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2018 -
Cross Disciplinary Fellowships - CDF

Quantitative implementation of causality in dynamic molecular pathways


Department of Bioinformatics - University of Texas Southwestern Medical Center - Dallas - USA

DANUSER Gaudenz (Host supervisor)

Biology has become a data science. The vastness of data acquired in life science require advanced analysis methods and the demand for computation and mathematical modeling is higher than ever before. In this circumstance, I am proposing a new framework in deciphering the information flow within molecular pathways utilizing the financial market analysis skills I acquired during my PhD.
The current approach to studying complex molecular pathways in cell biology is to perturb pathway components and then classify the effect as a phenotype. This approach has enabled cell biologist to discover the molecular players of pathways and even to infer hierarchical interaction cascades in pathways. However, under conditions of nonlinearity and high redundancy, the interpretation of these phenotypes can become exceedingly complicated.
The proposed research will focus on the following 2 aims. Establish the mechanisms of information flow within the GEF, GTPase network. Establish the mechanisms of detecting the transient topology with protrusion events.
The Significance of the proposed research derives from; 1) the project challenges the experimental paradigm of molecular cell biology in that it seeks to circumvent the limitations of molecular perturbation in deciphering pathways with nonlinearity and redundancy; 2) the project introduce to the field of molecular cell biology a theoretical foundation for the definition of causality; and 3) the unique data sets available between the Danuser and Hahn labs will allow me to develop this framework on the example of GEF-GTPase interaction networks, in which the current tools fail to address the redundancy and non-linearity.

2018 -
Long-Term Fellowships - LTF

High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration


- Institute of Science and Technology Austria - Klosterneuburg - AUSTRIA

DANZL Johann Georg (Host supervisor)

Directed cell migration is at the core of vital processes in immune response or development. We know key mechanisms of 2D migration, especially how remodeling the actin cytoskeleton forms leading/trailing edges. 3D migration deviates considerably from 2D behavior, is physiologically more relevant and barely understood, mainly since available imaging fails to provide sufficient spatial and temporal resolution but affects living specimen adversely.
I propose a novel microscope to provide 3D subdiffraction resolution at several frames per second, while being “gentle” due to low intensities. I strive to combine benefits of light sheet microscopy and coordinate-targeted nanoscopy with protected STED: A secondary off-state protects emitters from state-cycling and photobleaching during depletion. Selective illumination of the focus-plane and widefield detection limit phototoxicity at high imaging speeds, while two superimposed depletion patterns achieve axial and highly parallelized lateral superresolution.
It is unclear to which extend amoeboid cells rely on adhesion receptors vs remodeling of actin cytoskeleton during 3D migration. I will label membrane, actin and adhesion-associated proteins of both wildtype and talin knockout leukocytes and image migration in a 3D collagen matrix to study: 1) what are the characteristics of actin flow, 2) do cells form adhesions and 3) what forces are transmitted onto the substrate?
The proposed project advances both state-of-the-art imaging and understanding of 3D cell migration substantially. My microscope will enable further study of diverse live systems well beyond current methods, including development, cell biology and neuroscience.

2018 -
Long-Term Fellowships - LTF

Revealing the principles of biogenesis and regulation of the Eukaryotic CO2-concentrating organelle


Department of Molecular Biology - Princeton University - Princeton - USA

JONIKAS Martin (Host supervisor)

Biological carbon fixation is a key step in the global carbon cycle that produces our food and fuels, and regulates the atmosphere’s composition. Approximately 30-40 percent of global carbon fixation occurs in an overlooked algal organelle called the pyrenoid.
In this work, I will utilize the single-celled green alga C. reinhardtii to explore how the pyrenoid, a non-membrane bound organelle, is separated from its environment in order to carry out its fundamental function. Specifically, I will apply biophysical methods to experimentally test whether the pyrenoid forms by liquid-liquid phase separation. I will discover the necessary and sufficient molecular components for pyrenoid formation, and will explore their ability to form droplets in-vitro, a hallmark of liquid-liquid phase separation proteins.
Next, I will characterize the regulatory mechanisms of the pyrenoid dynamic assembly and disassembly. I will explore the mechanisms governing pyrenoid phase switching by mass-spectrometry PTMs (post-translational modification) mapping. To identify regulators, I will use the novel method of proximity proteomic mapping in living cells by the engineered peroxidase (APEX2).
By revealing the underlying mechanism for pyrenoid biogenesis and regulation, I will improve our understanding of its activity, a key step towards a systematic understanding of the global regulation of photosynthesis. Additionally, this work will enhance our understanding of formation and function of non-membrane bound organelles, and will expend this field into the photosynthetic kingdom.

