bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicted binding interface between coronavirus nsp3 and nsp4
Authors: Hensel Zach 
Published: March 2022

AbstractDouble membrane vesicles (DMVs) in coronavirus-infected cells feature pores that span both membranes. DMV pores were observed to have six-fold symmetry and include the nsp3 protein. Co-expression of SARS-CoV nsp3 and nsp4 induces DMV formation, and elements of nsp3 and nsp4 have been identified that are essential for membrane disruption. I describe a predicted luminal binding interface between nsp3 and nsp4 that is membrane-associated, conserved in SARS-CoV-2 during the COVID-19 pandemic and in diverse coronaviruses, and stable in molecular dynamics simulation. Combined with structure predictions for the full-length nsp4 monomer and cryo-EM data, this suggests a DMV pore model in which nsp4 spans both membranes with nsp3 and nsp4 inserted into the same bilayer. This approach may be able to identify additional protein-protein interactions between coronavirus proteins.
Chromosomal integration of blaCTX-M genes in diverse Escherichia coli isolates recovered from river water in Japan
Authors: Gomi Ryota , Yamamoto Masaki , Tanaka Michio , Matsumura Yasufumi 
Published: March 2022

AbstractOccurrence of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (ESBLEC) in environmental waters is of great concern. However, unlike clinical ESBLEC, their genetic characteristics, in particular the genetic contexts of ESBL genes, are not well understood. In this study, we sequenced and analyzed the genomes of CTX-M-producing E. coli isolates recovered from river water to fully characterize the genetic contexts of blaCTX-M genes. Among the 14 isolates with completed genomes, blaCTX-M genes were detected on the chromosome in nine isolates. All but one chromosomal blaCTX-M genes were associated with ISEcp1 and were carried on different transposition units ranging in size from 2,855 bp to 11,093 bp; the exception, blaCTX-M-2, was associated with ISCR1. The remaining five isolates carried blaCTX-M genes on epidemic IncI1 plasmids of different sequence types (STs) (ST3, ST16, ST113, and ST167) (n = 4) or on an IncB/O/K/Z plasmid (n = 1). This study revealed that environmental E. coli carry blaCTX-M genes in diverse genetic contexts. Apparent high prevalence of chromosomal blaCTX-M potentially indicates that some E. coli can stably maintain blaCTX-M genes in environmental waters, though further studies are needed to confirm this.
Mutation Rate Evolution Drives Immune Escape In Mismatch Repair-Deficient Cancer
Authors: Kayhanian Hamzeh , Barmpoutis Panagiotis , Lakatos Eszter , Cross William , Caravagna Giulio , Zapata Luis , Litchfield Kevin , Steele Christopher , Waddingham William , Patel Dominic , Milite Salvatore , Jin Chen , Baker Ann-Marie , Ross Christopher , Alexander Daniel , Khan Khurum , Hochhauser Daniel , Novelli Marco , Werner Benjamin , Guppy Naomi , Linares Josep ,   Genomics England Research Consortium, Ligtenberg Marjolijn J.L. , Nagtegaal Iris D. , Sottoriva Andrea , Graham Trevor , Pillay Nischalan , Rodriguez-Justo Manuel , Shiu Kai-Keen , Jansen Marnix 
Published: March 2022

SUMMARYMutation rate optimisation drives evolution and immune evasion of bacteria and lentiviral strains, including HIV. Whether evolving cancer lineages similarly adapt mutation rates to increase tumour cell fitness is unknown. Here, by mapping the clonal topography of mismatch repair-deficient (MMRd) colorectal cancer, we show that genomic MMRd mutability co-evolves with neoantigen selection to drive intratumour diversification and immune escape. Mechanistically, we find that microsatellite instability modulates subclonal DNA repair by toggling two hypermutable mononucleotide homopolymer runs in the mismatch repair genes MSH6 and MSH3 (C8 and A8, respectively) through stochastic frameshift switching. Spontaneous mutation and reversion at these evolvability switches modulates subclonal mutation rate, mutation bias, and clonal HLA diversity during MMRd cancer evolution. Combined experimental and simulation studies demonstrate that subclonal immune selection favours incremental MMR mutations. MMRd cancers thus fuel intratumour heterogeneity by adapting subclonal mutation rate and mutation bias to immune selection, revealing a conserved co-evolutionary arms race between neoantigen selection and adaptive genomic mutability. Our work reveals layers of mutational complexity and microsatellite biology in MMRd cancer evolution previously hidden in bulk analyses.
Ultrastructure Expansion Microscopy (U-ExM) in Trypanosoma cruzi: localization of tubulin isoforms and isotypes
Authors: Alonso Victoria Lucia 
Published: March 2022

