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2014 Seminars

Christmas Special CABD Seminar. December 17 @ 12:30 pm
The carotid body: a hypoxia-sensitive germinal niche in the adult peripheral nervous system
Dr. Ricardo Pardal
IBiS

Summary: The carotid body is the main peripheral chemoreceptor organ in mammals, and is crucial to survive in low oxygen conditions. Physiological adaptation to sustained hypoxia depends on the activity of a population of neural crest-derived adult stem cells residing in the organ. These cells are able to contribute to both neurogenesis and angiogenesis in response to the hypoxic stimulus, hence constituting an enticing example of physiological plasticity in an adult population of progenitor cells.
CABD Seminar November 28 @ noon
Growth control in Drosophila: miRNAS and signaling molecules
Dr. Marco Milán
IRB Barcelona
CABD Seminar November 21 @ noon
Leukocyte guidance and gradient sensing in vivo: lessons from zebrafish.
Dr Milka Sarri
MRC research fellow at the Dept of PDN, Univ of Cambridge, UK

Summary: Our group is interested in how individual cells navigate in complex tissue environments. We focus on immune cells (neutrophils) and ask how they search tissues and find their way to sites of infection or tissue damage. We are investigating the molecular cues that guide neutrophils, how they establish functional gradients and how they direct cell migration. We approach this through live imaging of immune cells in zebrafish combined with quantitative and genetic approaches. We are also developing new optogenetic tools to interrogate the spatiotemporal dynamics of neutrophil gradient sensing in vivo.
CABD Seminar November 3 @ 5 pm
Applications of data and text mining to the study of protein-protein interaction networks
Dr. Miguel Andrade
"Computational Biology and Data Mining” group, MDC, Berlin, Germany

Summary: I will introduce a series of methods and web tools that we have developed inspired by projects that deal with the study of protein-protein interaction (PPI) networks. Data and text mining tools use the bibliographic records in MEDLINE to prioritize abstracts from the biomedical literature, genes or chemicals, according to topics defined by users. PESCADOR extracts and displays networks of gene and protein interactions from collections of MEDLINE abstracts. HIPPIE is a database of human PPIs scored according to experimental evidence. Finally I will explain an application of PPI analysis where we discover the function of polyQ regions in proteins in the modulation of PPIs.
CABD Seminar October 27 @ noon
Neural induction in amphioxus
Dr. Hécto Escrivá
Observatoire Océanologique de Banyuls, France
CABD Seminar October 18 @ 11:30 am
Research on aging: toward a translational perspective
Dr. Luigi Ferrucci
National Institutes of Health, Baltimore, Maryland, USA

Summary: Over the last few years research on the biology of aging has made unprecedented progress. Up to 20 years ago, the appearance of a scientific report on the biology of aging in one of the top rank biological journals was a rare event, almost considered a curiosity or a singularity. More recently, research on the biological mechanisms that underlay aging has grown into a critical branch of science. Research in cell and animal models of mechanisms that may affect aging or modulate its progression is now the main focus of entire laboratories and research institutions around the world. Candidate mechanisms include epigenetic modifications, DNA repair, cell senescence, telomere shortening, impaired proteostasis, impaired mitochondrial function and others. Unfortunately, very little of such new wealth of knowledge has been translated to better care for older persons and to the development of interventions that can slow down aging and prevent or delay the decline in health and physical function that is unavoidably associated with the aging process. Indeed, it is still unclear whether candidates aging mechanism and the development of the susceptibility phenotypes typical of aging are in any way related. Promoting aging well will require delaying major diseases and disabilities and their consequences. Medical research has been successful in controlling and preventing specific diseases in persons that were otherwise relatively healthy. However, as the population ages, such disease specific approaches start showing limitations and needs to be supplemented by a more global approach that takes into account measures of susceptibility and resilience that may strongly affect competing risks. As people live longer and develop susceptibility, they are more likely to fall victim to multiple diseases and preventing or treating one diseases is increasingly likely to result in an alternative cause of death or disability with limited gain in healthy or total life expectancy. This view is consistent with recent findings suggesting that unrelated morbidities cluster in the same individuals and that mild chronic inflammation and hyper-metabolism are strong independent predictors of multi-morbidity. Technology is now available that allows assessing candidate biological mechanisms of aging. At the same time, geriatricians, population scientists and gerontologists are developing robust measures of susceptibility and resilience that can be collected in clinical populations. In most cases, these research fields work as separate entities and are unlikely to collide. Progress will require biologists, gerontologists, population scientists and geriatricians to find a common language and start operating as multidisciplinary team.
CABD Seminar October 16 @ 10:30 am
A life course approach to healthy ageing: evidence from the MRC National Survey of Health and Development and other UK cohort studies
Dr. Diana Kuh
MRC Unit for Lifelong Health and Ageing at UCL. UK

