2 M.S. thesis.

Representative Publications

"Structural and Dynamical Insights into the Membrane-bound α-Synuclein" N. Jain, K. Bhasne, M.
Hemaswasthi& S. Mukhopadhyay* PLoS One2013 (accepted).

"Nanophotonics of Protein Amyloids" M. Bhattacharya and S. Mukhopadhyay* Nanophotonics
2013 (accepted).

"Dynamics and Dimension of an Amyloidogenic Disordered State of Human β2-Microglobulin" D.
Narang, P.K. Sharma & S. Mukhopadhyay*Eur. Biophys. J. 2013, 42, 767-776.

Protein Misfolding, Prion "Nanoscopic Amyloid Pores formed via Stepwise Protein Assembly" M. Bhattacharya, N. Jain, P.
& Amyloid Biology Dogra, S. Samai and S. Mukhopadhyay* J. Phys. Chem. Lett. 2013, 4, 480-485.

"Nanoscale Fluorescence Imaging of Single Amyloid Fibrils" V. Dalal, M. Bhattacharya, D. Narang,
P.K. Sharma and S. Mukhopadhyay* J. Phys. Chem. Lett. 2012, 3, 1783-1787. (This work was
selected for ACS video slide share).

"Structural and Dynamical Insights into the Molten-globule form of Ovalbumin" M. Bhattacharya &
S. Mukhopadhyay* J. Phys. Chem. B 2012, 116, 520-531.

"Chain Collapse of an Amyloidogenic Intrinsically Disordered Protein" N. Jain, M. Bhattacharya &
S. Mukhopadhyay* Biophys. J. 2011, 101, 1720-1729. (Featured in Faculty of 1000:
http://f1000.com/13409028).

"Insights into the Mechanism of Aggregation and Fibril Formation from Bovine Serum Albumin" M.
Bhattacharya, N. Jain & S. Mukhopadhyay* J. Phys. Chem. B. 2011, 115, 4195-4205.

"A natively unfolded yeast prion monomer adopts an ensemble of collapsed and rapidly fluctuating
structures" S. Mukhopadhyay, R. Krishnan, E.A. Lemke, S. Lindquist and A.A. DenizProc. Natl.
Acad. Sci. U.S.A. 2007, 104, 2649-2654. (Cited over 120 times)

"Structure and Dynamics of a Molecular Hydrogel" S. Mukhopadhyay, UdayMaitra, Ira, G.
Krishnamoorthy, J. Scmidt and Y. TalmonJ. Am. Chem. Soc. 2004, 126, 15905-15914.

SamratMukhopadhyay has contributed a total of 25 papers to the literature (including 2 book
chapters).

4 Dept. Biol. Sci. IISER Mohali +91-172-2293150 [email protected]

Research Interests & Projects

Our laboratory is involved in unraveling the fundamental molecular
mechanism of amyloid formation that has been implicated in a variety of
deadly human disorders. We have started investigating the formation of
amyloid pore by AFM and Raman spectroscopy and have made an important
progress towards the nanoscopic imaging of amyloid fibrils beyond the
diffraction-limit. Using near-field scanning optical microscopy (NSOM), we
were able to resolve the fibrils that were spatially separated by ~ 75 nm. We are
also investigating membrane-induced folding and amyloid formation of α-
synuclein, an intrinsically disordered protein. It has been implicated in a
number of potentially important neuronal functions as well as in the etiology of
Parkinson's disease. Based on our results, we proposed a structural model of
α-synuclein in the membrane-bound form. Recently, we have embarked upon
studying functional prions and amyloids that are implicated in many important
biological functions.

5

Joined Jan 2009

N. G. Prasad

Associate Professor

Sept 2013 - Present, Associate Professor, IISER, Mohali.
Jan 2009 - Sept 2013, Assistant Professor, IISER, Mohali.
Aug 2007- Dec 2008, Assistant Professor, School of Life Sciences, IISER, Kolkata.
Oct 2003 - Aug 2007, Post Doctoral Fellow, Department of Biology, Queen's University,
Kingston, ON, Canada.
Aug 1998 - Oct 2003, PhD student, Jawaharlal Nehru Centre for Advanced Scientific
Research, Bangalore.
June 1997 - Aug 1998, Lecturer, Department of Zoology, MES College of Arts, Commerce
and Science, Bangalore University, Bangalore,
June 1995 - May 1997, M.Sc., Department of Zoology, Bangalore University, Bangalore.
Prasad has guided 2 PhD theses and 3 Master's theses.

Representative Publications

Nandy, B., Gupta V., Udaykumar, N., Samant, M., Sen, S. and Prasad, N.G. 2013. Evolution of mate-harm, longevity
and behaviour in male fruit flies subjected to different levels of interlocus conflict. BMC Evolutionary Biology 13:212

Gupta, V., Zeeshan, S. A. and Prasad, N. G. 2013. Sexual activity increases resistance against Pseudomonas
entomophila in male Drosophila melanogaster. BMC Evolutionary Biology 13: 185.

Nandy, B., Vanika, G., Udaykumar, N., Samant, M. A., Sen, S. and Prasad, N.G. 2013. Experimental evolution of
female traits under different levels of intersexual conflict in Drosophila melanogaster. Evolution
doi:10.1111/evo.12271.

Evolutionary Genetics Imroze, K. and Prasad, N. G. 2013. Adaptive male mate choice in relation to female infection status in Drosophila
melanogaster. Journal of Insect Physiology 59: 1017-1023. doi: 10.1016/j.jinsphys.2013.07.010

Nandy, B., Chakraborty, P., Ali, Z.S. and Prasad, N.G. 2013. Sperm competitive ability evolves in response to altered
operational sex ratio. Evolution. doi:10.1111/evo.12076

Khan, I. and Prasad N. G. 2012. The aging of the immune response in Drosophila melanogaster. Journals of
Gerontology: Biological Sciences. doi:10.1093/Gerona/gls144.

Nandy, B., Abhilasha, J., Zeeshan, S. A., Sharmi, S. and Prasad, N. G. 2012. Degree of adaptive male mate choice is
positively correlated with female quality variance. Scientific Reports. doi:10.1038/srep00447

Imroze, K. and Prasad, N. G. 2011. Mating with large males decreases the immune defence of females in Drosophila
melanogaster. Journal of Genetics. 90: 427-434.

Pan-Pan, J., Bedhomme, S., Prasad, N. G. and Chippindale, A. K. 2011. Sperm competition and mate harm
unresponsive to male-limited selection in Drosophila: An evolving genetic architecture under domestication.
Evolution. 65:2248

Nandy, B. and Prasad, N. G. 2011. Reproductive behaviour and fitness components in male Drosophila are non-
linearly affected by the number of male co-inhabitants early in adult life. Journal of Insect Science.
11: 67

Prasad has contributed a total of 30 papers to the literature.

6 Dept. Biol. Sci. IISER Mohali +91-172-2293170 [email protected]

Research Interests & Projects

In promiscuous species, the correlation for fitness between males and females is
less than one. Thus, males and females can potentially evolve traits that increase
their own Darwinian fitness but harm the fitness of the other sex. This leads to open-
ended cycles of adaptation and counter adaptation- a form of intra-species Red
Queen process- often called Intersexual Conflict. Such antagonistic co-evolution
between the sexes has been suggested to drive rapid divergence between
populations in their life-history and behaviour and act as an engine of speciation.
The long term goal of our lab is to understand the interplay between sexual conflict,
sexual selection and life-history evolution. Specifically, we are working on (a)
Interlocus Sexual conflict, (b) Life-History Evolution and (c) Evolutionary Ecology of
immunity.
We use Drosophila melanogaster as a model system. Our approaches include
Experimental Evolution, Cytogenetic cloning and Phenotypic manipulations. Our
techniques allow us to follow the process of adaptive evolution in real time across
replicate populations. More importantly, we can assess fitness and related traits
under conditions that are meaningful to the populations.

7

Joined Mar 2009

Arunika Mukhopadhaya

Assistant Professor

2009(March)-to date: Assistant Professor, Department of Biological Sciences, IISER Mohali,
Punjab

2006(April)-2009(March): Research Associate, Department of Microbiology and Immunology,
Albert Einstein College of Medicine, New York

2004(March)-2006(March): Research Associate, Radiation Oncology Department, Albert
Einstein College of Medicine, New York

1999(April)-2004(March): PhD Research Scholar, National Institute of Cholera and Enteric
Diseases, Kolkata.

Representative Publications

Immunology :
Host-microbe interactions

8 Dept. Biol. Sci. IISER Mohali +91-172-2293148 [email protected]

Research Interests & Projects

My group is interested in characterization of host-immunomodulatory responses by pathogenic
gram negative enteric bacteria. Pathogenic enteric bacteria are those which upon entering into the
host colonize in the gut region and secrete toxin(s) or invade gut epithelial cells to pathogenize the
host. Pathogens carry pathogen associated molecular patterns (PAMPs) which are recognized by
the pattern recognition receptor (PRRs) present on the cells such as macrophages, dendritic cells,
intestinal epithelial cells. PAMP recognition by PRRs initiate signal transduction cascades
resulting in production of an array of cytokines and chemokines which are not only important for
innate immune responses also shapes up adaptive immune responses in terms of inflammation
and B/T cell effector function and memory generation. Different PAMPs or antigens have the ability
to excite or suppress the immune responses. If the antigen is a potent stimulator of the host's
immune system, it can be considered for vaccine development. On the other hand if the antigen is
an immune suppressor that help us to understand more about the pathogenesis of the bacteria.
Currently we are working on three broad projects:
Project 1: Understanding the host-immunomodulatory role of Vibrio cholerae porin
Project 2: Understanding the host-immunomodulatory role of homologous porin from Vibrio
parahaemolyticus
Project 3: Understanding the host-immunomodulatory role of TypeIII secretion system
translocation effector proteins of Salmonella enterica serovar Typhimurium.

9

Joined Mar 2009

Kausik Chattopadhyay

Assistant Professor

B.Sc. (Honours in Chemistry) 1996, Calcutta University, India. M.Sc.
(Biochemistry) 1998, Calcutta University, India. Ph.D. research, 1998-2003,
National Institute of Cholera and Enteric Diseases, Kolkata, India. Ph.D.
(Biochemistry) from Calcutta University, India. Post-doctoral research,
2003-2009, Albert Einstein College of Medicine, New York, USA. Joined
IISER Mohali in March, 2009.

Dr. Kausik is guiding/has guided 5 Ph.D theses and 2 masters' theses.

Structure-function studies: Representative Publications
Pore-forming toxins
Rai, A. K.*, Paul, K.* and Chattopadhyay, K. (2013) Functional mapping of the lectin activity site on the β-Prism
domain of Vibrio cholerae cytolysin: implications for the membrane pore-formation mechanism of the toxin. J. Biol.
Chem, 288 (3), 1665-1673. (*These authors contributed equally to this work).

Paul, K. and Chattopadhyay, K. (2012) Single point mutation in Vibrio cholerae cytolysin compromises membrane
pore-formation mechanism of the toxin. FEBS Journal, 279 (21), 4039-4051.

Paul, K. and Chattopadhyay, K. (2011) Unfolding distinguishes the Vibrio cholerae cytolysin precursor from the
mature form of the toxin. Biochemistry, 50 (19), 3936-3945.

Chattopadhyay, K., Ramagopal, U. A., Nathenson, S. G., and Almo S. C. (2009) 1.8 A structure of murine GITRL
dimer expressed in Drosophila melanogaster S2 cells. Acta Crystallography D. Biol. Crystallogr. D65. 434-439.

Chattopadhyay, K., Lazar-Molnar, E., Yan, Q., Rubinstein, R., Zhan, C., Vigdorovich, V., Ramagopal, U. A.,
Bonanno, J., Nathenson, S. G., and Almo, S. C. (2009) Sequence structure function and immunity: structural
genomics of costimulation. Immunological Reviews, volume 229, issue 1, 356-386.

Chattopadhyay, K., Ramagopal, U. A., Brenowitz, M., Nathenson, S. G., and Almo S. C. (2008) Evolution of GITRL
immune function: murine GITRL exhibits unique structural and biochemical properties within the TNF superfamily.
Proc. Natl. Acad. Sci. USA, 105. 635-640. (This article was selected in the Editor's Choice section of Science
Signaling).

Chattopadhyay, K., Ramagopal, U. A., Mukhopadhaya, A., Malashkevich, V. N., DiLorenzo, T. P., Brenowitz, M.,
Nathenson, S. G., and Almo, S. C. (2007) Assembly and structural properties of glucocorticoid-induced TNF receptor
ligand: implications for function. Proc. Natl. Acad. Sci. USA, 104. 19452- 19457.

