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Biology subjects

Cohen, G.

Publications and source records attributed to Cohen, G..

10 recordsLinked to original sources

Retrospective image analysis for long-term demography using Google Earth imagery

O_LIEcosystems are rapidly degrading. Widely used approaches to monitor ecosystems to manage them effectively are both expensive and time consuming. The recent proliferation of publicly available imagery from satellites, Google Earth, and citizen-science platforms holds the promise to revolutionising ecological monitoring and optimising their efficiency. However, the potential of these platforms to detect species and track their population dynamics remains under-explored. C_LIO_LIWe introduce a fast, inexpensive method for retrospective image analysis combining current ground-truth data with historical RGB imagery from Google Earth to extract long-term demographic data. We apply this method to three case studies involving two major Mediterranean invasive plant taxa with contrasting growth forms. Specifically, we: (1) utilise deep learning to automatically detect individuals of prickly pear (Opuntia sp.) across various Mediterranean habitats and image resolutions; (2) reconstruct 10 years of spatially explicit recruitment rates for Opuntia along a climatic gradient; and (3) quantify nearly 20 years of growth dynamics for the clonal invader Carpobrotus sp. in two contrasting environments. C_LIO_LIOur object detection model, trained with Google Earth imagery, achieves 60-80% success in identifying individuals of Opuntia, regardless of habitat type. Model performance increases with target species colour consistency and contrast, as well with the usage of basic data augmentation techniques. Detection is constrained by individual area (<4 m{superscript 2}) but captures 80% of the examined population. C_LIO_LIBeyond detection, our time-series analysis of publicly available imagery enables detailed population monitoring. With 10-year image series available for Spain, Greece, and the UK, and 20 years for Portugal, we successfully estimate annual recruitment and growth rates and their climatic sensitivity, identify productive and unproductive years, estimate individual age, characterise population structure, model size-age relationships, and identify recruitment hotspots for targeted management. C_LIO_LIOur pipeline opens new avenues for cost-effective, large-scale demographic monitoring by retrospectively harnessing open-access imagery. While demonstrated here with invasive plants, we discuss the broad applicability of our approach across taxa and ecosystems. The use of retrospective image analysis for long-term demography with Google Earth imagery has the potential to expedite conservation decisions, support effective restoration, and enable robust ecological forecasting in the Anthropocene. C_LI

ecology↗

Discovery of potent SARS-CoV-2 nsp3 macrodomain inhibitors uncovers lack of translation to cellular antiviral response

A strategy for pandemic preparedness is the development of antivirals against a wide set of viral targets with complementary mechanisms of action. SARS-CoV-2 nsp3-mac1 is a viral macrodomain with ADP-ribosylhydrolase activity, which counteracts host immune response. Targeting the virus immunomodulatory functionality offers a differentiated strategy to inhibit SARS-CoV-2 compared to approved therapeutics, which target viral replication directly. Here we report a fragment-based lead generation campaign guided by computational approaches. We discover tool compounds which inhibit nsp3-mac1 activity at low nanomolar concentrations, and with responsive structure-activity relationships, high selectivity, and drug-like properties. Using our inhibitors, we show that inhibition of nsp3-mac1 increases ADP-ribosylation, but surprisingly does not translate to demonstrable antiviral activity in cell culture and iPSC-derived pneumocyte models. Further, no synergistic activity is observed in combination with interferon gamma, a main protease inhibitor, nor a papain-like protease inhibitor. Our results question the extent to which targeting modulation of innate immunity-driven ADP-ribosylation can influence SARS-CoV-2 replication. Moreover, these findings suggest that nsp3-mac1 might not be a suitable target for antiviral therapeutics development.

microbiology↗

Marginal Zone B cells are Necessary for the Formation of Anti-Donor IgG After Allogeneic Sensitization

The formation of anti-MHC antibody is a significant barrier to improved outcomes in organ transplantation. Patients with pre-formed anti-HLA antibodies have limited options for suitable donors, and the formation of donor-specific anti-HLA antibodies after transplantation is a harbinger of graft rejection. Despite the recognized importance of anti-HLA antibodies, the mechanisms responsible for the differentiation of B cells after exposure to allogeneic antigen are poorly understood. In order to evaluate the differentiation of B cells in response to allogeneic antigen, we used a model of H-2b C57/Bl6 sensitization with H-2d antigen. We found that although the formation of anti-H-2d IgG was robust, few class switched B cells and germinal center B cells were formed. Sensitization induced weak expression of classical memory B cell markers, but we observed populations of CD21+ and IRF4+ B cells, that corresponded to an increase in the frequency of marginal zone phenotype B cells after sensitization. Depletion of marginal zone B cells prior to sensitization resulted in a significant dimunition of anti-H-2d IgG and also fewer germinal center B cells. These results demonstrate a previously unappreciated role for marginal zone B cells as a reservoir of alloreactive B cells that are activated by allogeneic antigen.

