Biallelic variants in WARS1 cause a highly variable neurodevelopmental syndrome and implicate a critical exon for normal auditory function

Aminoacyl-tRNA synthetases (ARSs) are essential enzymes for faithful assignment of amino acids to their cognate tRNA. Variants in ARS genes are frequently associated with clinically heterogeneous phenotypes in humans and follow both autosomal dominant or recessive inheritance patterns in many instances. Variants in tryptophanyl-tRNA synthetase 1 (WARS1) cause autosomal dominantly inherited distal hereditary motor neuropathy and Charcot-Marie-Tooth disease. Presently, only one family with biallelic WARS1 variants has been described. We present three affected individuals from two families with biallelic variants (p.Met1? and p.(Asp419Asn)) in WARS1, showing varying severities of developmental delay and intellectual disability. Hearing impairment and microcephaly, as well as abnormalities of the brain, skeletal system, movement/gait, and behavior were variable features. Phenotyping of knocked down wars-1 in a C. elegans model showed depletion is associated with defects in germ cell development. A wars1 knockout vertebrate model recapitulates the human clinical phenotypes, confirms variant pathogenicity and uncovers evidence implicating the p.Met1? variant as potentially impacting an exon critical for normal hearing. Together, our findings provide consolidating evidence for biallelic disruption of WARS1 as causal for an autosomal recessive neurodevelopmental syndrome and present a vertebrate model that recapitulates key phenotypes observed in patients. This article is protected by copyright. All rights reserved

Interactive Similarity Analysis for 3D+t Cell Trajectory Data

Recent data acquisition techniques permit an improved analysis of living organisms. These techniques produce 3D+t information of cell developments in unprecedentedly high resolution. Biologists have a strong desire to analyze these cell evolutions in order to find similarities in their migration and division behaviors. The exploration of such patterns helps them in understanding how cells and hence organisms are able to ensure a regular shape development. However, the enormous size of the time-dependent data with several tens of thousands of cells and the need to analyze it in 3D hinder an interactive analysis. Visualizing the data to identify and extract relevant features provides a solution to this problem. For this, new visualization approaches are required that reduce the complexity of the data to detect important features in the visual analysis. In this thesis, novel visual similarity analysis methods are presented to interactively process very large 3D+t data of cell developments. Three main methods are developed that allow different visual analysis strategies. The usefulness of them is demonstrated by applications to cells from zebrafish embryos and Arabidopsis thaliana plants. Both data sets feature a high regularity in the shape formation of the organs and domain experts seek to research similar cell behaviors that are responsible for this development. For example, the identification of 3D division behaviors in plants is still an unresolved issue. The first method is a novel visualization approach that can automatically classify cell division types in plant data sets with high memory and time efficiency. The visualization is based on the generation of newly introduced cell isosurfaces that allow a quantitative and spatial comparison of cell division behaviors among individual plants. The method is applied to cells of the lateral root of Arabidopsis plants and reveals similar division schemes with respect to their temporal order. The second method enables a new visual similarity analysis for arbitrary 3D trajectory data in order to extract similar movement behaviors. The algorithm performs a grouping of thousands of trajectories with an optional level of detail modification. The clustering is based on a newly weighted combination of geometry and migratory features for which the weights are used to emphasize feature combinations. As a result, similar collective cell movements in zebrafish as well as a hitherto unknown correlation between division types and subsequent nuclei migrations in the Arabidopsis plants are detected. The third method is a novel visualization technique called the structure map. It permits a compact and interactive similarity analysis of thousands of binary tree structures. Unique trees are pre-ordered in the map based on spectral similarities and substructures are highlighted according to user-selected tree descriptors. Applied to cell developments from zebrafish depicted as trees, the map achieves compression rates up to 95% according to spectral analysis and facilitates an immediate identification of biologically implausible events and outliers. Additionally, similar quantities of feature appearances are detected in the center of the lateral root of several Arabidopsis plants

Women in Science 2017

Ever since its 1967 start, SURF has been a cornerstone of Smith’s science education. Women in Science 2017 summarizes research done by Smith College’s SURF Program participants during the summer of 2017. 151 students participated in SURF (144 hosted on campus and nearby eld sites), supervised by 58 faculty mentor-advisors drawn from the Clark Science Center and connected to its eighteen science, mathematics, and engineering departments and programs and associated centers and units. At summer’s end, SURF participants summarized their research experiences for this publication.https://scholarworks.smith.edu/clark_womeninscience/1006/thumbnail.jp