Chattopadhyay, K., Bhatia, S., Fiser, A., Almo, S. C., and Nathenson, S. G. (2006) Structural basis of inducible
costimulator ligand costimulatory function: determination of the cell surface oligomeric state and functional mapping
of the receptor binding site of the protein. J. Immunol. 177, 3920-3929.

Chattopadhyay, K. and Banerjee, K. K. (2003) Unfolding of Vibrio cholerae hemolysin induces oligomerization of the
toxin monomer. J. Biol. Chem. 278, 38470-38475.

Chattopadhyay, K., Bhattacharyya, D., and Banerjee, K. K. (2002) Vibrio cholerae hemolysin: implication of
amphiphilicity and lipid-induced conformational change for its pore-forming activity. Eur. J. Biochem. 269, 4351-
4358.

Dr. Kausik has contributed a total of 15 papers to the literature (including 1 book chapter).

10 Dept. Biol. Sci. IISER Mohali +91-172-2293147 [email protected]

Research Interests & Projects

Structure-Function Studies on Pore-Forming Protein Toxins
Pore-forming protein toxins (PFTs) represent a special class of membrane damaging cytolytic
proteins, and they are found in wide spectrum of organisms ranging from bacteria to humans.
They exert their toxic effects by punching 'holes' into target cell membrane, thus destroying the
natural permeability barrier function of the cell membrane. PFTs are, in general, synthesized as
water-soluble molecules, and in contact with target cell membranes they form membrane-inserted
pores. However, in spite of sharing this overall general scheme, PFTs differ significantly from each
other in the intricate details of their pore formation mechanisms. A major mechanistic challenge
associated with the membrane pore formation process by PFTs is elucidating the folding pathways
that ensure thermodynamic compatibility of the water-soluble and the membrane-inserted form of
the toxin with aqueous and membrane lipid milieu, respectively. One of the major research
interests of my group is focused on studying structure-function relationship of some of the
prominent bacterial PFTs. The critical issues we address are:
1. Mechanistic details of membrane channel formation by PFTs.
2. Mechanism(s) associated with cellular responses triggered by PFTs.

11

Joined July 2009

Lolitika Mandal

Assistant Professor

I did my Masters in Zoology with a specialization in Cytology and Molecular
Genetics from Burdwan University. Thereafter for my doctoral studies, I joined the
Cytogenetics Laboratory, Banaras Hindu University, Varanasi. My post doctoral
research was carried out in Department of Molecular, Cell and Developmental
Biology, University of California, Los Angeles. Upon completion of which, I
returned to India to join IISER (MOHALI) on 1st July 2009. Currently, I am guiding 5
Ph.D theses and 2 masters' theses. One master thesis has already been
submitted from my laboratory.

Stem and progenitor cell development: Representative Publications
Molecular pathways of hematopoeisis and cardiogenesis
Mondal BC, Mukherjee T, Mandal L, Evans CJ, Sinenko SA, Martinez-Agosto JA, Banerjee U. Interaction
between differentiating cell- and niche-derived signals in hematopoietic progenitor maintenance.
Cell. 2011 Dec 23;147(7):1589-600. Joint First author.

Mukherjee T, Kim WS, Mandal L, Banerjee U. Interaction between Notch and Hif-alpha in development and
survival of Drosophila blood cells. Science. 2011 Jun 3;332(6034):1210-3.

Grigorian M, Mandal L, Hakimi M, Ortiz I, Hartenstein V. The convergence of Notch and MAPK signaling
specifies the blood progenitor fate in the Drosophila mesoderm. Dev Biol. 2011 May 1;353(1):105-18.

Grigorian M, Mandal L, Hartenstein V. Hematopoiesis at the onset of metamorphosis: terminal
differentiation and dissociation of the Drosophila lymph gland. Dev Genes Evol. 2011 Aug;221(3):121-31.

Sinenko SA, Mandal L, Martinez-Agosto JA, Banerjee U.Dual role of wingless signaling in stem-like
hematopoietic precursor maintenance in Drosophila. Dev Cell. 2009 May;16(5):756-63.

Mandal L, Martinez-Agosto JA, Evans CJ, Hartenstein V, Banerjee U. A Hedgehog- and Antennapedia-
dependent niche maintains Drosophila haematopoietic precursors. Nature. 2007 Mar 15;446(7133):
320-4.

Hartenstein V, Mandal L.The blood/vascular system in a phylogenetic perspective. Bioessays. 2006
Dec;28(12):1203-10. Review.

Mandal L, Dumstrei K, Hartenstein V.Role of FGFR signaling in the morphogenesis of the Drosophila
visceral musculature. Dev Dyn. 2004 Oct;231(2):342-8.

Mandal L, Bannerjee U, Hartenstein V. Evidence for a fruit fly hemangioblast and similarities between
lymph-gland hematopoiesis in fruit fly and mammal aorta-gonadal-mesonephros mesoderm. Nat Genet.
2004 Sep;36(9):1019-23.

Cory J. Evans, Sergey A. Sinenko, Lolitika Mandal, Julian A. Martinez-Agosto and Utpal Banerjee.
Genetic Dissection of Hematopoiesis Using Drosophila as a Model System. Cardiovascular Development.
Advances in Developmental Biology. Edited by Rolf Bodmer.

Lolitika has contributed a total of 12 papers to the literature (including 1 book chapters).

12 Dept. Biol. Sci. IISER Mohali +91-172-2293172 [email protected]

Research Interests & Projects

Developmental Genetics Laboratory at IISER (MOHALI) is interested in Hematopoiesis,
Cardiogenesis and Molecular pathways in stem and progenitor cell development.
Ongoing Project: Molecular genetic dissection of signaling pathways involved in hematopoietic
niche maintenance in Drosophila. A proposal funded by WELLCOME DBTAlliance.
Stem cells are the source of virtually all highly differentiated cells that are replenished during the
lifetime of an animal. The critical balance between stem and differentiated cell populations is
crucial for the long-term maintenance of functional tissue types. A microenvironment that is
supportive of stem cells is commonly referred to as a stem cell niche. Although, several signaling
molecules emanating from the niche has been identified for regulation of stem cell state and
function, the information regarding niche maintenance is still in its infancy. We are interested to
know the mechanistic basis of niche maintenance.
Last decade established Drosophila as the best invertebrate model system for studying
hematopoiesis. Due to the limited access of mammalian hematopoietic niche this amenable
system allows us to unravel molecular regulation of stem cell progenitors and its relation with the
niche. The power of Drosophila as a model organism is very well established, most notably its
genetics and developmental biology. Taking advantage of these strengths our group also aims in
unraveling novel genes and mechanisms that controls hematopoietic progenitors cell
specification and differentiation. Given the high degree of conservation of blood development
between Drosophila and the vertebrates, we hope that the ability to manipulate the function of
such genes in Drosophila would aid in understanding function and dysfunction in human
hematopoiesis.

13

Joined July 2009

Sudip Mandal

Assistant Professor

I did my Masters from the Department of Zoology, Banaras Hindu University
with specialization in Cytogenetics and Molecular Genetics. After obtaining
my Doctoral degree from Banaras Hindu University, I moved to the
Department of Molecular Cell and Developmental Biology, University of
California Los Angeles for post doctoral training. I joined IISER Mohali on
July 1, 2009. Our group consists of 5 graduate students and 1 postdoctoral
fellow. Two students have completed their Masters’ thesis from our
laboratory.

Molecular Cell & Developmental Biology: Representative Publications
Mitochondrial regulation of cellular function Freije, W.A., Mandal, S., and Banerjee, U. (2012). Expression profiling of attenuated
mitochondrial function identifies retrograde signals in Drosophila. G3 2, 843-851.

Mandal, S., Lindgren, A.G., Srivastava, A.S., Clark, A.T., and Banerjee, U. (2011).
Mitochondrial function controls proliferation and early differentiation potential of
embryonic stem cells. Stem cells 29, 486-495.

Mandal, S., Freije, W.A., Guptan, P., and Banerjee, U. (2010). Metabolic control of
G1-S transition: cyclin E degradation by p53-induced activation of the ubiquitin-
proteasome system. The Journal of cell biology 188, 473-479.

Owusu-Ansah, E., Yavari, A., Mandal, S., and Banerjee, U. (2008). Distinct
mitochondrial retrograde signals control the G1-S cell cycle checkpoint. Nature
genetics 40, 356-361.

Liao, T.S., Call, G.B., Guptan, P., Cespedes, A., Marshall, J., Yackle, K., Owusu-
Ansah, E., Mandal, S., Fang, Q.A., Goodstein, G.L., et al. (2006). An efficient
genetic screen in Drosophila to identify nuclear-encoded genes with mitochondrial
function. Genetics 174, 525-533.

Mandal, S., Guptan, P., Owusu-Ansah, E., and Banerjee, U. (2005). Mitochondrial
regulation of cell cycle progression during development as revealed by the tenured
mutation in Drosophila. Developmental cell 9, 843-854.

14 Dept. Biol. Sci. IISER Mohali +91-172-2293175 [email protected]

Research Interests & Projects

Mitochondria, as we all studied in our school days, are bean shaped organelles considered as the
powerhouse of the cell and the biochemical pathways leading to ATP synthesis within the
mitochondria is well understood. However, studies in the recent past have established
mitochondria as dynamic polymorphic structures having branched reticulate network
interspersed with small bean shaped structures that integrate diverse extra and intra cellular
signals to regulate several cellular functions. Mitochondrial biology, therefore, has become a fast
growing area in genetics and medicine, linking cell biological processes to metabolic disorders
and cancer. We are interested in understanding the role of mitochondrion in controlling cell
biological processes like proliferation, growth and differentiation. We use the model organism,
Drosophila melanogaster, for genetic dissection of retrograde signaling pathways from
mitochondria to nucleus that are essential in modulating cellular responses. Taking advantage of
the advanced genetic tools available in this model system and using high-end microscopy and
molecular genetic approaches we aim to unravel the mechanistic basis of mitochondrial
regulation of cellular functions.
The other focus of our research involves embryonic stem cells. Embryonic stem cells, by virtue of
their capacity to proliferate indefinitely and to differentiate into almost all types of somatic cells,
hold the potential to be used for therapeutic purposes. Current research in this field aims to a)
develop means to direct embryonic stem cells to differentiate into specific cell types that can be
used for therapy and (b) to reprogram adult somatic cells to form induced pluripotent stem (IPS)
cells. In this pursuit scientists are trying to understand the genetic regulations and modifications in
the genome that contribute to the processes of reprogramming and differentiation. Although it is
equally important to understand how these processes are affected by the cellular metabolic state,
very limited studies address this issue. We aim to understand the metabolic control of pluripotency
and early lineage specification of ESCs and EpiSCs. To achieve this goal, we employ a
combination of microscopic, histological, biochemical, genetic and molecular cell biological
approaches.

15

Joined June 2010

Samarjit Bhattacharyya

Assistant Professor

1994-1997 Bachelor of Science (B.Sc.) in Honors in Physics (Major), Chemistry and
Mathematics (Minors) from University of Calcutta, West Bengal, India.

1997-1999 Master of Science (M.Sc.) in Biophysics, Molecular Biology and Genetics from
University of Calcutta, West Bengal, India.

1999-2005 Graduate student at the National Centre for Biological Sciences (NCBS), Tata
Institute of Fundamental Research (TIFR), Bangalore, India.

2005-2010 Post-doctoral fellow with Prof. Robert. C. Malenka, M.D, Ph.D, at Stanford
University, USA.

Joined IISER Mohali in June, 2010

Neurobiology: Molecular Mechanisms of Protein Trafficking Representative Publications
in the Central Nervous System
Ishier Raote, Samarjit Bhattacharyya & Mitradas M Panicker. Functional Selectivity in Serotonin Receptor 2A (5-
HT2A) Endocytosis, Recycling and Phosphorylation. Molecular Pharmacology, 83(1): 42-50, 2013.

Rishi Raj Trivedi & Samarjit Bhattacharyya. Constitutive internalization and recycling of metabotropic glutamate
receptor 5 (mGluR5). Biochem Biophys Res Commun. 427(1): 185-190, 2012.

Citri, A.,* Bhattacharyya, S.,* Ma, C., Morishita, W., Fang, S., Rizo, J., & Malenka, R.C. Calcium binding to PICK1 is
essential for the intracellular retention of AMPA receptors underlying long-term depression. Journal of
Neuroscience, 30(49): 16437-52, 2010. (* Joint first authors)

Citri, A., Soler-Llavina, G., Bhattacharyya, S., & Malenka, R. C. N-methyl- Daspartate receptor and metabotropic
glutamate receptor-dependent long-term depression are differentially regulated by the ubiquitin-proteasome system.
European Journal of Neuroscience, 30(8):1443-50, 2009.

