Research Opportunities

This collaborative project between Dr. Steven Holland’s laboratory at the NIH and Dr. Lalita Ramakrishnan’s lab at the University of Cambridge will seek to understand the mechanistic basis of human susceptibility to environmental mycobacteria that are nonpathogenic to most people but can cause serious disease in individuals with specific immune deficiencies. Dr. Holland runs an international referral service that takes care of a unique cohort of patients with genetic susceptibility to nontuberculous mycobacterial infections. In the lab, they are mapping these susceptibilities and have found then to map to distinct immune genes, e.g., IRF8 and GATA-2, myeloid growth factors, IL-12R, the GTPase Rac2, to name only a few. 

Dr. Ramakrishnan’s group has pioneered the optically transparent and genetically tractable zebrafish as a model for mycobacterial pathogenesis. The use of the zebrafish has enabled discoveries about TB immunopathogenesis and the genetic basis of susceptibility to TB which has led to the discovery of a variety of inexpensive, approved drugs that can be used to treat TB, often in a patient genotype-directed manner. They have also used the zebrafish to understand the mechanism of leprosy neuropathy.

Through this joint project, the two labs will work together to harness the power of the zebrafish to understand the molecular and cellular basis of the human susceptibilities identified by Holland. The student will move between humans and fish (and Bethesda and Cambridge) to uncover fundamental mechanisms of mycobacterial disease pathogenesis while acquiring mastery over the disciplines immunology, infectious diseases, genetics, molecular biology and cell biology.

There are more than 200 million clinical cases of malaria each year, leading to nearly half a million deaths, primarily among children in Africa. The two major tools for malaria control, antimalarial drugs and insecticides, are both seriously threatened by resistance, making the search for a highly effective malaria vaccine more urgent than ever. My lab focuses on the malaria parasite blood stages, during which parasites invade, multiply inside and consume human erythrocytes. The process of erythrocyte invasion represents a brief extracellular window in the parasite life cycle when parasites are exposed to the antibody-mediated immune system, making it a potential vaccine target. A number of vaccine-related projects are available that intersect with the interests of NIH collaborators in the NIAID Malaria Research Program, from systematic screening of new potential vaccine candidates, to deep structural understanding of current high-profile candidates, to understanding natural immunity to malaria by working with partners in endemic countries in order to inform better vaccine design. All could involve a mix of new technologies, including CRISPR/Cas9 engineering of parasite genomes, and represent an opportunity to contribute to the long-term battle against one of humanities oldest and most persistent infectious disease foes.

A signalling pathway linking nutrient availability to changes in gene expression that hinges on the phosphorylation of translation initiation 2 (eIF2) has long been known to exist. Recognized initially as the yeast General Control Response, recent convergent lines of research have implicated its metazoan counterpart, the Integrated Stress Response, in diverse physiological processes ranging from immunity to memory formation.

This PhD programme will exploit our emerging detailed understanding of translation initiation and termination to shed light on unanticipated mechanistic aspects of the ISR. An understanding of these details may inform efforts to target the ISR to therapeutic ends.

Apicomplexan pathogens are highly-adapted intracellular parasites of humans causing disease including malaria, toxoplasmosis and cryptosporidiosis. These parasites actively confront, subvert and defend themselves against host immune attack using a complex suite of parasite surface and secreted proteins that hijack immune signalling pathways. Moreover, transmission and generation of genetic novelty occurs in definitive hosts where differentiation into sexual parasite forms occurs. Relatively little is known, however, of the molecules and processes that drive these events, particularly during the sexual stages of parasite development. This project will use new methods in in vitro culture of sexual development in Toxoplasma, advanced methods for global spatial characterisation of parasite cell proteomes in order to identify specific proteins thought to be implicated in these interactions, and then utilise CRISPR/cas9 mutagenesis tools to engineer pools of strains deficient in these specific proteins. By assaying mutant pools both in vitro, and through the definitive host we will identify proteins and processes required for sexual stage conversion.

Primary progressive multiple sclerosis (PPMS) is a chronic demyelinating disease of the central nervous system, which currently lacks restorative therapies. Transplantation of neural stem cells (NSCs) has been shown to promote healing of the injured CNS, but previous work has demonstrated that NSCs from patients with PPMS are prematurely senescent. Cellular senescence causes a pro-inflammatory cellular phenotype that impairs tissue regeneration. Senescence in PPMS NSCs was found to be associated with increased secretion of HMGB1, a pro-inflammatory alarmin found to inhibit oligodendrocyte differentiation, and also found increased within white matter lesions of PPMS autopsy tissue. This project aims to understand the role of HMGB1 in PPMS NSC senescence using techniques such as CRISPR-Cas9, RNA sequencing, and functional NSC assays. The longterm goal of this project will be to determine the cause of senescence in NSCs from patients with PPMS and if these cells are suitable for therapeutic use.

