Fibroblast-expressed LRRC15 is a receptor for SARS-CoV-2 spike and controls antiviral and antifibrotic transcriptional programs.

Although ACE2 is the primary receptor for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection, a systematic assessment of host factors that regulate binding to SARS-CoV-2 spike protein has not been described. Here, we use whole-genome CRISPR activation to identify host factors controlling cellular interactions with SARS-CoV-2. Our top hit was a TLR-related cell surface receptor called leucine-rich repeat-containing protein 15 (LRRC15). LRRC15 expression was sufficient to promote SARS-CoV-2 spike binding where they form a cell surface complex. LRRC15 mRNA is expressed in human collagen-producing lung myofibroblasts and LRRC15 protein is induced in severe Coronavirus Disease 2019 (COVID-19) infection where it can be found lining the airways. Mechanistically, LRRC15 does not itself support SARS-CoV-2 infection, but fibroblasts expressing LRRC15 can suppress both pseudotyped and authentic SARS-CoV-2 infection in trans. Moreover, LRRC15 expression in fibroblasts suppresses collagen production and promotes expression of IFIT, OAS, and MX-family antiviral factors. Overall, LRRC15 is a novel SARS-CoV-2 spike-binding receptor that can help control viral load and regulate antiviral and antifibrotic transcriptional programs in the context of COVID-19 infection.

iPSC-derived PSEN2 (N141I) astrocytes and microglia exhibit a primed inflammatory phenotype.

BACKGROUND: Widescale evidence points to the involvement of glia and immune pathways in the progression of Alzheimer's disease (AD). AD-associated iPSC-derived glial cells show a diverse range of AD-related phenotypic states encompassing cytokine/chemokine release, phagocytosis and morphological profiles, but to date studies are limited to cells derived from PSEN1, APOE and APP mutations or sporadic patients. The aim of the current study was to successfully differentiate iPSC-derived microglia and astrocytes from patients harbouring an AD-causative PSEN2 (N141I) mutation and characterise the inflammatory and morphological profile of these cells. METHODS: iPSCs from three healthy control individuals and three familial AD patients harbouring a heterozygous PSEN2 (N141I) mutation were used to derive astrocytes and microglia-like cells and cell identity and morphology were characterised through immunofluorescent microscopy. Cellular characterisation involved the stimulation of these cells by LPS and Aß42 and analysis of cytokine/chemokine release was conducted through ELISAs and multi-cytokine arrays. The phagocytic capacity of these cells was then indexed by the uptake of fluorescently-labelled fibrillar Aß42. RESULTS: AD-derived astrocytes and microglia-like cells exhibited an atrophied and less complex morphological appearance than healthy controls. AD-derived astrocytes showed increased basal expression of GFAP, S100ß and increased secretion and phagocytosis of Aß42 while AD-derived microglia-like cells showed decreased IL-8 secretion compared to healthy controls. Upon immunological challenge AD-derived astrocytes and microglia-like cells showed exaggerated secretion of the pro-inflammatory IL-6, CXCL1, ICAM-1 and IL-8 from astrocytes and IL-18 and MIF from microglia. CONCLUSION: Our study showed, for the first time, the differentiation and characterisation of iPSC-derived astrocytes and microglia-like cells harbouring a PSEN2 (N141I) mutation. PSEN2 (N141I)-mutant astrocytes and microglia-like cells presented with a 'primed' phenotype characterised by reduced morphological complexity, exaggerated pro-inflammatory cytokine secretion and altered Aß42 production and phagocytosis.

Latent Space Representations for Marker-Less Realtime Hand-Eye Calibration.

Marker-less hand-eye calibration permits the acquisition of an accurate transformation between an optical sensor and a robot in unstructured environments. Single monocular cameras, despite their low cost and modest computation requirements, present difficulties for this purpose due to their incomplete correspondence of projected coordinates. In this work, we introduce a hand-eye calibration procedure based on the rotation representations inferred by an augmented autoencoder neural network. Learning-based models that attempt to directly regress the spatial transform of objects such as the links of robotic manipulators perform poorly in the orientation domain, but this can be overcome through the analysis of the latent space vectors constructed in the autoencoding process. This technique is computationally inexpensive and can be run in real time in markedly varied lighting and occlusion conditions. To evaluate the procedure, we use a color-depth camera and perform a registration step between the predicted and the captured point clouds to measure translation and orientation errors and compare the results to a baseline based on traditional checkerboard markers.