Bhattacharyya, S., Biou, V., Xu, W., Schlüter, O., & Malenka, R. C. A critical role for PSD-95/AKAP interactions in
endocytosis of synaptic AMPA receptors. Nature Neuroscience, 12(2):172-81, 2009.

Biou, V., Bhattacharyya, S., & Malenka, R. C. Endocytosis and recycling of AMPA receptors lacking GluR2/3. Proc.
Natl. Acad. Sci, USA, 105(3):1038-43, 2008.

Bhattacharyya, S., Raote, I., Bhattacharya, A., Miledi, R., & Panicker, M. M. Activation, internalization, and recycling of
the serotonin 2A receptor by dopamine. Proc. Natl. Acad. Sci, USA, 103(41):15248-53. 2006.

Bhattacharyya, S., Puri, S., Miledi, R., & Panicker, M. M. Internalization and recycling of 5-HT2A receptors
activated by serotonin and protein kinase C mediated mechanisms. Proc. Natl. Acad. Sci, USA, 99(22):14470-5,
2002.

Patent: A novel assay for screening antipsychotic drugs. Mitradas. M. Panicker and Samarjit Bhattacharyya.
United States Patent Number: 7524639. European patent approved.

Dr. Samarjit Bhattacharyya has contributed a total of 8 papers and 1 patent.

16 Dept. Biol. Sci. IISER Mohali +91-172-2293149 [email protected]

Research Interests & Projects

Cellular and Molecular Mechanisms of Protein Trafficking in the Central
Nervous System

An essential requirement for maintenance of homeostasis in any living organism is the
ability of cells to sense the external environment and, in the case of multicellular
organisms, for cells to communicate with each other via mediators released into the
extracellular milieu. In the brain, a variety of neurotransmitters and neuromodulators act
on target receptors to activate cellular signaling events which transfer information from
one cell to the next. Normal signaling depends on accurate localization of such receptors in
specific regions of the cell, and the process of receptor trafficking plays a critical role in
controlling this localization. Despite the obvious significance of this process, we still know
very little about the protein machineries that mediate trafficking of neurotransmitter
receptors in the brain, the regulatory events that control these protein machineries, and the
functional consequences of these regulatory events. Our labs specific interest lies in
studying the cellular and molecular mechanisms that regulate the trafficking of
neurotransmitter receptors in the central nervous system. Currently, the lab is studying the
cellular and molecular mechanisms that regulate the trafficking of (1) ionotropic
glutamate receptors and (2) metabotropic glutamate receptors (mGluRs). We
employ multidisciplinary approaches ranging from biochemistry and molecular biology to
cell biology and imaging to address these questions.

17

Joined Sept 2010

Anand Bachhawat

Professor

Dr Anand K Bachhawat has obtained a Masters in Chemistry from IIT Kanpur
followed by a PhD in Biochemistry from Calcutta University (Bose Institute). He
has done a post-doctoral stint at the MGH Cancer Center, Harvard Medical
School, Boston, followed by a post-doctoral stint at the Carnegie Mellon
University, Pittsburgh. He joined the Institute of Microbial Technology in 1993. In
September 2010 he moved to IISER Mohali as a Professor in Biological
Sciences. Dr Bachhawat has guided 18 PhD theses (including several ongoing
and 2 M.Sc. theses).

Yeast Genetics and Biochemistry: Representative Publications
Glutathione and sulfur metabolism
Ganguli D, Kumar C, Bachhawat A.K.. ( 2007). The alternative pathway of glutathione degradation is mediated by a
novel protein complex involving three new genes in Saccharomyces cerevisiae. Genetics. 175,1137-1151,2007.

Kaur, J. and Bachhawat, A.K.( 2007) Yct1p, a novel, high-affinity, cysteine specific transporter from the yeast
Saccharomyces cerevisiae. Genetics 176, 877-890, 2007.

Kaur H, Kumar C, Junot C, Toledano M, Bachhawat AK (2009) Dug1p is a Cys-Gly peptidase of the gamma -glutamyl
cycle of Saccharomyces cerevisiae, and represents a novel family of Cys-Gly peptidases. J Biol Chem. 284:14493-
502.

Kaur, J. and Bachhawat, A.K. (2009). Q222 in transmembrane domain 4 and Q526 in transmembrane domain 9 are
critical for substrate recognition in the yeast high affinity glutathione transporter, Hgt1p. J Biol Chem 284(35):23872-
84

Yadav, AK, Desai, PR, Rai, MN, Kaur R, Ganesan, K and Bachhawat, AK (2011) Glutathione biosynthesis in the yeast
pathogens Candida glabrata and Candida albicans: Essential in C. glabrata, and essential for virulence in C. albicans
. Microbiology 157, 484-495.

Kumar, C, Igbaria, A, D'Autreaux, B., Planson, A-G., Junot, C., Bachhawat, AK, Deluanay-Moisan, A and Toledano, M.
(2011). Glutathione revisited : a vital function in iron metabolism but a secondary role in thiolredox maintenance.
EMBO J. 30: 2044-56, 2011.

Yadav, AK and Bachhawat, AK (2011) CgCYN1, a plasma membrane cystine-specific transporter of Candida glabrata
with orthologues prevalent amongst pathogenic yeasts and fungi. J Biol Chem. 286:19714-23,2011.

Desai PR, Thakur A, Ganguli D, Paul S, Morschhauser J, Bachhawat AK (2011). Glutathione utilization by Candida
albicans requires a functional DUG pathway and OPT7, an unusual member of the oligopeptide transporter family. J
Biol Chem. 286:41183-94.

Kaur H, Ganguli D, Bachhawat AK. (2012). Glutathione degradation by the alternative pathway (DUG pahway) in
Saccharomyces cerevisiae is initiated by the (Dug2p-Dug3p)2 complex, a novel GATase enzyme acting on
glutathione. J Biol Chem. 287:8920-31.

Kumar A, Tikoo S, Maity S, Sengupta S, Sengupta S, Kaur A, Bachhawat AK. (2012) Mammalian proapoptotic factor
ChaC1 and its homologues function as γ-glutamyl cyclotransferases acting specifically on glutathione.EMBO
Reports. 13:1095-101.

Prof Bachhawat has contributed a total of 55 papers to the literature (including 3 book chapters).

18 Dept. Biol. Sci. IISER Mohali +91-172-2293154 [email protected]

Research Interests & Projects

Glutathione, Sulphur and Redox are the key areas around which our lab interests are centred.
The major question that we are asking is 'How is glutathione homeostasis maintained in living
cells ?' Surrounding this major question are several other questions that become important for our
understanding. The principal model systems that we use to address these questions are the
yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. Glutathione, γ-glutamyl
cysteinyl glycine, an unusual thiol containing tripeptide that is present in high concentrations in
almost all eukaryotic cells, plays multiple roles including protection from oxidative stress,
maintenance of the cellular redox buffer, in mitochondrial iron-sulphur metabolism, in gene
regulation, and in metal and drug detoxification. Glutathione metabolism is intimately linked to
sulphur metabolism owing to the presence of the key cysteine residue, and we thus also
investigate aspects of sulphur metabolism related to glutathione homeostasis. As the focus is on
understanding how glutathione levels are maintained in the cell, we are examining different
pathways that contribute towards this maintenance. This includes the high affinity plasma
membrane transporter of glutathione that was identified in our lab, the classical and two recently
discovered non-classical pathways of glutathione degradation (also discovered in our lab)
biosynthesis, organellar compartmentalization and utilization of glutathione. We are attempting to
not only understand these different pathways and their regulation in detail, but are interested in
integrating these pathways and their regulation into a larger picture of glutathione homeostasis in
living cells.
We have also an interest in the human lysosomal disorder, cystinosis, that is due to a defect in the
lysosomal cystine transporter and we are using yeasts to investigate different aspects of this
disease. Very recently, we have also initiated a project on the synthetic biology of commercially
important terpenoids.

19

Joined Oct 2010

Purnananda Guptasarma

Professor

Purnananda Guptasarma completed a Bachelors' degree in engineering and an integrated Masters'
degree in Science, under the dual-degree program of the Birla Institute of Technology & Science
(BITS, Pilani), during 1983-1988. He worked for a Ph.D in molecular biophysics and biochemistry at
the Centre for Cellular and Molecular Biology (CCMB, Hyderabad), during 1988-1993. After
spending some additional months at CCMB as a research associate of the DBT, he moved to the
University of Cambridge in 1994, as a Wellcome Trust International Travelling Research Fellow at
the Department of Biochemistry. Towards the end of 1996, he joined the Institute of Microbial
Technology (IMTECH, Chandigarh) as a principal investigator in its Division of Protein Science and
Engineering, and worked in four positions as a scientist. In 2008, he became an adjunct faculty at
IISER Mohali, and left IMTECH to move to a full Professorship at IISER in October 2010.

Guptasarma has guided 17 doctoral theses (including 7 that are ongoing, with 2 of these due for
submission), and 3 Masters' theses.

Protein Engineering and Structural Biochemistry : Representative Publications
Folding, Structure, Stability, Function, Aggregation
Kundu, B. & Guptasarma, P. (1999). Hydrophobic dye inhibits the aggregation of molten carbonic anhydrase during
thermal unfolding and refolding. Proteins : Structure, Function, Bioinformatics. 37, 321-324.

Shukla, A., Raje, M. & Guptasarma, P. (2003). A backbone-reversed form of an all-beta alpha crystallin domain from a
small heat-shock protein (retro-HSP12.6) folds and assembles into structured multimers. Journal of Biological
Chemistry 278, 26505-26510.

Mukherjee, S., Sharma, S., Kumar, S. & Guptasarma P. (2005). Slow irreversible unfolding of Pyrococcus furiosus
triosephosphate isomerase: separation and quantitation of conformers through a novel electrophoretic approach.
Analytical Biochemistry 347, 49-59.

Sharma, S. & Guptasarma, P. (2008). Dimorphic aggregation behavior of a fusion polypeptide incorporating a stable
protein domain (EGFP) with an amyloidogenic sequence (retro CspA). FEBS Letters 582, 2203-2211.

Ahmed, S., Kapoor. D., Singh, B. & Guptasarma, P. (2008). Conformational behavior of polypeptides derived through
simultaneous global conservative site-directed mutagenesis of chymotrypsin inhibitor 2. Biochimica et Biophysica
Acta : Proteins and Proteomics 1784, 796-805.

Chandrayan, S. K. & Guptasarma, P. (2009). Attenuation of ionic interactions profoundly lowers the kinetic thermal
stability of Pyrococcus furiosus triosephosphate isomerase. Proteins : Structure, Function, Bioinformatics 72,
539-546.

Kapoor, D., Singh, B., Subramanian K. & Guptasarma, P. (2009) Creation of a new eye lens crystallin (Gambeta)
through structure-guided mutagenic grafting of the surface of beta B2 crystallin onto the hydrophobic core of gamma B
crystallin. FEBS Journal 276, 3341-3353.

Fatima, U., Singh, B., Subramanian, K. & Guptasarma P. (2012). Insufficient (sub-native) helix content in
soluble/solid aggregates of recombinant and engineered forms of IL-2 throws light on how aggregated IL-2 is
biologically active. Protein Journal. 31, 529-543.

Dhaunta, N., Arora, K., Chandrayan, S.K. & Guptasarma, P. (2013). Introduction of a thermophile-sourced ion pair
network in the fourth beta/alpha unit of a psychophile-derived triosephosphate isomerase from Methanococcoides
burtonii significantly increases its kinetic thermal stability. Biochimica et Biophysica Acta: Proteins and
Proteomics. 1834:1023-1033.

Prakash, S., Sundd, M. & Guptasarma, P. (2014) The Key to the Extraordinary Thermal Stability of P. furiosus Holo-
Rubredoxin: Iron Binding-Guided Packing of a Core Aromatic Cluster Responsible for High Kinetic Stability of the
Native Structure. PLoS One 9, e89703.

The above list contains one representative paper each from the first ten doctoral students in the group, during
Guptasarma's work at IMTECH and at IISER. Guptasarma has published over 55 research papers to date.

Patents - Title : A recombinant meso-active thermo-stable protein and the process of design and biosynthesis
thereof. Inventors :Divya Kapoor, Sanjeev K. Chandrayan, Shubbir Ahmed, Swati Sharma, Manish Datt, Balvinder
Singh, Karthikeyan Subramanian & Purnananda Guptasarma. Countries : China Patent 200780048162; PCT Patent
WO/2008/056376; Indian Patent 2411/DEL/2006; patent(s) pending in Australia, UK and USA.