2018 -
Cross Disciplinary Fellowships - CDF

De novo computational design of functional metalloproteins


Institute of Protein Design - University of Washington - Seattle - USA

BAKER David (Host supervisor)

De novo design of proteins enables access to the vast regions of sequence space previously unexplored by nature. These proteins are computationally designed based on physicals principles of protein structure and folding, and are tailor-made with a specific function in mind. As a result, it would be possible to design customized proteins that can give insights into the fundamentals of protein biochemistry as well as tackle practical challenges in medicine and materials sciences. To further push the boundaries of de novo protein design, its concepts will be combined with the world of metal-catalysis. As a result, novel functional metalloproteins will be developed with the protein structure designed to support an active site that is most optimal for high reactivity and selectivity. The design efforts will be directed towards both known biochemical transformations as well as those natively not catalyzed by enzymes. To achieve this goal, quantum chemical methods will be used to develop precise active site models for the transition states of the catalyzed reactions. Rosetta protein design algorithms will then be employed to identify sequences that would best support the atomic arrangements of these theoretical enzyme models. Further rounds of sequence optimization will be performed to ensure high stability and predictability of the active site as well as the entire protein structure. Finally best designs will be expressed and experimentally tested for their activity. In general, the knowledge gained in the process will be beneficial for establishing the general underlying principles behind de novo metalloprotein design.

2018 -
Career Development Awards

Genomic conflict and stability during germline development


Department of Genetics - Cambridge University - Cambridge - UK

A large fraction of our genome consists of selfish DNA modules known as transposable elements (TEs) – mobile units that aim to increase in copy number by jumping from one location to the other. Since their discovery, TEs have been involved in the organization, functioning, and evolution of genomes, but their uncontrolled activity is detrimental to the host and must therefore be tightly regulated. This is especially true in the germline, the grounds where host and TE mechanisms compete for maximizing their influence over the genetic information that will be passed to the following generations. A classic example of disruptive TE activity is provided by hybrid dysgenesis in Drosophila, a syndrome that specifically affects germline development and that is triggered by the P-element DNA transposon. Using this textbook model of genomic conflict, we have recently uncovered the existence of a novel mechanism by which an evolutionary conserved small RNA system controls TE expression by regulating chromatin states and alternative splicing. Building on this foundation, the proposal first aims to dissect the emerging and exciting relationship between chromatin states, transcription, and splicing regulation in vivo. In parallel, I will use this system in combination with developmental, genetics, and high-throughput molecular approaches to understand, at the single-cell level, how host-mechanisms access and control genome integrity during catastrophic germline damage. Dissecting such mechanisms will not only provide unique insight into our comprehension of germline development, but will help us understand one of the major forces that shape the evolution of eukaryotic genomes.

2018 -
Long-Term Fellowships - LTF

A biophysical study on the role of mechanical feedback in learning and the emergence of locomotion


Kavli Institute for Theoretical Physics and Dept. of Physics - University of California, Santa Barbara - Santa Barbara - USA

SHRAIMAN Boris (Host supervisor)
STREICHAN Sebastian (Host supervisor)

Animals move by coordinated muscle activity, which they have to learn during early development. The motor learning period involves spontaneous muscle and neuronal activity, neuromuscular coupling, and experience-dependent network plasticity. Through these processes, the brain ‘discovers’ physical constraints of the body, to generate motion. How does the interplay between neuronal dynamics and body mechanics leads to coordinated motion during development remains unclear. Here, I propose to study the role of mechanical feedback during motor learning of the D. melanogaster embryo. I will explore how physical parameters such as muscle force and elasticity are encoded into neural activity during development, and how non-linear tissue mechanics and spontaneous myogenic contractions enrich neural dynamics and drive the emergence of coordinated motion. To test these ideas, I will assemble a novel light-sheet/light-field microscope, which will enable high-frequency 10-50hz in toto imaging of neuronal and muscle activity in the developing embryo. In addition, I will apply optogenetic tools to directly manipulate muscle contraction activity, and study their effect on the learning dynamics. This comprehensive data set will allow me to develop a physical model of motor learning. The model will combine biological parameters such as spontaneous neural activity and network plasticity, together with physical parameters such as muscle force response, tissue elasticity and substrate friction. This research will reveal novel aspects of motor learning, with implications to developmental biology and medical research.

