bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biochemical Characterization of Emerging SARS-CoV-2 Nsp15 Endoribonuclease Variants
Authors: Wilson Isha M. , Frazier Meredith N. , Li Jian-Liang , Randall Thomas A. , Stanley Robin E. 
Published: May 2022

AbstractGlobal sequencing efforts from the ongoing COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, continue to provide insight into the evolution of the viral genome. Coronaviruses encode 16 nonstructural proteins, within the first two-thirds of their genome, that facilitate viral replication and transcription as well as evasion of the host immune response. However, many of these viral proteins remain understudied. Nsp15 is a uridine-specific endoribonuclease conserved across all coronaviruses. The nuclease activity of Nsp15 helps the virus evade triggering an innate immune response. Understanding how Nsp15 has changed over the course of the pandemic, and how mutations affect its RNA processing function, will provide insight into the evolution of an oligomerization-dependent endoribonuclease and inform drug design. In combination with previous structural data, bioinformatics analyses of 1.9+ million SARS-CoV-2 sequences revealed mutations across Nsp15’s three structured domains (N-terminal, Middle, EndoU). Selected Nsp15 variants were characterized biochemically and compared to wild type Nsp15. We found that mutations to important catalytic residues decreased cleavage activity but increased the hexamer/monomer ratio of the recombinant protein. Many of the highly prevalent variants we analyzed led to decreased nuclease activity as well as an increase in the inactive, monomeric form. Overall, our work establishes how Nsp15 variants seen in patient samples affect nuclease activity and oligomerization, providing insight into the effect of these variants in vivo.
The SARS-CoV-2 Spike Protein Activates the Epidermal Growth Factor Receptor-Mediated Signaling
Authors: Palakkott Abdulrasheed , Alneyadi Aysha , Muhammad Khalid , Eid Ali H. , Amiri Khaled , Ayoub Mohammed Akli , Iratni Rabah 
Published: May 2022

AbstractObjectivesThe coronavirus disease-19 (COVID-19) pandemic is caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). At the molecular and cellular levels, the SARS-Cov-2 uses its envelope glycoprotein, the spike S protein, to infect the target cells in the lungs via binding with their transmembrane receptor, the angiotensin-converting enzyme 2 (ACE2). Here, we wanted to invesitgate if other molecular targets and pathways may be used by SARS-Cov-2.MethodsWe investigated the possibility for the spike 1 S protein and its receptor-binding domain (RBD) to target the epidermal growth factor receptor (EGFR) and its downstream signaling pathway in vitro using the lung cancer cell line (A549 cells). Protein expression and phosphorylation was examined upon cell treatment with the recombinant full spike 1 S protein or RBD.ResultsWe demonstrate for the first time the activation of EGFR by the Spike 1 protein associated with the phosphorylation of the canonical ERK1/2 and AKT kinases and an increase of survivin expression controlling the survival pathway.ConclusionsOur study suggests the putative implication of EGFR and its related signaling pathways in SARS-CoV-2 infectivity and Covid-19 pathology. This may open new perspectives in the treatment of Covid-19 patients by targeting EGFR.
Novel tumorigenic FOXM1-PTAFR-PTAF axis revealed by multi-omic profiling in TP53/CDKN2A-double knockout human gastroesophageal junction organoid model
Authors: Zhao Hua , Cheng Yulan , Kalra Andrew , Ma Ke , Zheng Yueyuan , Ziman Benjamin , Tressler Caitlin , Glunde Kristine , Shin Eun Ji , Ngamruengphong Saowanee , Khashab Mouen , Singh Vikesh , Anders Robert A. , Jit Simran , Wyhs Nicolas , Chen Wei , Li Xu , Lin De-Chen , Meltzer Stephen J. 
Published: May 2022

