Intriguingly, somatic cells can be directly reprogrammed back to naive pluripotency by defined, exogenously expressed transcription and growth factors. Induced pluripotent cells can initiate differentiation into a variety of somatic cell types, providing a powerful platform for understanding basic aspects of embryonic development that harbors substantial promise for human therapeutics for diverse diseases. During reprogramming, a fully differentiated regulatory landscape is converted to a permissive landscape capable of directed differentiation toward a multitude of cell types. During directed differentiation, this permissive landscape is narrowed, resulting in a fully differentiated cells expressing a fraction of potential genes and gene regulatory modules. However, a high-resolution picture of these epigenetic transformations is effectively entirely missing. A mapping of the regulatory changes caused during reprogramming and directed differentiation would provide the first regulatory “movie” of cells executing these programs, fundamentally changing our understanding of how biological state is set and how it evolves. We will combine highly efficient programming and reprogramming systems developed in the Hanna lab with cutting edge epigenetic analysis methods developed in the Greenleaf lab to 1) map chromatin dynamics at base-pair resolution during near-deterministic somatic cell reprogramming using a sensitive assay of transposase accessible chromatin (ATAC-seq). These data will allow a temporal understanding of the chromatin, TF binding, and nucleosome positioning changes that occur during the reprogramming process, providing causal information regarding the regulatory regions and protein factors that drive phenotypic changes. We will then 2) identify regulators that drive the human naive and primed pluripotent cell differentiation competence towards authentic primordial germ cell (PGC) lineage, using a similar workflow. Finally, we will 3) reveal regulatory variability in human pluripotent cell populations expanded in a variety of newly developed growth conditions by probing the epigenome at the single-cell level. Our analysis of controlled developmental systems will decipher the dynamics and interdependence between different layers of chromatin regulation, leading to basic understanding of epigenesis with immediate application toward therapeutic ends.

Tendons are specialized tissues that connect bone to muscle, transmitting the force generated by these structures to allow for body movement. Tendon injuries due to acute trauma overuse or age related degeneration account for 30-50% of all sports related injuries and nearly half of all job related illness in the US. Studies have shown that tendons initiate a regenerative response but rarely regain their original biomechanical properties. Despite how common tendon injuries are, we still have limited knowledge of the molecular pathways regulating tendon cell maintenance and injury response. To address this, we will employ a robust method to study the cell proliferation dynamics of adult tendon tissue using the TetO-H2B-GFP reporter mice. The TetO-H2B-GFP transgenic mice have been used in several systems to monitor cell division history, including hematopoietic stem cells and muscle stem cells systems (Foudi et al., 2009, Chakkalakal et al., 2012). Next, we will use pulse-chase labeling of these transgenic mice to identify label retaining cells residing in the tendon and determine if they exhibit stem cell activity in an injury model. Finally, we will isolate the H2B-GFP label-retaining stem cells and perform RNAseq to identify unique molecular signatures of tendon stem cell populations. This work will impact our understanding of tendon cell behaviors during maintenance and injury conditions, and aims to discover new gene pathways unique to the label retaining stem cell populations. These discoveries could ultimately provide new therapeutic targets for the treatment of tendon injuries.