2018 -
Long-Term Fellowships - LTF

Dissecting the interaction between leukemia initiating cells and their bone marrow microenvironment


Harvard Stem Cell Institute and Center for Regenerative Medicine - Harvard University & Massachusetts General Hospital - Boston - USA

SCADDEN David T. (Host supervisor)

Leukemia is a paradoxical cancer case, being among the most studied but still most lethal types. Current research focuses on unraveling the cell-intrinsic genome alterations leading to malignant transformation of healthy blood to leukemia initiating cells (LICs), while mostly ignoring their interaction with the bone marrow (BM) microenvironment. This is mainly due to the complexity of the hematopoietic niche itself as well as technical challenges associated with BM imaging without distorting tissue architecture. I hypothesize that distinct BM cell population(s) play a critical role in protecting LICs from cytotoxic effects of current treatments driving minimal residual disease and subsequent deadly relapses. Here, I aim to apply novel quantitative deep-tissue imaging with single-cell resolution to localize LICs and reveal the exact cellular composition of the leukemic BM niche at disease progression, remission and relapse. Identifying the relevant cell populations, I then aim to elucidate the underlying molecular players governing this interaction at the protein level. Using genetic manipulation for both LICs and their niche, I aim to block the protective role of the leukemic niche on disease progression and relapse. To recapitulate key features of human acute myeloid leukemia (AML), a novel mouse model established in the host laboratory allowing non-invasive quantitative monitoring of disease progression in living animals will be utilized. Deciphering the identity of leukemic niche cues protecting cancer stem cells, a currently largely unexplored field of research, could help shaping future therapeutic approaches against rapidly-developing lethal cancers.

2018 -
Long-Term Fellowships - LTF

Human gut microbial determinants of non-alcoholic fatty liver disease


Department of Molecular and Clinical Medicine - University of Gothenburg - Gothenburg - SWEDEN

BÄCKHED Fredrik (Host supervisor)

Non-alcoholic fatty liver disease (NAFLD) affects 25-40% of the world’s population and is associated with significant morbidity and mortality, yet definitive diagnosis requires invasive liver biopsy, and there are currently no approved pharmacologic agents or validated biomarkers. Further, the pathogenesis of the NAFLD remains unknown, precluding the development of diagnostic and therapeutic tools. Current evidence suggests that pathogenesis involves complex interactions between environmental factors, such as diet and lifestyle, with abnormalities in glucose and lipid homeostasis. The gut microbiota, which is a key mediator of environmental exposures to the host, has been shown to be altered in a mouse model of NAFLD. Gut microbial metabolites play a role as signaling molecules in the setting of metabolic disease and have also recently been shown to regulate host chromatin, ultimately affecting gene expression. Thus, NAFLD-associated changes in the microbiota and its function may play a role in disease development via signaling at the level of cellular receptors and chromatin. Here, I propose to 1) identify NAFLD-associated changes in human gut bacterial community composition and function, 2) develop microbiota-based biomarkers with utility in screening, diagnosis, and prognosis, and 3) elucidate the molecular mechanisms by which altered bacterial taxa and metabolites contribute to disease pathogenesis. Completion of this work will impact clinical management of NAFLD, pave the way for the development of microbiota-based therapies, and yield the first evidence of gut microbial control of global host chromatin states in humans.

