bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of local convergent shifts in evolutionary rates with phyloConverge characterizes the phenotypic associations and modularity of regulatory elements
Authors: Saputra Elysia , Mao Weiguang , Clark Nathan , Chikina Maria 
Published: May 2022

AbstractPhysiological and morphological adaptations to extreme environments arise from the molecular evolution of protein-coding regions and regulatory elements (REs) that regulate gene expression. Comparative genomics methods can characterize genetic elements that underlie the organism-level adaptations, but convergence analyses of REs are often limited by their evolutionary properties. A RE can be modularly composed of multiple transcription factor binding sites (TFBS) that may each experience different evolutionary pressures. The modular composition and rapid turnover of TFBS also enables a compensatory mechanism among nearby TFBS that allows for weaker sequence conservation/divergence than intuitively expected. Here, we introduce phyloConverge, a comparative genomics method that can perform fast, fine-grained local convergence analysis of genetic elements. phyloConverge calibrates for local shifts in evolutionary rates using a combination of maximum likelihood-based estimation of nucleotide substitution rates and phylogenetic permutation tests. Using the classical convergence case of mammalian adaptation to subterranean environments, we validate that phyloConverge identifies rate-accelerated conserved non-coding elements (CNEs) that are strongly correlated with ocular tissues, with improved specificity compared to competing methods. We use phyloConverge to perform TFBS-scale and nucleotide-scale scoring to dissect each CNE into subregions with uneven convergence signals and demonstrate its utility for understanding the modularity and pleiotropy of REs. Subterranean-accelerated regions are also enriched for molecular pathways and TFBS motifs associated with neuronal phenotypes, suggesting that subterranean eye degeneration may coincide with a remodeling of the nervous system. phyloConverge offers a rapid and accurate approach for understanding the evolution and modularity of regulatory elements underlying phenotypic adaptation.
A transcriptional complex of FtMYB102 and FtbHLH4 coordinately regulates the accumulation of rutin in Fagopyrum tataricum
Authors: Mi Yaolei , Li Yu , Qian Guangtao , Vanhaelewyn Lucas , Meng Xiangxiao , Liu Tingxia , Yang Wei , Shi Yuhua , Ma Pengda , Wahab Atia tul , Chen Shilin , Sun Wei , Zhang Dong 
Published: May 2022

AbstractTartary buckwheat is rich in flavonoids, which not only play an important role in plant-environment interaction, but are also beneficial to human health. Rutin is a therapeutic flavonol which is massively accumulated in Tartary buckwheat. It has been demonstrated that transcription factors control rutin biosynthesis. However, the transcriptional regulatory network of rutin is not fully clear. In this study, through transcriptome and target metabolomics, we validated the role of FtMYB102 and FtbHLH4 TFs at the different developmental stages of Tartary buckwheat. The elevated accumulation of rutin in the sprout appears to be closely associated with the expression of FtMYB102 and FtHLH4. Yeast two-hybrid, transient luciferase activity and co-immunoprecipitation demonstrated that FtMYB102 and FtbHLH4 can interact and form a transcriptional complex. Moreover, yeast one-hybrid showed that both FtMYB102 and FtbHLH4 directly bind to the promoter of chalcone isomerase (CHI), and they can coordinately induce CHI expression as shown by transient luciferase activity assay. Finally, we transferred the FtMYB102 and FtbHLH4 into the hairy roots of Tartary buckwheat and found that they both can promote the accumulation of rutin. Our results indicate that FtMYB102 and FtbHLH4 can form a transcriptional complex by inducing CHI expression to coordinately promote the accumulation of rutin.
Kidney Transplant Recipients and Omicron: Outcomes, effect of vaccines and the efficacy and safety of novel treatments
Authors: Gleeson Sarah , Martin Paul , Thomson Tina , Thind Amarpreet , Prendecki Maria , Spensley Katrina J. , Clarke Candice L. , Roufosse Candice , Pickard Graham , Thomas David , McAdoo Stephen P. , Lightstone Liz , Kelleher Peter , Willicombe Michelle 
Published: May 2022