AbstractUltrastructure Expansion Microscopy (U-ExM) is a recently developed technique that enables the increase of the spatial resolution within a cell or a tissue for microscopic imaging by physically expanding the sample. For the first time, I report a detailed protocol validating the use of U-ExM in Trypanosoma cruzi and quantifying the expansion factors of different subcellular compartments. I was able to determine the localization patterns of different tubulin isoforms, such as α-tubulin and β-tubulin. Also, I immunolocalized acetylated and tyrosinated α-tubulin isotypes in epimastigotes and use mitochondrial cell-permeable dyes to identify this organelle. Finally, U-ExM was also performed in trypomastigotes and amastigotes validating this technique in all life cycle stages of T. cruzi.
Transcriptional circuitry of NKX2-1 and SOX1 defines an unrecognized lineage subtype of small cell lung cancer
Authors: Kong Ranran , Patel Ayushi S. , Sato Takashi , Yoo Seungyeul , Bao Li , Sinha Abhilasha , Jiang Feng , Tian Yang , Fridrikh Maya , Liu Shuhui , Feng Jie , He Xijing , Jiang Jiantao , Ma Yuefeng , Grullon Karina , Yang Dawei , Powell Charles A. , Beasley Mary Beth , Zhu Jun , Snyder Eric L. , Li Shaomin , Watanabe Hideo 
Published: March 2022

AbstractRationaleThe current molecular classification of small cell lung cancer (SCLC) based on expression of four lineage transcription factors still leaves its major subtype SCLC-A as a heterogeneous group, necessitating more precise characterization of lineage subclasses.ObjectivesTo refine the current SCLC classification with epigenomic profiles and to identify features of the re-defined SCLC subtypes.MethodsWe performed unsupervised clustering of epigenomic profiles on 25 SCLC cell lines. Functional significance was evaluated by cell growth, apoptosis and xenograft using CRISPR-Cas9-mediated deletion. The specific cistromic profiles by ChIP-seq and its functional transcriptional partners using co-immunoprecipitation followed by mass spectrometry were determined. Rb1fl/flTrp53fl/fl and Rb1fl/flNkx2-1fl/fl mouse models were engineered to explore the function of Nkx2-1 in tumor initiation and differentiation. H3K27ac profiles were analyzed to reveal 6 human SCLC specimen and 20 mice tumors epigenomic landscapes.Measurements and Main ResultsWe identified an epigenomic subclusters of the major SCLC-A subtype, named SCLC-Aα and SCLC-Aσ. SCLC-Aα was characterized by the presence of a super-enhancer at the NKX2-1 locus, which was observed in human SCLC specimens and a murine SCLC model. We found NKX2-1, a dual lung and neural lineage factor, is uniquely relevant in SCLC-Aα. We further found maintenance of this neural identity in SCLC-Aα is mediated by collaborative transcriptional activity with another neuronal transcriptional factor SOX1.ConclusionsWe comprehensively describe an additional epigenomic heterogeneity of the major SCLC-A subtype, and define SCLC-Aα subtype by the core regulatory circuitry representing NKX2-1 and SOX1 super-enhancers and their functional collaborations to maintain neuronal linage state.
Sensory Tetanization to Induce LTP-Like Plasticity: A Review and Reassessment of the Approach
Authors: Dias James W. , McClaskey Carolyn M. , Rumschlag Jeffrey A. , Harris Kelly C. 
Published: March 2022

