bluuebunny/crossref_metadata_2025_split huggingface dataset:
Capsid-E2 interactions rescue core assembly in viruses that cannot form cytoplasmic nucleocapsid cores
Authors: Button Julie M. , Mukhopadhyay Suchetana 
Published: June 2021

ABSTRACTAlphavirus capsid proteins (CPs) have two domains: the N-terminal domain (NTD) that interacts with the viral RNA, and the C-terminal domain (CTD) that forms CP-CP inter-actions and interacts with the cytoplasmic domain of the E2 spike protein (cdE2). In this study, we examine how mutations in the CP NTD affect CP CTD interactions with cdE2. We changed the length and/or charge of the NTD of Ross River virus CP and found that changing the charge of the NTD has a greater impact on core and virion assembly than changing the length of the NTD. The NTD CP insertion mutants are unable to form cyto-plasmic cores during infection but they do form cores or core-like structures in virions. Our results are consistent with cdE2 having a role in core maturation during virion assembly and rescuing core formation when cytoplasmic cores are not assembled. We go on to find that the isolated cores from some mutant virions are now assembly competent in that they can be disassembled and reassembled back into cores. These results show how the two domains of CP may have distinct yet coordinated roles.IMPORTANCEStructural viral proteins have multiple roles during entry and assembly. The capsid protein (CP) of alphaviruses has one domain that interacts with the viral genome and another domain that interacts with the E2 spike protein. In this work we determine that the length and/or charge of the CP affects cytoplasmic core formation. However, defects in cytoplasmic core formation can be overcome by E2-CP interactions, thus assembling a core or core-like complex in the virion. In the absence of both cytoplasmic cores and CP-E2 interactions, CP is not even packaged in the released virions, but some infectious particles are still released presumably as RNA packaged in a glycoprotein containing membrane shell. This suggests that the virus has multiple mechanisms in place to ensure the viral genome is surrounded by a capsid core during its lifecycle.
Survival mechanism of a novel marine multistress-tolerant Meyerozyma guilliermondii GXDK6 under high NaCl stress as revealed by integrative omics analysis
Authors: Cai Xinghua , Sun Huijie , Bai Huashan , Chen Yanyi , Kashif Muhammad , Bu Ru , Mo Xueyan , Su Guijiao , Ou Qian , Yan Bing , Jiang Chengjian 
Published: June 2021

ABSTRACTA novel strain named Meyerozyma guilliermondii GXDK6 was provided in this work, which was confirmed to survive independently under high salt stress (12% NaCl) or co-stress condition of strong acid (pH 3.0) and high salts (10% NaCl) without sterilization. Its survival mechanism under high salt stress was revealed by integrated omics for the first time. Whole-genome analysis showed that 14 genes (e.g., GPD1 and FPS1) of GXDK6 relevant to salt tolerance were annotated and known to belong to various salt-resistant mechanisms (e.g., regulation of cell signal transduction and glycerol metabolism controls). Transcriptome sequencing results indicated that 1220 genes (accounting for 10.15%) of GXDK6 were differentially transcribed (p < 0.05) when GXDK6 growth was under 10% stress for 16 h, including important novel salt-tolerant-related genes (e.g., RTM1 and YHB1). Proteomics analysis demonstrated that 1005 proteins (accounting for 27.26%) of GXDK6 were differentially expressed (p < 0.05) when GXDK6 was stressed by 10% NaCl. Some of the differentially expressed proteins were defined as the novel salt-tolerant related proteins (e.g., sugar transporter STL1 and NADPH-dependent methylglyoxal reductase). Metabolomic analysis results showed that 63 types of metabolites (e.g., D-mannose, glycerol and inositol phosphate) of GXDK6 were up- or downregulated when stressed by 10% NaCl. Among them, D-mannose is one of the important metabolites that could enhance the salt-tolerance survival of GXDK6.IMPORTANCEMicrobial contamination is a huge obstacle in industrial fermentation. The emergence of multistress-tolerant microorganism is expected to realize industrial fermentation without sterilization by controlling specific conditions. However, microorganisms eligible for non-sterile fermentation are required to survive independently under the selected special conditions for the fermentation conditions to be controlled to avoid microbial contamination. Here, a novel marine Meyerozyma guilliermondii was presented, which is able to survive well under high salt stress, its survival mechanism was systematically revealed by integrated omics technology. In addition, finding that NaCl stress could also stimulate the biosynthesis of functional metabolites from GXDK6 (e.g., calcitriol and didemnin B). Among the functional metabolites, calcitriol biosynthesis via microbial method was rarely reported. Thus, its biosynthetic mechanism was further revealed. The findings in this study contributed to understanding the survival mechanism of M. guilliermondii under high salt stress, and the development of new molecular drugs from M. guilliermondii GXDK6.Graphic abstract
Relating in vitro neutralisation level and protection in the CVnCoV (CUREVAC) trial
Authors: Cromer Deborah , Reynaldi Arnold , Steain Megan , Triccas James A , Davenport Miles P , Khoury David S 
Published: June 2021