20 Dept. Biol. Sci. IISER Mohali +91-172-2293151 [email protected]

Research Interests & Projects

I work in the areas of protein structural biochemistry, and protein engineering. Over the last two
decades and more, I have been fascinated by three sets of questions in molecular and cellular biology : (i) How
do proteins fold to native structure, become stable (or hyper-stable), and function (especially as enzymes),
OR misfold to undergo aggregation ? (ii) How is gene expression regulated by controlling the topological states
of (and physical access of proteins to), either DNA or RNA ? (ii) How do the developmental fates of cells, during
organismal development, become determined genetically even prior to the onset of zygotic gene expression,
when cells lose totipotency under maternal genetic control? I have worked and published extensively in the
first of the three areas above, and continue to do so, even as I approach the 'three-quarters line' of my second
decade as a Principal Investigator. In the second of the areas above, I've published some theories and
experiments, and have launched into many more, the results of which are not yet published. In the third area,
I've done much thinking, but no experiments yet. As an experimentalist, I use every instrumentation-based tool
or technique that I can get myself to learn, or master, given my background in both engineering and science
before my Ph.D in molecular biophysics and biochemistry. Currently, I use all conceivable techniques in
cellular and molecular biology and microscopy, as well as all forms of UV-Vis-IR spectroscopy, calorimetry,
light scattering, surface probing, and mass spectrometry, all analytical and chromatographic modes of
ultracentrifugation, chromatography, and electrophoresis, as well as some NMR, ESR, and X-ray
crystallography (the last three of these largely in collaborative mode). I also use molecular modeling.

Currently, three-fifths of the work in my lab is on ex-vivo studies of protein structure, stability, folding
and function, or misfolding and aggregation, using many different experimental systems; mostly
hyperthermophile-derived proteins. The remaining two-fifths relate to studies of DNA-protein interactions or
gene expression, or cellular responses to protein aggregates.

In recent years, we have discovered a novel fluorescence in proteins (from H-bonded peptide bonds);
invented a new technique for grafting beta sheet-based active surfaces between proteins; unraveled the
molecular mechanisms of high kinetic stability in hyperthermophile proteins (and used these to engineer
proteins, to make them more or less kinetically stable, by design); discovered novel health implications and
modes of aggregation of certain medically-relevant proteins; and developed new methods in fluorescence
spectroscopy, mass spectrometry, gene expression and bioinformatics.

www.guptasarmalab.in

21

Joined July 2011

Kavita Babu

Assistant Professor

1998 - 2004: PhD in Drosophila Development, Supervisor: Professor William Chia,
National University of Singapore, Singapore and Kings College, London, UK.

2005 - 2011: Postdoctoral Fellow in C. elegans neurobiology, Advisor: Professor Joshua
Kaplan, Massachusetts General Hospital and Harvard University Boston, USA.

2011 - Present: Assistant Professor in the Department of Biological Sciences since
August 2011, Indian Institute of Science Education and Research (IISER), Mohali.

Kavita is currently an Assistant Professor and Wellcome-DBT Intermediate Fellow at
IISER Mohali.

Neurobiology: Representative Publications
Function & regulation of cell adhesion molecules Babu, K., Hu, Z., Chien, S-C., Garriga, G. and Kaplan, J.M. (2011) The Immunoglobulin
super family protein RIG-3 prevents synaptic potentiation and regulates Wnt signaling.
Neuron 2011 Jul 14; 71(1): 103-16.

Hu, Z.*, Pym, E.C.G.*, Babu, K.*, Vahlishan Murray, A.B.* and Kaplan, J.M. (2011) A
neuropeptide-mediated stretch response links muscle contraction to changes in
neurotransmitter release. Neuron 2011 Jul 14; 71(1): 92-102.* Equal contribution

Babu, K., Bahri, S., Alphey, L. and Chia, W. (2005) Bifocal and PP1 interaction regulates
targeting of the R-cell growth cone in Drosophila. Dev Biol 2005 Dec 15; 288(2): 372-
86.Corresponding author

Babu, K., Cai, Y., Bahri, S. and Chia, W. (2004) Roles of Bifocal, Homer and F-actin in
anchoring Oskar to the posterior cortex of Drosophila oocytes. Genes Dev. 2004 Jan 15;
18(2): 138-43.

Helps, N.R.*, Cohen, P.T., Bahri, S.M., Chia, W. and Babu, K.* (2001) Interaction with
protein phosphatase 1 Is essential for bifocal function during the morphogenesis of the
Drosophila compound eye. Mol Cell Biol. 2001 Mar; 21(6): 2154-64.* Equal contribution.

22 Dept. Biol. Sci. IISER Mohali +91-172-2293153 [email protected]

Research Interests & Projects

Synapses are essential for brain functions. Normal functioning of synapses is required
for all activities from the generation of movement to learning and memory. Synaptic
function requires a co-ordination between pre-synaptic neurotransmitter release and
post-synaptic receptor levels. In my lab we use C. elegans as a model system to study
the development and function of synapses.
Multiple studies have revealed that that cell adhesion molecules are required for normal
synapse formation and function. My post-doctoral work has shown that the cell
adhesion molecules, RIG-3 functions through a receptor tyrosine kinase, CAM-1/Ror to
maintain normal post-synaptic receptor levels at the neuromuscular junction (see
cartoon). We are interested in understanding the mechanism of RIG-3 function at the
synapse.
We are also interested in understanding the role of other cell adhesion molecules at the
synapse. Our Laboratory has also recently started trying to understand the molecular
basis of learning and memory using C. elegans as a model to study the same.
Techniques used in our Laboratory include C. elegans genetics, RNA interference and
behavioral assays in combination with Molecular Biology, Cell Biology and
Biochemistry.
For more information on our Laboratory, Lab members and the projects we work on,
please visit www.babulab.org

23

Joined Oct 2011

Mahak Sharma

Assistant Professor

B.Tech. degree in Biotechnology from Guru Gobind Singh Indraprastha University
(G.G.S.I.P.U.), Delhi, India (2000-2004); Ph.D. from Department of Biochemistry
and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska,
U.S.A. (2005-2009); Postdoctoral Research Fellow in the Department of
Rheumatology, Immunology and Allergy, Brigham and Women's Hospital/Harvard
Medical School, Boston, MA, U.S.A. (2009-2011); and Assistant Professor in
Department of Biological Sciences, IISER Mohali (October 2011-Present). I am
currently guiding three students for PhD theses and one Master student's thesis.

Cell Biology: Molecular Mechanisms Regulating Membrane Representative Publications
Trafficking Towards Lysosomes
Amit Tuli, Jerome Thiery, Ashley M. James, Xavier Michelet, Mahak Sharma, Salil Garg, Keri B. Sanborn, Jordan S.
Orange, Judy Lieberman, and Michael B. Brenner. Arf-like GTPase Arl8b regulates lytic granule polarization and
natural killer cell-mediated cytotoxicity. Molecular Biology of the Cell, in press 2013 (selected for cover image).

Salil Garg*, Mahak Sharma*, Cindy Ung, Amit Tuli, Duarte C. Barral, David L. Hava, Natacha Veerapen, Gurdyal S.
Besra, Nir Hacohen and Michael B. Brenner. Lysosomal trafficking, antigen presentation, and microbial killing are
controlled by the Arf-like GTPase Arl8b. *Equal contribution. Immunity, 35(2):182-193 (2011). This research article
was highlighted in the Cell Press published monthly podcasts (September 1, 2011) and was chosen by Faculty of
1000 Biology, an expert guide to the most important advances in biology, and was evaluated as "recommended" with a
7.0 rating.

Mahak Sharma, Sai Srinivas Panapakkam Giridharan, Juliati Rahajeng, Naava Naslavsky and Steve Caplan.
MICAL-L1: an unusual Rab effector that links EHD1 to tubular recycling endosomes. Article Addendum.
Communicative and Integrative Biology, 3(2):1-3 (2010). This article was highlighted as one of the “most popular”
downloaded paper by the Communicative and Integrative Biology journal website (April, 2010).

Fabien Kieken*, Mahak Sharma*, Marko Jovic*, Sai Srinivas Panapakkam Giridharan, Naava Naslavsky, Steve
Caplan and Paul Sorgen. Mechanism for the selective interaction of C-terminal EH-domain proteins with specific
NPF-containing partners. *Equal contribution. Journal of Biological Chemistry, 285(12):8687-8694 (2010).

Marko Jovic*, Mahak Sharma*, Juliati Rahajeng and Steve Caplan. The early endosome: a busy sorting station for
proteins at the crossroads [review]. *Equal contribution. Histology and Histopathology, 25(1):99-112 (2010).

Saumya Pant, Mahak Sharma, Kruti Patel, Steve Caplan, Chavela Carr and Barth Grant. AMPH-1/Amyphysin/Bin1
functions with RME-1/Ehd1 in endocytic recycling. Nature Cell Biology, 11(12):1399-1410 (2009).

Mahak Sharma, Sai Srinivas Panapakkam Giridharan, Juliati Rahajeng, Naava Naslavsky and Steve Caplan.
MICAL-L1 links EHD1 to tubular recycling endosomes and regulates receptor recycling. Molecular Biology of the Cell,
20(24):5181-5194 (2009).

Amit Tuli, Mahak Sharma, Haley Capek, Naava Naslavsky, Steve Caplan and Joyce C. Solheim. Mechanism for
amyloid precursor-like protein 2 enhancement of major histocompatibility complex class I molecule degradation.
Journal of Biological Chemistry, 284(49):34296-34307 (2009). This paper was chosen by Faculty of 1000 Biology and
was evaluated as "recommended" with a 6.0 rating.

Amit Tuli, Mahak Sharma, Mary M. McIlhaney, James E. Talmadge, Naava Naslavsky, Steve Caplan and Joyce C.
Solheim. Amyloid precursor-like protein 2 increases the endocytosis, instability and turnover of the H2-Kd MHC class I
molecule. Journal of Immunology, 181(3):1978-1987 (2008).

Mahak Sharma, Naava Naslavsky and Steve Caplan. A role for EHD4 in the regulation of early endosomal transport.
Traffic, 9(6):995-1018 (2008).

Dr. Mahak Sharma has contributed a total of 15 papers to the literature.

24 Dept. Biol. Sci. IISER Mohali +91-172-2293145 [email protected]

Research Interests & Projects

The primary research interests of my lab focus on studying the molecular mechanisms regulating the
trafficking towards late endosomes and lysosomes. We are studying the role of small GTP-binding
proteins that localize to lysosomes in mammalian cells. We have recently characterized one such
protein known as Arl8, a member of Arl (Arf-like) family of small GTPases in regulating lysosomal
trafficking. The small GTPases regulate multiple steps of vesicle trafficking, starting from recruitment
of the coat proteins for vesicle formation, motility on microtubule tracks and finally vesicle tethering on
target membranes, leading to vesicle fusion
Upon GTP-binding, small GTPases recruit downstream tethering factors to intracellular membranes
which permit vesicle docking with the target membranes. We have recently identified one such
tethering complex known as the HOPS (HOmotypic fusion and vacuole Protein Sorting) complex as an
Arl8 interaction partner. To understand these processes, we are using state-of-the-art techniques
including qualitative and quantitative confocal microscopy, flow cytometry, protein-protein interaction
techniques and molecular biology approaches.
The importance of this protein complex is reflected by the fact that pathogens such as
Mycobacterium.tuberculosis evade killing in the host lysosome by targeting HOPS complex subunits.
Moreover, patients suffering from ARC syndrome which presumably lack a functional HOPS complex
suffer from recurrent bacterial infections. Thus, our findings will contribute to a better understanding of
the mechanism by which mammalian HOPS complex regulates lysosomal trafficking, proper
functioning of which is critical for cellular survival and defence against pathogens.

25

Joined Nov 2011

Somdatta Sinha

Professor

After completing high school, B.Sc. and M.Sc in Physics from Visva Bharati University, Santiniketan (West
Bengal), Somdatta Sinha joined the School of Theoretical and Environmental Sciences, Jawaharlal Nehru
University at New Delhi for M. Phil. and Ph. D. During this period she also worked at the Centre for Theoretical
Studies, Indian Institute of Science, Bangalore. On completion of her doctoral thesis, Dr. Sinha joined the
Centre for Cellular & Molecular Biology (CCMB), Hyderabad (Andhra Pradesh) in 1983 as a Scientist, and
continued her interdisciplinary research work as a Group Leader in Mathematical and Computational Biology
till 2011. She joined IISER Mohali in November 2011 as a professor in the Department of Biological Sciences.
She has mentored 5 (3 completed and 2 ongoing) PhD students at CCMB, 4 Masters thesis students at IISER,
and trained a large number of project students and summer trainees in interdisciplinary studies in Theoretical
Biology.