Andrew Holmes’ Lab (NIH/NIAAA) and Armin Lak’s Lab, Oxford University

Several decades of research has shown that medial frontal cortical neurons, as well as the neuromodulatory system that innervate the medial frontal cortex, notably the dopamine system, are important in reward valuation and decision making. However, it is not known whether different regions of medial frontal cortex play distinct roles in guiding decisions. Moreover, the role of frontal dopamine signals in shaping and regulating decisions has yet to be established. To address these questions, this project will use a combination of large-scale Neuropixels recording across the medial frontal cortex, as well as optical measurement of dopamine release in the medial frontal cortex during decision making in mice. At Oxford, the project will use Neuropixels probes to record the activity of many neurons across different regions of medial frontal cortex while mice perform a task that systematically manipulates the value of choice options. This data will allow us to investigate the relation between frontal neuronal activity and decision-making variables, and characterize distinct roles of different medial frontal regions in choice behavior. At NIH, the project will take advantage of optical and genetic methods to measure the dynamics of dopamine release in frontal cortical regions identified in the electrophysiological recordings. These experiments will reveal the roles that frontal dopamine play during decision making. In analyzing the electrophysiological and optical data, we will use computational models of learning and decision making to relate neuronal signals with trial-by-trial model-driven estimates of decision variables. The project is primarily experimental in nature but will provide an opportunity to develop computational skills. Together, the project will provide fundamental insights into behaviorally-relevant computations that neurons across the medial frontal cortex perform during decision making, and will reveal the roles of frontal dopamine signals in shaping choice behavior. For more information please visit: https://www.niaaa.nih.gov/laboratory-behavioral-and-genomic-neuroscience and https://www.laklab.org.

*This project is available for the 2021 Oxford-NIH Pilot Programme*

My lab is interested in understanding how membrane-bound organelles form and acquire their distinctive proteome essential to carry their specialized functions. In particular, we focus on how organelle function is maintained through quality control processes, such as protein degradation. We are also interested in inter-organelle communications- which and how molecules are exchanged between organelles, which signals regulate those exchanges, etc.  Although my lab does mostly basic research, we are interested how these processes are disrupted in human disease.

The aim of this project is to exploit the human artificial chromosomes (HAC) to understand human disease associated with chromosome instability and to develop new strategy for therapeutic treatments.

The regulation of gene expression by controlling the production and stability of messenger RNA (mRNA) in the context of the cellular environment is critical for normal cell function. Imbalance in mRNA levels is deleterious for the cell as well as the organism. The exosome is a key mediator of 3′-to-5′ exo- and endonucleolytic RNA degradation and has a central role in maintaining proper mRNA levels in the nucleus and the cytoplasm in eukaryotes (Kilchert et al., 2016 Nature RMCB). However, the exosome is rather unspecific and has a low intrinsic nucleolytic activity and, currently, we do not understand how the exosome targets specific mRNAs for efficient degradation. This has important clinical implications as dysregulation of the exosome function leads to severe neurological diseases such as spinal muscular atrophy, pontocerebellar hypoplasia, and infantile leukodystrophy. Learning more about the mechanisms that underpin exosome regulation will, in turn, help us to understand how these pathogenic states arise in humans in instances where exosome function is perturbed. Highly conserved proteins that interact with the 5′-terminal methylguanylate cap structure on mRNAs such as Cbc20, Cbc80, and Ars2 have been implicated in the regulation of RNA degradation and gene silencing mediated by the exosome complex.

In this project, we aim to understand the function of Cbc20, Cbc80 and Ars2 by studying in molecular detail how these factors guide the targeting and activation of the exosome. The project will bring together two highly complementary host laboratories (headed by Dr. Lidia Vasilieva at the University of Oxford and Dr. Eugene Valkov at the NCI/NIH in Frederick, U.S.A.) to address this important biological problem. Both laboratories will synergize to apply the latest biochemical, structural, genetic and transcriptomic approaches to ensure an excellent training opportunity in multidisciplinary molecular biology. In the course of their doctoral studies, the student will receive extensive training in protein production and purification, X-ray crystallography and/or single-particle cryoEM, functional biochemistry, genetics and functional genomics. Production and reconstitution of multisubunit complexes, as well as functional biochemical and transcriptomic analyses, will be carried at Oxford whilst the structural aspects of the project will be at the NIH. New mechanistic insights into the function of the exosome cofactors will be highly impactful and advance our understanding of how they regulate the exosome function in controlling the stability of individual mRNA targets. This fundamental new knowledge will advance our understanding of how cells execute different programs of gene expression in health and disease.

Bacterial chemotaxis response is crucial for colonization and infection, and the signal transduction systems that mediate such responses are potential new targets for antimicrobial drug development. Such system has emerged as a paradigm for understanding the principles of intracellular signal transduction both in bacterial and eukaryotic cells. In bacterial cells, hundreds of basic core signalling units consisting of three essential components, the chemoreceptors, the histidine kinase and the adaptor protein, assemble into a two-dimensional lattice array which allows cells to amplify and integrate many varied and possibly conflicting signals to locate optimal growing conditions. We aim to determine the structure and dynamics of the chemotaxis signalling arrays using state-of-the-art cryo-electron microscopy and tomography. We will take both in vitro and in situ structural approaches and combined with large-scale all atom molecular dynamic simulations. The ultimate goal is to assemble a time-resolved molecular movie of the entire signalling pathway in bacterial chemotaxis at an atomic level. 

Infections by retroviruses, such as HIV-1, critically depend on the viral capsid. Many host cell defence proteins, including restriction factors Trim5α, TrimCyp and MxB, target the viral capsid at the early stages of infection and potently inhibit virus replication. These restriction factors appear to function through a remarkable capsid pattern sensing ability that specifically recognizes the assembled capsid, but not the individual capsid protein. Using cutting-edage cryoEM technologies, we aim to determine the molecular interactions between the viral capsid and host restriction factors that underpin their capsid pattern-sensing capability and ability to inhibit HIV-1 replication. Specifically, we will combine cryoEM and cryoET with all-atom molecular dynamics simulations to obtain high-resolution structures, together with mutational and functional analysis, as well as correlative light and cryoEM imaging of viral infection process, to reveal the essential mechanism for HIV-1 capsid recognition and inhibition of HIV-1 infection. Information derived from our studies will allow to design more robust therapeutic agents to block HIV-1 replication.