AbstractWe aimed to describe the outcomes of Omicron infection in kidney transplant recipients (KTR), compare the efficacy of the community therapeutic interventions and report the safety profile of molnupiravir.From 142 KTRs diagnosed with COVID-19 infection after Omicron had become the dominant variant in the UK, 116 (78.9%) cases were diagnosed in the community; 47 receiving sotrovimab, 21 molnupiravir and 48 no treatment. 10 (20.8%) non-treated patients were hospitalised following infection, which was significantly higher than the sotrovimab group (2.1%), p=0.0048, but not the molnupiravir treated group (14.3%), p=0.47. The only admission following sotrovimab occurred in a patient infected with BA.2. One patient from the molnupiravir and no-treatment groups required ICU support, and both subsequently died, with one other death in the no-treatment group. No patient receiving sotrovimab died. 6/116 (5.2%) patients required dialysis following their diagnosis; 2 (9.5%) patients receiving molnupiravir and 4 (8.3%) no-treatment. This requirement was significantly higher in the molnupiravir group compared with the sotrovimab treated patients, in whom no patient required dialysis, p=0.035. Both molnupiravir treated patients requiring dialysis had features of systemic thrombotic microangiopathy.Post-vaccination serostatus was available in 110 patients. Seropositive patients were less likely to require hospital admission compared with seronegative patients, 6 (7.0%) and 6 (25.0%) respectively, p=0.023. Seropositive patients were also less likely to require dialysis therapy, p=0.016.In conclusion, sotrovimab treatment in the community was associated with superior patient and transplant outcomes; it’s clinical efficacy against the BA.2 variant requires a rapid review. The treatment benefit of molnupiravir was not evident, and wider safety reporting in transplant patients is needed.
Carbapenem heteroresistance of KPC-producing Klebsiella pneumoniae results from tolerance, persistence and resistance
Authors: Chiarelli Adriana , Cabanel Nicolas , Rosinski-Chupin Isabelle , Obadia Thomas , Ruimy Raymond , Naas Thierry , Bonnin Rémy A. , Glaser Philippe 
Published: May 2022

ABSTRACTCarbapenemase-producing Klebsiella pneumoniae (CPKp) have disseminated globally and represent a major threat in hospitals with few therapeutic options and high mortality rates. Isolates producing the carbapenemase KPC (KPC-Kp) might be classified as susceptible according to clinical breakpoints by antibiotic susceptibility testing (AST), allowing the use of imipenem or meropenem for treatment of infections. However, some KPC-Kp show heteroresistance (HR) to carbapenems, with colonies growing in the inhibition halo of agar-based AST. HR KPC-Kp have been associated with a higher risk of treatment failure. Here, we characterized the diversity of mechanisms behind HR to imipenem of these isolates. By analyzing a diverse collection of CPKp, we showed that HR is frequent among KPC-Kp. By monitoring single HR colony appearance using the ScanLag setup, we discriminated surviving cells in two subpopulations leading to a Gaussian-like distribution of early-appearing colonies, with a delayed emergence compared to colonies arising in the absence of antibiotics, and a long tail of late-appearing colonies. A subset of colonies showed a reduced growth rate. Characterization of surviving populations by AST and whole-genome sequencing of 333 colonies revealed a majority of parental genotypes and a broad landscape of genetic alterations in 28% of the colonies, including gene loss, DNA amplification and point mutations. This unveils the complexity of imipenem HR among KPC-Kp isolates, which involves tolerant and persistent cells, but also resistant bacteria. These observations contribute to a better understanding of reasons behind carbapenem treatment failure of KPC-Kp isolates.IMPORTANCEThe ability of a bacterium to defeat antibiotics not only depends upon resistance, but also on tolerance and persistence, which allow a bacterial population to temporarily survive high drug doses. Carbapenems are antibiotics of last resort and Klebsiella pneumoniae isolates producing the carbapenemase KPC are a threat to hospitals, although they might remain susceptible to carbapenems. However, seemingly homogeneous populations of KPC-K. pneumoniae isolates frequently show varying degrees of susceptibility to carbapenem, i.e., a phenomenon called heteroresistance. We characterized bacteria surviving a high dose of imipenem, progressively degraded by the released carbapenemase, by monitoring the growth of the resulting colonies using the ScanLag system, their genome sequence and carbapenem susceptibility. We show that the observed phenotypic diversity combines tolerance, persistence and resistance making the treatment with high doses of carbapenems frequently inefficient.
Space-time resolved inference-based whole-brain neurophysiological mechanism imaging: application to resting-state alpha rhythm
Authors: Zhao Yun , Boley Mario , Pelentritou Andria , Karoly Philippa J. , Freestone Dean R. , Liu Yueyang , Muthukumaraswamy Suresh , Woods William , Liley David , Kuhlmann Levin 
Published: May 2022

