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7,874 results match your criteria: "Sanger Institute[Affiliation]"
Trends Parasitol
December 2024
Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK. Electronic address:
Reconciling organism-scale biology at cellular-scale resolution has been a monumental challenge. Recently, Gramberg et al. uncovered the spatial organisation of gene expression in the common liver fluke, Fasciola hepatica.
View Article and Find Full Text PDFPLoS Biol
December 2024
Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom.
To keep ahead of the evolution of resistance to insecticides in mosquitoes, national malaria control programmes must make use of a range of insecticides, both old and new, while monitoring resistance mechanisms. The outdoor-biting malaria vector Anopheles arabiensis is of increasing concern for malaria transmission because it is apparently less susceptible to many indoor control interventions, yet knowledge of its mechanisms of resistance remains limited. Furthermore, comparatively little is known in general about resistance to non-pyrethroid insecticides such as pirimiphos-methyl (PM), which are crucial for effective control in the context of globally high resistance to pyrethroids.
View Article and Find Full Text PDFWellcome Open Res
November 2024
School of Biology, University of St Andrews, St Andrews, Scotland, UK.
We present a genome assembly from an individual male (whiskered bat; Chordata; Mammalia; Chiroptera; Vespertilionidae). The genome sequence has a total length of 2,081.20 megabases.
View Article and Find Full Text PDFGenome Med
December 2024
Human Genomics and Evolution, St Vincent's Institute of Medical Research, Fitzroy, 3065, Australia.
Background: Multiplexed Assays of Variant Effects (MAVEs) can test all possible single variants in a gene of interest. The resulting saturation-style functional data may help resolve variant classification disparities between populations, especially for Variants of Uncertain Significance (VUS).
Methods: We analyzed clinical significance classifications in 213,663 individuals of European-like genetic ancestry versus 206,975 individuals of non-European-like genetic ancestry from All of Us and the Genome Aggregation Database.
Nat Neurosci
December 2024
Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
Single-cell or single-nucleus transcriptomics is a powerful tool for identifying cell types and cell states. However, hypotheses derived from these assays, including gene expression information, require validation, and their functional relevance needs to be established. The choice of validation depends on numerous factors.
View Article and Find Full Text PDFNat Neurosci
December 2024
Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.
Nat Neurosci
December 2024
Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
Over the past decade, single-cell genomics technologies have allowed scalable profiling of cell-type-specific features, which has substantially increased our ability to study cellular diversity and transcriptional programs in heterogeneous tissues. Yet our understanding of mechanisms of gene regulation or the rules that govern interactions between cell types is still limited. The advent of new computational pipelines and technologies, such as single-cell epigenomics and spatially resolved transcriptomics, has created opportunities to explore two new axes of biological variation: cell-intrinsic regulation of cell states and expression programs and interactions between cells.
View Article and Find Full Text PDFClin Microbiol Infect
December 2024
Departments of Medicine and Medical Microbiology/Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
Objectives: The objective of this study is to assess the frequency of the novel sodium bicarbonate (NaHCO)-responsive phenotype, wherein clinical methicillin-resistant Staphylococcus aureus (MRSA) isolates are rendered susceptible to standard-of-care β-lactams in the presence of NaHCO, in a collection of 103 clinical U.S. MRSA skin and soft-tissue infection (SSTI) isolates and 22 clinical European SSTI isolates.
View Article and Find Full Text PDFNat Immunol
December 2024
Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Genome Biol
December 2024
Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
We present MoCHI, a tool to fit interpretable models using deep mutational scanning data. MoCHI infers free energy changes, as well as interaction terms (energetic couplings) for specified biophysical models, including from multimodal phenotypic data. When a user-specified model is unavailable, global nonlinearities (epistasis) can be estimated from the data.
View Article and Find Full Text PDFNat Commun
November 2024
Division of Infection and Immunity, University College London, London, UK.
Blood transcriptional biomarkers of acute viral infections typically reflect type 1 interferon (IFN) signalling, but it is not known whether there are biological differences in their regulation that can be leveraged for distinct translational applications. We use high frequency sampling in the SARS-CoV-2 human challenge model to show induction of IFN-stimulated gene (ISG) expression with different temporal and cellular profiles. MX1 gene expression correlates with a rapid and transient wave of ISG expression across all cell types, which may precede PCR detection of replicative infection.
View Article and Find Full Text PDFCell Syst
December 2024
School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 2B9, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada. Electronic address:
T cells develop from hematopoietic progenitors in the thymus and protect against pathogens and cancer. However, the emergence of human T cell-competent blood progenitors and their subsequent specification to the T lineage have been challenging to capture in real time. Here, we leveraged a pluripotent stem cell differentiation system to understand the transcriptional dynamics and cell fate restriction events that underlie this critical developmental process.
