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Residue co-evolution has become the primary principle for estimating inter-residue distances of a protein, which are crucially important for predicting protein structure. Most existing approaches adopt an indirect strategy, i.e., inferring residue co-evolution based on some hand-crafted features, say, a covariance matrix, calculated from multiple sequence alignment (MSA) of target protein. This indirect strategy, however, cannot fully exploit the information carried by MSA. Here, we report an end-to-end deep neural network, CopulaNet, to estimate residue co-evolution directly from MSA. The key elements of CopulaNet include (i) an encoder to model context-specific mutation for each residue; (ii) an aggregator to model residue co-evolution, and thereafter estimate inter-residue distances. Using CASP13 (the 13th Critical Assessment of Protein Structure Prediction) target proteins as representatives, we demonstrate that CopulaNet can predict protein structure with improved accuracy and efficiency. This study represents a step toward improved end-to-end prediction of inter-residue distances and protein tertiary structures.During the COVID-19 pandemic, semi-structured interviews were undertaken with 20 adults awaiting a diagnosis for their chronic breathlessness. Three key themes were identified using thematic analysis (1) de-prioritisation of diagnosis, (2) following UK 'lockdown' guidance for the general population but patients fearful they were more at risk, and (3) the impact of lockdown on coping strategies for managing breathlessness. The existing unpredictable pathway to diagnosis for those with chronic breathlessness has been further interrupted during the COVID-19 pandemic.Molecular profiling of circulating extracellular vesicles (EVs) provides a promising noninvasive means to diagnose, monitor, and predict the course of metastatic breast cancer (MBC). However, the analysis of EV protein markers has been confounded by the presence of soluble protein counterparts in peripheral blood. Here we use a rapid, sensitive, and low-cost thermophoretic aptasensor (TAS) to profile cancer-associated protein profiles of plasma EVs without the interference of soluble proteins. We show that the EV signature (a weighted sum of eight EV protein markers) has a high accuracy (91.1 %) for discrimination of MBC, non-metastatic breast cancer (NMBC), and healthy donors (HD). For MBC patients undergoing therapies, the EV signature can accurately monitor the treatment response across the training, validation, and prospective cohorts, and serve as an independent prognostic factor for progression free survival in MBC patients. Together, this work highlights the potential clinical utility of EVs in management of MBC.Flaviviruses use a ~70 nucleotide stem-loop structure called stem-loop A (SLA) at the 5' end of the RNA genome as a promoter for RNA synthesis. Flaviviral polymerase NS5 specifically recognizes SLA to initiate RNA synthesis and methylate the 5' guanosine cap. We report the crystal structures of dengue (DENV) and Zika virus (ZIKV) SLAs. DENV and ZIKV SLAs differ in the relative orientations of their top stem-loop helices to bottom stems, but both form an intermolecular three-way junction with a neighboring SLA molecule. To understand how NS5 engages SLA, we determined the SLA-binding site on NS5 and modeled the NS5-SLA complex of DENV and ZIKV. Our results show that the gross conformational differences seen in DENV and ZIKV SLAs can be compensated by the differences in the domain arrangements in DENV and ZIKV NS5s. We describe two binding modes of SLA and NS5 and propose an SLA-mediated RNA synthesis mechanism.Soil sustainability is reflected in a long-term balance between soil production and erosion for a given climate and geology. Here we evaluate soil sustainability in the Andean Altiplano where accelerated erosion has been linked to wetter climate from 4.5 ka and the rise of Neolithic agropastoralism in the millennium that followed. We measure in situ cosmogenic 14C directly on cultivated hilltops to quantify late Holocene soil loss, which we compare with background soil production rates determined from cosmogenic 26Al and 10Be. Our Monte Carlo-based inversion method identifies two scenarios to account for our data an increase in erosion rate by 1-2 orders of magnitude between ~2.6 and 1.1 ka, or a discrete event stripping ~1-2 m of soil between ~1.9 and 1.1 ka. Coupled environmental and cultural factors in the Late Holocene signaled the onset of the pervasive human imprint in the Andean Altiplano seen today.Guanine-rich DNA sequences occur throughout the human genome and can transiently form G-quadruplex (G4) structures that may obstruct DNA replication, leading to genomic instability. Here, we apply multi-color single-molecule localization microscopy (SMLM) coupled with robust data-mining algorithms to quantitatively visualize replication fork (RF)-coupled formation and spatial-association of endogenous G4s. Using this data, we investigate the effects of G4s on replisome dynamics and organization. We show that a small fraction of active replication forks spontaneously form G4s at newly unwound DNA immediately behind the MCM helicase and before nascent DNA synthesis. These G4s locally perturb replisome dynamics and organization by reducing DNA synthesis and limiting the binding of the single-strand DNA-binding protein RPA. We find that the resolution of RF-coupled G4s is mediated by an interplay between RPA and the FANCJ helicase. FANCJ deficiency leads to G4 accumulation, DNA damage at G4-associated replication forks, and silencing of the RPA-mediated replication stress response. Our study provides first-hand evidence of the intrinsic, RF-coupled formation of G4 structures, offering unique mechanistic insights into the interference and regulation of stable G4s at replication forks and their effect on RPA-associated fork signaling and genomic instability.The prevalence of asthma and airway hyperreactivity (AHR) is increasing at an alarming rate. Group 2 innate lymphoid cells (ILC2s) are copious producers of type 2 cytokines, which leads to AHR and lung inflammation. Here, we show that mouse ILC2s express CD200 receptor (CD200R) and this expression is inducible. CD200R engagement inhibits activation, proliferation and type 2 cytokine production, indicating an immunoregulatory function for the CD200-CD200R axis on ILC2s. selleck chemicals Furthermore, CD200R engagement inhibits both canonical and non-canonical NF-κB signaling pathways in activated ILC2s. Additionally, we demonstrate both preventative and therapeutic approaches utilizing CD200R engagement on ILC2s, which lead to improved airway resistance, dynamic compliance and eosinophilia. These results show CD200R is expressed on human ILC2s, and its engagement ameliorates AHR in humanized mouse models, emphasizing the translational applications for treatment of ILC2-related diseases such as allergic asthma.