2018 -
Career Development Awards

A prosthetic photon-based neurotransmitter system to overcome synaptic transmission barriers


Neurophotonics and Mechanical Systems Biology Research Group - The Institute of Photonic Sciences - Castelldefels - Barcelona - SPAIN

In many neurodegenerative diseases, synaptic transmission is perturbed. Optogenetics is a powerful strategy to control neuronal function in health and disease using light-activated ion channels called channelrhodopsins. Although optogenetics could be used to overcome synaptic-transmission defects in many psychiatric and neurodegenerative disorders, several factors hold back this strategy, including the need to open the skull for efficient light delivery and the need to minimize light scattering. To overcome these limitations, I propose to integrate light-generating enzymes and light-activated ion channels into a photon-based neurotransmitter system using presynaptic expression of luciferases and postsynaptic expression of channelrhodopsins, respectively. I will develop microfluidic and novel optogenetic tools to target individual neurons in freely behaving animals. I will demonstrate the feasibility of this approach with the well-characterized sensory circuits in the roundworm Caenorhabditis elegans, a powerful model for neurodegenerative diseases. Taken together, these investigations will empower researchers and ultimately clinicians to replace the “flavor” of chemical neurotransmitters by tuning the color of luciferase-emitted photons and the channels that respond to them. I anticipate that this strategy will unleash the full potential of optogenetics for controlling neuronal function during health and disease.

2018 -
Long-Term Fellowships - LTF

A systems-level approach to stress granule maturation in neurodegenerative diseases


Department of Biochemistry - ETH - Zurich - SWITZERLAND

PETER Matthias (Host supervisor)

Neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) affect motor neurons. The degeneration of these neurons is typically characterized by the abnormal cytoplasmic deposition of protein aggregates. These pathological aggregates are amyloid-like, and evidence suggests that they evolve from physiological stress granules (SGs). Thus, to understand how SGs mature into disease causing aggregates is highly important. In the proposed project, I aim to unravel these mechanisms by establishing a motor neuron-like cell line for the comprehensive analysis of SG maturation. To do so, I will take advantage of preliminary data in yeast and develop protocols for the maturation of physiological dynamic SGs into solid-like and aberrant amyloid-like states in motor neuron-like cells. This process will be characterized by fluorescent microscopy and cryo-tomography, and biochemical methods such as limited proteolysis coupled to mass-spectrometry (LiP) to visualize structural alterations. Physiological, solid-like and amyloid-like states will be purified and analysed by mass spectrometry to reveal alterations in the SG composition and in the post-translational modifications (PTMs) of SG components. For the observed changes, I will identify whether they are causative for SG maturation. Finally, applying an advanced mass-spectrometry method, the "sentinel protein assay”, will allow me to identify cellular pathways that are specifically activated during SG maturation. I believe that these results will not only provide important mechanistic insights into SG maturation but may also help to develop innovative therapeutic strategies to prevent this transition and the onset of ALS.

2018 -
Long-Term Fellowships - LTF

Real-time spectral imaging and prediction of successive state changes in model microbial communities

LANDRY Zachary (USA)

Department of Environmental Engineering - ETH - Zurich - SWITZERLAND

STOCKER Roman (Host supervisor)

In this project, we will use model microbial communities based around the degradation of polymers abundant in marine ecosystems. Raman microscopy is a hyperspectral imaging method that can be used to profile the chemical environment of live samples, and will be used to record the progression of a model microbial community within a microfluidic device. Our device contains a single polymeric primary substrate as well as a number of ports that allow for introduction of soluble substrates. By integrating this microenvironment with Raman microscopy we intend to clearly document the biochemical progression of the microbial community during primary succession and colonization of the substrate. The use of this model environment will be leveraged into a general method identify and predict state transitions in real-time as the community moves through the phases of succession, with the goal of being able to elucidate the biochemical drivers of these transitions, and subsequently demonstrate the validity of these drivers by perturbing the natural progression of these state transitions.

2018 -
Long-Term Fellowships - LTF

Resolving the structures and mechanisms of heteromeric amino acid transporter by phase-plate cryo-EM


Department of Structural Biology - Max Planck Institute of Biophysics - Frankfurt - GERMANY

KUEHLBRANDT Werner (Host supervisor)