Summary: Research on factors that determine healthy ageing is a priority of governments and funding agencies to inform strategies for reducing societal and individual costs of an ageing population. This field lacks an agreed conceptual framework and has spawned many definitions of healthy ageing. This presentation discusses how healthy ageing may be conceptualised and investigated within a life course framework that acknowledges the growing evidence that social, psychological and biological factors from early life onwards affect the chance of healthy ageing. Research findings will be presented from two sources: from the MRC National Survey of Health and Development (NSHD), a nationally representative sample of British men and women followed since their birth in March 1946, so far for 68 years^1 ; and from cross cohort studies which attempt to replicate these findings to strengthen causal inference and policy relevance. Diana has been at the forefront of the development of life course epidemiology.^2,3,4 Her latest co-edited book /A life course approach to healthy ageing^5 /integrates conceptual frameworks and models from life course epidemiology and ageing research, and reviews the evidence linking factors operating from early life to optimal adult functioning at the individual, body system and cellular levels, and to wellbeing.
CABD Seminar October 10 @ 11 am
Dr. Mark C. Field
Dundee University

Summary: The nuclear lamina maintains nuclear structural integrity, mediates interactions with the cytoskeleton and co-ordinates the spatiotemporal organisation of chromatin. Similar events and organisational principles appear to be common across the eukaryotes, suggesting that the last eukaryotic common ancestor would have possessed a lamina and the means to construct and maintain heterochromatin. How this ancestral system has subsequently been diversified into the lamina systems present in diverse modern taxa remains an incompletely answered question. Likely components of the lamina have been identified from a range of taxa, using both in silico and direct experimental approaches. It has become apparent that there are likely at least three distinct lamina systems, which so far appear mutually exclusive: The NUP-1 system of trypanosomatids, the NUA system of higher plants and the lamins of metazoa and amoebozoa. Here we will present evidence for a more extensive metazoan-related lamin distribution across eukaryotes. Secondly we will describe the identification and characterisation NUP-2, a second component of the trypanosome lamina and which likely functions in a cooperative manner with NUP1. Taken together, these observations indicate an extremely complex evolutionary trajectory for the lamins, with multiple examples of secondary loss, together with the apparently independent evolution of a highly complex lamina in trypanosomes. The implications of these observations for the evolution and origins of the nucleus will be discussed.
CABD Seminar September 19 @ noon
Functional Organization of the mouse Neuromuscular Junction and Spinal Muscular Atrophy
Dr. Lucía Tabares
Departamento de Fisiología Medica y Biofísica Facultad de Medicina Universidad de Sevilla

Summary: Synapses are complex structures organized by adhesive and scaffolding molecules that align presynaptic vesicular release sites, namely, active zones (AZs), with postsynaptic neurotransmitter receptors, thereby allowing rapid and reliable intercellular communication. Synapses undergo through a complex and well-coordinated maturation process, during which the molecular elements and the biophysical properties of the secretory machinery are continuously adjusted to the synapse size and to the functional requirements. We studied the synaptic maturation process by investigating how the structural and functional organization of AZs is achieved in a large synapse, the neuromuscular junction (NMJ). We used confocal microscopy of AZs immunostained with fluorescently tagged antibodies to proteins such as Bassoon and Piccolo, two scaffolding proteins of the AZ. We found that from early postnatal ages Bassoon and Piccolo are distributed in a regular punctate pattern in the nerve terminal, suggesting that the spatial organization of the AZs is a highly regulated process. We determined the number of Bassoon spots at different ages and found that the increase in AZs occurs in parallel to the postsynaptic area increase, what results in a relatively constant density of AZs during development. We also studied the functional changes in the mouse NMJ during postnatal maturation. We found a good correlation between the size of the readily releasable pool (RRP) and the number of AZs at different ages. In addition, quantal content rapidly increases between the 3rd & 4rd week of age while the release probability remains almost constant during the maturation process. At mature motor nerve terminals real time exo-/endocytosis was studied by monitoring fluorescence increase resulting for dequenching of pHluorin molecules after exposure to the extracellular pH.
CABD Seminar September 12 @ noon
Modern genetic engineering tools facilitate assessing the role of Wnt signaling at long range
Dr Luís Baena
MRC. NIMR (National Institute for Medical Research) Developmental Biology Department. The Ridgeway, Mill Hill. London. UK