immunology↗

Metagenomics of Parkinson's disease implicates the gut microbiome in multiple disease mechanisms

Parkinsons disease (PD) may start in the gut and spread to the brain. To investigate the role of gut microbiome, we enrolled 490 PD and 234 control individuals, conducted deep shotgun sequencing of fecal DNA, followed by metagenome-wide association studies requiring significance by two methods (ANCOM-BC and MaAsLin2) to declare disease association. Thirty-percent of species and pathways tested had altered abundances in PD, depicting a widespread dysbiosis. Network analysis showed PD-associated species form polymicrobial clusters that grow or shrink together, and some compete. Metagenomic profile of PD indicates a disease permissive microbiome, evidenced by overabundance of pathogens and immunogenic components, dysregulated neuroactive signaling, preponderance of molecules that induce alpha-synuclein pathology, and over-production of toxicants; with the reduction in anti-inflammatory and neuroprotective factors limiting the capacity to recover. These data provide a broad foundation with a wealth of concrete testable hypotheses to discern the role of the gut microbiome in PD.

genomics↗

Identification of Potent CD43+ Effector CD8+ T cells Elicited After Transplantation

SUMMARYCD8+ T cells mediate acute rejection of allografts, which threatens the long-term survival of transplanted organs. The factors that govern differentiation of graft-directed effector CD8+ T cells could lead to targeted approaches to limit acute rejection. Using MHC Class I tetramers, we found that allogeneic CD8+ T cells were present at an elevated precursor frequency in naive mice, only modestly increased in number after grafting, and maintained high T cell receptor diversity throughout the immune response. While antigen-specific effector CD8+ T cells poorly express the canonical effector marker KLRG-1, expression of the activated glycoform of CD43 defined potent effectors after transplantation. Activated CD43+ effector T cells maintained high expression of ICOS in the presence of CTLA-4 Ig, and dual CTLA-4 Ig/anti-ICOS treatment prolonged graft survival. These data demonstrate that graft-specific CD8+ T cells have a distinct response profile relative to anti-pathogen CD8+ T cells, and that CD43 and ICOS are critical surface receptors that define potent effector CD8+ T cell populations that form after transplantation.

immunology↗

COVID Moonshot: Open Science Discovery of SARS-CoV-2 Main Protease Inhibitors by Combining Crowdsourcing, High-Throughput Experiments, Computational Simulations, and Machine Learning

We report the results of the COVID Moonshot, a fully open-science, crowd sourced, structure-enabled drug discovery campaign targeting the SARS-CoV-2 main protease. We discovered a non-covalent, non-peptidic inhibitor scaffold with lead-like properties that is differentiated from current main protease inhibitors. Our approach leveraged crowdsourcing, machine learning, exascale molecular simulations, and high-throughput structural biology and chemistry. We generated a detailed map of the structural plasticity of the SARS-CoV-2 main protease, extensive structure-activity relationships for multiple chemotypes, and a wealth of biochemical activity data. All compound designs (>18,000 designs), crystallographic data (>840 ligand-bound X-ray structures), assay data (>10,000 measurements), and synthesized molecules (>2,400 compounds) for this campaign were shared rapidly and openly, creating a rich open and IP-free knowledgebase for future anti-coronavirus drug discovery.

biochemistry↗

An automatic pipeline for the design of irreversible derivatives identifies a potent SARS-CoV-2 Mpro inhibitor.

Designing covalent inhibitors is a task of increasing importance in drug discovery. Efficiently designing irreversible inhibitors, though, remains challenging. Here, we present covalentizer, a computational pipeline for creating irreversible inhibitors based on complex structures of targets with known reversible binders. For each ligand, we create a custom-made focused library of covalent analogs. We use covalent docking, to dock these tailored covalent libraries and to find those that can bind covalently to a nearby cysteine while keeping some of the main interactions of the original molecule. We found ~11,000 cysteines in close proximity to a ligand across 8,386 protein-ligand complexes in the PDB. Of these, the protocol identified 1,553 structures with covalent predictions. In prospective evaluation against a panel of kinases, five out of nine predicted covalent inhibitors showed IC50 between 155 nM - 4.2 M. Application of the protocol to an existing SARS-CoV-1 Mpro reversible inhibitor led to a new acrylamide inhibitor series with low micromolar IC50 against SARS-CoV-2 Mpro. The docking prediction was validated by 11 co-crystal structures. This is a promising lead series for COVID-19 antivirals. Together these examples hint at the vast number of covalent inhibitors accessible through our protocol.

