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Mashup Score: 0Effects of land use change and elevation on endemic shrub frogs in a biodiversity hotspot - 4 hour(s) ago
Agroforestry, often promoted as a sustainable agriculture practice, is rapidly expanding, often at the cost of primary tropical forests. While agroforestry impacts amphibian diversity negatively, its effects on population demography, microhabitat use and body condition are relatively understudied. This information is crucial for determining and promoting amphibian-friendly land use practices. We compared habitats, population densities, microhabitat use, and body condition of two endemic species of shrub frogs (Pseudophilautus amboli and Raorchestes bombayensis) across 1) elevations (low- and high-elevation forests) and 2) land use categories (cashew, rubber, and low-elevation forests) in the northern part of the Western Ghats Biodiversity Hotspot. Using distance sampling, we demonstrated that abundances of the two shrub frog species differed across elevation categories, with Pseudophilautus more common in low-elevation forests and Raorchestes more prevalent in high-elevation forests. B
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Mashup Score: 3
SARS-CoV-2 infection of immunocompromised individuals often leads to prolonged detection of viral RNA and infectious virus in nasal specimens, presumably due to the lack of induction of an appropriate adaptive immune response. Mutations identified in virus sequences obtained from persistently infected patients bear signatures of immune evasion and have some overlap with sequences present in variants of concern. We characterized virus isolates from two COVID-19 patients undergoing immunosuppressive cancer therapy, with all isolates obtained greater than 100 days after the initial COVID-19 diagnoses and compared to an isolate from the start of the infection. Isolates from an individual who never mounted an antibody response specific to SARS-CoV-2 despite the administration of convalescent plasma showed slight reductions in plaque size and some showed temperature-dependent replication attenuation on human nasal epithelial cell culture compared to the virus that initiated infection. An iso
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Mashup Score: 0
Introduction: Inflammatory myopathies (IM) are a group of severe autoimmune diseases, sharing some similarities, whose cause is unknown and treatment is empirical. While C-protein-induced myositis (CIM), the most currently used model of IM, has removed some roadblock to understand and improve the treatment of IM, it has only been partially characterised and its generation limited by reproducibility issues. This study aimed at optimising the generation and the characterisation of CIM. Methods: In silico analysis was run to identify the top-3 specific and immunogenic regions of C-protein. The cognate polypeptides were synthetised and used to immunise C57BL/6N mice. Grip strength, walking ability, serum creatine-kinase levels and muscle pathology (histological and electron microscopic features) were assessed. Immune cell proportions and interferon signature in muscles were also determined. Results: Among the three C-protein polypeptides with the highest immunogenic score, amino acids 965-
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Mashup Score: 2HIV-1 infection is associated with depletion of germinal center B cells and a decrease in IgA+ plasma cells in the GI tract - 5 hour(s) ago
Gastrointestinal (GI) B cells and plasma cells (PCs), critical to mucosal homeostasis, play an important role in the host response to HIV-1 infection. Here, high resolution mapping of human B cells and PCs from colon and ileum during both viremic and suppressed HIV-1 infection identified a significant reduction in germinal center (GC) B cells and Follicular Dendritic Cells (FDCs) during HIV-1 viremia. Further, IgA+ PCs, the major cellular output of intestinal GCs were significantly reduced during viremic HIV-1 infection. PC-associated transcriptional perturbations, including type I interferon signaling persisted in antiretroviral therapy (ART) treated individuals, suggesting ongoing disruption of the intestinal immune milieu during ART. GI humoral immune perturbations associated with changes in intestinal microbiome composition and systemic inflammation. Herein, we highlight a key immune defect in the GI mucosa due to HIV-1 viremia, with major implications. ### Competing Interest State
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Mashup Score: 0Genome sequencing of 'Fuji' apple clonal varieties reveals evolutionary history and genetic mechanism of the spur-type morphology - 5 hour(s) ago
Somatic variations arising during asexual reproduction can lead to the emergence of bud sports exhibiting advantageous traits, forming the basis for bud sport breeding in perennial plants. Here, we report a near-complete, fully phased genome assembly of ‘Fuji’ apple, enabling comprehensive identification of somatic variants across 74 clonally propagated ‘Fuji’ varieties. Phylogenetic analysis of ‘Fuji’ sport varieties indicates that the emergence of spur-type and early maturation traits results from multiple independent formation events. A number of putative functional somatic variants are identified, including one spur-type specific deletion located in the promoter of the TCP transcription factor gene MdTCP11. DNA methylation level of the deletion-associated miniature inverted-repeat transposable element is lower in the spur-type varieties compared to the standard-type varieties, while the expression of MdTCP11 is significantly higher. Overexpression of MdTCP11 in apple decreases the