Summary: Misregulation of Wnt signalling frequently leads to developmental abnormalities and diseases and, therefore, intensive efforts have been devoted to investigate the significance and mechanisms of Wnt signaling in multiple cellular contexts. Despite this thorough research during the last decades, there are many aspects of their action mode that remain obscure. The recent progress in genome editing has brought new experimental approaches to analyze gene function at physiological level, as well as classical problems of developmental biology. During the talk, I will describe the latest efforts of the laboratory aimed to improve the current protocols of genomic engineering in Drosophila, and their application to assess the long range of Wnt signaling. Unexpectedly, our results show that the spread at long range of the main Drosophila Wnt member, Wingless, is not essential to obtain properly developed adult flies in specific experimental conditions. Instead, the combination of several biological processes (extended transcription, persistent signaling through a mechanism akin to cellular memory and spreading) ensure the levels of Wnt signalling required for keeping the reproducibility of pattern formation and size of organs.
CABD Seminar June 20 @ noon
Decoding the mechanisms of natural direct cell reprogramming: dynamic histone modiying activities ensures the robustness of natural transdifferentiation
Dr. Sophie Jarriault
IGBMC 1 rue Laurent Fries, BP 10142 67404 Illkirch Cedex, CU Strasbourg France

Summary: Natural interconversions between functionally distinct somatic cell types (aka transdifferentiation or Td) have been reported in species as diverse as jellyfish and mice. Whereas in vitro induced transdifferentiation events are very inefficient and often incomplete, natural Td events occur with remarkable precision and efficiency. For example, our laboratory has recently shown that a rectal cell suddenly looses its differentiated identity and is reprogrammed into a motoneuron with invariant precision, in 100% of the wild type Caenorhabditis elegans animals. We have used this unique model of cellular plasticity at the single cell level to decipher the cellular transitions and requirements, the molecular networks necessary to drive this event and the epigenetic mechnisms that determine its impressive efficiency and invariance.
CABD Seminar June 16 @ 10am
Nuclear architecture and chromatin organization in the early Caenorhabditis elegans embryo
Dr. Christian Lanctôt
Institute of Cellular Biology and Pathology, Charles University in Prague

Summary: The folding of the genome in three dimensions plays an important role in global gene regulation through the differential positioning of genes in the nucleus and their relationships to nuclear landmarks. We are using the C. elegans embryo to search for cell lineage-specific patterns of gene positioning and chromatin organization. The developmental constancy of this model organism allows comparing cells that are equivalent in terms of history, developmental potential and gene expression profile. Using multi-color 3D DNA FISH, we have found that genome topography is highly plastic in the early C. elegans embryo. In the course of this work, we have also observed that the germ line founder cell displays a unique nuclear organization, which is characterized by chromatin compaction and concomitant expansion of the intercellular compartment. Additional features of the nuclear architecture of the germ line founder cell will be described.
CABD Seminar June 13 @ noon
Playing both sides: Stat signaling in stem cell maintenance AND differentiation
Dr. Lilach Gilboa
Department of Biological Regulation Weizmann Institute of Science Rehovot 76100 Israel