AbstractA recent study analysed the relationship between neutralising antibody response and protection from SARS-CoV-2 infection across eight vaccine platforms1. The efficacy results from a phase 2b/3 trial of a ninth vaccine candidate, CVnCoV (CUREVAC), was announced on 16 June 20212. The low efficacy of this new mRNA vaccine, which showed only 47% protection from symptomatic SARS-CoV-2 infection, was surprising given the high efficacy of two previous mRNA-based vaccines3,4. A number of factors have been suggested to play a role in the low efficacy in the CVnCoV study, particularly around the dose and immunogenicity of the vaccine (which uses an unmodified mRNA construct5,6) and the potential role of infection with SARS-CoV-2 variants (which were the dominant strains observed in the CVnCoV trial)2.
Raloxifene reduces sex- and age-related intervertebral disc degeneration in mice by estrogen signaling
Authors: Bhadouria Neharika , Niziolek Paul , El Jordi Omar , Berman Alycia G. , McKinzie David , Wallace Joseph M. , Holguin Nilsson 
Published: June 2021

AbstractEstrogen agonist raloxifene is an FDA-approved treatment for osteoporosis in postmenopausal women that may also be a promising prophylactic for painful intervertebral disc (IVD) degeneration. Here, we hypothesized that raloxifene would augment IVD structure and reduce neurokinin-1 (substance P) in young and old mice by stimulating estrogen signaling. 2.5 month (male and female) and 22.5 month (female) C57Bl/6J mice were subcutaneously injected with raloxifene hydrochloride (5x/week, 6week, n=7-9/grp). Next, to determine the impact of estrogen-deficiency to IVD structure and substance P, female mice were ovariectomized (OVX) at 4mo and tissues from OVX and sham-operated mice were harvested at 6mo (n=5-6/grp). First, compared to male IVD, female IVD expressed less col2 and osterix transcription, early markers of IVD degeneration. Irrespective of sex, raloxifene increased the transcriptional expression for extracellular matrix anabolism, proliferation, notochordal cells (vs chondrocyte-like cells) and estrogen signaling in young IVD. Next, we determined that biological sex and aging each induced structural features of lumbar IVD degeneration. Therapeutically, injection of raloxifene countered these features by increasing IVD height in young mice, preventing mild sex-related IVD degeneration in young female mice and partially reversing age-related IVD degeneration in old female mice. Further, estrogen agonist raloxifene upregulated er-α protein and downregulated substance P protein in young and old IVD. By contrast, estrogen-deficiency by OVX increased IVD degeneration and substance P protein in IVD cells. Similarly, substance P protein in vertebral osteocytes was upregulated in females relative to males and by estrogen-deficiency and downregulated by raloxifene. Overall, raloxifene augmented IVD structure and reduced substance P expression in young and old female murine IVD, whereas estrogen-deficiency increased substance P in the spine. These data suggest that raloxifene may potentially relieve painful IVD degeneration in postmenopausal women induced by biological sex, estrogen-deficiency and advanced age.Abstract FigureGraphical AbstractInjection of raloxifene promotes IVD health by engaging estrogen and Wnt signaling to promote cell proliferation and IVD structure. Differential estrogen signaling by raloxifene and ovariectomy regulated nerve signaling protein substance P in the spine. Raloxifene may also bind water to collagen to promote hydration. Acan: aggrecan, AF: annulus fibrosus, NC: notochordal cell, NP: nucleus pulposus
Mechanical Stimulation via Muscle Activity is Necessary for the Maturation of Tendon Multiscale Mechanics during Embryonic Development
Authors: Peterson Benjamin E. , Rolfe Rebecca A. , Kunselman Allen , Murphy Paula , Szczesny Spencer E. 
Published: June 2021