AbstractNeural mechanisms are complex and difficult to image. This paper presents a new space-time resolved whole-brain imaging framework, called Neurophysiological Mechanism Imaging (NMI), that identifies neurophysiological mechanisms within cerebral cortex at the macroscopic scale. By fitting neural mass models to electromagnetic source imaging data using a novel nonlinear inference method, population averaged membrane potentials and synaptic connection strengths are efficiently and accurately imaged across the whole brain at a resolution afforded by source imaging. The efficiency of the framework enables return of the augmented source imaging results overnight using high performance computing. This suggests it can be used as a practical and novel imaging tool. To demonstrate the framework, it has been applied to resting-state magnetoencephalographic source estimates. The results suggest that endogenous inputs to cingulate, occipital, and inferior frontal cortex are essential modulators of resting-state alpha power. Moreover, endogenous input and inhibitory and excitatory neural populations play varied roles in mediating alpha power in different resting-state sub-networks. The framework can be applied to arbitrary neural mass models and has broad applicability to image neural mechanisms in different brain states.HighlightsThe whole-brain imaging framework can disclose the neurophysiological substrates of complicated brain functions in a spatiotemporal manner.Developed a semi-analytical Kalman filter to estimate neurophysiological variables in the nonlinear neural mass model efficiently and accurately from large-scale electromagnetic time-series.The semi-analytical Kalman filter is 7.5 times faster and 5% more accurate in estimating model parameters than the unscented Kalman filter.Provided several group-level statistical observations based on neurophysiological variables and visualised them in a whole-brain manner to show different perspectives of neurophysiological mechanisms.Applied the framework to study resting-state alpha oscillation and found novel relationships between local neurophysiological variables in specific brain regions and alpha power.
Sensitivity of novel SARS-CoV-2 Omicron subvariants, BA.2.11, BA.2.12.1, BA.4 and BA.5 to therapeutic monoclonal antibodies
Authors: Yamasoba Daichi , Kosugi Yusuke , Kimura Izumi , Fujita Shigeru , Uriu Keiya , Ito Jumpei , Sato Kei ,   The Genotype to Phenotype Japan (G2P-Japan) Consortium
Published: May 2022

AbstractAs of May 2022, Omicron BA.2 variant is the most dominant variant in the world. Thereafter, Omicron subvariants have emerged and some of them began outcompeting BA.2 in multiple countries. For instance, Omicron BA.2.11, BA.2.12.1 and BA.4/5 subvariants are becoming dominant in France, the USA and South Africa, respectively. In this study, we evaluated the sensitivity of these new Omicron subvariants (BA.2.11, BA.2.12.1 and BA.4/5) to eight therapeutic monoclonal antibodies (bamlanivimab, bebtelovimab, casirivimab, cilgavimab, etesevimab, imdevimab, sotrovimab and tixagevimab). Notably, we showed that although cilgavimab is antiviral against BA.2, BA.4/5 exhibits higher resistance to this antibody compared to BA.2. Since mutations are accumulated in the spike proteins of newly emerging SARS-CoV-2 variants, we suggest the importance of rapid evaluation of the efficiency of therapeutic monoclonal antibodies against novel SARS-CoV-2 variants.
Structural snapshots of nitrosoglutathione binding and reactivity underlying S-nitrosylation of photosynthetic GAPDH
Authors: Mattioli Edoardo Jun , Rossi Jacopo , Meloni Maria , De Mia Marcello , Marchand Christophe H. , Tagliani Andrea , Fanti Silvia , Falini Giuseppe , Trost Paolo , Lemaire Stéphane D. , Fermani Simona , Calvaresi Matteo , Zaffagnini Mirko 
Published: May 2022