Mathematical and Computational Biology Representative Publications

A Realistic Host-Vector Transmission Model for Describing Malaria Prevalence Pattern. Bulletin of
Mathematical Biology. DOI 10.1007/s11538-013-9905-7. Sandip Mandal, Somdatta Sinha and Ram
Rup Sarkar, (2013).

Multi-fractal analysis of HIV-1 genomes. Molecular Phylogenetics and Evolution. Vol. 62, pp 756-
763. Aridaman Pandit, Anil Kumar D., Somdatta Sinha, (2012).

Differential Trends in the Codon Usage Patterns in HIV-1 Genes. PLoS ONE. Vol 6 (12): e28889. doi:
10.1371/journal.pone. 0028889. Aridaman Pandit, Somdatta Sinha, (2011).

Stability of synchronization in a multi-cellular system. Europhysics Letters. Vol 92. 40012. Suma
Ghosh, G. Rangarajan, Somdatta Sinha, (2010).

Propagation of extrinsic perturbation in a negatively auto-regulated pathway. Physical Biology, 4, pp
48-59. R Maithreye, Somdatta Sinha (2007).

Assortative mixing in Protein Contact Networks and protein folding kinetics. Bioinformatics (Oxford).
Vol. 23 no. 14 2007, pages 1760–1767. Ganesh Bagler, Somdatta Sinha, (2007).

The role of heterogeneity on the spatiotemporal dynamics of host parasite metapopulation.
Ecological Modelling. Vol 180, 435-443. B. K. Singh, J. Subba Rao, R. Ramaswamy, Somdatta
Sinha, (2004).

Controlling Dynamics in Spatially Extended Systems. Physical Review E. Vol 65, pp 036227-1to9.
Nita Parekh, Somdatta Sinha, (2002).

Global and Local Control of Spatiotemporal Chaos in Coupled Map Lattices. Physical Review
Letters. Vol 81, pp 1401-1404. Parekh N., Parthasarathy, S., Somdatta Sinha, (1998).

Unusual Dynamics of Extinction in a Simple Ecological Model. Proc. Nat. Acad. Sci. (USA). Vol 93, pp
1504 –1508. Somdatta Sinha, Parthasarathy, S., (1996).

As of December 2013, Prof. Sinha's group has contributed a total of 56 papers to the literature
(including 7 book chapters). She has also co-authored Science Textbooks of Classes 7, 8, and 10 for
the Central Board of Secondary Education (CBSE) published by the National Council for Educational
Research & Training (NCERT), India.

26 Dept. Biol. Sci. IISER Mohali +91-172-2293166 [email protected]

Research Interests & Projects

Sinha group's scientific interests are in the areas of Theoretical Biology, Nonlinear
Dynamics and Complex Systems, with a view to understand the logic and design of
biological processes. They study the evolution and maintenance of spatiotemporal
organization in biological systems spanning multiple scales - from genetic to
ecological. Her doctoral thesis was on modelling circadian rhythms, and
experimental studies and mathematical modelling of the pattern-forming processes
during development of Hydra. Her group used both experimental studies, and
mathematical modelling and computational analysis to study - a) intracellular
networks in protein structures and biochemical pathways using graph theory and
molecular dynamics; b) collective spatiotemporal behaviour and pattern-formation
in coupled cell systems (e.g., tissues and organelles); c) single and meta-population
dynamics in ecological and epidemiological models - general and disease-specific
(Malaria); d) whole genome analysis to study HIV-1 evolution and development of
alignment-free methods for classification. Her current research involves analysing
epidemiological data of infectious diseases, study host-parasite evolution using
genomic data and computational modelling, and using graph theory to understand
macroscopic properties of intracellular networks.

27

Joined Jan 2012

Rachna Chaba

Assistant Professor

Rachna Chaba obtained Masters in Biotechnology from Guru Nanak Dev University,
Amritsar in 1998. She then moved to the Institute of Microbial Technology, Chandigarh, to
pursue Ph.D. (1998-2003) in Biotechnology. There she worked on the characterization of
serine-threonine kinase and phosphatase from Mycobacterium tuberculosis in the
laboratory of Dr. Pradip K. Chakraborti. She subsequently moved to the University of
California San Francisco, USA, to work in the laboratory of Dr. Carol A. Gross as a
postdoctoral fellow (2004-2011). There she studied the design of the Envelope Stress
Response pathway in Escherichia coli. Rachna joined IISER-Mohali as a faculty member in
the Department of Biological Sciences in Jan. 2012.

Bacterial Genetics and Physiology Representative Publications

Lima, S., Guo, M. S., Chaba, R., Gross, C. A. and Sauer, R. T. (2013). Dual Molecular Signals Mediate the Bacterial
Response to Outer-Membrane Stress. Science 340 (6134): 837-841.

Oh, E., Becker, A. H., Sandikci, A., Huber, D., Chaba, R., Gloge, F., Nichols, R. J., Typas, A., Gross, C. A., Kramer, G.,
Weissman, J. S. and Bukau, B. (2011). Selective ribosome profiling reveals the co-translational chaperone action of
trigger factor in vivo. Cell 147(6):1295-1308. (Faculty of 1000 factor 12)

Chaba, R.$, Alba, B.M., Guo, M., Sohn, J., Ahuja, N., Sauer, R. T. and Gross, C. A.$ (2011). Signal integration by DegS
and RseB governs the sigmaE mediated envelope stress response in Escherichia coli. PNAS 108(5): 2106-2111. $co-
corresponding authors (Faculty of 1000 factor 8)

Nichols, R. J., Choo, Y. J., Sen, S., Beltrao, P., Zietek, M., Chaba, R., Lee, S., Kazmierczak, K. M., Lee, K. J., Wong, A.,
Shales, M., Lovett, S., Winkler, M. E., Krogan, N. J., Typas, A. and Gross, C. A. (2011). Phenotypic Landscape of a
Bacterial Cell. Cell 144(1):143-156. (Faculty of 1000 factor 13)

Ahuja, N., Korkin, D., Chaba, R., Cezairliyan, B. O., Sauer, R. T., Kim, K. K. and Gross, C. A. (2009). Analyzing the
interaction of RseA and RseB, the two negative regulators of the sigmaE envelope stress response, using a combined
bioinformatic and experimental strategy. J. Biol. Chem. 284(8): 5403-5413.

Thakur, M., Chaba, R., Mondal, A. K. and Chakraborti, P. K. (2008). Interdomain interaction reconstitutes the
functionality of PknA, a eukaryotic type Ser/Thr kinase from Mycobacterium tuberculosis. J. Biol. Chem. 283(12):
8023-8033.

Chaba, R., Grigorova, I. L., Flynn, J. M., Baker, T. A. and Gross, C. A. (2007). Design principles of the proteolyt
cascade governing the sigmaE mediated envelope stress response in Escherichia coli: keys to graded, buffered, and
rapid signal transduction. Genes Dev. 21(1): 124-136. *This article was highlighted in the perspective in Genes and
Development.

Hasenbein, S., Merdanovic, M. and Ehrmann, M. (2007). Determinants of regulated proteolysis in signal transduction.
Genes Dev. 21(1): 6-10.

Grigorova, I. L., Chaba, R., Zhong, H. J., Alba, B. M., Rhodius, V., Herman, C. and Gross, C. A. (2004). Fine-tuning of
the Escherichia coli sigmaE envelope stress response relies on multiple mechanisms to inhibit signal-independent
proteolysis of the transmembrane anti-sigma factor, RseA. Genes Dev. 18(21): 2686-2697.

Chaba, R., Raje, M. and Chakraborti, P. K. (2002). Evidence that a eukaryotic-type serine/threonine protein kinase
from Mycobacterium tuberculosis regulates morphological changes associated with cell division. Eur. J. Biochem.
269(4): 1078-1085.

Sarin, J., Aggarwal, S., Chaba, R., Varshney, G. C. and Chakraborti, P. K. (2001). β-subunit of phosphate-specific
transporter from Mycobacterium tuberculosis is a thermostable ATPase. J. Biol. Chem. 276(48): 44590-44597.

Rachna Chaba has contributed a total of 11 papers to the literature.

28 Dept. Biol. Sci. IISER Mohali +91-172-2293146 [email protected]

Research Interests & Projects

Systems-level analysis and mechanistic dissection of metabolic pathways in bacteria
Metabolism provides energy, creates building blocks, and regulates macromolecular processes.
Integrating metabolism with other cellular responses provides the robustness enabling bacterial
survival in diverse nutrient and toxic environments, key to their success as commensals,
pathogens and industrial workhorses. Metabolic processes have often been probed by
qualitative, non-saturating genetic techniques that may miss players and connections, thereby
leading to a focus on the identification/characterization of individual components rather than
considering metabolism as a cellular system. Thus despite decades of active research, our
knowledge of metabolism even in the well-studied microbe, E. coli, is far from complete. A major
obstacle impeding systems-level analysis of metabolism has been the lack of a comprehensive,
quantitative, functional-genomics approach that provides an entire parts list and hints of
connections. In this direction, my lab utilizes high-throughput quantitative genetic screening
methodology (response of every gene deletion/overexpression strain to chemical perturbations,
~4000 genes), to identify novel players and networks in metabolism. The information extracted
from these genomic approaches is integrated with knowledge from other high-throughput
datasets like phenotype microarray analysis, transcriptional profiling and proteome analysis to
generate testable hypotheses about the function of novel genes, the process they participate in,
and interconnections between pathways. As a complement, we also perform detailed molecular
studies of important targets to establish their functional roles. Our research mainly focuses on the
metabolic processes that govern utilization of carbon sources implicated in pathogenesis and
those providing tolerance to toxic agents important in biofuel production. Overall, our study
intends to identify novel transporters, metabolic enzymes and regulators required for the
degradation of carbon sources and toxic agents; cross-talk between metabolic pathways; and
stress response pathways important for survival in toxic conditions. Thus, the combined use of a
functional-genomics approach and mechanistic analysis will expand our knowledge of
metabolism beyond a mere description of parts and will provide new metabolic information that
can be harnessed to design novel antibacterials and create strains with superior toxicity tolerance.

29

Joined Mar 2012

Ram K Yadav

Assistant Professor

Assistant Professor, South Asian University, New Delhi (July 2011 to March
2012)
Postdoctoral Fellow, University of California, Riverside (July 2007 to June 2011)
Ph.D. in Plant Developmental Genetics, Technical University of Munich,
Germany (2007)
M.Sc. in Animal Biotechnology, NDRI, Karnal (2001)
Currently, I am supervising three PhD's students and a MS student.

Plant Developmental Genetics Representative Publications

Yadav, R.K.#, Perales, M.#, Gruel, G.#, Ohno, C., Heisler, M., Grike, T., Jönsson, H., and Reddy, G.V. (2013) Plant
stem cell maintenance involves direct transcriptional repression of differentiation program. Molecular Systems
Biology 9, 654. (# Co-first author)

Yadav, R.K.#, Perales M.#, Girke, T., & Reddy, G.V., (2011) WUSCHEL protein movement mediates stem cell
homeostasis. Genes & Development 25, 2025-2030. (# Co-first author)

Liu, M., Chakraborty, A., Yadav, R. K., Meenakshisundaram, G., Reddy, G. V. & Roy-Chowdhury, A. (2011). Adaptive
cell segmentation and tracking for volumetric confocal microscopy images of a developing plant meristem. Molecular
Plant 4, 922-931.

Prasad, K., Grigg, S.P., Barkoulas, M., Yadav, R.K., Sanchez-Perez, G.F., Pinon, V., Blilou, I., Hofhuis, H.,
Dhonukshe. P., Galinha, C., Mähönen, A.P., Muller, W.H., Raman, S., Verkleij. A.J., Snel, B., Reddy, G.V., Tsiantis, M.,
Scheres, B. (2011). Arabidopsis PLETHORA transcription factors control phyllotaxis. Current Biology 21, 1123-
1128.

Yadav, R.K. Tavakkoli, M. & Reddy, G.V. (2010). WUSCHEL mediates stem-cell homeostasis by regulating stem-cell
number and patterns of cell division and differentiation of stem-cell progenitors. Development 137, 3581-3589.

Liu, M., Yadav, R. K., Roy-Chowdhury, A. & Reddy, G. V. (2010). Automated tracking of stem cell lineages of
Arabidopsis shoot apex using local graph matching. Plant Journal 62, 135-147.

Oben Tataw, Min Liu, Ram. K. Yadav, Venugopala Reddy & Amit Roy-Chowdhurry (2010). Pattern analysis of stem
cell growth dynamics in the shoot apex of Arabidopsis. Intl. Conf. on Image Processing.