Global Water Challenges in Sub-Saharan Africa and how to strengthen science-policy dialogues on transboundary governance and cooperation.

The United Nations Water Conference 2023 highlighted the need for concrete actions to boost integrated water resources management for achieving the Sustainable Development Goals and called for strategies to enhance cooperation among stakeholders. Technical cooperation between countries and institutions in transboundary systems, e.g., on environmental data collection, is an effective way to promote international diplomacy and prevent disputes between riparian states. Still, establishing collaborations to inform bilateral dialogues on the identification of environmental challenges, their causes, and development priorities may be a difficult task in itself. This is particularly true in the African context because of limited resources and lack of data. In this paper, we analyse the case of nine transboundary river basins in Sub-Saharan Africa to identify which water-management challenges are perceived as most important by the different riparian countries from a policy and scientific perspective. Our insights are based on the most up-to-date scientific papers, open access reports and technical literature, river basin authority's strategy papers, projects' summary reports, and national policy documents. We also complement these sources with the pieces of information we gained through collaborations with regional and local experts, and management bodies (such as river basin authorities). We highlight the current water-related conflicts and the gap between the priorities identified by the scientific community and different riparian countries on how to tackle hydro-climatic change and improve food and energy security, human and environmental health. Based on our experience, we discuss some keys to building trust among stakeholders, strengthening cooperation, and identifying shared water-governance measures in transboundary river basins. They are: (i) connect science and policy to provide sound knowledge for the right questions, (ii) value local knowledge and exploit the complementarity of different perspectives, (iii) consider multiple spatial scales and multi-level stakeholders to leave no one behind, (iv) promote a culture which values trade-offs and handles complexity, and (v) co-create data and knowledge to facilitate stakeholder dialogue from problem definition to intervention identification.

Molecular Bridge Engineering for Tuning Quantum Electronic Transport and Anisotropy in Nanoporous Graphene.

Recent advances on surface-assisted synthesis have demonstrated that arrays of nanometer wide graphene nanoribbons can be laterally coupled with atomic precision to give rise to a highly anisotropic nanoporous graphene structure. Electronically, this graphene nanoarchitecture can be conceived as a set of weakly coupled semiconducting 1D nanochannels with electron propagation characterized by substantial interchannel quantum interferences. Here, we report the synthesis of a new nanoporous graphene structure where the interribbon electronic coupling can be controlled by the different degrees of freedom provided by phenylene bridges that couple the conducting channels. This versatility arises from the multiplicity of phenylene cross-coupling configurations, which provides a robust chemical knob, and from the interphenyl twist angle that acts as a fine-tunable knob. The twist angle is significantly altered by the interaction with the substrate, as confirmed by a combined bond-resolved scanning tunneling microscopy (STM) and ab initio analysis, and should accordingly be addressable by other external stimuli. Electron propagation simulations demonstrate the capability of either switching on/off or modulating the interribbon coupling by the corresponding use of the chemical or the conformational knob. Molecular bridges therefore emerge as efficient tools to engineer quantum transport and anisotropy in carbon-based 2D nanoarchitectures.

Scalable workflow for characterization of cell-cell communication in COVID-19 patients.

COVID-19 patients display a wide range of disease severity, ranging from asymptomatic to critical symptoms with high mortality risk. Our ability to understand the interaction of SARS-CoV-2 infected cells within the lung, and of protective or dysfunctional immune responses to the virus, is critical to effectively treat these patients. Currently, our understanding of cell-cell interactions across different disease states, and how such interactions may drive pathogenic outcomes, is incomplete. Here, we developed a generalizable and scalable workflow for identifying cells that are differentially interacting across COVID-19 patients with distinct disease outcomes and use this to examine eight public single-cell RNA-seq datasets (six from peripheral blood mononuclear cells, one from bronchoalveolar lavage and one from nasopharyngeal), with a total of 211 individual samples. By characterizing the cell-cell interaction patterns across epithelial and immune cells in lung tissues for patients with varying disease severity, we illustrate diverse communication patterns across individuals, and discover heterogeneous communication patterns among moderate and severe patients. We further illustrate patterns derived from cell-cell interactions are potential signatures for discriminating between moderate and severe patients. Overall, this workflow can be generalized and scaled to combine multiple scRNA-seq datasets to uncover cell-cell interactions.

A decision support tool to enhance agricultural growth in the Mékrou river basin (West Africa).