Insect-transmitted parasites endanger our health and our food supply and are the causal agents of e.g. malaria and yellow fever and numerous plant diseases in economically important crops. Surprisingly, only a few laboratories worldwide investigate which characteristics at the parasite molecular level are required for insect transmission and represent key drivers of parasite epidemics. We hypothesize that evolution of the triangular host-parasite-insect relationship is a battle between genes rather than individual organisms.
Aster yellows phytoplasmas (AYPs) represent parasites that excel at controlling their plant hosts, dramatically modifying their development and thereby not only affecting the plant-AYP interaction, but also the interactions between plants and AYP vector leafhopper populations, for example by increasing plant attractiveness to the leafhoppers. When studying such an extended phenotype that even changes the development of other species within its own ecological web, it becomes evident how developmental outcomes are intertwined with ecological ones. Therefore, we selected this triangular host-parasite-insect system as a paradigm to unravel how mechanistic aspects of gene function are linked to the ecological niche of the organism and the environment.
AYP express vir genes, encoding effectors, which products have a dramatic impact on plant architecture and hence, crop yield, but which facilitate AYP spread by their vector insects. The relative AYP fitness increase that can be achieved by those different modifications of plant development can only be determined by understanding their impact on the population dynamics and migratory behavior of the insect vectors, which in its turn allow for the expansion and spread of the AYPs.
Unraveling these complex interactions requires an interdisciplinary approach and multi-scale modeling framework, in which we can zoom out from the molecular up to the ecological level. We will compare and contrast a leafhopper migration-driven context found in Wisconsin (USA) with a residential-population driven context found in Poland (Europe), allowing us to separate the relative importance of the plant and the insect dynamics. These distinct ecological settings also allow for testing hypotheses regarding how the ecological embedding is determining which effector genes are selected for, both regarding type and severity.
This study will result in a better understanding of general principles of any triangular host-parasite-vector interaction web in their full multi-level context. Moreover, it will set up a modeling framework that can be straightforwardly applied to a broader class of disease studies, including human diseases such as malaria.

Human influenza viruses are transmitted by inhalation of virus-laden aerosol, whereas avian viruses are disseminated by the fecal-oral route. Thus, in order to become transmissible between humans, an avian virus must adapt to a different mode of transmission. It is well established that the hemagglutinins in the envelope of avian viruses recognize differently glycosylated receptors on host cells. However, we propose that host adaptation also requires changes in the structure, fluidity, and lipid selection of the viral envelope glycoproteins hemagglutinin and neuraminidase, the proton channel, and the matrix protein.
There are several requirements on the envelope’s biophysical properties for optimal transmissibility: The membrane must be fluid at body temperature (42 °C in birds versus 33 °C in the human respiratory tract) to allow virus budding, but it should solidify to protect virions against damage during transmission between organisms. After internalization by a new host the membrane must liquefy again to allow infection. The phase state of the membrane depends on temperature, but lipid compositions determine at which temperature phase changes occur. In turn, this will have an effect on the structure and organization of the viral envelope proteins and their interaction with the viral membrane, particularly regarding their ability to laterally interact, cluster and adopt certain conformations. Hitherto, these aspects have been widely neglected when studying the adaptation of influenza virus to new hosts.
We will take a multi-pronged approach to address this problem. Avian and human viruses will be grown at different temperatures and in different types of host cells. The lipidomes of these viruses will be determined. The phase and mechanical properties of the viral envelopes under changing environmental conditions will be examined. Structural changes of the viral envelope proteins will be determined at high resolution and the reasons for their altered behaviors will be sought by determining differing interactions with specific lipids in each case. Hypotheses about the molecular reasons for envelope adaptation to different host conditions will be formulated based on these results and ultimately tested for their relevance in viral envelope lipid selection and virus morphology by generation of recombinant viruses lacking lipid binding sites.

Prions are protein-based epigenetic inheritance units with the unique ability to switch between native and prion forms. This switch results in profound alterations in function. Under normal conditions, this switch may reduce the fitness of the organism. However, under acute stress, the organism may survive by trying untapped and hidden phenotypes revealed by the prion state. Intriguingly, many RNA binding proteins are predicted to have prion domains and prion switching of such proteins can dramatically alter cellular networks. I propose to experimentally characterize all yeast RNA binding prions using well-established prion assays. Furthermore, using stringent and quantitative RNA-protein interaction assays together with prion assays, I will characterize the functionality of RNA-binding proteins in their prion form and determine which RNAs they bind in the two different states. Differential RNA binding of prions will be a proof-of-principle for the concept of beneficial gains-of-phenotypes under stress conditions.
Moreover, several neurodegenerative disease pathologies have been associated with mutations in the prion-like domains of RNA binding proteins. The mutations are thought to alter RNA homeostasis upon prion-like folding of the protein. I will test one such prion candidate RNA binding protein, the eIF4G translation initiation factor. Two point mutations in eIF4G are linked to parkinsonism. I will test if these mutations increase the prionogenicity of eIF4G and/or cause differential binding of RNAs.
My work will provide valuable insights into the prion biology of RNA binding proteins and how mutations in them can alter cellular physiology in disease.