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Mashup Score: 0Proteomic analysis to classify extracellular vesicles and plasmodesmata in Arabidopsis cell culture supernatants - 5 hour(s) ago
The plant apoplast contains diverse proteins. In this study, we analyzed the extracellular vesicle (EV) proteome using cell culture supernatants. Unexpectedly, many plasmodesmata proteins were identified. The comparison between the cell culture EV proteome and the plasmodesmata proteome revealed that EV and plasmodesmata proteins were indistinguishable. Highly sensitive imaging analyses showed that PDLP3, a representative plasmodesmata marker, was localized to plasmodesmata, but it was also present as small granules in apoplast regions. The small PDLP3 granules were similar in size to the EVs, implying that the PDLPs identified during the proteomic analysis may be small PDLP granules secreted into apoplast regions, rather than proteins derived from the plasmodesmata itself. Next, we attempted to distinguish EV proteins from plasmodesmata proteins. The step-wise density gradient ultracentrifugation and clustering analysis separated EV protein clusters (represented by tetraspanins and me
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Mashup Score: 0
The emergence of ‘Mexican Fire’ disease in Brazilian tomato fields, attributed to potato virus Y (PVY), has raised concerns. Characterized by severe necrosis on median leaves, the definitive etiological agent of this disease remained unverified despite PVY detection in symptomatic plants. Our study aimed to elucidate the causal agent, occurrence, spread, and symptomatology of Mexican Fire. Deep sequencing of tomato leaves with typical necrotic symptoms confirmed the association with PVY, reinforcing its role as the causal agent. Serological tests with a PVY-specific polyclonal antibody consistently correlated symptoms with virus presence in a fresh market tomato field, with higher PVY incidence near older tomato and maize plants. Necrotic leaf distribution analysis revealed a predominant occurrence in median leaves, progressing upwards. Deep sequencing of symptomatic field samples exclusively detected PVY, reaffirming its role in symptom induction. Importantly, PVY inoculation under fi
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Mashup Score: 0Cardioprotection by Poloxamer 188 is Mediated through Increased Endothelial Nitric Oxide Production - 5 hour(s) ago
Ischemia/reperfusion (I/R) injury significantly contributes to the morbidity and mortality associated with cardiac events. Poloxamer 188 (P188), a nonionic triblock copolymer, has been proposed to mitigate I/R injury by stabilizing cell membranes. However, the underlying mechanisms remain incompletely understood, particularly concerning endothelial cell function and nitric oxide (NO) production. We employed human induced pluripotent stem cell (iPSC)-derived cardiomyocytes (CMs) and endothelial cells (ECs) to elucidate the effects of P188 on cellular survival, function, and NO secretion under simulated I/R conditions. iPSC-CMs contractility and iPSC-ECs’ NO production were assessed following exposure to P188. Further, an isolated heart model using Brown Norway rats subjected to I/R injury was utilized to evaluate the ex-vivo cardioprotective effects of P188, examining cardiac function and NO production, with and without the administration of a NO inhibitor. In iPSC-derived models, P188
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Mashup Score: 0
Animal skin patterns take an astounding variety of forms, a result of dynamical processes at the cellular level acting as the organism grows. How cellular dynamics interact with organism growth to form skin patterns remains unclear. Here, we study this interplay by tracking the evolving cellular point pattern of chromatophores, the pigment cells present in squid skin. The arrangement of chromatophores appears locally ordered, but disordered at large spatial scales. In particular, its degree of disorder increases with spatial scales more rapidly than for a purely random system. This atypical behaviour resembles highly irregular critical systems in statistical physics. We combine experiments and theory to reveal how this exotic pattern develops through chromatophore insertion as the organism grows. The mechanism we describe may apply to a broad class of growing tissues. ### Competing Interest Statement The authors have declared no competing interest.
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Mashup Score: 0TRAPT: A multi-stage fused deep learning framework for transcriptional regulators prediction via integrating large-scale epigenomic data - 5 hour(s) ago
It is a challenging task to identify functional transcriptional regulators, which control expression of gene sets via regulatory elements and epigenomic signals, involving context-specific studies such as development and diseases. Integrating large-scale multi-omics epigenomic data enables the elucidation of the complex epigenomic control patterns of regulatory elements and regulators. Here, we propose TRAPT, a multi-modality deep learning framework that predicts functional transcriptional regulators from a queried gene set by integrating large-scale multi-omics epigenomic data, including histone modifications, ATAC-seq and TR-ChIP-seq. We design two-stage self-knowledge distillation model to learn nonlinear embedded representation of upstream and downstream regulatory element activity, and merge multi-modality epigenomic features from TR and the queried gene sets for inferring regulator activity. Experimental results on 1072 TR-related datasets demonstrate that TRAPT outperforms curre
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Effects of land use change and elevation on endemic shrub frogs in a biodiversity hotspot https://t.co/NkZP0szwiz #bioRxiv