We describe in this paper the implementation of E-Water, an open software Decision Support System (DSS), designed to help local managers assess the Water Energy Food Environment (WEFE) nexus. E-Water aims at providing optimal management solutions to enhance food crop production at river basin level. The DSS was applied in the transboundary Mékrou river basin, shared among Benin, Burkina Faso and Niger. The primary sector for local economy in the region is agriculture, contributing significantly to income generation and job creation. Fostering the productivity of regional agricultural requires the intensification of farming practices, promoting additional inputs (mainly nutrient fertilizers and water irrigation) but, also, a more efficient allocation of cropland. In order to cope with the heterogeneity of data, and the analyses and issues required by the WEFE nexus approach, our DSS integrates the following modules: (1) the EPIC biophysical agricultural model; (2) a simplified regression metamodel, linking crop production with external inputs; (3) a linear programming and a multiobjective genetic algorithm optimization routines for finding efficient agricultural strategies; and (4) a user-friendly interface for input/output analysis and visualization. To test the main features of the DSS, we apply it to various real and hypothetical scenarios in the Mékrou river basin. The results obtained show how food unavailability due to insufficient local production could be reduced by, approximately, one third by enhancing the application and optimal distribution of fertilizers and irrigation. That would also affect the total income of the farming sector, eventually doubling it in the best case scenario. Furthermore, the combination of optimal agricultural strategies and modified optimal cropland allocation across the basin would bring additional moderate increases in food self-sufficiency, and more substantial gains in the total agricultural income. The proposed software framework proves to be effective, enabling decision makers to identify efficient and site-specific agronomic management strategies for nutrients and water. Such practices would augment crop productivity, which, in turn, would allow to cope with increasing future food demands, and find a balanced use of natural resources, also taking other economic sectors-like livestock, urban or energy-into account.

Protection by dietary restriction in the YAC128 mouse model of Huntington's disease: Relation to genes regulating histone acetylation and HTT.

Huntington's disease (HD) is a fatal neurodegenerative disease characterized by metabolic, cognitive, and motor deficits. HD is caused by an expanded CAG repeat in the first exon of the HTT gene, resulting in an expanded polyglutamine section. Dietary restriction (DR) increases lifespan and ameliorates age-related pathologies, including in a model of HD, but the mechanisms mediating these protective effects are unknown. We report metabolic and behavioral effects of DR in the full-length YAC128 HD mouse model, and associated transcriptional changes in hypothalamus and striatum. DR corrected many effects of the transgene including increased body weight, decreased blood glucose, and impaired motor function. These changes were associated with reduced striatal human (but not mouse) HTT expression, as well as alteration in gene expression regulating histone acetylation modifications, particularly Hdac2. Other mRNAs related to Huntington's pathology in striatal tissue showed significant modulation by the transgene, dietary restriction or both. These results establish a protective role of DR in a transgenic model that contains the complete human HTT gene and for the first time suggest a role for DR in lowering HTT level, which correlates with severity of symptoms.

Imaging three-dimensional surface objects with submolecular resolution by atomic force microscopy.

Submolecular imaging by atomic force microscopy (AFM) has recently been established as a stunning technique to reveal the chemical structure of unknown molecules, to characterize intramolecular charge distributions and bond ordering, as well as to study chemical transformations and intermolecular interactions. So far, most of these feats were achieved on planar molecular systems because high-resolution imaging of three-dimensional (3D) surface structures with AFM remains challenging. Here we present a method for high-resolution imaging of nonplanar molecules and 3D surface systems using AFM with silicon cantilevers as force sensors. We demonstrate this method by resolving the step-edges of the (101) anatase surface at the atomic scale by simultaneously visualizing the structure of a pentacene molecule together with the atomic positions of the substrate and by resolving the contour and probe-surface force field on a C60 molecule with intramolecular resolution. The method reported here holds substantial promise for the study of 3D surface systems such as nanotubes, clusters, nanoparticles, polymers, and biomolecules using AFM with high resolution.

Role of the hypothalamus in mediating protective effects of dietary restriction during aging.

Dietary restriction (DR) can extend lifespan and reduce disease burden across a wide range of animals and yeast but the mechanisms mediating these remarkably protective effects remain to be elucidated despite extensive efforts. Although it has generally been assumed that protective effects of DR are cell-autonomous, there is considerable evidence that many whole-body responses to nutritional state, including DR, are regulated by nutrient-sensing neurons. In this review, we explore the hypothesis that nutrient sensing neurons in the ventromedial hypothalamus hierarchically regulate the protective responses of dietary restriction. We describe multiple peripheral responses that are hierarchically regulated by the hypothalamus and we present evidence for non-cell autonomous signaling of dietary restriction gathered from a diverse range of models including invertebrates, mammalian cell culture, and rodent studies.