Modularity of gene regulation has evolved in response to organisms adapting to varying environments, and enables independent variation of functional systems as well as synchronized responses to single stimuli. I propose to study the changes in modular gene regulation involved in natural adaptation by testing (I) the long-standing hypothesis that suppression of recombination can create linked groups of adaptive alleles in differentially adapting populations, and (II) a novel hypothesis that linked groups of adaptive alleles can give rise to modular regulation. By adapting recently developed genetic methods to use in stickleback fish, I will not only test these hypotheses in an empirical setting for the first time, but also produce a wealth of novel information on the effects of adaptive divergence on recombination and gene regulation, as well as further advance the stickleback as the premier model organism for studying natural adaptation with molecular resolution. With this project I will switch from analyzing organ development in the mouse to exploring genome-wide effects of adaptation on recombination and gene regulation in fish. Learning the methods and skills required to carry out this project in the high-quality environment provided by my host laboratory I will significantly expand my expertise and gain the tools necessary for a future as an independent researcher.

Many microbes produce toxins that kill members of other species. Intriguingly, however, some microbes specifically target members of their own species - termed fratricide. Such behavior seems obviously deleterious; unchecked, it can have detrimental effects on the fitness of individuals and their populations, even leading to self-inflicted extinctions of clonal populations. Surprisingly, however, growing evidence suggests that fratricide is widespread. Under what circumstances can fratricide emerge as the product of evolution? Under what conditions should this trait be expressed, and how should it be regulated?
In this proposal, we aim to address these questions using advanced biophysical techniques and theoretical modeling.
We will use Streptococcus pneumoniae as a model system. Previous biochemical studies indicate that, in S. pneumoniae, fratricide is regulated by a complex intracellular regulatory network and coordinated by cell-to-cell signaling. We aim to:
1) Characterize the dynamics and regulation determining the fates of individual cells during fratricide.
Using advanced biophysical techniques, we will characterize the real-time dynamics of the pertinent regulatory processes, cell fates, and multicellular interactions with single-cell resolution.
2) Elucidate how fratricide can emerge as a stable product of evolution. We will perform competition experiments between the wild-type strain and various mutants under a wide range of spatio-temporal settings and analyse them using quantitative models.
Bridging molecular, cellular and multicellular scales, our proposed research will produce an integrated understanding of the regulatory mechanisms and evolutionary origins of fratricide. The conceptual and quantitative framework obtained from this work will be largely system-independent, applicable to various types of competition among conspecifics.

Aging is a process fundamental to all organisms. Exhaustion of stem cells and their niche is a hallmark of aging, as it limits cell turnover and thus tissue homeostasis. In humans, aging-related dysfunctions of stem cells are linked to many diseases such as neurodegeneration and cancer. The testis of Drosophila melanogaster offers an excellent model to study aging of stem cells, with well characterized signaling pathways implicated in their maintenance and where phenomena like de-differentiation were discovered. Much attention has been paid to the decline of stem cell number and of self-renewal factors, but there is a gap in our knowledge of other (i.e., non-gonadal) extrinsic signals and of mechanisms other than de-differentiation that replenish the stem cell population as a function of time. In this project, I will determine if de-differentiation of non-stem cells contributes to the maintenance of the germline stem cell population. I will attempt to identify the roles of the anti-oxidant activity pathway Nrf2 and of other potential non-autonomous signals in aging, focusing on the hypothesis that tissues other than the niche can contribute to the maintenance of stem cells and prevent their loss during aging.