AbstractInactivation of the tumor suppressor genes TP53 and CDKN2A occurs early during gastroesophageal junction (GEJ) tumorigenesis. However, due to a paucity of GEJ-specific disease models, cancer-promoting consequences of TP53 and CDKN2A inactivation at the GEJ have been incompletely characterized. Here we report the development of the first wild-type primary human GEJ organoid model, as well as a CRISPR-edited transformed GEJ organoid model. CRISPR/Cas9 engineering to inactivate TP53 and CDKN2A (TP53/CDKN2AKO) in GEJ organoids induced morphologic dysplasia as well as pro-neoplastic features in vitro and tumor formation in vivo. Notably, lipidomic profiling identified several Platelet-Activating Factors (PTAFs) among the most upregulated lipids in CRISPR-edited organoids; and importantly, PTAF/PTAFR abrogation by siRNA knockdown or a pharmacologic inhibitor (WEB2086) significantly blocked proliferation and other pro-neoplastic features of TP53/CDKN2AKO GEJ organoids in vitro and tumor formation in vivo. In addition, murine xenografts derived from Eso26, an established esophageal adenocarcinoma (EAC) cell line, were suppressed by WEB2086. Mechanistically, TP53/CDKN2A dual inactivation disrupted both the transcriptome and the DNA methylome, likely mediated by key transcription factors, particularly Forkhead Box M1 (FOXM1). Importantly, FOXM1 activated PTAFR transcription by binding to the PTAFR promoter, further amplifying the PTAF-PTAFR pathway. In summary, we established a robust model system for investigating early GEJ neoplastic events, identified crucial metabolic and epigenomic changes occurring during GEJ model tumorigenesis, and discovered a potential cancer-therapeutic strategy, while providing insights into pro-neoplastic mechanisms associated with TP53/CDKN2A inactivation in early GEJ neoplasia.One Sentence SummaryNovel tumorigenic FOXM1-PTAFR-PTAF axis revealed by multi-omic profiling in TP53/CDKN2A-double knockout human gastroesophageal junction organoid model.Graphic Abstract
Identification of transcriptional network disruptions in drug-resistant prostate cancer with TraRe
Authors: Blatti Charles , de la Fuente Jesús , Gao Huanyao , Marín Irene , Chen Zikun , Zhao Sihai. D. , Tan Winston , Weinshilbaum Richard , Kalari Krishna R. , Wang Liewei , Hernaez Mikel 
Published: May 2022

AbstractMetastatic castration-resistant prostate cancer (mCRPC) presents very low survival rates due to lack of response or acquired resistance to the available therapies. To date no molecular mechanisms of resistance have been identified, pointing out their complex dynamics. To identify key genes and processes associated with phenotypically-driven regulatory differences, we developed TraRe, a computational method that provides a three-tier analysis: i) at the network level, inferring differentially regulated modules; ii) at the regulon level, identifying regulatory relationships linked to phenotypic differences; and iii) at the single gene level, identifying TFs consistently linked to rewired modules. We applied TraRe (available in Bioconductor with full documentation) to transcriptomic data from 46 mCRPC patients with Abiraterone-response clinical data and uncovered abrogated immune response regulatory modules that showed strong differential regulation in Abi-resistant patients. These modules were replicated in an independent mCRPC study. Further, we experimentally validated key rewiring predictions and their associated transcription factors. Among them, ELK3, MXD1, and MYB were found to have a differential role in cell survival for Abi-response-specific settings. Moreover, we identified the role of ELK3 in cell migration capacity, which could have direct impact on mCRPC. Collectively, these findings shed light on the underlying regulatory mechanisms driving abiraterone response.
Back from the dead: the atypical kinase activity of a pseudokinase regulator of cation fluxes during inducible immunity
Authors: Brauer Elizabeth K. , Ahsan Nagib , Popescu George V. , Thelen Jay J. , Popescu Sorina C. 
Published: May 2022