Summary: Tissue homeostasis is maintained by balancing stem cell self-renewal and differentiation. Understanding how surrounding cells support these opposing process has immense therapeutic importance. The ovary of the fruit fly Drosophila melanogaster is a leading model for the study of adult stem cell biology. Previous work has established that both BMP and Stat signaling are required within somatic niche cells for germ line stem cell (GSC) self-renewal. Our data now suggests that Stat is also required for GSC differentiation, and is thus fulfilling two opposing roles. In a genetic screen we identified the chromatin and telomere-binding factor Without Children (Woc) as required for maintaining the association of somatic Escort Cells (ECs) with germ cells in adult ovaries. This tight association is essential for GSC differentiation. Woc is also required in larval ovaries for the association of Intermingled Cells (ICs) with Primordial Germ Cells. Reduction in the levels of two other proteins: Stat and its target Zfh-1 produce phenotypes similar to woc in both larval and adult ovaries, suggesting a molecular connection between the three proteins. Indeed, we found that Woc is required for a Stat-mediated up-regulation of zfh-1 transcription. Our results further demonstrate that over-expression of Zfh-1 in ECs can rescue GSC differentiation in woc-deficient ovaries. Thus, Zfh-1 is a major Woc target in ECs. Our results highlight the Woc-Stat-Zfh-1 module as promoting somatic encapsulation of germ cells throughout their development. Each somatic cell type can then provide the germline with the support it requires at that particular stage. Stat is thus a permissive factor, explaining its’ apparently opposite roles in GSC maintenance and differentiation.
CABD Seminar June 6 @ noon
Dr. Miguel Vicente
CNB, Madrid
CABD Seminar June 5 @ noon
Trafficking machinery in Planar Cell Polarity
Dr. José María Carvajal González
Mount Sinai medical Center, NY, USA

Summary: Epithelial cells are dynamic building blocks of our bodies that require 3D information and precise arrangement during development. This fundamental function of epithelia rests upon the specific polarized distribution of plasma membrane proteins within their apical/basolateral (AP/BL) and planar axes, however how these two polarity axes communicate during morphogenesis to coordinate spatial information is largely unexplored. A key step in generating Planar Cell Polarity (PCP) is the formation of restricted junctional domains that contain Frizzled/Dishevelled (Fz/Dsh) or Van Gogh/Prickle (Vang/Pk) complexes within the same cell. Although several models have been proposed for how these complexes acquire and maintain their polarized localization, most involving proximal-­â€distal trafficking in wing cells and protein-­â€protein interactions, the machinery involved in moving the core PCP proteins around the cell remain unknown. We have recently identified Arf1 and AP-­â€1 adaptor complex as major regulators of PCP proteins trafficking in vivo. Arf1 and AP-­â€1 disruption affects the accumulation of Fz/Fmi and Vang/Fmi in proximo-­â€distal complexes, hence producing severe PCP phenotypes. Using novel tools we demonstrate a direct and specific involvement of Arf1 in Frizzled trafficking in vivo. Our data support a model whereby the trafficking machinery plays an important part during PCP establishment, promoting the formation of polarized PCP core complexes.
CABD Seminar May 23 @ noon
PICT: structural analysis of protein complexes in vivo.
Dr. Oriol Gallego
IRB, Barcelona

Summary: Most of the approaches currently used to study protein complexes are based on in vitro assays (e.g. NMR, X-ray, electron microscopy, isothermal titration calorimetry etc). The accurate measurement of parameters that define protein complexes in a physiological context has been largely limited due to technical constrains. I will present PICT (Protein interactions from Imaging of Complexes after Translocation) a method that provides a simple fluorescence microscopy readout for the study of protein complexes in living cells. We take advantage of the inducible dimerization of FK506-binding protein (FKBP) and FKBP-rapamycin binding (FRB) domain to translocate protein assemblies to membrane associated anchoring platforms in yeast. PICT can be used to easily assess molecular details mediating interactions between proteins, it can be automated for high-throughput studies; can be used to quantify dissociation rates or even determine the structure of large protein complexes in vivo. I will illustrate the power of PICT with the analysis of three biological pathways in Saccharomyces cerevisiae: MAPK cascade, exocytosis and endocytosis.
CABD Seminar May 16 @ 10:30am
Nucleosome dynamics and genome evolution
Dr. Francisco Antequera
Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC) Salamanca. Spain