biochemistry↗

Hyaluronan-NK cell Interaction Controls the Primary Vascular Barrier during Early Pregnancy

Successful implantation is associated with a unique spatial pattern of vascular remodeling, characterized by profound peripheral neo-vascularization surrounding a peri-embryo avascular niche. We hypothesized that hyaluronan controls the formation of the unique vascular pattern encompassing the embryo. This hypothesis was evaluated by genetic modification of hyaluronan metabolism specifically targeted to embryonic trophoblast cells. The outcome of altered hyaluronan deposition on uterine vascular remodeling and post-implantation development were analyzed by MRI, detailed histological examinations, and RNA-sequencing of uterine NK cells. Our experiments revealed that eliminating the anti-angiogenic hyaluronan, led to elevated expression of MMP-9, VEGF-A and its receptor VEGFR-2, accompanied by reduced recruitment of uterine NK cells. Further local decrease in VEGFR-3 resulted in impaired formation of vascular sinuous folds, ectopic angiogenesis and dysfunctional uterine NK cells. Conversely, enhanced deposition of hyaluronan caused the expansion of the maternal-embryo barrier, leading to an increased diffusion distance and aborted implantation. These results demonstrate a pivotal role for hyaluronan in successful pregnancy by fine-tuning the peri-embryo avascular niche and maternal vascular morphogenesis.

developmental biology↗

Nanoscale Polarization of the Vaccinia Virus Entry Fusion Complex Drives Efficient Fusion

The spatial distribution of binding and fusion proteins on most viruses and the functional relevance of this organization remains largely unexplored. Employing super-resolution microscopy we define the nanoscale membrane architecture of the prototypic poxvirus, vaccinia. We show that binding and entry fusion complex (EFC) proteins are organized into distinct functional domains with fusion proteins polarized to the tips of virions. Repression of individual EFC components disrupted fusion protein polarization, correlating with a loss of fusion activity. Repression of vaccinia A27, a non-EFC protein implicated in fusion, revealed that disruption of EFC localization impacts virus fusion pore formation. We propose that the polarized distribution of EFCs is essential for poxvirus fusion efficiency.

microbiology↗

Long-term cardiovascular re-programming by short-term perinatal exposure to nicotine‘s main metabolite cotinine

BackgroundCotinine - a nicotine by-product and biomarker of passive perinatal tobacco smoke exposure - is historically considered to lack significant health effects. We challenged this notion and sought \"proof-of-concept\" evidence of the adverse developmental potential of exposure to this substance at real-life levels.\n\nMethodsPregnant C57 mice drank nicotine or cotinine-laced water for 6wks from conception (NPRE = 2% saccharin+100g nicotine/ml; CPRE = 2% saccharin + 10g cotinine/ml) or for 3wks after birth (CPOST = 2% saccharin + 30g cotinine/ml). Controls drank 2% saccharin (CTRL). At 17{+/-}1weeks male pups (CTRL n=6; CPOST n=6; CPRE n=8; NPRE n=9) were instrumented for EEG and blood pressure (BP) telemetry. We evaluated (i) cardiovascular control during sleep (at rest / during stress); (ii) arterial reactivity ex vivo; (iii) expression of genes involved in arterial constriction/dilation.\n\nResultsBlood cotinine levels (ELISA) recapitulated passive smoker mothers-infants. Pups exposed only to cotinine exhibited (i) mild bradycardia - hypotension at rest (p<0.001); (ii) attenuated (CPRE, p<0.0001) or reverse (CPOST; p<0.0001) BP reactivity to asphyxia; (iii) pronounced adrenergic hypo-contractility (p<0.0003), low Protein Kinase C (p<0.001) and elevated adrenergic receptor mRNA (p<0.05) (all drug-treated arteries). NPRE pups also exhibited endothelium-mediated dysfunction.\n\nConclusionsCotinine has subtle, enduring developmental consequences. Some cardiovascular effects of nicotine can plausibly arise via conversion to cotinine. Low-level exposure to this metabolite may pose unrecognized perinatal risks. Adults must avoid inadvertently exposing a fetus or infant to cotinine as well as nicotine.

physiology↗