Programmed hepatocytes cell death associated with FLIP downregulation in response to extracellular preS1/2.

Chronic hepatitis B virus (HBV) infection involves liver damage resulting in continuous cell injury and death. During HBV infection, hepatocytes exhibit changes in death receptor expression and in their susceptibility to death. These changes are observed not only in infected cells but also in bystander cells. Because excess viral surface protein (HBsAg) is secreted in large amounts as soluble particles containing preS proteins, the role of soluble preS1/2 in hepatocyte (HepG2) death modulation is an important issue to be explored. An increase of cell death induced by preS1/2 was observed. Also, cell death was associated with the down-regulation of FLIP and activation of caspase 8, caspase 9, and BID. Additionally, hepatocytes exhibited a sensitization to death mediated by the Fas receptor. These results, may contribute to understanding the role of envelope proteins (preS1/2) in the pathogenesis of HBV infection.

[Breast cancer in México: a 10-year trend analysis on incidence and age at diagnosis].

INTRODUCTION: Breast cancer is an important public health problem. Some countries have achieved a downward trend while in others, continues ascending. In México, information on incidence and age at diagnosis is isolated in time, and knowledge on trend analysis is lacking. OBJECTIVE: To examine the 2003-2012 trend of the incidence rate and age at diagnosis of breast cancer in the northeast of México. We also analyze the trend of positivity to nodes, hormone receptors and HER2; and its association with age at diagnosis. MATERIAL AND METHODS: This is an epidemiological study of breast cancer patients in a tertiary care hospital in Monterrey, México (n = 3,488). Only new cases with a histology report were included; if this was not available, the cytology result was considered. Trend analysis was performed using the JoinPoint regression program Version 3.5. RESULTS: The breast cancer incidence rate increased from 26.7 to 49.8 per 100,000 between 2003 and 2011 (p < 0.05). The adjusted rate showed an annual percentage rate of change of +6.2% (95%CI 4.2, 8.2). The mean age was 55.7 ± 13.7 years and remained stable over time. Nodes, hormone receptors and HER2 positivity rate also remained stable over time. Age < 50 years increased twice the risk for positivity to nodes (OR 2.0, 95%CI 1.4, 2.7), ER-PR- (OR 1.8, 95% CI 1.4, 2.4) and ER-PR-HER2- (OR 1.9, 95%CI 1.5, 2.5). CONCLUSIONS: The 10-year analysis showed a significant upward trend. This study represents a first effort in our country, for determining patterns on incidence and age at diagnosis of breast cancer, as well as that of biomarkers.

CRISPR activation screens: navigating technologies and applications.

Clustered regularly interspaced short palindromic repeats (CRISPR) activation (CRISPRa) has become an integral part of the molecular biology toolkit. CRISPRa genetic screens are an exciting high-throughput means of identifying genes the upregulation of which is sufficient to elicit a given phenotype. Activation machinery is continually under development to achieve greater, more robust, and more consistent activation. In this review, we offer a succinct technological overview of available CRISPRa architectures and a comprehensive summary of pooled CRISPRa screens. Furthermore, we discuss contemporary applications of CRISPRa across broad fields of research, with the aim of presenting a view of exciting emerging applications for CRISPRa screening.

Introducing Design Strategies to Preserve N-Heterocycles Throughout the On-Surface Synthesis of Graphene Nanostructures.

Despite the impressive advances in the synthesis of atomically precise graphene nanostructures witnessed during the last decade, advancing in compositional complexity faces major challenges. The concept of introducing the desired functional groups or dopants in the molecular precursor often fails due to their lack of stability during the reaction path. Here, a study on the stability of different pyridine and pyrimidine moieties during the on-surface synthesis of graphene nanoribbons on Au(111) is presented. Combining bond-resolved scanning tunneling microscopy with X-ray photoelectron spectroscopy, the thermal evolution of the nitrogen dopants throughout the whole reaction sequence is tracked. A comparative experimental and ab initio electronic characterization confirms the presence of dopants in the final structures, revealing also that the pyridinic nitrogen leads to a significant band downshift. The results demonstrate that, by using synthetic strategies to lower the reaction temperatures, one can preserve specific N-heterocycles throughout all the reaction steps of the synthesis of graphene nanoribbons and beyond the interibbon coupling reaction that leads to nanoporous graphene.