AbstractWhile most pseudokinases lack phosphotransfer activity due to altered catalytic residues within their kinase domain, a subset of pseudokinases maintain kinase activity through atypical mechanisms. The Arabidopsis ILK1 is a pseudokinase from the Raf-like MAP3K family and is the only known plant pseudokinase with confirmed kinase activity. ILK1 activity promotes microbial pattern-induced root growth inhibition through its stabilization of the HAK5 potassium transporter with the calmodulin-like protein CML9. ILK1 also has a kinase-independent function in salt stress suggesting that it interacts with additional proteins. We determined that members of the ILK subfamily are the sole pseudokinases within the Raf-like MAP3K family and identified 179 novel putative ILK1 protein interactors. We also identified 70 novel peptide targets for ILK1, the majority of which were phosphorylated in the presence of Mn2+instead of Mg2+in line with modifications in ILK1’s DFG cofactor binding domain. Overall, the ILK1-targeted or interacting proteins included diverse protein types including transporters (HAK5, STP1), protein kinases (MEKK1, MEKK3), and a cytokinin receptor (AHK2). The expression of 31 genes encoding putative ILK1-interacting or phosphorylated proteins, including AHK2, were altered in the root and shoot in response to molecular patterns suggesting a role for these genes in immunity. We describe a potential role for ILK1 interactors in the context of cation-dependent immune signaling responses, highlighting the importance of K+in MAMP responses. This work further supports the notion that ILK1 is an atypical kinase with an unusual cofactor dependence that may interact with multiple proteins in the cell.
Structure and specialization of mycorrhizal networks in phylogenetically diverse tropical communities
Authors: Perez-Lamarque Benoît , Petrolli Rémi , Strullu-Derrien Christine , Strasberg Dominique , Morlon Hélène , Selosse Marc-André , Martos Florent 
Published: May 2022

AbstractBackgroundThe root mycobiome plays a fundamental role in plant nutrition and protection against biotic and abiotic stresses. In temperate forests or meadows dominated by angiosperms, the numerous fungi involved in root symbioses are often shared between neighboring plants, thus forming complex plant-fungus interaction networks of weak specialization. Whether this weak specialization also holds in rich tropical communities with more phylogenetically diverse sets of plant lineages remains unknown.We collected roots of 30 plant species in semi-natural tropical communities including angiosperms, ferns, and lycophytes, in three different habitat types on La Réunion island: a recent lava flow, a wet thicket, and an ericoid shrubland. We identified root-inhabiting fungi by sequencing both the 18S rRNA and the ITS2 variable regions. We assessed the diversity of mycorrhizal fungal taxa according to plant species and lineages, as well as the structure and specialization of the resulting plant-fungus networks.ResultsThe 18S and ITS2 datasets are highly complementary at revealing the root mycobiota. According to 18S, Glomeromycotina colonize all plant groups in all habitats forming the least specialized interactions, resulting in nested network structures, while Mucoromycotina (Endogonales) are more abundant in the wetland and show higher specialization and modularity compared to the former. According to ITS2, mycorrhizal fungi of Ericaceae and Orchidaceae, namely Helotiales, Sebacinales, and Cantharellales, also colonize the roots of most plant lineages, confirming that they are frequent endophytes. While Helotiales and Sebacinales present intermediate levels of specialization, Cantharellales are more specialized and more sporadic in their interactions with plants, resulting in highly modular networks.ConclusionsThis study of the root mycobiome in tropical environments reinforces the idea that mycorrhizal fungal taxa are locally shared between co-occurring plants, including phylogenetically distant plants (e.g. lycophytes and angiosperms), where they may form functional mycorrhizae or establish endophytic colonization. Yet, we demonstrate that, irrespectively of the environmental variations, the level of specialization significantly varies according to the fungal lineages, probably reflecting the different evolutionary origins of these plant-fungus symbioses. Frequent fungal sharing between plants questions the roles of the different fungi in community functioning and highlights the importance of considering networks of interactions rather than isolated hosts.
Structures reveal a key mechanism of WAVE Regulatory Complex activation by Rac1 GTPase
Authors: Ding Bojian , Yang Sheng , Schaks Matthias , Liu Yijun , Brown Abbigale , Rottner Klemens , Chowdhury Saikat , Chen Baoyu 
Published: May 2022

AbstractRho-family GTPase Rac1 activates the WAVE regulatory complex (WRC) to drive Arp2/3-mediated actin polymerization in many essential processes. Rac1 binds to WRC at two distinct sites—the A and D sites. Precisely how Rac1 binds and how the binding triggers WRC activation remain unknown. Here we report WRC structures by itself, and when bound to single or double Rac1 molecules, at ∼3 Å resolutions by cryogenic-electron microscopy. The structures reveal that Rac1 binds to the two sites by distinct mechanisms, and binding to the A site, but not the D site, drives WRC activation. Activation involves a series of unique conformational changes leading to the release of sequestered WCA (WH2- central-acidic) polypeptide, which stimulates the Arp2/3 complex to polymerize actin. Together with biochemical and cellular analyses, the structures provide a novel mechanistic understanding of how the Rac1-WRC-Arp2/3-actin signaling axis is regulated in diverse biological processes and diseases.
Saccade-related modulation of oscillatory activity in primary auditory cortex
Authors: Barczak Annamaria , O’Connell Monica Noelle , McGinnis Tammy , Mackin Kieran , Schroeder Charles E. , Lakatos Peter 
Published: May 2022