Heteromeric amino acid transporters (HATs) mediate the antiport of amino acids across the cell membrane, and play pivotal roles in amino acid absorption, neurotransmission, and metabolite supply to cancer cells. HATs are unique among all solute carrier (SLC) transporters, in that they are composed of the two subunits, the ‘helper’ heavy chain and the ‘catalytic’ light chain, linked by a disulfide bridge. Malfunction of HATs are implicated in hereditary diseases like cystinuria and lysinuric protein intolerance, and thus HATs are important pharmacological targets for both hereditary and acquired diseases. However, the structures and mechanisms of HATs are poorly understood. The crystallization of HATs proved extremely challenging, likely due to extensive glycosylation and difficulty in preparing heteromeric complexes in general. I propose to use single-particle cryo-electron microscopy (cryo-EM) to solve the first three-dimensional structure of a HAT in its full dimeric assembly. Conventional cryo-EM suffers from a practical size barrier at ~150 kDa due to low image contrast, and a HAT (~125 kDa) represents one of the most challenging targets. I will employ cutting-edge techniques like Volta phase plate, antibodies and nanodiscs to overcome the issue. I aim to solve the structures in multiple conformations, (1) apo, (2) substrate-bound and (3) inhibitor-bound states, to gain fundamental insights into the heterodimer formation, substrate transport and pharmacological inhibition. With concomitant biochemical experiments, these studies will facilitate understanding and therapeutic application of this important SLC transporter.

2018 -
Long-Term Fellowships - LTF

How to grow a flat leaf?


Center for Integrative Genomics - Faculty of Biology and Medicine - Lausanne - SWITZERLAND

FANKHAUSER Christian (Host supervisor)

Growing flat leaves is crucial for plant success, since it directly affects light interception and photosynthesis. This process is tightly regulated by endogenous signals revealing a strongly genetically defined developmental program, but is also modulated by the light environment. As shown using null mutants, both blue light receptors phototropins (phot) and red/far-red light receptor phytochromeB (phyB) affect leaf flattening, and it was recently found that plants lacking PKS3, a protein involved in phot signaling, suffer severe flattening defects. The main objective of this project is thus to determine how light signals interact with endogenous cues to control development of a flat leaf. First, I will perform an exhaustive temporal and spatial characterization of the phot and phyB-mediated light control of leaf development applying various light treatments and complementing phot1phot2, phyB and pks3 with tissue-specific promoters. Next, I will apply the latest microscopy techniques to determine the expression pattern of leaf development markers under various light conditions and in photoreceptor mutant backgrounds. Also, given the major role of auxin in leaf development, and the various ways in which phot and phyB control it, I will study auxin abundance, transport and sensitivity at the tissue and cellular level. Finally, I expect to identify new components of phot signaling evaluating the interactome of PKS3 through IP-MS. Thereby I expect to determine how a conserved developmental program and photosensory cues crosstalk to control leaf flattening.

2018 -
Long-Term Fellowships - LTF

Anatomical and functional characterization of the neural circuits controlling ejaculation


Neuroethology Laboratory - Champalimaud Centre for the Unknown - Lisbon - PORTUGAL

LIMA Susana (Host supervisor)

Sexual behavior is fundamental for evolution and an important component of human well-being. Ejaculation is a critical mechanism in male sexual function, which is hypothesized to be controlled by a neural circuit known as the 'spinal ejaculation generator' (SEG), located in the lumbar spinal cord. The SEG has also been hypothesized to control the post-ejaculatory refractory period, a phase of sexual satiety, through ascending projections to the brain. However, the mechanisms by which the SEG controls ejaculation and the refractory remain elusive.
We will tackle this problem first by using anatomical tracing to find the spinal neurons that provide input to the ejaculatory muscles and immunochemistry to characterize their molecular identity. We will use this information to provide specific genetic access to SEG neurons. By expressing fluorescent probes in
these neurons, we will be able to obtain targeted electrophysiological recordings and use them to characterize the intrinsic and synaptic properties of the SEG circuitry in vivo. By expressing genetically encoded calcium indicators, which provide fluorescence probes of activity, we will monitor the activity of the SEG during sexual behaviour. Finally, by expressing and optically stimulating excitatory and inhibitory opsins in SEG neurons or their terminals, we will test their causal role in triggering both ejaculation and the post-ejaculatory refractory period. This project will provide the first mechanistic description of the key neural circuitry controlling male ejaculation and the refractory period, with potential implications for the treatment of sexual dysfunction.