Deletion of miPEP in adipocytes protects against obesity and insulin resistance by boosting muscle metabolism.

Mitochondria facilitate thousands of biochemical reactions, covering a broad spectrum of anabolic and catabolic processes. Here we demonstrate that the adipocyte mitochondrial proteome is markedly altered across multiple models of insulin resistance and reveal a consistent decrease in the level of the mitochondrial processing peptidase miPEP. OBJECTIVE: To determine the role of miPEP in insulin resistance. METHODS: To experimentally test this observation, we generated adipocyte-specific miPEP knockout mice to interrogate its role in the aetiology of insulin resistance. RESULTS: We observed a strong phenotype characterised by enhanced insulin sensitivity and reduced adiposity, despite normal food intake and physical activity. Strikingly, these phenotypes vanished when mice were housed at thermoneutrality, suggesting that metabolic protection conferred by miPEP deletion hinges upon a thermoregulatory process. Tissue specific analysis of miPEP deficient mice revealed an increment in muscle metabolism, and upregulation of the protein FBP2 that is involved in ATP hydrolysis in the gluconeogenic pathway. CONCLUSION: These findings suggest that miPEP deletion initiates a compensatory increase in skeletal muscle metabolism acting as a protective mechanism against diet-induced obesity and insulin resistance.

Molecular dissection of cobra venom highlights heparinoids as an antidote for spitting cobra envenoming.

Snakebites affect about 1.8 million people annually. The current standard of care involves antibody-based antivenoms, which can be difficult to access and are generally not effective against local tissue injury, the primary cause of morbidity. Here, we used a pooled whole-genome CRISPR knockout screen to define human genes that, when targeted, modify cell responses to spitting cobra venoms. A large portion of modifying genes that conferred resistance to venom cytotoxicity was found to control proteoglycan biosynthesis, including EXT1, B4GALT7, EXT2, EXTL3, XYLT2, NDST1, and SLC35B2, which we validated independently. This finding suggested heparinoids as possible inhibitors. Heparinoids prevented venom cytotoxicity through binding to three-finger cytotoxins, and the US Food and Drug Administration-approved heparinoid tinzaparin was found to reduce tissue damage in mice when given via a medically relevant route and dose. Overall, our systematic molecular dissection of cobra venom cytotoxicity provides insight into how we can better treat cobra snakebite envenoming.

Comparative proteomic analysis of the ATP-sensitive K+ channel complex in different tissue types.

ATP-sensitive K(+) (K(ATP)) channels are expressed ubiquitously, but have diverse roles in various organs and cells. Their diversity can partly be explained by distinct tissue-specific compositions of four copies of the pore-forming inward rectifier potassium channel subunits (Kir6.1 and/or Kir6.2) and four regulatory sulfonylurea receptor subunits (SUR1 and/or SUR2). Channel function and/or subcellular localization also can be modified by the proteins with which they transiently or permanently interact to generate even more diversity. We performed a quantitative proteomic analysis of K(ATP) channel complexes in the heart, endothelium, insulin-secreting min6 cells (pancreatic ß-cell like), and the hypothalamus to identify proteins with which they interact in different tissues. Glycolysis is an overrepresented pathway in identified proteins of the heart, min6 cells, and the endothelium. Proteins with other energy metabolic functions were identified in the hypothalamic samples. These data suggest that the metabolo-electrical coupling conferred by K(ATP) channels is conferred partly by proteins with which they interact. A large number of identified cytoskeletal and trafficking proteins suggests endocytic recycling may help control K(ATP) channel surface density and/or subcellular localization. Overall, our data demonstrate that K(ATP) channels in different tissues may assemble with proteins having common functions, but that tissue-specific complex organization also occurs.

New-Onset Crohn's Disease following Initiation of Secukinumab: A Case Report and Review of the Role of IL-17 in the Pathogenesis of Crohn's Disease.

Patients with autoimmune conditions show a high expression of proinflammatory cytokines including interleukin (IL)-17. While IL-17 inhibitors have demonstrated efficacy in managing autoimmune disorders, rare instances of de novo or exacerbated inflammatory bowel disease (IBD) have been reported. The factors that affect the onset and severity remain unclear. Here, we present a case of a 38-year-old female who developed manifestations of Crohn's disease within 1 month of initiating secukinumab treatment for psoriatic arthritis, in addition to a review of the role of IL-17 in the pathophysiology of Crohn's disease.