AbstractThe auditory and visual sensory systems are both used by the brain to obtain and organize information from our external environment, yet there are fundamental differences between these two systems. Visual information is acquired using systematic patterns of fixations and saccades, which are controlled by internal motor commands. Sensory input occurs in volleys that are tied to the timing of saccades. In contrast, the auditory system does not use such an overt motor sampling routine so the relationship between sensory input timing and motor activity is less clear. Previous studies of primary visual cortex (V1) in nonhuman primates (NHP) have shown that there is a cyclical modulation of excitability tied to the eye movement cycle and suggests that this excitability modulation stems from the phase reset of neuronal oscillations. We hypothesized that if saccades provide a supramodal temporal context for environmental information then we should also see saccade-related modulation of oscillatory activity in primary auditory cortex (A1) as NHPs shift their gaze around their surroundings. We used linear array multielectrodes to record cortical laminar neuroelectric activity profiles while subjects sat in a dark or dimly lit and silent chamber. Analysis of oscillatory activity in A1 suggests that saccades lead to a phase reset of neuronal oscillations in A1. Saccade-related phase reset of delta oscillations were observed across all layers while theta effects occurred primarily in extragranular layers. Although less frequent, alpha oscillations also showed saccade-related phase reset within the extragranular layers. Our results confirm that saccades provide a supramodal temporal context for the influx of sensory information into A1 and highlight the importance of considering the effects of eye position on auditory processing.Significance StatementUsing laminar multielectrodes, the current study examined saccade-related neuronal activity during resting state while NHPs sat in a dark or dimly lit room. Our results confirm that saccade-related modulation of delta band oscillatory activity occurs across all layers of A1. Interestingly, our data also show a saccade-related phase reset of theta and alpha bands that preferentially occurs in extragranular layers. These results confirm that saccades provide a supramodal temporal context for the influx of environmental information into A1 and emphasizes the importance of considering eye position when examining auditory processing.
Ghrelin is related to lower brain reward activation during touch
Authors: Pfabigan D.M. , Frogner E.R. , Schéle E. , Thorsby P. M. , Skålhegg B. S , Dickson S. L. , Sailer U. 
Published: May 2022

AbstractThe gut hormone ghrelin drives food motivation and increases food intake, but it is also involved in the anticipation of and response to rewards other than food. This pre-registered study investigated how naturally varying ghrelin concentrations affect the processing of touch as a social reward in humans.Sixty-seven volunteers received slow caressing touch (so-called CT-targeted touch) as a social reward and control touch on their shins during 3T functional imaging on two test days. On one occasion participants were fasted and on another they received a meal. On each occasion plasma ghrelin was measured at three time points.All touch was rated as more pleasant after the meal, but there was no association between ghrelin concentrations and pleasantness. CT-targeted touch was rated as most pleasant and activated somatosensory and reward networks (whole-brain). A region-of-interest in the right medial orbitofrontal cortex (mOFC) showed lower activation during all touch the higher ghrelin concentrations were. During CT-targeted touch, a larger satiety response (ghrelin decrease after the meal) was associated with higher mOFC activation, and this OFC activation was associated with higher experienced pleasantness.Overall, higher ghrelin concentrations appear to be related to lower reward value of touch. Ghrelin may reduce the value of social stimuli, such as touch, to promote food search and intake in a state of low energy. This suggests that the role of ghrelin goes beyond assigning value to food reward.
The fidelity of transcription in human cells
Authors: Chung C. , Verheijen B.M. , Zhang X. , Huang B. , Coakley A. , McGann E. , Wade E. , Dinep-Schneider O. , LaGosh J. , Anagnostou M. , Simpson S. , Thomas K. , Ernst J. M. , Rattray A. , Lynch M. , Kashlev M. , Benayoun B. A. , Li Z. , Strathern J. , Gout J-F. , Vermulst M. 
Published: May 2022