2018 -
Long-Term Fellowships - LTF

High-content phenogenomic analysis of mitochondrial unfolded protein response (UPRmt) in C. elegans


Institut Interfacultaire de Bioingénierie - École Polytechnique Fédérale de Lausanne - Lausanne - SWITZERLAND

AUWERX Johan (Host supervisor)

Complex human diseases are the result of a combination of genetic, environmental and lifestyle factors, and the development of new treatments for such diseases has been challenging. Large-scale screens in pharmaceutical industry have essentially not changed over the last 50 years and many drug candidates fail in clinic, as animal testing is mostly performed on animals with a single genetic background, compromising translational utility. While multiplexing experiments in vertebrate animal models with different genetic backgrounds seems unrealistic, small model organisms, such as C. elegans, are emerging as valid alternatives to cells and inbred mouse models in drug development, significantly lowering time and costs of research. My host laboratory has developed an automated platform for roundworm culture and high-throughput phenomic data collection and analysis. I here propose to use this platform to map mitochondrial stress pathways, such as the UPRmt, in a large C. elegans genetic reference population and in depth characterize selected candidate hits from this genetic screen through the study of loss-of-function worm models in vivo. This will allow me at the same time to develop and validate protocols for high-content and high-throughput phenotypic analysis of C. elegans. Furthermore, my project will spur replacement, reduction, and refinement (3Rs) of vertebrate animal testing and will promote the roundworm (and eventually other small organisms) as new model organism for high-throughput biology as well as for drug discovery.

2018 -
Cross Disciplinary Fellowships - CDF

Dynamic network theory of microbial communities


Department of Zoology - University of Oxford - Oxford - UK

FOSTER Kevin (Host supervisor)

Microbial communities affect us in many important ways, from health and disease to food production, industrial fouling, agriculture, and the environment. There is a great need, therefore, to both understand and control microbial communities. The challenge is that these communities often contain many dynamically-interacting species, making them complex systems that are difficult to predict. To understand microbial communities, we need breakthroughs in advanced theoretical methods. The current state-of-the-art treats microbes as static networks but microbial communities are dynamic systems where species interactions can rapidly change and shift a community to an undesirable state. To deal with this, I will develop a new dynamic network theory to both understand and control microbial communities. Firstly, I will analyse how the key properties of microbial communities are influenced by different sources of network dynamics. I will study both microbe-driven changes in network structures, e.g. ecological succession, and changes driven by external factors, including the abiotic environment and host factors for symbiotic communities. I will then apply control theory to these dynamic networks in order to understand how to stabilize dynamic networks and shift networks from an undesirable (e.g. disease) to a desirable state. As a final step, I will work with my host laboratory to design experiments and test the ability of my theory to both predict and engineer gut communities for specific outcomes. In this way, I aim to make major contributions to both microbiology and complex system theory.

2018 -
Long-Term Fellowships - LTF

Dissecting microbial driven maternal-fetal immune crosstalk and consequences on offspring immunity


National Institute of Allergy and Infectious Disease - National Institutes of Health - Bethesda - USA

BELKAID Yasmine (Host supervisor)

Mammalian pregnancy is a unique physiological context that undergoes substantial hormonal, metabolic, microbiota and immunological changes. Epidemiology studies have shown that pregnant women have altered susceptibility to various infections. These environmental exposures could have profound and long-term effects on the offspring with impaired growth and disorders. Despite ample evidence linking the maternal immune perturbation to offspring outcomes, the mechanistic pathways for this in utero influence remain unclear. Further, little is known about the impact of these microbial exposures on the offspring immune system. Moreover, how distinct microbiota could imprint the offspring immune system for the long term remains unknown. The objective of this grant is to set up murine maternal immune activation models via infectious diseases that commonly occur during human pregnancy, including influenza virus and Listeria monocytogenes infections, to understand the impact on immune ontogeny, microbiota composition, infectious and inflammatory diseases susceptibility of offspring in neonatal and adult stages. We will dissect the mechanistic links of maternal-fetal crosstalk through vertical transmission of maternal cytokines, microbiota and/or epigenetic regulation with an ultimate goal to rescue the potential detrimental consequence in offspring. Further integration of our findings from murine models to human samples will provide significant impact in the clinic. Insight into maternal-fetal immune crosstalk is a fundamental line of research with profound implications in understanding and prevention of complex immune disorders that are on the rise in high-income countries.

