Postdoctoral Program - Nic-PDF : Joint Projects
Joint Project No.1:
Applications are invited for post-doctoral researchers to work on a four year collaborative project entitled “Identification of microbial cell surface protein families that participate in host-microbe interactions: a special focus on antibiotic resistance”, which combines the bioinformatics expertise of Prof. R. Sowdhamini’s group at the National Centre for Biological Sciences, Bangalore, India and in Dr. Alex Bateman’s group in European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge. Half of the postdoctoral tenure will be spent at NCBS, while the other half will be at EMBL-EBI.
This project will involve the analysis of microbial cell surface proteins and their sequence variations. We plan to measure and study the rapid evolution of bacterial cell surface proteins with the hypothesis that amino acid changes to bacterial cell surface proteins confer antibiotic resistance. One of the serious impediments in the study of bacterial genome analysis is the enormous sequence diversity due to evolutionary changes in protein domain families and superfamilies. This means that sequence searches for particular protein families might not achieve complete coverage. The domain and family databases are likely to be incomplete and inaccurate, particularly for fast evolving proteins in bacteria. This project and fellowship will enable Bateman’s and Sowdhamini’s groups to combine their expertise on studying protein domains and evolutionary studies of domain superfamilies in bacterial genomes through sensitive mathematical models such as Hidden Markov Models (HMMs). The generation of HMMs and sequence searches for select protein domain superfamilies will be carried out in NCBS in the first two years. Once we have a broader set of members of a protein superfamily, motif and domain repeat analyses will be carried out. Amino acid variations at different positions of protein domains in pathogenic bacterial genomes will be correlated with the level of pathogenicity and virulence of attack. These two components will be carried out in Cambridge. The broad goal of the project is to study protein families that mediate these interactions and confer antibiotic resistance to microbial species.
Applicants should have (or be about to receive) a PhD in bioinformatics, genome analysis and protein domains and superfamilies. Significant expertise in sequence and structural analyses is essential. Experience in using or developing databases containing Hidden Markov Models will be an added advantage. The successful applicant must be proficient in a scripting language such as Perl or Python.
The closing date for initial applications is 7th April 2017. Applications should include a CV, publication list, and contact details for three referees. Candidates will first be invited for an in person or electronic interview at NCBS or Cambridge soon after. The selected candidate will then develop a two page proposal jointly with Sowdhamini and Bateman and will submit a complete application (proposal, CV and two letters of recommendation, including one from their Ph. D. thesis advisor) to the Bangalore-Cambridge selection committee by 21st April 2017. Candidates will present a talk and be interviewed by a panel in either Bangalore or Cambridge in the third week of May, 2017. Appointment decisions will be announced soon after.
Joint Project No.2:
Conservation status of Gyps vultures through a genomic lens: understanding diet, population dynamics and recent evolution
Gyps vultures have declined by over 97% in the Indian subcontinent in the last two decades. Detailed investigation points to veterinary use of the nephrotoxic NSAID diclofenac as the main cause. This drug is now banned in the Indian subcontinent, and Gyps vulture populations are slowly recovering. However, some important aspects of the ecology and recent evolution of these recovering populations are porrly understood. We seek to use genomic tools to investigate ecological, population dynamic and recent evolutionary changes in these endangered species. Our project builds on extensive research by Green (Cambridge) on vulture ecology, demography and conservation, and the conservation genetic/evolutionary biological expertise of Ramakrishnan (NCBS) and Amos (Cambridge). Specifically, we will use molecular tools to investigate the diet of vultures close to and further away from protected areas to discern whether higher abundance and lower declines observed close to national parks are partly because of access to uncontaminated wild prey. We will also use genetic methods to identify individuals and monitor connectivity between vulture populations. Finally, we will acquire genome-wide data from extant and historical vultures to investigate the extent of demographic decline and whether this diclofenac-induced decline selected for vultures resistant to the toxin. Our research will help better plan vulture conservation locally and shed light on evolutionary impacts of such declines on endangered species.
The fellow will be between Cambridge and NCBS, and will spend the first six months standardizing diet identification protocols in Cambridge. The next six months will be spent in India conducting fieldwork. In the second year and third year, the fellow will spend seven months in India and five months at Cambridge conducting fieldwork, investigating diet and population genetic connectivity using genomic methods. In the final year, the postdoc will spend eight months in Cambridge working with museum skins to investigate the extent of historical variation.
We seek a postdoctoral fellow with interest in conservation genetics. Interest and knowledge of population genetics, landscape genetics, bird population ecology and NGS methods/bioinformatics are beneficial. This is an excellent opportunity for the fellow to train in cutting-edge conservation methods. We hope to apply results to conservation policy and encourage applicants with a keen interest in connecting their research to the on-the-ground conservation.
Joint Project No.3:
Chromatin architecture and functional enhancers in metastatic cancer progression
Applications are invited for post-doctoral researchers to work on a four-year collaborative project entitled “Chromatin architecture and functional enhancers in metastatic cancer progression”, which includes Dr. Dimple Notani’s group at the National Centre for Biological Sciences, Bangalore, India and Dr. Sakari Vanharanta’s group at the MRC Cancer Unit, University of Cambridge, UK. Half of the postdoctoral tenure will be spent at NCBS, while the other half will be at Cambridge.
The broad goal of the project is to study how chromatin architecture and eRNAs on functional enhancers drive metastatic cancer progression using state-of-the art functional genomics and experimental models of metastasis. The candidate will perform a series of chromatin architectural and transcriptional studies at NCBS, followed by functional validation in experimental metastasis models in Cambridge.
Applicants should have (or be about to receive) a PhD in Molecular biology or biochemistry. Experience in experimental animal models, chromatin and transcriptional studies or bioinformatics is desirable.
The closing date for initial applications is 7th April 2017. Applications, sent by email to Dr. Notani (firstname.lastname@example.org) and Dr. Vanharanta (email@example.com), should include a CV, publication list, and contact details for three referees. Candidates will first be invited for an in person or electronic interview at NCBS or Cambridge soon after. The selected candidate will then develop a two page proposal jointly with Dr. Notani and Dr. Vanharanta and will submit a complete application (proposal, CV and two letters of recommendation, including one from their Ph. D. thesis advisor) to the Bangalore-Cambridge selection committee by 21st April 2017. Candidates will present a talk and be interviewed by a panel in either Bangalore or Cambridge in the third week of May, 2017. Appointment decisions will be announced soon after.
Joint Project No.4:
Making hair cells outside the inner ear: investigating the molecular mechanisms underlying development of the spiracular/paratympanic organ placode
In all vertebrates, hair cells develop within sensory patches in the otic placode-derived inner ear. In fishes and aquatic-stage amphibians, hair cells also form in the mechanosensory organs derived from lateral line placodes. In amniotes, the only site of hair cell formation outside the inner ear is the paratympanic organ (PTO) of birds and alligators: this tiny sense organ is buried in the wall of the middle ear.
The Baker and Ladher groups previously showed that the PTO originates from a previously unidentified placode associated with the first pharyngeal cleft, not from the geniculate placode as had been thought (O’Neill et al., 2012, Nature Communications 3, 1041). This discovery confirmed previous proposals of homology between the PTO and the spiracular organ (SpO) of jawed fishes, which is buried in the wall of the spiracle (first pharyngeal cleft).
The proposed project will investigate the molecular basis of SpO/PTO development in sturgeon (SpO, Baker lab), and chicken (PTO, Ladher lab), in order to identify common core pathways that define the SpO/PTO placode and control the development of this unique model for hair cell formation outside the inner ear.