ABSTRACTAccurate transcription is required for the faithful expression of genetic information. To provide insight into the molecular mechanisms that control the fidelity of transcription, we analyzed the landscape of transcription errors in human embryonic stem cells. These measurements provide the first reasonable estimate of the fidelity of transcription in human cells and identify multiple genetic and epigenetic factors that control its accuracy. In addition, we developed a new reporter mouse to identify cell types and tissues that commit these errors the most. These experiments revealed that CA1 and dentate gyrus neurons are highly sensitive to transcriptional mutagenesis, lending new support to the hypothesis that transcription errors play a role in the progression of Alzheimer’s disease. Taken together, these experiments provide unprecedented insight into the fidelity of gene expression in human cells and the molecular mechanisms that govern the central dogma of life.
High resolution mapping reveals hotspots and sex-biased recombination inPopulus trichocarpa
Authors: Abeyratne Chanaka Roshan , Macaya-Sanz David , Zhou Ran , Barry Kerrie W. , Daum Christopher , Haiby Kathy , Lipzen Anna , Stanton Brian , Yoshinaga Yuko , Zane Matthew , Tuskan Gerald A. , DiFazio Stephen P. 
Published: May 2022

ABSTRACTFine-scale meiotic recombination is fundamental to the outcome of natural and artificial selection. Here, dense genetic mapping and haplotype reconstruction were used to estimate recombination for a full factorialPopulus trichocarpacross of seven males and seven females. Genomes of the resulting 49 full-sib families (N=829 offspring) were re-sequenced, and high-fidelity biallelic SNP/INDELs and pedigree information were used to ascertain allelic phase and impute progeny genotypes to recover gametic haplotypes. The fourteen parental genetic maps contained 1820 SNP/INDELs on average that covered 376.7 Mb of physical length across 19 chromosomes. Comparison of parental and progeny haplotypes allowed fine-scale demarcation of cross-over (CO) regions, where 38,846 CO events in 1,658 gametes were observed. CO events were positively associated with gene density and negatively associated with GC content and long terminal repeats. One of the most striking findings was higher rates of COs in males in 8 out of 19 chromosomes. Regions with elevated male CO rates had lower gene density and GC content than windows showing no sex bias. High-resolution analysis identified 67 candidate CO hotspots spread throughout the genome. DNA sequence motifs enriched in these regions showed striking similarity to those of maize, Arabidopsis and wheat. These findings, and recombination estimates, will be useful for ongoing efforts to accelerate domestication of this and other biomass feedstocks, as well as future studies investigating broader questions related to evolutionary history, perennial development, phenology, wood formation, vegetative propagation, and dioecy that cannot be studied using annual plant model systems.
A long non-coding RNA is a key factor in the evolution of insect eusociality
Authors: Cardoso-Junior Carlos A. M. , Tibério Gustavo J. , Lago Denyse C. , Vieira Luiz Carlos , Rosa José C. , Paschoal Alexandre R. , Ronai Isobel , Oldroyd Benjamin P. , Hartfelder Klaus 
Published: May 2022

SUMMARYInsect sociality is a major evolutionary transition based on the suppression of worker reproduction in favor of the reproductive monopoly of the queen. In the honey bee (Apis mellifera) model organism, the development of the two female caste phenotypes, queen and worker, is triggered by differences in their larval diets. However, the mechanistic details underlying their respective developmental trajectories, as well as the maintenance of sterility in the adult workers, are still not fully understood. Here we show that the long non-coding RNA lncov1 interacts with the Tudor staphylococcus nuclease (Tudor-SN) protein to form a regulatory module that promotes apoptosis in the ovaries of worker larvae. In adult workers, the lncov1/Tudor-SN module responds positively to environmental cues that suppress reproductive capacity. As lncov1 is considerably conserved in the Apidae, we propose that, by promoting worker sterility, the lncov1/Tudor-SN module has likely played critical roles in the social evolution of bees.