Recent advances in sequencing technologies have greatly expanded our knowledge about mRNA transcription rates, abundance, translational activity and half-lives. By contrast, a mechanistic understanding of the cytosolic mRNA fate is still scarce: what are the cis determinants (i.e. mRNA sequence, chemical modifications) and trans factors (mRNA binding proteins, small RNAs) that signal for translation, repression or decay? How are these signals read out and implemented? One puzzling aspect of mRNA biology is that upon stress, mRNAs become sequestered into granular assemblies, so-called P-bodies (PBs). PB formation is conserved from yeast to human, and they fulfill pivotal mRNA storage tasks in e.g. neurons and oocytes. Still, they are poorly characterized in terms of composition, assembly dynamics and most importantly their precise function is unknown.
In order to better understand the life of an mRNA and the function of PBs, I propose to
a) perform mass-spectrometric analyses of the composition of mRNA-particles (mRNPs) destined for translation, repression and decay to identify key factors specific for each pathway
b) to reconstitute PB formation in vitro from yeast lysate, a unrivaled opportunity to manipulate and study their assembly and function
c) to establish a system to visualize and quantitate mRNA-protein-interactions in real time, by microscopy.
These studies will help us to decipher the regulatory code of mRNA turnover and the mysterious function of granular assemblies like PBs, and to better comprehend the many diseases associated with these fundamental pathways. Further, it might allow us to develop novel tools to manipulate the activity state of an mRNA.

Avian feather patterning has long been studied as a model of two-dimensional periodic pattern formation. Each feather emerges from the site where embryonic dermal cells aggregate. Previous studies have suggested that the dermal condensation at regular intervals is based on the spatial patterns of interacting morphogens. However my recent finding implied that the existence of cell-cell interactions between two types of dermal cells: one is the dermal cells of outer boundary of feather buds and the other is those of interior of buds. Time-lapse observation showed a unique behavior of dermal cells of outer boundary. At the beginning of feather patterning, the dermal cells was uniformly distributed throughout the region beneath epidermis. As skin develop, the cells actively moved to avoid the center of feather buds and localized in the outer boundary, suggesting segregating mechanisms between two types of dermal cells. This looks like a meshwork in the skin. The patterning process of mesh structures seems to be directly involved in the size of buds and distance between each buds. Thus, in this proposal, I aim to uncover the molecular basis of the pattern formation. To this end, I will use reconstitution assay in which dissociated dermal cells can regenerate complete feather buds, allowing the analysis of cell interaction and easy gene-transfer into dermal cells. We have candidate genes that regulate the spacing feather buds, so I will also examine whether these genes are involved in the interaction of dermal cells by gene suppression. This study will provide new insight into developmental biology.

The heart is the first organ to acquire its function during embryonic development and has a vital role in pumping nutrients/oxygen. In the early vertebrate embryo, the heart is a single primitive contractile cardiac tube. In mammals, it originates from a horseshoe-shaped cardiac crescent continuous across the midline that merges at the midline to form a tube. While in recent years significant progress has been made in our understanding of the gene regulatory logic that controls early heart development, approaches toward a comprehensive framework of the cell behaviors underlying the formation of the primitive heart tube from the cardiac crescent are still missing. In this project, we propose to combine genetic approaches to label in vivo the individual cardiac progenitor cells, state-of-the-art microscopy techniques (i.e. 2-photon and light sheet microscopy) to live-image the morphogenesis of the entire heart tube at cellular resolution in mouse and computational methods to extract quantitative meaningful morphogenetic parameters. Through this approach, we aim to elucidate the complex 4D tissue movements and associated cell dynamics- such as migration, division and changes in cell shape- that occur during heart tube morphogenesis. We aim to subsequently use these findings to analyze the putative cellular defects in embryos mutant for transcriptional regulators that show cardiac abnormalities. While much of the cardiac defects observed have been described by looking at the terminal phenotype, our goal is to understand how these defects arise from seeing directly the dynamics of the collective behavior of the cells that form the heart.

Structural genome variation and DNA methylation enable plants as sessile organisms to adapt to changing environments. Our current understanding of the interaction between structural variation and methylation, the underlying mechanisms and genome-wide extent, is limited by the lack of true reference genomes. In this project I will extend our knowledge by exploiting the Arabidopsis thaliana 1,001-genomes and methylomes project as an unprecedented resource created in the host lab. By utilizing groundbreaking single-molecule real time sequencing (PacBio) together with Bionano Irys optical DNA mapping, I propose to create true de novo reference genomes for 50 selected A. thaliana ecotypes. I will then characterize effects of DNA methylation on genome stability in methylation deficient mutants. Subsequently, I propose to generate A. thaliana populations from differentially methylated lines, and a mutant, and generate Bionano optical genome and methylome maps for F1 and inbred F2 progeny. From these large data sets, I will bioinformatically infer the genome and population-wide extent of SVs and DNA methylation to understand their potential associations. I will further expand on their causal relationship after selfing of heterozygous F1 progeny, and identify e.g. whether there is a bias towards the homologous chromosome containing the variation. I propose to use the created datasets to also test the hypothesis that changes in DNA methylation can trigger structural genome variation other than through retrotransposition. Results of this project will benefit our understanding of the evolutionary drive and consequences behind different shapes in the (epi)genome.