AbstractDuring embryonic development, tendons transform into a hypocellular tissue with robust tensile load-bearing capabilities. Previous work suggests that this mechanical transformation is due to increases in collagen fibril length and is dependent on mechanical stimulation via muscle activity. However, the relationship between changes in the microscale tissue structure and changes in macroscale tendon mechanics is still unclear. Additionally, the specific effect of mechanical stimulation on the multiscale structure-function relationships of developing tendons is also unknown. Therefore, the objective of this study was to measure the changes in tendon mechanics and structure at multiple length scales during embryonic development with and without skeletal muscle paralysis. Tensile testing of tendons from chicken embryos was performed to determine the macroscale tensile modulus as well as the magnitude of the fibril strains and interfibrillar sliding with applied tissue strain. Embryos were also treated with either decamethonium bromide or pancuronium bromide to produce rigid or flaccid paralysis. Histology was performed to assess changes in tendon size, spacing between tendon subunits, and collagen fiber diameter. We found that the increase in the macroscale modulus observed with development is accompanied by an increase in the fibril:tissue strain ratio, which is consistent with an increase in collagen fibril length. Additionally, we found that flaccid paralysis reduced the macroscale tendon modulus and the fibril:tissue strain ratio, whereas less pronounced effects that were not statistically significant were observed with rigid paralysis. Finally, skeletal paralysis also reduced the size of collagen fibril bundles (i.e., fibers). Together, these data suggest that more of the applied tissue strain is transmitted to the collagen fibrils at later embryonic ages, which leads in an increase the tendon macroscale tensile mechanics. Furthermore, our data suggest that mechanical stimulation during development is necessary to induce structural and mechanical changes at multiple physical length scales. This information provides valuable insight into the multiscale structure-function relationships of developing tendons and the importance of mechanical stimulation in producing a robust tensile load-bearing soft tissue.
Distinct epicardial gene regulatory programmes drive development and regeneration of the zebrafish heart
Authors: Weinberger Michael , Simões Filipa C. , Sauka-Spengler Tatjana , Riley Paul R. 
Published: June 2021

SummaryUnlike the adult mammalian heart, which has limited regenerative capacity, the zebrafish heart can fully regenerate following injury. Reactivation of cardiac developmental programmes is considered key to successfully regenerating the heart, yet the regulatory elements underlying the response triggered upon injury and during development remain elusive. Organ-wide activation of the epicardium is essential for zebrafish heart regeneration and is considered a potential regenerative source to target in the mammalian heart. Here we compared the transcriptome and epigenome of the developing and regenerating zebrafish epicardium by integrating gene expression profiles with open chromatin ATAC-seq data. By generating gene regulatory networks associated with epicardial development and regeneration, we inferred genetic programmes driving each of these processes, which were largely distinct. We identified wt1a, wt1b, and the AP-1 subunits junbb, fosab and fosb as central regulators of the developing network, whereas hif1ab, zbtb7a, tbx2b and nrf1 featured as putative central regulators of the regenerating epicardial network. By interrogating developmental gene regulatory networks that drive cell-specific transcriptional heterogeneity, we tested novel subpopulation-related epicardial enhancers in vivo. Taken together, our work revealed striking differences between the regulatory blueprint deployed during epicardial development and regeneration. These findings challenge the dogma that heart regeneration is essentially a reactivation of developmental programmes, and provide important insights into epicardial regulation that can assist in developing therapeutic approaches to enable tissue regeneration in the adult mammalian heart.
Persistence of Hippocampal and Striatal Multivoxel Patterns During Awake Rest after Motor Sequence Learning
Authors: King Bradley R. , Gann Mareike A. , Mantini Dante , Doyon Julien , Albouy Geneviève 
Published: June 2021

AbstractMemory consolidation, the process by which newly encoded and fragile memories become more robust, is thought to be supported by the reactivation of brain regions - including the hippocampus - during post-learning rest. While hippocampal reactivations have been demonstrated in humans in the declarative memory domain, it remains unknown whether such a process takes place after motor learning. Using multivariate analyses of task-related and resting state fMRI data, here we show that patterns of brain activity within both the hippocampus and striatum elicited during motor learning persist into post-learning rest, indicative of reactivation of learning-related neural activity patterns. Moreover, results indicate that hippocampal reactivation reflects the spatial representation of the learned motor sequence. These results thus provide insights into the functional significance of neural reactivation after motor sequence learning.
Substrate access mechanism in a novel membrane-bound phospholipase A of Pseudomonas aeruginosa concordant with specificity and regioselectivity
Authors: Ahmad Sabahuddin , Strunk Christoph Heinrich , Schott-Verdugo Stephan N. , Jaeger Karl-Erich , Kovacic Filip , Gohlke Holger 
Published: June 2021