AbstractS-nitrosylation is a redox post-translational modification widely recognized to play an important role in cellular signaling as it can modulate protein function and conformation. At the physiological level, nitrosoglutathione (GSNO) is considered the major physiological NO-releasing compound due to its ability to transfer the NO moiety to protein thiols. GSNO can also induce protein S-glutathionylation but the structural determinants regulating its redox specificity are not fully elucidated. In this study, we employed photosynthetic glyceraldehyde-3-phosphate dehydrogenase from Chlamydomonas reinhardtii (CrGAPA) to investigate the molecular mechanisms underlying GSNO-dependent thiol oxidation. We first observed that GSNO causes enzyme inhibition by specifically inducing S-nitrosylation. Treatment with reducing agents restores CrGAPA activity completely. While the cofactor NADP+ only partially protects from GSNO-mediated S-nitrosylation, the resultant inactivation is completely blocked by the presence of the substrate 1,3-bisphosphoglycerate, indicating that the S-nitrosylation of the catalytic Cys149 is responsible of CrGAPA inactivation. The crystal structures of CrGAPA in complex with NADP+ and NAD+ reveal a general structural similarity with other photosynthetic GAPDH. Starting from the 3D structure, we carried out molecular dynamics simulations to identify the protein residues involved in GSNO binding. Quantum mechanical/molecular mechanical calculations were performed to investigate the reaction mechanism of GSNO with CrGAPA Cys149 and to disclose the relative contribution of protein residues in modulating the activation barrier of the trans-nitrosylation reaction. Based on our findings, we provide functional and structural insights into the response of CrGAPA to GSNO-dependent regulation, possibly expanding the mechanistic features to other protein cysteines susceptible to be oxidatively modified by GSNO.
Cellular reprogramming with ATOH1, GFI1, and POU4F3 implicate epigenetic changes and cell-cell signaling as obstacles to hair cell regeneration in mature mammals
Authors: Iyer Amrita A. , Hosamani Ishwar , Nguyen John D. , Cai Tiantian , Singh Sunita , Beyer Lisa , Zhang Hongyuan , Jen Hsin-I , Yousaf Rizwan , Birol Onur , Sun Jenny J. , Ray Russell S. , Raphael Yehoash , Segil Neil , Groves Andrew K. 
Published: May 2022

ABSTRACTReprogramming of the cochlea with hair cell-specific transcription factors such as ATOH1 has been proposed as a potential therapeutic strategy for hearing loss. ATOH1 expression in the developing cochlea can efficiently induce hair cell regeneration but the efficiency of hair cell reprogramming declines rapidly as the cochlea matures. We developed Cre-inducible mice to compare hair cell reprogramming with ATOH1 alone or in combination with two other hair cell transcription factors, GFI1 and POU4F3. In newborn mice, all transcription factor combinations tested produced large numbers of cells with the morphology of hair cells and rudimentary mechanotransduction properties. However, one week later, only a combination of ATOH1, GFI1 and POU4F3 could reprogram non-sensory cells of the cochlea to a hair cell fate, and these new cells were less mature than cells generated by reprogramming one week earlier. We used scRNA-seq and combined scRNA-seq and ATAC-seq to suggest at least two impediments to hair cell reprogramming in older animals. First, hair cell gene loci become less epigenetically accessible in non-sensory cells of the cochlea with increasing age. Second, signaling from hair cells to supporting cells, including Notch signaling, can prevent reprogramming of many supporting cells to hair cells, even with three hair cell transcription factors. Our results shed light on the molecular barriers that must be overcome to promote hair cell regeneration in the adult cochlea.
Bioprinting microporous functional living materials from protein-based core-shell microgels
Authors: Ou Yangteng , Cao Shixiang , Zhang Yang , Zhu Hongjia , Guo Chengzhi , Yan Wei , Xin Fengxue , Dong Weiliang , Zhang Yanli , Narita Masashi , Yu Ziyi , Knowles Tuomas 
Published: May 2022