Yadav, R.K., Girke, T., Pasala, S., Xie, M. & Reddy, G.V. (2009). Gene expression map of the Arabidopsis shoot apical
meristem stem cell niche. Proc Natl Acad Sci U S A 106, 4941-4946.

Fulton, L., Batoux, M., Vaddepalli, P., Yadav, R.K., Busch, W., Andersen, S.U., Jeong, S., Lohmann, J.U. & Schneitz,
K. (2009). DETORQUEO, QUIRKY, and ZERZAUST represent novel components involved in organ development
mediated by the receptor-like kinase STRUBBELIG in Arabidopsis thaliana. PLoS Genet 5, e1000355.

Yadav, R.K., Fulton, L., Batoux, M. & Schneitz, K. (2008). The Arabidopsis receptor-like kinase STRUBBELIG
mediates inter-cell-layer signaling during floral development. Dev Biol 323, 261-270.

Book Chapters

Yadav, R.K., Snipes, S., Girke, T. & Reddy, G.V. (2013). Organization of gene expression and its regulation in shoot
apical meristem. Methods in Molecular Biology 959, 235-245.

Chakraborty, A., Yadav, R.K., Liu, M., Tataw, M., Mkrtchyan, K., Amit Roy Chowdhury and Reddy, G.V. (2012)
Computational tools for quantitative analysis of cell growth patterns and morphogenesis in actively developing plant
stem cell niches. Methods in Molecular Biology. 876: 217-227.

Fulton, L., Batoux, M., Yadav, R.K. and Schneitz, K. (2006) The genetic control of flower size and shape. Annual
Plant Reviews 20, 71-97.

Ram has published 16 research papers and contributed three book chapters to the literature.

30 Dept. Biol. Sci. IISER Mohali +91-172-2293155 [email protected]

Research Interests & Projects

Unlike animals, plants continuously grow and develop organs throughout their life.
This remarkable ability is achieved by maintaining a stable pool of stem cells, which
are embedded in the meristem. In higher plants, shoot apical meristem (SAM)
harbors pluripotent stem cells in the center. Early in development SAM stem cell
progenitors will differentiate in to organ primordia at the periphery of meristem,
which will form leaves. However, later on meristem integrates environmental cues in
to development thus organ primordia will emerge as flower meristem that will
produce flower organs. Similar to animals, differentiation of stem cells in to distinct
cell types is essential to form the body parts of a plant. Currently, we are studying the
gene regulatory network underlying the cell type specification in plant model
organism Arabidopsis thaliana. We have identified several transcription factors
(TFs) enriched in SAM cell types using fluorescent activated cell sorting followed
with microarray analysis. We are taking a systems biology approach to understand
the role of cell specific TFs in cell identity acquisition. Our lab has embarked upon to
determine the expression pattern of epidermal and subepidermal cell type enriched
TFs and their interaction with their cognate partners and immediate targets. We are
using a variety of techniques such as molecular biology, genetics, genomics and
live-imaging to resolve the gene regulatory networks involved in cell type
specification in SAM.

31

Joined Mar 2012

Shravan Kumar Mishra

Assistant Professor

1994-1997: B.Sc. Biochemistry & Microbiology, University of Mumbai, India.
1997-1999: M.Sc. Biotechnology, M. S. University of Baroda, India.
1999: Project Assistant, TIFR Bombay, India.
2000-2004: PhD Biology, J. W. Goethe University of Frankfurt, Germany.
2004-2012: Post-doctoral Fellow, Max Planck Institute of Biochemistry, Martinsried/Munich
Germany.
March 2012 - Assistant Professor (Department of Biological Sciences), IISER Mohali.
January 2013 - Head of Max Planck - DST partner group, Max Planck Institute of
Biochemistry, Martinsried/Munich, Germany and IISER Mohali.

Representative Publications
Mishra, S.K., Ammon, T., Popowicz, G.M., Krajewski, M., Nagel, R.J., Ares, M., Holak,
T., and Jentsch, S. (2011). Role of the ubiquitin-like protein Hub1 in splice-site usage
and alternative splicing. Nature(Article) 474: 173-178.

Ubiquitin-Like Modifiers and RNA Splicing Tripp, J*.,Mishra, S.K*., and Scharf, K.-D. (2009). Functional dissection of the cytosolic
chaperone network in tomato mesophyll protoplasts. Plant Cell Environ. 32: 123-133.
(*Equal contribution).

Baniwal, S.K., Bharti, K., Chan, K.Y., Fauth, M., Ganguli, A., Kotak, S., Mishra, S.K.,
Nover, L., Port, M., Scharf, K.-D., Tripp, J., Zielinski, D., and von Koskull-Doering, P.
(2004). Heat stress response in plants: a complex game with chaperones and more
than 20 heat stress transcription factors. J. Biosci. 29: 471–487 (Review).

Mishra, S.K., Tripp, J., Winkelhaus, S., Tschiersch, B., Theres, K., Nover, L., and
Scharf, K.-D. (2002). In the complex family of heat stress transcription factors, HsfA1
has a unique role as master regulator of thermo tolerance in tomato. Genes & Dev. 16:
1555-1567.

Nover, L., Bharti, K., Doering, P., Mishra, S.K., Ganguli, A., and Scharf, K.-D. (2001).
Arabidopsis and the heat stress transcription factor world: how many heat stress
transcription factors do we need? Cell Stress Chap. 6: 177-189 (Review).

32 Dept. Biol. Sci. IISER Mohali +91-172-2293156 [email protected]

Research Interests & Projects

Function of Ubiquitin-Like Proteins and Regulation of RNA Splicing
Ubiquitin and ubiquitin-like modifiers, for example, Hub1, SUMO, NEDD8 etc. (referred as UBL)
are a group of small proteins with ubiquitin fold and function as central regulators of a vast number
of cellular processes. Covalent attachment of ubiquitin to a target protein requires a set of
dedicated enzymes by the process is called ubiquitination. This process determines fate of the
targets through proteasomal degradation. However, ubiquitination also confers functional
diversity to its targets in non-proteolytic ways and is known to play key roles in various cellular
processes like DNA repair, signal transduction, protein sorting etc. In contrast most ubiquitin-like
proteins function as non-destructive tags, which are known to play regulatory roles in large
number of processes in the cell.
UBLs also have the ability to act non-covalently. A notable example is Hub1, which lacks the
potential for covalent conjugation and functions in RNA splicing in a unique way. Efficient splicing
of a subset of introns and a class of alternative splicing events require non-covalent modification of
the splicing machinery (spliceosome) by Hub1.
We are interested in studying (1) novel functions of proteins related to ubiquitin (2) functions of
novel proteins related to ubiquitin and (3) regulators of RNA splicing. Initially we plan to understand
roles of these proteins in cellular processes like RNA splicing and stress signaling. For these
questions we perform experiments in cell biology, genetics and biochemistry in the yeasts
Saccharomyces cerevisiae and Schizosaccharomyces pombe. We aim to utilize mammalian cell
cultures and multi-cellular organisms to address questions related to functional conservation of
UBLs and applications of our studies in humans.

33

Joined June 2012

Rajesh Ramachandran

Assistant Professor

Dr. Rajesh Ramachandran did his Masters in Marine Biology from Cochin
University of Science and Technology, Cochin, India (July, 1997- May, 1999). He
was a doctoral scholar at the Centre for Cellular and Molecular Biology,
Hyderabad, India (May, 1999-April, 2005). He did his first postdoctoral research at
CCMB, Hyderabad, India (April, 2005-February 2007) and the second one at
Molecular and Behavioral Neuroscience Institute, University of Michigan, Ann
Arbor, USA (February 2007-May, 2012). He joined IISER Mohali in June 2012.

Rajesh Ramachandran has guided no PhD students and no Masters thesis after
joining IISER-M.

Molecular Mechanisms Underlying Representative Publications
Retina Regeneration
Rajesh Ramachandran, Xiao-Feng Zhao , Daniel Goldman. (2012). Insm1a-mediated gene repression is essential
for the formation and differentiation of Muller glia-derived stem cells in the injured retina. Nature Cell Biology 14:
1013-1023.

Jin Wan, Rajesh Ramachandran, Daniel Goldman (2012). HB-EGF Is Necessary and Sufficient for Müller Glia
Dedifferentiation and Retina Regeneration. Developmental Cell 22: 334-347

Rajesh Ramachandran , Xiao-Feng Zhao , Daniel Goldman (2011) An Ascl1a/Dkk/β-Catenin signaling pathway is
necessary and glycogen synthase kinase-3β inhibition is sufficient for zebrafish retina regeneration. Proceedings of
the National Academy of Sciences, USA 108: 15858-15863

Rajesh Ramachandran, Blake Fausett and Daniel Goldman (2010). Ascl1a regulates Müller glia dedifferentiation
and retina regeneration via a Lin28-dependent, let-7 miRNA signaling pathway. Nature Cell Biology 12: 1101-1107

Rajesh Ramachandran, Aaron Reifler, Jack M. Parent and Daniel Goldman (2010). Conditional gene expression
and lineage tracing of tuba1a expressing cells during zebrafish development and retina regeneration. Journal of
Comparative Neurology 518:4196-4212.

StevenT.Suhr, Rajesh Ramachandran, Cynthia L. Fuller, Matthew B. Veldman, Christine A. Byrd and Daniel
Goldman (2008) Highly-restricted, cell-specific expression of the simian CMV-IE promoter in transgenic zebrafish
with age and after heat shock. Gene Expression Patterns 9: 54-64.

Rajesh Ramachandran and K.C. Majumdar. (2008). The growth hormone-encoding gene isolated and
characterized from Labeo rohita Hamilton is expressed in CHO cells under the control of constitutive promoters in
'autotransgene' constructs. Fish Physiology and Biochemistry 34: 413-436.

Rajesh Ramachandran and K.C. Majumdar. (2007) A Comparative account of the structure of the growth hormone
encoding gene and genetic interrelationship in six species of the genus Labeo. Fish Physiology and Biochemistry
33: 311-333.

Rajesh Ramachandran and K.C. Majumdar.(2005). Transgene integration- an analysis in transgenic Labeo rohita
Hamilton (Pisces: Cyprinidae). Fish Physiology and Biochemistry 31: 281-287.

Book Chapter
Rajesh Ramachandran, Aaron Reifler, Jin Wan and Daniel Goldman (2012). Application of Cre-loxP Recombination
for Lineage Tracing of Adult Zebrafish Retinal stem cells. In: Retinal Development: Methods and Protocols,
Methods in Molecular Biology vol: 884 Shu-Zen Wang (ed.) (DOI 10.1007/978-1-61779-848-1_8). Humana Press,
a part of Springer Science+Business Media New York 2012

Rajesh Ramachandran has contributed 10 Research publications (including 1 book chapter)

34 Dept. Biol. Sci. IISER Mohali +91-172-2293181 [email protected]

Research Interests & Projects

Retinal damage is one of the most common causes of blindness in the modern world. The
obvious solution to this problem is to harness the regenerative potential of the retinal stem
cells. The piscine model zebrafish offers the maximum potential in unraveling the mystery
of retinal regeneration compared to mammalian and avian counterparts. I am working on
signaling pathways like wnt, notch and hedgehog to assess their impact on fish retina
regeneration. I am also working on a few selected candidate genes like pluripotency
inducing factors like sox2, oct4, nanog, klf4, cMyc and lin28 involved in retina
regeneration. Currently the major research projects I am carrying out are (1) An
investigation on the role of transcription factors Ascl1a, FoxN4, Zic2b and tumor
suppressor Pten in retina regeneration and functional analysis of pluripotency factors in
retinal stem cells, funded by Wellcome Trust-DBT India Alliance and (2) Understanding the
molecular mechanisms of epigenetically regulated genes during Muller glia
dedifferentiation and retina regeneration in zebrafish, funded by IISER Mohali.
Ph.D. students: Soumitra Mitra, Simran Kaur
MS student: Sapna Meena
Rotating Ph.D. student: Mohammad Anwar Khursheed

35

Joined June 2012

Shashi Bhushan Pandit

Assistant Professor

Dr. Shashi Bhushan Pandit completed his Masters and PhD (Integrated PhD)
in Computational Biology from Indian Institute of Science, Bangalore in 2005.
He had been postdoctoral fellow at Georgia Institute of Technology (USA),
Genoscope (France) and Institute of Systems and Synthetic Biology
(France). He joined IISER, Mohali in June, 2012.

Presently, he is supervising 2 PhD and 1 MS thesis students.