2018 -
Long-Term Fellowships - LTF

Deciphering the mechanism and significance of a common stress program


Department of Immunobiology - Yale School of Medicine - New Haven - USA

MEDZHITOV Ruslan (Host supervisor)

Cells continually encounter a variety of suboptimal conditions which restrict growth and proliferation. In response to such stressors, proper adaptive mechanisms are typically activated. Adaptive mechanisms can be categorized into two groups, specific and general. The specific responses, such as DNA repair or unfolded protein response, directly deal with the primary cause. By contrast, a general response is assumed to inhibit growth and render cells highly tolerant to the stress as a dormant state of an organism. While most studies have focused on the specific effectors, little is understood about how cells initiate and maintain the central stress response pathway.
By analyzing high-throughput sequencing data available in our lab on various types of stress conditions, I have found several genes that are commonly regulated in mammalian cells. I hypothesize the common genes may modulate a general stress response, which protects cells from stressors. To understand the role of those candidates, I will 1) reveal molecular mechanisms underlying the common stress program and 2) evaluate their biological significance in vivo. With biochemical and computational approaches combined with loss of function studies, I will determine their targets to unveil regulatory networks established in the common stress program. Finally, I will perform in vivo experiments with various stresses to confirm whether the candidates function in the physiological context. By understanding the core stress response, this research will address an important but often overlooked aspect of stress response and provide a fundamental understanding of cell survival and maintenance.

2018 -
Long-Term Fellowships - LTF

Imaging functional integration of newborn neurons into neural circuits of the axolotl brain

LUST Katharina (GERMANY)

Molecular Mechanisms of Vertebrate Regeneration - Research Institute of Molecular Pathology (IMP) - Vienna - AUSTRIA

TANAKA Elly M. (Host supervisor)

Post embryonic growth and regeneration require new cells to integrate into the network of existing cells. In the case of the brain it is extremely important to maintain and restore circuit function, such that behaviors can be executed correctly. To study such processes a system that fulfills both post-embryonic growth as well as regeneration is needed. Furthermore, since neural circuit functions are highly dynamic the need for in vivo approaches is evident. In mammalian systems where neurogenesis occurs throughout life in restricted brain regions such approaches are technically challenging.
Here, I propose to use the axolotl (Ambystoma mexicanum) brain to understand the dynamic remodeling of neural circuits through the addition of newborn neurons during post-embryonic growth and regeneration. I will establish a high resolution intra-vital in vivo imaging approach to address the dynamics of neurogenesis and remodeling of neural circuits in the telencephalon and the optic tectum. Using this setup in combination with genetically encoded calcium indicators I will generate activity maps of these regions in the presence or absence of defined stimuli and address their functional remodeling during growth and their restoration after injury. Furthermore, I will develop and adapt methods to visualize the functional connections of neurons in axolotl. Together, this work will provide fundamental insights into the functional maintenance and regeneration of neural circuits and the dynamics of how new neurons integrate in vivo which has not yet been achieved in any vertebrate system.

2018 -
Long-Term Fellowships - LTF

Mapping and manipulating stem cell fate acquisition using synthetic gene constructs


Department of Bioengineering - Stanford University - Stanford - USA

QI Lei Stanley (Host supervisor)

A driving goal of regenerative medicine is to use stem cells to replace worn-out cells, tissues and organs. Stem cells could in principle be instructed to generate all cell types required. However, two crucial questions must first be addressed: 1) How can we precisely target specific cell types with these signals to control differentiation? 2) What molecular signals instruct cells to differentiate, sequentially, into cell types of interest? These fundamental questions have been difficult to address in a generalizable way. However, two new advances open up powerful new ways to address them. First, a new design principle for signaling systems shows how combinations of seemingly redundant ligands and receptors could be used to target signals to specific cell types. Second, a new technique called MEMOIR enables cells to actively record their own signaling histories within their genomes, providing information on which signals are perceived within each cell lineage.
Here, I propose to combine my own experience in stem cell research with Michael Elowitz’s expertise in synthetic biology to develop technology for mapping and manipulating the processes by which cells acquire their identities. More specifically, I will analyze promiscuous receptor-ligand interactions in the FGF or ErbB receptor families to better understand how the use of ligand combinations could enable more cell type specific activation of these pathways. In addition, I will implement MEMOIR in developing neurons to extract the signaling histories that accompany their differentiation. Knowledge of the way differentiating cells process signals may enable more precise control over cell identity.