A well-recognized problem in rational drug design is inability to successfully predict the potency of the drug even for enzymes where the structure is known with atomic resolution. One of the missing pieces in the puzzle is the dynamical nature of the water hydrating the protein surface. This hydration water has properties significantly distinct from the bulk and mediates most of the biomolecular interfacial interactions, while its dynamics is intimately linked to the protein dynamics. The complexity of the problem becomes even clearer if one considers that the native environment where the protein functions is the heterogeneous and crowded environment of the living cell. Intracellular environment is known to alter the water dynamics due to high extent of macromolecular crowding. Therefore, if one wants to have a realistic picture of the drug-enzyme interaction in situ, it is essential to take into account the dynamical properties of both the solvating water and the protein itself in its native environment.
Recently a sensitive in-vitro method to probe hydration dynamics with (sub-) nanometer resolution based on Overhauser Dynamic Nuclear Polarization (ODNP) was developed in the laboratory of Prof. Songi Han (UCSB). The main goal of this proposal is to develop ODNP into a method that will be applicable to in-vivo studies in living cells. When developed this method will allow to monitor changes in hydration dynamics of the biomacromolecules that are induced by the heterogeneous in-cell environment and to compare them with the ones induced by the mimics commonly employed in the in-vitro studies such as cell extracts and solutions artificially crowded with high MW polymers.

Persistence in Mycobacterium tuberculosis is a phenomenon of cells where a fraction is resistant to a killing assault as a consequence of a transient gene expression or protein modifications. I believe that the persistence phenomenon is being unmasked at the presence of bactericidal drugs or host adaptive immunity and it is the single most important impediment to tuberculosis control. While several genes were previously proposed as contributing to the emergence of persistence, the complete regulatory network is still unknown and it is clearly not attributed to one 'persister gene'. My goal is to define the genetic network causing the persistence phenotype in Mycobacterium tuberculosis. I plan to tackle this problem by exploring the roles of the transcription initiation sigma factors in persistence in the presence of bactericidal drugs. This will be done by a combination of precise null deletions of the twelve nonessential sigma factors together with ChIP-seq and RNA-seq analysis. In addition to the in vitro assays, I will be also testing my hypothesis in vivo, by examining the effect of sigma factor mutant strains as well as mutants of the genes transcribed by each sigma factor. All these mutants will be made in the background of the sigma factor deletion strain (double mutants) and tested in an in vivo mouse model for Mycobacterium tuberculosis cells that are unable to persist.
By combining the in vitro high throughput screens with the in vivo experiments, I expect to define the genetic network causing persistence in Mycobacterium tuberculosis.

Animals as diverse as mammals, birds and insects use odors to find mates, hosts and food sources. This is a difficult task, because natural odors occur in complex turbulent air plumes, and the relevant target odors intermingle with plumes of multiple background odors that stem from a variety of natural and anthropogenic sources (vegetation, exhaust fumes, etc.). It is essential for animals to be able to separate target from background odors. We hypothesize that animals may use temporal information from natural odor fluctuations to achieve odor-background segregation, as odorants from the same source fluctuate together in synchrony, while odorants from different sources do not. Behavioral studies have shown that insects can indeed use fast temporal stimulus cues. However, it is not yet known how the brain accomplishes the difficult task of odor-background segregation.
In this project we will investigate the neural mechanisms of odor-background segregation using the honey bee as model organism. Honey bees visit many different flower species for nectar and pollen. However, over a series of trips an individual forager bee only visits a single flower species on which it has found nectar previously, a phenomenon called floral constancy. To localize the target flowers in a natural environment bees use several cues, including odors. As the bee is challenged by multiple backgrounds in every flower patch, bees must be equipped with efficient mechanisms of odor-background segregation. We will use behavioral experiments to identify naturally evolved strategies of odor-background segregation (Brian H Smith, USA). Physiological recordings will inform us about neuronal processing and the receptor neurons’ and the brain’s different roles (Paul Szyszka, Germany). We will use computational models (Thomas Nowotny, UK) to formulate mechanistic explanations of the process of odor-background segregation and generate predictions to test in experiments. To overcome the limitations of computer simulations, we will finally transfer successful models to the embodied context of odor tracking robots (Ryohei Kanzaki, Japan). Understanding how small and fast fluctuations in relative concentrations of odor mixtures are used by animals to reliably identify odor sources will help us identify common principles of how animals’ brains represent and process their environment.