AbstractLiving materials bring together material science and biology to allow the engineering and augmenting of living systems with novel functionalities. Bioprinting promises accurate control over the formation of such complex materials through programmable deposition of cells in soft materials, but current approaches had limited success in fine-tuning cell microenvironments while generating robust macroscopic morphologies. Here, we address this challenge through the use of core-shell microgel ink to decouple cell microenvironments from the structural shell for further processing. Cells are microfluidically immobilized in the viscous core that can promote the formation of both microbial populations and mammalian cellular spheroids, followed by interparticle annealing to give covalently stabilized functional scaffolds with controlled microporosity. The results show that the core-shell strategy mitigates cell leakage while affording a favorable environment for cell culture. Furthermore, we demonstrate that different microbial consortia can be printed into scaffolds for a range of applications. By compartmentalizing microbial consortia in separate microgels, the collective bioprocessing capability of the scaffold is significantly enhanced, shedding light on strategies to augment living materials with bioprocessing capabilities.
Impact of Pericytes on the Stabilisation of Microvascular Networks in Microfluidic Systems in Response to Nanotoxicity
Authors: Dibble Matthew , Di Cio Stefania , Luo Piaopiao , Balkwill Frances , Gautrot Julien E. 
Published: May 2022

AbstractRecapitulating the normal physiology of the microvasculature is pivotal in the development of more complex in vitro models and organ-on-chip design. Pericytes are an important component of the vasculature, promoting vessel stability, inhibiting vascular permeability and maintaining the vascular hierarchical architecture. This report presents a microfluidic model exploring interactions between endothelial cells and pericytes. We identify basal conditions required to form stable and reproducible endothelial networks. We then investigate interactions between endothelial cells and pericytes via direct co-culture. In our system, pericytes inhibited vessel hyperplasia and maintained vessel length in prolonged culture (>10 days). In addition, these vessels displayed barrier function and expression of junction markers associated with vessel maturation, including VE-cadherin, β-catenin and ZO-1. Furthermore, pericytes maintained vessel integrity following stress (nutrient starvation) and inhibited vessel regression, in contrast to the striking dissociation of networks in endothelial monocultures. This response was also observed when endothelial/pericyte co-cultures were exposed to high concentrations of moderately toxic cationic nanoparticles used for gene delivery. This study highlights the importance of pericytes in protecting vascular networks from stress and external agents and their importance to the design of advancedin vitromodels, including for the testing of nanotoxicity, to better recapitulate physiological response and avoid false positives.
Clair3-Trio: high-performance Nanopore long-read variant calling in family trios with Trio-to-Trio deep neural networks
Authors: Su Junhao , Zheng Zhenxian , Ahmed Syed Shakeel , Lam Tak-Wah , Luo Ruibang 
Published: May 2022

AbstractAccurate identification of genetic variants from family child-mother-father trio sequencing data is important in genomics. However, state-of-the-art approaches treat variant calling from trios as three independent tasks, which limits their calling accuracy for Nanopore long-read sequencing data. For better trio variant calling, we introduce Clair3-Trio, the first variant caller tailored for family trio data from Nanopore long-reads. Clair3-Trio employs a Trio-to-Trio deep neural network model, which allows it to input the trio sequencing information and output all of the trio’s predicted variants within a single model to improve variant calling. We also present MCVLoss, a novel loss function tailor-made for variant calling in trios, leveraging the explicit encoding of the Mendelian inheritance. Clair3-Trio showed comprehensive improvement in experiments. It predicted far fewer Mendelian inheritance violation variations than current state-of-the-art methods. We also demonstrated that our Trio-to-Trio model is more accurate than competing architectures. Clair3-Trio is accessible as a free, open-source project at https://github.com/HKU-BAL/Clair3-Trio.
The damage-independent evolution of ageing by selective destruction
Authors: Wordsworth James , O’ Keefe Hannah , Clark Peter , Shanley Daryl 
Published: May 2022

AbstractAgeing is currently believed to reflect the accumulation of molecular damage due to energetic costs of maintenance, as proposed in disposable soma theory (DST). Here we use agent-based modelling to describe an alternative theory by which ageing could undergo positive selection independent of energetic costs. We suggest that the selective advantage of aberrant cells with fast growth might necessitate a mechanism of counterselection we name selective destruction that specifically removes the faster cells from tissues, preventing the morbidity and mortality risks they pose. The resulting survival advantage of slower mutants could switch the direction of selection, allowing them to outcompete both fast mutants and wildtype cells, causing them to spread and induce ageing in the form of a metabolic slowdown.Selective destruction could therefore provide a proximal cause of ageing that is both consistent with the gene expression hallmarks of ageing, and independent of accumulating damage. Furthermore, negligible senescence would acquire a new meaning of increased basal mortality.