AbstractGreat interest has been given to developing non-invasive approaches for studying cortical plasticity in humans. High frequency presentation of auditory and visual stimuli, or sensory tetanization, can induce long-term-potentiation-like (LTP-like) changes in cortical activity. However, contrasting effects across studies suggest that sensory tetanization may be unreliable. We review these contrasting effects, conduct our own study of auditory and visual tetanization, and perform meta-analyses to determine the average effect of sensory tetanization across studies. We measured auditory-evoked amplitude changes in a group of younger (18-29 years of age) and older (55-83 years of age) adults following tetanization to 1 kHz and 4 kHz tone bursts and following a slow-presentation control. We also measured visual-evoked amplitude changes following tetanization to horizontal and vertical sign gradients. Auditory and visual response amplitudes decreased following tetanization, consistent with some studies but contrasting with others finding amplitude increases (i.e., LTP-like changes). Older adults exhibited more modest auditory-evoked amplitude decreases, but visual-evoked amplitude decreases like those of younger adults. Changes in response amplitude were not specific to tetanized stimuli. Importantly, slow presentation of auditory tone-bursts produced response amplitude changes approximating those observed following tetanization in younger adults. Meta-analyses of visual and auditory tetanization studies found that the overall effect of sensory tetanization was not significant across studies or study sites. The results suggest that sensory tetanization may not produce reliable changes in cortical responses and more work is needed to determine the validity of sensory tetanization as a method for inducing human cortical plasticity in vivo.
LanA (Language Atlas): A probabilistic atlas for the language network based on fMRI data from >800 individuals
Authors: Lipkin Benjamin , Tuckute Greta , Affourtit Josef , Small Hannah , Mineroff Zachary , Kean Hope , Jouravlev Olessia , Rakocevic Lara , Pritchett Brianna , Siegelman Matthew , Hoeflin Caitlyn , Pongos Alvincé , Blank Idan A. , Struhl Melissa Kline , Ivanova Anna , Shannon Steven , Sathe Aalok , Hoffmann Malte , Nieto-Castañón Alfonso , Fedorenko Evelina 
Published: March 2022

AbstractTwo analytic traditions characterize fMRI language research. One relies on averaging activations voxel-wise across individuals. This approach has limitations: because of inter-individual variability in the locations of language areas, a location in a common brain space cannot be meaningfully linked to function. An alternative approach relies on identifying language areas in each individual using a functional ‘localizer’. Because of its greater sensitivity, functional resolution, and interpretability, functional localization is gaining popularity, but it is not always feasible, and cannot be applied retroactively to past studies. We provide a solution for bridging these currently disjoint approaches in the form of aprobabilistic functional atlascreated from fMRI data for an extensively validated language localizer in 806 individuals. This atlas enables estimating the probability that any given location in a common brain space belongs to the language network, and thus can help interpret group-level peaks and meta-analyses of such peaks, and lesion locations in patient investigations. More meaningful comparisons of findings across studies should increase robustness and replicability in language research.
SRSF10 is essential for progenitor spermatogonia expansion by regulating alternative splicing
Authors: Liu Wenbo , Lu Xukun , Zhao Zheng-Hui , Li Qian-Nan , Xue Yue , Gao Zheng , Sun Si-Min , Lei Wen-Long , Li Lei , An Geng , Liu Hanyan , Han Zhiming , Ouyang Ying-Chun , Hou Yi , Wang Zhen-Bo , Sun Qing-Yuan , Liu Jianqiao 
Published: March 2022

AbstractAlternative splicing expands the transcriptome and proteome complexity and plays essential roles in tissue development and human diseases. However, how alternative splicing regulates spermatogenesis remains largely unknown. Here, using germ cell-specific knockout mouse model, we demonstrated that the splicing factor Srsf10 is essential for spermatogenesis and male fertility. Depletion of Srsf10 in germ cells had little effect on the formation of SSCs but impeded the expansion of progenitor spermatogonia, leading to the failure of spermatogonia differentiation and meiosis initiation. This was further evidenced by the decreased expression of progenitor cell markers in bulk RNA-seq, and much less progenitor and differentiating spermatogonia in single-cell RNA-seq data. Furthermore, the expression of genes involved in cell cycle was abnormal in all subtypes of spermatogonia identified in single-cell RNA-seq data. Notably, using isolated spermatogonia, we found that Srsf10 depletion disturbed the alternative splicing of hundreds of genes, which were preferentially associated with cell cycle, mitotic cell cycle checkpoint and germ cell development, including Dazl, Kit, Ret, Sycp1, Nasp and Bora. These data suggest that SRSF10 is critical for the expansion of progenitor spermatogonia by regulating alternative splicing, expanding our understanding of the mechanism underlying spermatogenesis.
Taste quality and hunger interactions in a feeding sensorimotor circuit
Authors: Shiu Philip K. , Sterne Gabriella R. , Engert Stefanie , Dickson Barry J. , Scott Kristin 
Published: March 2022