Summary:Nucleosomes are the structural units of chromatin. They facilitate the packaging of the genome inside the nucleus and modulate the accessibility of regulators to the DNA molecule. Nucleosome positioning along the genome depends on the combined contribution of several factors, which include nucleosome remodelers, the binding of regulatory proteins to DNA, and the differential affinity of nucleosomes for different DNA sequences. In the case of Schizosaccharomyces pombe, the nucleosomal profile genome-wide is largely maintained under different physiological conditions and patterns of gene expression. This relatively constant landscape favours the concentration of regulators in constitutive and inducible nucleosome-depleted regions (NDRs). We have also found that this strict positioning of nucleosomes in six species of budding and fission yeasts is associated with a species-specific nucleosomal sequence signature, which contributes critically to nucleosome positioning in the genome. These observations highlight nucleosomes as major actors in genome evolution and suggest that the variety of nucleosomal signatures among species results from the coevolution of nucleosomes and their underlying DNA sequence.
CABD Seminar April 12 @ noon
The structure of RNA polymerase I provides insight into ribosomal RNA synthesis
Dr. Carlos Fernandez-Tornero
Centro de Investigaciones Biológicas, Madrid

Summary:Protein biosynthesis depends on ribosome availability, which crucially relies on ribosomal RNA production. In eukaryotes, this process is carried out in the nucleolus by RNA polymerase I (Pol I), a 14-subunit enzyme whose activity is a major determinant of cell growth. We were able to obtain the crystal structure of yeast Pol I at 3.0 Å resolution. The structure represents the latent state of the enzyme, characterized by three major features. First, it forms dimers that involve the C-terminal tail of the stalk subunit A43. Second, the two enzyme halves pivot along the DNA-binding cleft to produce an open cleft and an unfolded bridge helix. Third, an extended loop mimics the DNA backbone in the cleft and may be involved in regulating Pol I transcription. The Pol I crystal structure also reveals intrinsic modules that only bind transiently in other RNA polymerases. Subunit A12.2 inserts a TFIIS-like zinc ribbon into the active site, providing insight into its role in RNA cleavage and Pol I insensitivity to α-amanitin. The A49-A34.5 heterodimer binds the outer side of subunit A135 through a TFIIF-like dimerization module, suggesting how it may function during transcriptional initiation and elongation.
Fernández-Tornero C, Moreno-Morcillo M, Rashid UJ, Taylor NMI, Ruiz FM, Gruene T, Legrand P, Steuerwald U, Müller CW (2013) Nature 502:644–649.
CABD Seminar March 28 @ noon
Exploring the Dark Matter of the Human Genome
Dr Axel Visel
Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA

Summary:The complete 3.2 billion base-pair sequence of the human genome has been known for more than ten years. The location and structure of nearly all protein-coding genes within the genome is now well understood, but protein-coding sequences account for less than 2% of the human genome. The remaining 98% remains largely unexplored territory, with minimal or no associated information about its function beyond the raw DNA sequence. Initially widely considered to be “junk DNA”, there is now strong evidence that important functions are embedded in this vast amount of non-coding DNA. In particular, it harbors tens of thousands of distant-acting gene regulatory sequences that play important roles in the development and function of the human body. Common variants of these regulatory elements substantially affect the risk for major severe diseases, such as heart disease and neuropsychiatric disorders. However, the underlying molecular mechanisms are difficult to study due to our limited understanding of the in vivo functions associated with non-coding DNA. Our work aims at the development and application of strategies for the identification and functional characterization of distant-acting transcriptional enhancers, a major category of regulatory elements found in the non-coding portion of the genome. Using a combination of sequence-based molecular approaches (ChIP-seq) and large-scale transgenic mouse studies, we create genome-wide maps of enhancers involved in developmental and disease processes and study the activity patterns of these enhancers in detail. I will discuss general strategies for enhancer identification and provide examples for application of these strategies for genome-scale identification of enhancers involved in heart development, brain development, and enhancers affecting craniofacial morphology. I will also discuss how the functional annotation of enhancer sequences in the human genome achieved through these studies is expected to facilitate the interpretation of human genetic data and improve our understanding how variation in non-coding sequences mechanistically contributes to common and rare diseases.
CABD Seminar March 21 @ noon
The evolution of body plans and body parts: Perspectives from studying the evolution of developmental regulation in spiders and flies
Dr. Alistair P. McGregor
Department of Biological and Medical Sciences Oxford Brookes University, UK