Phenomics: An integrative approach to Comparative Developmental Physiology

Phenomics, the high-throughput acquisition of phenotypic data at the scale of the whole organism, has led to considerable advancements in plant biology and medicine, yet applications within animal environmental physiology and evolutionary biology are rare. The main aim of this thesis is to understand what phenomics can contribute to our understanding of Comparative Developmental Physiology (CDP), in terms of how environmental and evolutionary change affects the development of physiological function in aquatic embryos. Additionally, I aim to understand the consequences of changes in high-dimensional phenotyping methods used throughout the thesis within the context of embryonic life history. To achieve this, I characterised evolutionary and temperature induced changes in high-dimensional phenotypic space in embryos of three species of freshwater snail with pre-established sequence heterochronies, evolutionary differences in the relative timings of developmental events. This was achieved through the use of a novel video based approach to phenomics in developing embryos termed ‘Energy Proxy Traits’ (EPTs) that integrate aspects of embryonic physiology and behaviour as a spectrum of energy. I found that evolutionary and intraspecific differences in developmental event timings were associated with high-dimensional phenotypic change, which may themselves act as objects of selection (Chapter 2). Additionally, EPTs revealed interspecific differences in whole-embryo sensitivities to chronic elevated temperature regimes, and considerable differences in responses between different physiological windows of development. EPTs were transferable between species that vary greatly in their developmental itineraries, and physiological windows of development that vary in their observable phenotypes (Chapter 3). Finally, I quantified changes in EPTs alongside life history traits, following serial experimental manipulation of nutrient content of developing embryos, with the aim of understanding how induced changes in EPTs affect other aspects of embryonic development (Chapter 4). Increases in total energy and concomitant reductions in size and rates of growth following removal of nutrient content suggest a trade-off between these variables, and a potential re-allocation of energetic reserves following removal of nutrient content in these embryos. In summary, EPTs enabled the continuous acquisition of physiological time series’, revealing evolutionary and environmentally induced changes in high-dimensional phenotypic space, changes which may have consequences for aspects of embryonic life history

The development of tissue explant and embryonic stem cell derived models to investigate the molecular and cellular mechanisms that coordinate vertebrate haematopoiesis and angiogenesis

Understanding the processes that control the formation of blood (haematopoiesis), and blood vessels (vasculogenesis and angiogenesis) in vivo has huge clinical importance. The complex three-dimensional architecture of blood vessels is dynamic and aberrant regulation of either the growth or function of the vascular system may potentiate the spread of tumours, resulting in failure of physiological processes such as implantation and placental development, leading to a range of angiogenesis associated disorders for example diabetic retinopathy. Both embryonic and adult haematopoiesis are also three-dimensional, dynamic processes in which deregulation may result in blood disorders or leukaemia. The experiments herein describe my contribution to investigations into the molecular mechanisms involved in haematopoiesis and angiogenesis over a period of approximately 15 years, taking advantage of technical advances as they became available and adapting them to specific cell models. For example, microarray technology has facilitated discovery of new pathways and transcripts implicated in normal and pathological angiogenesis; central to this mechanism is the role of vascular endothelial growth factor (VEGF), a mitogen specific to endothelial cells. Chromosome immunoprecipitation (ChIP) technology subsequently revealed pathways of early mesoderm formation and the importance of gastrulation in this process. Transcriptional targets of the T-box transcription factor Brachyury were subsequently determined. Throughout this work, the human female reproductive tract provided a unique resource, as one of the rare sites of physiological angiogenesis with which to investigate endothelial cell biology and haematopoiesis. Embryonic stem cell-derived embryoid bodies subsequently proved to be an excellent model for the study of early blood vessel development in three dimensions (2003-5), and to follow early mesoderm development (2006-2010). Targets of Brachyury revealed the close association between blood vessel development, haematopoiesis and early mesoderm formation via a common haemangioblast precursor for blood and endothelial cell lineages. Data gathered by myself, and colleagues, from gene expression and transcription factor analysis is now being used to create lineage codes or routemaps for differentiation of stem cells to mature cells in-vitro and it is now possible to produce mature megakaryocytes and erythrocytes in vitro. The current challenge is to produce fully functional human platelets and enucleated red blood cells. Combined with the use of autologous induced pluripotent stem cells (iPSCs) this makes patientspecific tailoring of cell-based therapies a real possibility