SummaryTaste detection and hunger state dynamically regulate the decision to initiate feeding. To study how context-appropriate feeding decisions are generated, we combined synaptic resolution circuit reconstruction with targeted genetic access to specific neurons to elucidate a gustatory sensorimotor circuit for feeding initiation in adult Drosophila melanogaster. This circuit connects gustatory sensory neurons to proboscis motor neurons through three intermediate layers. Most neurons in this pathway are necessary and sufficient for proboscis extension, a feeding initiation behavior, and respond selectively to sugar taste detection. Pathway activity is amplified by hunger signals that act at select second-order neurons to promote feeding initiation in food-deprived animals. In contrast, the feeding initiation circuit is inhibited by a bitter taste pathway that impinges on premotor neurons, illuminating a local motif that weighs sugar and bitter taste detection to adjust behavioral outcome. Together, these studies reveal central mechanisms for the integration of external taste detection and internal nutritive state to flexibly execute a critical feeding decision.
POSITIVE RATE DEPENDENT ACTION POTENTIAL PROLONGATION BY MODULATING POTASSIUM ION CHANNELS
Authors: Cabo Candido 
Published: March 2022

ABSTRACTPharmacological agents that prolong action potential duration (APD) to a larger extent at slow rates than at the fast excitation rates typical of ventricular tachycardia exhibit reverse rate dependence. Reverse rate dependence has been linked to the lack of efficacy of class III agents at preventing arrhythmias. In this report we show that, in computer models of the ventricular action potential, APD prolongation by accelerating phase 2 repolarization (by increasing IKs) and decelerating phase 3 repolarization (by blocking IKr and IK1) results in a robust positive rate dependence (i.e., larger APD prolongation at fast rates than at slow rates). In contrast, APD prolongation by blocking a specific potassium channel type results in reverse rate dependence or a marginal positive rate dependence. Interventions that result in a strong positive rate dependence tend to decrease the repolarization reserve because they require substantial IK1 block. However, limiting IK1 block to ∼50% results in a strong positive rate dependence with moderate decrease in repolarization reserve. In conclusion, the use of a combination of IKs activators and IKr and IK1 blockers could result in APD prolongation that potentially maximizes anti-arrhythmic effects (by maximizing APD prolongation at fast excitation rates) and minimizes pro-arrhythmic effects (by minimizing APD prolongation at slow excitation rates).
Structural maturation of SYCP1-mediated meiotic chromosome synapsis through conformational remodelling by molecular adapter SYCE3
Authors: Crichton James H. , Dunce James M. , Dunne Orla M. , Salmon Lucy J. , Devenney Paul S. , Lawson Jennifer , Adams Ian R. , Davies Owen R. 
Published: March 2022

AbstractIn meiosis, a supramolecular protein structure, the synaptonemal complex (SC), assembles between homologous chromosomes to facilitate their recombination. Mammalian SC formation is thought to involve hierarchical zipper-like assembly of an SYCP1 protein lattice that recruits stabilising central element (CE) proteins as it extends. Here, we combine biochemical approaches with separation-of-function mutagenesis in mice to uncover that, rather than stabilising the SYCP1 lattice, the CE protein SYCE3 actively remodels this structure during synapsis. We find that SYCP1 tetramers undergo conformational change into 2:1 heterotrimers upon SYCE3-binding, removing their assembly interfaces and disrupting the SYCP1 lattice. SYCE3 then establishes a new lattice by its self-assembly mimicking the role of the disrupted interface in tethering together SYCP1 dimers. SYCE3 also interacts with CE complexes SYCE1-SIX6OS1 and SYCE2-TEX12, providing a mechanism for their recruitment. Thus, SYCE3 remodels the SYCP1 lattice into a CE-binding integrated SYCP1-SYCE3 lattice to achieve long-range synapsis by a mature SC.
Identifying the C. elegans vulval transcriptome
Authors: Zhang Qi , Hrach Heather , Mangone Marco , Reiner David J. 
Published: March 2022