Plants are sessile organisms that must sense and respond to their environment to grow and survive. To facilitate the integration of diverse environmental stimuli including water, sunlight, and nutrients, plants have evolved a complex signaling system that utilizes small molecules called phytohormones. Among the various phytohormones, Gibberellic Acid (GA) has a number of effects on plant growth and development, such as seed germination, root and shoot elongation, flowering and fruit patterning. GA is widely used in agriculture at specific developmental stages, such as promoting fruit set, increasing the size of seedless grapes and improving the outlook of apples and citrus. Importantly, genetic perturbation of GA signaling played a critical role in so called 'first green revolution', which has given rise to the modern day high-yielding cultivars of maize, wheat, and rice. Although spatiotemporal distribution of GA must be tightly regulated, it is largely unknown how GAs are delivered through plant tissues and where they accumulate during plant growth and development. Our overarching aim is to dissect the mechanisms underlying active GA transport and uncover physiological roles of GA redistribution during plant development. Taking advantage of our unique fluorescently labeled GA surrogates, we have discovered a novel protein that transports GA in vitro and in vivo. To the best of our knowledge, this is the first bona fide GA transporter so far. We hypothesize that this newly discovered GA transporter plays major roles in GA transport during plant growth and development. We will approach our goals by combining unique expertise from each lab, including electrophysiology and mass spectrometry-based in vitro transport assays, X-ray crystallography, and developmental genetics and in vivo transport assays using fluorescently labeled GAs. Our proposed research is innovative because it is the first detailed investigation for an active GA transport mechanism. We expect to determine the spatiotemporal distribution of GA at the cellular level, as well as uncovering the structural and mechanistic insights into the GA transporters, which may be used to rationally intervene GA delivery in plants. We believe that controlling GA delivery through manipulation of GA transporters has the potential to generate a second green revolution to improve agricultural traits.

Morphogenesis sculpts 2D epithelial sheets into 3D structures. While much work has been devoted to understanding the mechanisms underlying morphogenetic processes, little is known about how they arose during the course of evolution and whether the structures that they produce underwent dynamic changes to gain new functions. To address this open question, we envision a new model system that synthesizes the powers of Drosophila genetics, evolutionary, developmental, and data-intensive computational biology. Our work focuses on the cephalic furrow as an epithelial structure that forms transitorily during Drosophila gastrulation and eventually reverts back to an unfolded state. This cephalic furrow arose recently in a derived lineage of the insect order Diptera, appears to perform a critical, yet unknown function during embryogenesis, but does not contribute to an organ. We will utilize cephalic furrow formation as model system to reconstruct the past and explore the future evolutionary possibilities of a complex epithelial structure. Our analysis is based on a triad of species within a well-defined phylogeny: two distantly related diperan species of the derived lineage that form the cephalic furrow (Drosophila melanogaster and Megaselia abdita) and a basal dipteran species that naturally lacks a cephalic furrow (Chironomus riparius). We first employ a comparative genomics approach to identify the previously unknown cephalic furrow effector genes to unveil the evolutionary history of genome rewiring that led to the emergence of the cephalic furrow. We then link the cephalic furrow genetic network to the control of cellular and tissue dynamics using in vivo quantitative imaging and in silico modeling approaches, thereby deciphering the function of the cephalic furrow in the context of morphogenetic movements during dipteran gastrulation. We use our model to predict a minimal genetic circuit that can reconstitute cephalic furrow formation in Chironomus riparius and ultimately, artificially evolve the cephalic furrow in Drosophila melanogaster by reprogramming its cells into distinct differentiation pathways, thereby systematically exploring its past and future evolution.