Computational structural and Representative Publications
systems biology
Carbonell P, Fichera D, Pandit S. B., Faulon JL. (2012) Enumerating metabolic pathways for the
production of heterologous target chemicals in chassis organisms. BMC Syst Biol. 6:10 (Highly
accessed).

S. B. Pandit and J. Skolnick (2010) TASSER_low-zsc: An approach to improve structure
prediction using low z-score ranked templates Proteins 78(13):2769-2780.

S. B. Pandit, Brylinski, M, Gao M, Arakaki, A and J. Skolnick (2010) PSiFR: An integrated resource
for prediction of protein structure and function. Bioinformatics, 26(5): 687-688.

S. B. Pandit and J. Skolnick (2008) Fr-TM-align : A new protein structural alignment method based
on fragment alignments and the TM-score. BMC Bioinformatics 9:531 (Highly accessed).

H. Zhou, S. B. Pandit, S. Lee, J. Borreguerro, H. Chen, L. Wroblewska and J. Skolnick (2007).
Analysis of TASSER based CASP7 protein structure prediction results. Proteins 69(S8): 90-97.

S. B. Pandit, Y. Zhang and J. Skolnick. (2006) TASSER-Lite: An automated tool for protein
comparative modeling. Biophysical Journal 91: 4180-4190.

O., Krishnadev, N. Rekha, , S. B. Pandit, S. Abhiman, S. Mohanty, L. Swapna, S., Gore, and N.
Srinivasan, (2005) PRODOC: a resource for the comparison of tethered protein domain
architectures with in-built information on remotely related domain families. Nucleic Acids Res., 33
(Web Server issue):W126-129.

S. B. Pandit and N. Srinivasan. (2003) Survey for G-proteins in the prokaryotic genomes:
prediction of functional roles based on classification. Proteins: Structure function and genetics 52,
585-597. (Recommend article in Faculty of 1000 Biology).

S. Gupta, S. B. Pandit, N. Srinivasan and D. Chatterji (2002) Proteomics analysis of carbon
starved Mycobacterium smegmatis: Induction of Dps like protein. Prot. Eng. 15, 503-511.

S. B. Pandit, D. Gosar, S. Abhiman, S. Sujatha, S.S. Dixit, N.S. Mhatre, R. Sowdhamini and N.
Srinivasan (2002) SUPFAM - Database of potential protein superfamily relationships derived by
comparing sequence-based and structure-based families: Implications for structural genomics
and function annotation in genomes. Nucl. Acids Res. 30, 289-293.

36 Dept. Biol. Sci. IISER Mohali +91-172-2293182 [email protected]

Research Interests & Projects

Computational structural and systems biology

The main research interest of the group is to understand structural/sequence basis of enzyme
promiscuity, ligand-protein interactions and modeling of multi-domain proteins with an aim to
develop robust computational prediction methodologies. Microorganisms show remarkable
resilience towards deletion of genes involved in metabolic pathways. Usually, this is attributed to
enzyme's capability to catalyze alternate substrate/reaction (promiscuous activity). Hence,
including these promiscuous reactions in metabolic pathway reconstructions can provide
complete metabolic capability of an organism. Recently, using chemoinformatics approach we
have developed a method to predict putative promiscuous reactions using molecular reaction
signatures. In this approach, we assumed that enzymes would accommodate any substrate and
catalyze the same. To evaluate this assumption, we are systematically investigating the structural
and sequence properties of enzymes or substrates binding sites, which could confer them
promiscuity. Furthermore, we will investigate the mechanistic aspect of enzyme promiscuity and
study their evolution. We will study the role of protein dynamics in ligand-protein interactions.
Many enzymes are multi-domain proteins. Hence, we are developing methods for tertiary
structure prediction of multi-domain proteins using our recently developed method TASSER
(Threading ASSembly and Refinement).
Dr. Shashi Bhushan Pandit has contributed a total of 25 research papers to the literature (including
2 books/book chapters).

37

Joined July 2012

Kuljeet Sandhu

Assistant Professor

Kuljeet Sandhu obtained his Masters from Institute of Bioinformatics and Applied
Biotechnology, Bangalore in 2004. He worked at Institute of Genomics and
Integrated Biology (IGIB), Delhi for a year and thereafter moved to Karolinska
Institute, Stockholm, Sweden for his doctorate followed by a post-doc in Genome
Institute of Singapore. His doctoral and post-doctoral work was primarily focussed
on systems analyses of long range chromatin interactions in the mammalian
genome. He joined IISER-Mohali in July 2012. Kuljeet has guided 1 MS thesis and is
guiding 1 Ph.D thesis.

Systems Biology: Representative Publications
Genome regulation
Sandhu KS*, Guoliang Li, Huay Mei Poh, Yu Ling Kelly Quek, Yee Yen Sia, Su Qin Peh, Fabianus
Hendriyan Mulawadi, Mile Sikic, Francesca Menghi, Anbupalam Thalamuthu, Wing Kin Sung,
Xiaoan Ruan, Melissa Jane Fullwood, Edison Liu, Peter Csermely, Yijun Ruan* . Large scale
functional organization of long-range chromatin interaction networks. Cell Rep. 2012 Nov
29;2(5):1207-19.

Sandhu KS*. Did the modulation of expression noise shape the evolution of three dimensional
genome organizations? Nucleus 2012; 3:3,1-4.

Li G#, Ruan X#, Auerbach R#, Sandhu KS# et al. Extensive promoter centered chromatin
interactions provide a architectural basis for transcription regulation in eukaryotes. Cell. 2012 Jan
20;148(1-2):84-98 (#co-first author).

Sandhu KS*. Systems properties of proteins encoded by imprintedse genes. Epigenetics 2010
Oct 01,5 (7).

Sandhu KS, Shi C, Sjolinder M, Zhao Z, Gondor A, Liu L, Tiwari VK, Guibert S, Emilsson L, Imreh
MP, Ohlsson R*. Nonallelic transvection of multiple imprinted loci is organized by the H19
imprinting control region during germline development. Genes Dev. 2009; Nov 15; 23: 2592-2597.

Sandhu KS*. Intrinsic disorder explains diverse nuclear roles of chromatin remodeling proteins. J
Mol Recognit. 2009 Jan-Feb;22(1):1-8.

Sandhu KS, Dash D*. Dynamic alpha-helices: conformations that do not conform. Proteins. 2007
Jul 1;68(1):109-22

Sandhu KS, Dash D*. Conformational flexibility may explain multiple cellular roles of PEST
motifs. Proteins. 2006 Jun 1;63(4):727-32

Sandhu KS, Acharya KK*. ExPrimer: to design primers from exon--exon junctions.
Bioinformatics. 2005 May 1;21(9):2091-2.

Kuljeet has contributed a total of 21 papers to the literature.

38 Dept. Biol. Sci. IISER Mohali +91-172-2293182 [email protected]

Research Interests & Projects

Kuljeet is a computational biologist and interested in wide spectrum of biological questions. Some
of the questions that his group is presently working on are as following:
1. What are the evolutionary constraints governing non-random linear and 3-dimensional

organization of eukaryotic genome?
2. What explains the global disconnect between location and effect of chromatin factors.
3. What determines the epigenetic accessibility, or lack thereof, of mono and bi-allelically

expressed genes to the activation/repression machinery?
4. What are the major determinants of transcriptional noise in the eukaryotic genome?
5. How do epigenetic errors radiate across different networks in the cell?
6. How do long structurally disordered regions in the proteins recognize DNA elements?
7. Are the left-handed glycyl residues evolutionarily selected to surrogate D-amino acid

conformation in proteins?

39

Joined Oct 2013

Manjari Jain

Assistant Professor

Sept 1998 - Aug 2001: B.Sc. (Zoology), University of Calcutta, India.
Sept 2001 - Aug 2003: M.Sc. (Zoology), University of Calcutta, India.
Sept 2003 - Jan 2004: JRF, College of Engineering and Leather Technology, India.
Feb 2004 - June 2004: JRF, Salim Ali Centre for Ornithology and Natural History, India
Aug 2004 - April 2011: Ph.D., Indian Institute of Science, Bangalore, India.
May & June 2011: Visiting Postdoc, School of Biological Sciences, University of Bristol, UK.
Aug 2011 - July 2012: Postdoctoral Trainee, University of Zurich, Switzerland.
Jan 2013 - June 2013: Postgraduate Guest Lecturer, Maulana Azad College, Kolkata, India.
Joined IISER Mohali on 15th October 2013.

Behavioural Ecology : Representative Publications
Evolutionary Biology & Biodiversity and Conservation
Balakrishnan R., Bahuleyan J., Nandi D. and Jain M. Modelling the effects of chorus species
composition and caller density on acoustic masking interference in multispecies choruses of
crickets and katydids. Ecological Informatics (in press).

Jain M., Diwakar S., Bahuleyan J., Deb R. and Balakrishnan R. (2013). A Rain Forest Dusk
Chorus: Cacophony or sounds of silence? Evolutionary Ecology (online) doi: 10.1007/s10682-
013-9658-7.

Rajaraman K., Mhatre N., Jain M., Postles M., Balakrishnan R. and Robert D. (2013). Low pass
filters and differential tympanal tuning in a paleotropical bushcricket with an unusually low
frequency call. Journal of Experimental Biology, 216: 777-787.

Jain M. and Balakrishnan R. (2012). Does acoustic adaptation drive vertical stratification? A test
in a tropical cricket assemblage. Behavioral Ecology, 23(2): 343-354.

Jain M. and Balakrishnan R. (2011). Microhabitat selection in an assemblage of crickets
(Orthoptera: Ensifera) of a tropical evergreen forest in Southern India. Insect Conservation and
Diversity, 4(2): 152-158.

Jain M., Kuriakose G. and Balakrishnan R. (2010). Evaluation of methods to estimate foliage
density in the understorey of a tropical evergreen forest. Current Science, 98(4): 508-515.

Diwakar S., Jain M. and Balakrishnan R. (2007). Psychoacoustic sampling as a reliable, non-
invasive method to monitor orthopteran species diversity in tropical forests. Biodiversity and
Conservation, 16 (14): 4081-4093.

Jain M., Balakrishnan R. (2013). From leaf litter to canopy: noninvasive and reliable sampling in a
tropical rainforest. In Lowman M., Soubadra M. D. and Ganesh T. (Eds.) Treetops at Risk.
Challenges of Global Forest Canopies (pp 313 – 320). Springer Verlag, New York. Book Chapter.

Dr. Manjari Jain has contributed a total of 9 papers and 2 book chapters to the literature.

40 Dept. Biol. Sci. IISER Mohali +91-172-2293116 [email protected]

Research Interests & Projects

I am a behavioural ecologist and my research interests lie in the interface of ethology, ecology and
evolutionary biology. I am primarily interested in understanding the ecology and evolution of acoustic
communication in animals. Variation and complexity in acoustic communication, the numerous constraints
on communication and how animals deal with these are the main drivers of my curiosity and my research
largely revolves around these topics. The approaches used are a combination of field and lab-based
experiments, empirical observations and theoretical modeling. My work is question-driven and I work on a
range of study systems including insects, birds and mammals.
PROJECTS
1)Evolution of signal design: An astonishing variety of signals exist in the animal kingdom. One of the major

aims of my research is to understand the structure of signals used by animals, the ecological contexts in
which they are used, the constraints under which the animals must communicate and the evolutionary
forces driving the communication system.
2)Acoustic communication and sociality: Over the course of evolution, non-human social animals have
achieved remarkable complexity in the organization of their societies and sophistication in
communication. I am interested in understanding the social evolution of acoustic communication. A
variety of animal societies, across different taxa, allow us to study this by examining interaction between
animals that are mediated by acoustic communication.
3)Biodiversity and conservation: Living in the tropics, we are blessed with a rich diversity of habitats, flora
and fauna. One cannot turn a blind eye towards the rapid loss of biodiversity and degradation of habitats
due to rapid urbanization. Through my research I aim to develop novel, non-invasive and whenever
possible, inexpensive techniques to monitor biological diversity in order to concentrate conservation
efforts to biodiversity-rich areas.
One of the major drawbacks of living an urban life is developing a disconnect with nature and an
indifference towards issues related to loss of biodiversity, sometimes even entire ecosystems. Thus,
apart from my research, I hope to create awareness about these issues through nature education and
public outreach.

41

Joined Nov 2013

Sharvan Sehrawat

Assistant Professor

Post-doctoral Fellow (Oct 2009 – March2013), Whitehead Institute for Biomedical
Research of MIT, Cambridge, MA, USA.

Post-doctoral Research Associate (Dec 2008 - Oct 2009), Dept of Pathobiology, The
University of Tennessee, Knoxville, TN, USA.