ABSTRACTDevelopment of the C. elegans vulva is a classic model of organogenesis. This system, which starts with six equipotent cells, encompasses diverse types of developmental event, including developmental competence, multiple signaling events to control precise and faithful patterning of three cell fates, execution and proliferation of specific cell lineages, and a series of sophisticated morphogenetic events. Early events have been subjected to extensive mutational and genetic investigations and later events to cell biological analyses. We infer the existence of dramatically changing profiles of gene expression that accompanies the observed changes in development. Yet except from serendipitous discovery of several transcription factors expressed in dynamic patterns in vulval lineages, our knowledge of the transcriptomic landscape during vulval development is minimal. This study describes the composition of a vulva-specific transcriptome. We used tissue specific harvesting of mRNAs via immunoprecipitation of epitope-tagged poly(A) binding protein, PAB-1, heterologously expressed by a promoter known to express GFP in vulval cells throughout their development. The identified transcriptome was small but tightly interconnected. From this data set we identified several genes with identified functions in development of the vulva and validated more with promoter-GFP reporters of expression. For one target, lag-1, promoter-GFP expression was limited but fluorescent tag of the endogenous protein revealed extensive expression. Thus, we have identified a transcriptome of the C. elegans as a launching pad for exploration of functions of these genes in organogenesis.
A sporadic Alzheimer’s blood-brain barrier model for developing ultrasound-mediated delivery of Aducanumab and anti-Tau antibodies
Authors: Wasielewska Joanna M. , Chaves Juliana C. S. , Johnston Rebecca L. , Milton Laura A. , Hernández Damián , Chen Liyu , Song Jae , Lee Wendy , Leinenga Gerhard , Nisbet Rebecca M. , Pébay Alice , Götz Jürgen , White Anthony R. , Oikari Lotta E. 
Published: March 2022

AbstractRationaleThe blood-brain barrier (BBB) is a major impediment to therapeutic intracranial drug delivery for the treatment of neurodegenerative diseases, including Alzheimer’s disease (AD). Focused ultrasound applied together with microbubbles (FUS+MB) is a novel technique to transiently open the BBB and increase drug delivery. Evidence suggests that FUS+MBis safe, however the effects of FUS+MBon human BBB cells, especially in the context of AD, remain sparsely investigated.MethodsHere we generated BBB cells (induced brain endothelial cells (iBECs) and astrocytes (iAstrocytes)) from apolipoprotein E gene allele E4 (APOE4, high AD risk) and allele E3 (APOE3, lower AD risk) carrying patient-derived induced pluripotent stem cells (iPSCs). We then developed a human sporadic AD BBB cell platform to investigate the effects of FUS+MBon BBB cells and screen for the delivery of two potentially therapeutic AD antibodies.ResultsWe utilized this robust and reproducible human BBB model to demonstrate increased delivery of therapeutic AD antibodies across the BBB following FUS+MBtreatment, including an analogue of Aducanumab (AduhelmTM; anti-amyloid-β) and a novel anti-Tau antibody RNF5. Our results also demonstrate the safety of FUS+MBindicated by minimal changes in the cell transcriptome as well as little or no changes in cell viability and inflammatory responses within the first 24 h post FUS+MB. Finally, we report a more physiologically relevant hydrogel-based 2.5D BBB model as a key development for FUS+MB-mediated drug delivery screening, with potentially higher translational utility.ConclusionOur results demonstrate an important translatable patient BBB cell model for identifying FUS+MB-deliverable drugs and screening for cell- and patient-specific effects of FUS+MB, accelerating the use of FUS+MBas a therapeutic modality in AD.One Sentence SummaryFocused ultrasound increases thein vitrodelivery of therapeutic antibodies Aducanumab and anti-Tau in a sporadic Alzheimer’s disease patient-derived blood-brain barrier cell model.
The Receptor Kinase FER Mediates Phase Separation of Glycine-Rich RNA-Binding Protein 7 to Confer Temperature Resilience in Arabidopsis
Authors: Xu Fan , Wang Long , Li Yingbin , Shi Junfeng , Staiger Dorothee , Chen Weijun , Wang Lifeng , Yu Feng 
Published: March 2022

AbstractTemperature fluctuations repress plant growth. Although glycine-rich RNA-binding proteins (GRPs) and cold shock proteins (CSPs) have been implicated in cold adaptation, their physiological roles in the response to temperature fluctuations are largely unknown. The receptor kinase FERONIA (FER), a master regulator of cell growth, phosphorylates GRP7 within its intrinsically disordered region to modulate mRNA alternative splicing in the nucleus. Here we show that natural variations at a GRP7 residue phosphorylated by FER influences GRP7 liquid-liquid phase separation (LLPS), aiding Arabidopsis to grow over a wider temperature range. LLPS of GRP7 in the cytoplasm leads to the formation of stress granules that recruits RNAs, along with the translation machinery component eIF4E1 and mRNA chaperones, CSP1 and CSP3, to inhibit translation. Mutations in FER and the GRP7-LLPS-recruited components attenuate root growth under temperature shift conditions. Our findings illustrate the roles of GRP7 LLPS in improving plant root capacity to withstand temperature fluctuations.