View Article and Find Full Text PDFDev Cell
November 2024
European Molecular Biology Laboratory (EMBL), Developmental Biology Unit, Heidelberg 69117, Germany. Electronic address:
The complexity of regeneration extends beyond local wound responses, eliciting systemic processes across the entire organism. However, the functional relevance and coordination of distant molecular processes remain unclear. In the cnidarian Nematostella vectensis, we show that local regeneration triggers a systemic homeostatic response, leading to coordinated whole-body remodeling.
View Article and Find Full Text PDFNat Commun
November 2024
INESC-ID, 1000-029, Lisboa, Portugal.
Integrating diverse types of biological data is essential for a holistic understanding of cancer biology, yet it remains challenging due to data heterogeneity, complexity, and sparsity. Addressing this, our study introduces an unsupervised deep learning model, MOSA (Multi-Omic Synthetic Augmentation), specifically designed to integrate and augment the Cancer Dependency Map (DepMap). Harnessing orthogonal multi-omic information, this model successfully generates molecular and phenotypic profiles, resulting in an increase of 32.
View Article and Find Full Text PDFMicrobiol Spectr
November 2024
Department of Medicine, Division of Pulmonary/Allergy/Critical Care, University of Alabama at Birmingham, Birmingham, Alabama, USA.
Commun Biol
November 2024
Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
The Neotropical realm, one of the most biodiverse regions on Earth, houses a broad range of zoonoses that pose serious public health threats. Protozoan parasites of the Leishmania (Viannia) braziliensis clade cause zoonotic leishmaniasis in Latin America with clinical symptoms ranging from simple cutaneous to destructive, disfiguring mucosal lesions. We present the first comprehensive genome-wide continental study including 257 cultivated isolates representing most of the geographical distribution of this major human pathogen.
View Article and Find Full Text PDFNat Commun
November 2024
Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain.
Common variable immunodeficiency (CVID) is the most prevalent primary immunodeficiency, marked by hypogammaglobulinemia, poor antibody responses, and increased infection susceptibility. The COVID-19 pandemic provided a unique opportunity to study the effects of prolonged viral infections on the immune responses of CVID patients. Here we use single-cell RNA-seq and spectral flow cytometry of peripheral blood samples before, during, and after SARS-CoV-2 infection showing that COVID-19 CVID patients display a persistent type I interferon signature at convalescence across immune compartments.
View Article and Find Full Text PDFGut
November 2024
CRUK Edinburgh Centre, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
Science
November 2024
Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
Nucleic Acids Res
November 2024
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SA, UK.
The European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) is one of the world's leading sources of public biomolecular data. Based at the Wellcome Genome Campus in Hinxton, UK, EMBL-EBI is one of six sites of the European Molecular Biology Laboratory, Europe's only intergovernmental life sciences organization. This overview summarizes the latest developments in services that EMBL-EBI data resources provide to scientific communities globally (https://www.
View Article and Find Full Text PDFNucleic Acids Res
November 2024
Chan Zuckerberg Initiative, 1180 Main Street, Redwood City, CA 94063, USA.
Hundreds of millions of single cells have been analyzed using high-throughput transcriptomic methods. The cumulative knowledge within these datasets provides an exciting opportunity for unlocking insights into health and disease at the level of single cells. Meta-analyses that span diverse datasets building on recent advances in large language models and other machine-learning approaches pose exciting new directions to model and extract insight from single-cell data.
View Article and Find Full Text PDFbioRxiv
November 2024
Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA 06269.
Two invasive hemipteran adelgids cause widespread damage to North American conifers. (the hemlock woolly adelgid) has decimated and (the Eastern and Carolina hemlocks, respectively). was introduced from East Asia and reproduces parthenogenetically in North America, where it can kill trees rapidly.
View Article and Find Full Text PDFNat Rev Microbiol
November 2024
Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Department of Medicine, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK.
Shigella sonnei is a major cause of diarrhoea globally and is increasing in prevalence relative to other Shigella because of multiple demographic and environmental influences. This single-serotype species has traditionally received less attention in comparison to Shigella flexneri and Shigella dysenteriae, which were more common in low-income countries and more tractable in the laboratory. In recent years, we have learned that Shigella are highly complex and highly susceptible to environmental change, as exemplified by epidemiological trends and increasing relevance of S.
View Article and Find Full Text PDFSci Rep
November 2024
Institut für Zoologie, Universität zu Köln, Zülpicher str. 47b, 50674, Cologne, Germany.
Hox genes are central to metazoan body plan formation, patterning and evolution, playing a critical role in cell fate decisions early in embryonic development in invertebrates and vertebrates. While the archetypical Hox gene cluster consists of members of nine ortholog groups (HOX1-HOX9), arrayed in close linkage in the order in which they have their anterior-posterior patterning effects, nematode Hox gene sets do not fit this model. The Caenorhabditis elegans Hox gene set is not clustered and contains only six Hox genes from four of the ancestral groups.
View Article and Find Full Text PDFEvol J Linn Soc
October 2024
Tree of Life Programme, Wellcome Sanger Institute, Hinxton, United Kingdom.