Ph.D., University of Tennessee, Knoxville, TN, USA Comparative and Experimental
Medicine (Immunology)2005-2008.

M.V.Sc., CCS Haryana Agricultural University, Hisar, IndiaVeterinary Immunology2001-
2004.

B.V.Sc and A.H., CCS Haryana Agricultural University, Hisar, IndiaVeterinary
Medicine1996-2001.

Immunology and Immunopathology Representative Publications

Veiga-Parga T, Sehrawat S and Rouse BT (2013) Regulatory T cell function in anti-viral immunity.
Immunol Reviews 255(1):182-96

Swee KL, Guimaraes CP, Sehrawat S, Spooner E, Brassa, I and Ploegh HL (2013) Sortase-
mediated installation of antigens onto anti-DEC205 enables optimization of antigen presentation
and immunization against a complex set of viral epitopes. Proc Natl Acad Science USA
110(4):1428-33

Sehrawat S, Koenig, PA, Kirak O, Schlieker C and Ploegh HL (2013) A catalytically inactive mutant
of deubiquitylase YOD-1 enhances the antigen cross presentation. Blood 121(7):1145-56

Sehrawat S, Kirak O, Koenig PA, Issacson MK, Marques S, Bozkurt G, Simas JP, Jaenisch R and
Ploegh HL (2012). CD8+ T cells from mice transnuclear for a TCR that recognizes a single H-2Kb-
restricted MHV68 epitope derived from gB (ORF8) help control the infection. Cell rep 1: 461-471.

Sehrawat S* and Rouse BT (2011) Tregs and Infections: On the potential value of modifying their
function? J Leukoc Biol. 90: 1079-1087.

Rouse BT and Sehrawat S (2010) Immunity and immunopathology to viruses: What decides the
outcome? Nature Rev Immunology 10, 514-526.

Sehrawat S, Reddy PB, Rajasagi N, Suryawanshi A, Hirashima M, Rouse BT (2010) Galectin-
9/TIM-3 interaction regulates virus-specific primary and memory CD8 T cell response. PloS
Pathogens. 6 (5): e1000882

Sehrawat S*, Suryawanshi A and Rouse BT (2009) Role of TIM-3/galectin-9 inhibitory interaction
in a virus induced immunoinflammatory lesion: Shifting the balance towards regulators. J
Immunol. 182(5): 3191-201.

Sehrawat S, Suvas S, Sarangi PP, Suryawanshi, A and Rouse BT (2008) In vitro generated
antigen specific CD4+CD25+Foxp3+ regulatory T cells control the severity of HSV-induced ocular
immunoinflammatory lesion. J. Virol. 82(14): 6838-51.

Sehrawat S* and Rouse BT (2008) Anti-inflammatory effect of FTY720 in a viral induced
immunopathology: Role of drug induced conversion of CD4+Foxp3- cells to become CD4+Foxp3+ T
cells. J Immunol: 180(11): 7636-47.

42 Dept. Biol. Sci. IISER Mohali +91-172-2293116 [email protected]

Research Interests & Projects

Area: Infectious Immunology and Immunopathology
In a quest to clear infections of various kinds, the host responds to the insults and induces
activation of cells of innate and adaptive immune system that eradicate invading pathogens. At the
same time regulatory mechanisms also operate to curtail excessive inflammatory responses. The
timely induction of an adaptive immune response and its maintenance in the memory phase forms
the basis of lasting protective immunity against infectious diseases and provides clue for
successful vaccination. After receiving help from CD4 T cells, pathogen-specific CD8 T cells are
appropriately activated to control the spread of intracellular pathogens such as viruses. Animal
models are used to investigate host-pathogen interaction. For studying the function and
differentiation of adaptive T and B cells, one has to secure sufficient number of antigen-specific
cells in naïve state but in a normal host the frequency of T cells specific to any given antigen is very
low and frustrates attempts at isolating such cells in meaningful numbers. In our laboratory we aim
to understand the function and differentiation of CD8 T cells during infection with endemic
pathogens such as dengue virus, Chikungunya virus and protozoan parasites such as
Plasmodium in addition to herpes viruses, the latter being the most successful pathogen.
Employing various molecular and immunological approaches, we try to understand the host-
pathogen interaction. We are also putting efforts in developing novel animal models to study
immunity and immunopathology during viral infections. We welcome creative colleagues who are
interested in learning and contributing to the advancement of immunology to join our group.

43

Joined Dec 2013

Rhitoban Ray Choudhury

Assistant Professor

I was born and grew up in Kolkata where I did my B. Sc (Honours) in Zoology from
Presidency College (now Presidency University) in 1999. I did my M. Sc also in
Zoology from Calcutta University in 2001 and then went to the University of
Rochester and did a MS on ecology and evolution in 2005. I finished my Phd from
the same university in 2010 in evolutionary genetics and then joined Purdue
University as a post-doc to work on functional genomics. After finishing my post-
doc, I joined IISER-Mohali in December 2013.

Representative Publications

Buellesbach J, Gadau J, Beukeboom LW, Echinger F, Raychoudhury R, Werren JH, Schmitt T. Cuticular
hydrocarbon divergence in the jewel wasp Nasonia: Evolutionary shifts in chemical communication
channels? Journal of Evolutionary Biology, 2013 Nov;26(11):2467-78. (DOI: 10.1111/jeb.12242).

Sen R*, Raychoudhury R*, Cai Y, Sun Y, Ulrike-Lietz V, Boucias DG and Scharf ME. Differential impacts of
juvenile hormone, soldier head extract and alternate caste phenotypes on host and symbiont
transcriptome composition in the gut of the termite Reticulitermes flavipes and its symbionts. BMC
Genomics, 2013, 14:491. (DOI: 10.1186/10.1186/1471-2164-14-491)

Evolution, Genetics and Genomics Boucias DG, Cai Y, Sun Y, Ulrike-Lietze V, Sen R, Raychoudhury R and Scharf ME. The hindgut-lumen
microbiome of the lignocellulose-degrading termite Reticulitermes flavipes and its responses to dietary
lignocellulose composition. Molecular Ecology, 2013, 22(7):1836-1853. (DOI: 10.1111/mec.12230)

Raychoudhury R*, Sen R*, Cai Y, Sun Y, Ulrike-Lietze V, Boucias DG and Scharf ME. Comparative
metatranscriptomic signatures of wood and paper feeding in the gut of the termite Reticulitermes flavipes
(Isoptera: Rhinotermitidae). Insect Molecular Biology, 2013, 22(2):155-171. (DOI: 10.1111/imb.12011)

Raychoudhury R and Werren JH (2012). Host genotype changes bi-directional to uni-directional
cytoplasmic incompatibility in Nasonia longicornis. Heredity, 108: 105-114. (DOI: 10.1038/hdy.2011.53)

Werren et al. (2010). Functional and evolutionary insights from the genomes of three parasitoid Nasonia
species. Science, 327: 343-348, (DOI: 10.1126/science.1178028).

Raychoudhury R, Desajrdins CA, Buellesbach J, Loehlin DW, Grillenberger BK, Beukeboom L, Schmitt T,
Werren JH (2010a). Behavioral and genetic characteristics of a new species of Nasonia. Heredity,
104:278-288. (DOI: 10.1038/hdy.2009.147).

Raychoudhury R*, Grillenberger BK*, Gadau J, Bijlsma R, van de zande L, Werren JH, Beukeboom LW
(2010b). Phylogeography of Nasonia vitripennis (Hymenoptera) indicates a mitochondrial sweep in North
America. Heredity, 104:318-326. (DOI:10.1038/hdy.2009.160)

Raychoudhury R, Baldo L, Oliveira DCSG, Werren JH (2009). Modes of acquisition of Wolbachia:
Horizontal transfer, hybrid introgression and co-divergence in the Nasonia species complex. Evolution,
63(1): 165-183 (DOI:10.1111/j.1558-5646.2008.00533.x)

Oliveira DCSG, Raychoudhury R, Lavrov DV, Werren JH (2008). Rapidly evolving mitochondrial genome
and directional selection in mitochondrial genes in the parasitic wasp Nasonia (Hymenoptera:
Pteromalidae). Molecular Biology and Evolution, 25(10): 2167-2180. (DOI:10.1093/molbev/msn159)
(*equal contribution)

44 Dept. Biol. Sci. IISER Mohali +91-172-2293160 [email protected]

Research Interests & Projects

I am an evolutionary geneticist by training but my interests range from molecular
ecology to functional genomics. I am particularly interested in 1) the evolution of
arthropod-endosymbiont interactions with a special emphasis on Wolbachia, 2)
evolutionary genetics with the parasitic wasp Nasonia as the model system and 3)
molecular evolution and functional genomics of arthropod-bacterial symbiosis. I am
also interested in phylogeography with particular emphasis on Indian taxa. The
biological questions that I seek to answer often involves the use of various techniques
ranging from field work to genomic tools. Presently the two broad research areas are:
1. Symbiosis: Wolbachia is one of the most abundant endosymbionts of the world
and infects majority of terrestrial arthropods. They also cause various reproductive
alterations in their hosts like cytoplasmic incompatibility, feminization, male-killing and
parthenogenesis. I am interested in various aspects of Wolbachia biology like its
abundance in Indian insects, the genetic basis of these reproductive alterations,
evolutionary history of host-bacterial symbiosis, etc.
2. Evolutionary Genetics: The parasitic wasp Nasonia is an excellent model
system for the genetic dissection of complex traits. The four species are relatively easy
to interbreed and also have a wealth of molecular markers along with sequenced
genomes. I am interested in investigating the genetic basis of various biological traits
using Nasonia as a model system.

45

Some illustrations relating to faculty research interests

-S

G-Glu-Cys-Gly

-Glu-Cys-Gly Glutamate + Cys-Gly
(Glutathione)
The high affinity glutathione
Dug1p transporter from yeast and
sulphur assimilation
Cysteine + Glycine

The DUG pathway of glutathione
degradation

Anand Bachhawat

High noise

Low noise

Functional and evolutionary constraints of 3-dimensional Arunika Mukhopadhaya
organization of eukaryotic genome. Left panel: Large scale
functional compartmentalization of long range physical
interactions among genes (Sandhu et al, Cell Reports 2012).
Right panel: Association of transcriptional noise of genes with
the chromatin mobililty. Genomic loci tethered to nuclear
compartments (like transcription factory) are expected to be
less mobile and, therefore, might exhibit low transcriptional
noise across cells (Sandhu, Nucleus 2012).

Kuljeet Sandhu

The hematopoietic organ/ lymph The niche (red) also signals to the
gland of Drosophila larvae harbors differentiated hemocytes (green)
stem like progenitors (red) that are which are present in the peripheral
maintained by niche (green). region of the lymph gland.

46 Lolitika Mandal

Kausik Chattopadhyay Mahak Sharma

Representative calls of sympatric rainforest crickets and Schematic representation of acoustic masking interference
katydids to highlight diversity in signal structure A) between different sound sources in three-dimensional space
Oscillograms of calls depicting signal structure in time domain. in terms of overlap of broadcast volume. Animals
B) Power spectra of calls depicting signal structure in communicating in dense choruses must evolve strategies to
frequency domain. minimize acoustic masking (overlap between spheres) in
order to communicate effectively.

Manjari Jain

Sexual activity increases survivorship of males post bacterial The ability to resist male induced harm evolves with in 45
infection. When infected with a pathogenic bacteria generations of selection in females. Females from the populations
(Pseudomonas entomophila), sexually active males (black with low levels of intersexual conflict (F) produce significantly
squares) have significantly better survivorship than virgin males higher number of progeny than females from populations with high
(open squares). This result is consistent across three different (M) or intermediate (C) levels of conflict when assayed under
populations of Drosophila melanogaster (Panels A, B and C). The benign conditions (Single Mating). However, when subjected to
survivorship of sham-infected controls is shown as the dashed line. conditions of increased mate harm (Continuous Exposure), fitness
of the females from F populations suffers the most while the fitness
of females from the M populations remains unaffected.

N. G. Prasad 47

Some illustrations relating to faculty research interests (Cont'd)

Methodology for high-throughput quantitative genetic Rajesh Ramachandran
screen to identify new players in metabolism

Rachna Chaba

Cell types revealed in shoot apex using fluorescent reporters. Confocal image stacks of wild type shoot apex were reconstructed in
to three-dimensional view; L1-layer (A-D), a three-dimensional side view of the same imagesis represented in (E-H).

Ram K Yadav

Primary hippocampal neurons expressing AFM and NSOM images of Structural model of membrane-bound alpha
AMPA receptors
amyloid pores and fibrils synuclein

48 Samarjit Bhattacharyya Samrat Mukhopadhyay