Ribosomes are the molecular machines that synthesize cellular proteins, and their proper function is essential for life. Ribosome assembly, maturation and translation involves hundreds of reactions, each with the potential for error. Although the ribosome has been studied for decades, the processes that governs the recognition and disposal of malfunctioning ribosomes and the immediate cellular consequences of damaged ribosomes remain poorly understood. The goal of my proposed project is thus to produce defective ribosomes and characterize in molecular detail how these damaged ribosomes are recognized and selectively degraded. First, I will produce green fluorescence protein (GFP)-labeled defective ribosomes to identify components of the degradation machinery using high-throughput microscopy-based cell screening. I will further develop a novel spatial-restricted pulse-chase purification method in living cells, which allows time-resolved isolation of defective ribosomes. Moreover, I will characterize purified damaged ribosomes by state-of-art mass-spectrometry to identify specific post-translational modifications and interaction partners. Using this molecular information, I will then specifically misregulate ribosome degradation to study the immediate and long-term effects on the cellular proteome and the resulting physiological consequences.

Overall, the proposal holds the promise to significantly enhance our understanding of the molecular mechanisms governing ribosome quality control and their role in maintaining proteostasis in eukaryotic cells.

My project aims to identify the neural circuits underlying parental behavior. I will first perform anterograde and trans-synaptic retrograde viral tracing from genetically specified neurons that have been shown to control parental behavior in both sexes. These experiments will reveal which areas these neurons target, from which neurons they receive input, and whether they fall into functionally different subgroups (Aim 1). Crucially, these experiments will also reveal structural sex differences in parenting circuits.

Parental behavior consists of discrete motor sequences, such as pup retrieval, grooming or nursing. I will artificially activate projections to identified downstream areas in behaving mice to uncover (a) which of these areas control parental behavior and (b) whether different target areas control discrete aspects of parental behavior (Aim 2).

While female mice are spontaneously maternal, males exhibit a drastic change in their behavior towards pups after mating: virgin males normally attack and kill pups but they become paternal after mating (post-mating switch). In the final phase of this project, I aim to uncover the neural circuit correlates of the post-mating switch (Aim 3). I will stimulate presynaptic areas while recording evoked postsynaptic responses in single parenting neurons in a brain slice preparation. Due to its sensitivity, this electrophysiological mapping approach is ideally suited to detect functional changes that occur without obvious structural changes.

Together, these results will advance our understanding of how parental behavior is controlled by neural circuits in the brain and how it can be influenced by social experience.

How does the brain encode sensory perceptions? Although we know approximately how sensory input is routed through different brain areas the “language” used by the brain to represent sensory experiences remains elusive. Brain cells are known to translate external sensory stimuli into electrical pulses called “spikes” to process sensory information. The patterns of spikes contain a code, the neural code, that is used for communication. Theoretically, if we can “crack” the neural code then we will be able to read and write sensory information to the brain. This project aims to combine approaches from cellular, systems, behavioural and computational neuroscience in order to demonstrate that the brain uses two distinct neural codes simultaneously to represent the sensation of touch. To do this, we will study different types of inhibitory cells in the brain that we hypothesize are responsible for carrying the two different codes. Using electrical recordings of individual cells, computer models of neural circuits, and optical recordings of electrical activity in the circuits of mice feeling objects with their whiskers, we will study how these two types of cells integrate information encoded in different ways, and examine how they affect activity in the brain. Using what we learn about these two types of inhibitory cells we will then develop and a novel, optical approach to bias the codes in a mouse’s brain as it performs sensory discrimination tasks with its whiskers. By shifting the mouse’s brain from one code to the other we hope to be able to generate illusory percepts in the mice—making them think they are feeling something with their whiskers that they are not actually feeling. If we can do this for both of the codes that we hypothesize are used by the brain, then we will have demonstrated for the first time that the brain uses two codes simultaneously.