Summary: My research focuses on a number of questions central to understanding the evolution of animal form: How does the genetic regulation of development evolve? What are the molecular changes in developmental factors underlying phenotypic variation? What is the relationship between the evolution of variation within species and differences between species? I address these questions by comparing the spider Parasteatoda tepidariorum to other metazoans to help explain long term evolutionary differences, and studying species of the Drosophila melanogaster subgroup to investigate more proximate evolutionary changes. In this talk, I will first discuss how we study the regulation of the gene even-skipped in Parasteatoda to explore the regulation and evolution of segmentation. I will then describe how we have used closely related species of Drosophila to investigate the genetic basis of evolutionary differences in compound eye morphology.
CABD Seminar March 14 @ noon
Embryonic development of the epicardium and implications of epicardial derived cells in cardiac fibrosis and regeneration in the zebrafish
Dr Nadia Mercader Huber
Department of Cardiovascular Development and Repair, Centro Nacional de Investigaciones Cardiovasculares - CNIC

Summary: While in humans cardiac fibrosis is irreversible, other vertebrates have a remarkable capacity to regenerate damaged tissue. We recently established a zebrafish injury model mimicking the consequences of tissue loss upon MI and found that cardiac fibrosis is reversible and occurs as an intermediate step during regeneration. We are studying how this balance between regeneration and repair is being established, where myofibroblasts are coming from and how they regress. One source of myofibroblasts is the epicardium, the outer layer covering the myocardium. The epicardium is an important source of trophic factors and progenitor cells, and a first step towards regeneration includes the reestablishment of the epicardial layer and the reexpression of developmental genes in epicardial derived cells. We are therefore also interested in analyzing its embryonic formation. Using live imaging in zebrafish embryos we study the mechanisms through which proepicardial cells emerge from the pericardial wall and attach to the myocardium. Proepicardium formation is dependent on pericardial fluid flow forces generated by the beating heart; we are now elucidating the underlying signaling pathways, which might also play an important role during disease and injury response.
CABD Seminar February 27 @ 5 pm
Chromatin state dynamics during development
Dr. Ger Jan Veenstra

Summary: Chromatin state is essential for pluripotency, competence and cell lineage commitment. In addition it may have a major impact on evolution, as it specifies how genes are marked for activation or repression by epigenetic mechanisms. Little is known, however, about the developmental origins of chromatin state, its regulation, and its influence on genomic evolution. We have explored this issue by generating genome-wide chromatin state maps in Xenopus laevis and Xenopus tropicalis embryos in order to relate genome sequence, functional genomic elements and developmental dynamics.
CABD Seminar February 21 @ 10 am
Making mesoderm with Brachyury
Dr. Jim Smith
MRC, London, UK
CABD Seminar February 20 @ 5 pm
Long range gene regulation in development and Evolution
Dr Denis Duboule
EPFL, Lausanne, Switzerland
CABD Seminar February 18 @ 5 pm
Drug screens in Xenopus to detect new genetic pathways required for neural crest formation.
Dr Grant N. Wheeler
Senior Lecturer in Cell and Developmental Biology; School of Biological Sciences. University of East Anglia. Norwich.
CABD Seminar January 10 @ noon
Linking metabolic transformation and cell signaling deregulation in cancer
Dr Raul V. Duran
Institut Européen de Chimie et Biologie Unit U916 – INSERM Bordeaux, France

Summary: During last years, a particular attention has been dedicated to examining the crosstalk between metabolism and cell signaling, with especial emphasis in highly proliferating cells. Our investigations focused on how cells sense nutrient availability and how this signal is transduced toward mTOR, a master regulator of cell growth. Our results showed that glutamine, a critical amino acid for the bioenergetics of cancer cells, upregulates mTORC1 pathway through glutaminolyis. Glutaminolysis is the double deamination of glutamine to form α-ketoglutarate. Intracellular α-ketoglutarate stimulates the activity of prolyl hydroxylases (PHDs), necessary for the activation of mTORC1. Therefore, our results established that the glutamine/PHD/mTORC1 pathway constitute a central signaling cascade which regulates cell growth in response to nutrient availability, with important implications in the metabolism of cancer cells.