AbstractPlaF is a cytoplasmic membrane-bound phospholipase A1 from Pseudomonas aeruginosa that alters the membrane glycerophospholipid (GPL) composition and fosters the virulence of this human pathogen. PlaF activity is regulated by a dimer-to-monomer transition followed by tilting of the monomer in the membrane. However, how substrates reach the active site and how the characteristics of the active site tunnels determine the activity, specificity, and regioselectivity of PlaF for natural GPL substrates has remained elusive. Here, we combined unbiased and biased all-atom molecular dynamics (MD) simulations and configurational free energy computations to identify access pathways of GPL substrates to the catalytic center of PlaF. Our results map out a distinct tunnel through which substrates access the catalytic center. PlaF variants with bulky tryptophan residues in this tunnel revealed decreased catalysis rates due to tunnel blockage. The MD simulations suggest that GPLs preferably enter the active site with the sn-1 acyl chain first, which agrees with the experimentally demonstrated PLA1 activity of PlaF. We propose that the acyl chain-length specificity of PlaF is determined by the structural features of the access tunnel, which results in favorable free energy of binding of medium-chain GPLs. The suggested egress route conveys fatty acid products to the dimerization interface and, thus, contributes to understanding the product feedback regulation of PlaF by fatty acid-triggered dimerization. These findings open up opportunities for developing potential PlaF inhibitors, which may act as antibiotics against P. aeruginosa.
The ACF chromatin remodeling complex is essential for Polycomb repression
Authors: Wiles Elizabeth T. , Mumford Colleen C. , McNaught Kevin J. , Tanizawa Hideki , Selker Eric U. 
Published: June 2021

ABSTRACTEstablishing and maintaining appropriate gene repression is critical for the health and development of multicellular organisms. Histone H3 lysine 27 (H3K27) methylation is a chromatin modification associated with repressed facultative heterochromatin, but the mechanism of this repression remains unclear. We used a forward genetic approach to identify genes involved in transcriptional silencing of H3K27-methylated chromatin in the filamentous fungus Neurospora crassa. We found that the N. crassa homologs of ISWI (NCU03875) and ACF (NCU00164) are required for repression of a subset of H3K27-methylated genes and that they form an ACF chromatin remodeling complex. This N. crassa ACF complex interacts with chromatin throughout the genome, yet association with facultative heterochromatin is specifically promoted by the H3K27 methyltransferase, SET-7. H3K27-methylated genes that are upregulated when iswi or acf1 are deleted show a downstream shift of the +1 nucleosome, suggesting that proper nucleosome positioning is critical for repression of facultative heterochromatin. Our findings support a direct role for the ACF complex in Polycomb repression.
The MuvB Complex Binds and Stabilizes Nucleosomes Downstream of the Transcription Start Site of Cell-Cycle Dependent Genes
Authors: Asthana Anushweta , Ramanan Parameshwaran , Hirschi Alexander , Guiley Keelan Z. , Wijeratne Tilini U. , Shelansky Robert , Doody Michael J. , Narasimhan Haritha , Boeger Hinrich , Tripathi Sarvind , Müller Gerd A. , Rubin Seth M. 
Published: June 2021

AbstractThe chromatin architecture in promoters is thought to regulate gene expression, but it remains uncertain how most transcription factors (TFs) impact nucleosome position. The MuvB TF complex regulates cell-cycle dependent gene-expression and is critical for differentiation and proliferation during development and cancer. MuvB can both positively and negatively regulate expression, but the structure of MuvB and its biochemical function are poorly understood. Here we determine the overall architecture of MuvB assembly and the crystal structure of a subcomplex critical for MuvB function in gene repression. We find that the MuvB subunits LIN9 and LIN37 function as scaffolding proteins that arrange the other subunits LIN52, LIN54 and RBAP48 for TF, DNA, and histone binding, respectively. Biochemical and structural data demonstrate that MuvB binds nucleosomes through an interface that is distinct from LIN54-DNA consensus site recognition and that MuvB increases nucleosome occupancy in a reconstituted promoter. We find in arrested cells that MuvB primarily associates with a tightly positioned +1 nucleosome near the transcription start site (TSS) of MuvB-regulated genes. These results support a model that MuvB binds and stabilizes nucleosomes just downstream of the TSS on its target promoters to repress gene-expression.
Neutralizing antibody 5-7 defines a distinct site of vulnerability in SARS-CoV-2 spike N-terminal domain
Authors: Cerutti Gabriele , Guo Yicheng , Wang Pengfei , Nair Manoj S. , Huang Yaoxing , Yu Jian , Liu Lihong , Katsamba Phinikoula S. , Bahna Fabiana , Reddem Eswar R. , Kwong Peter D. , Ho David D. , Sheng Zizhang , Shapiro Lawrence 
Published: June 2021

SummaryAntibodies that potently neutralize SARS-CoV-2 target mainly the receptor-binding domain or the N-terminal domain (NTD). Over a dozen potently neutralizing NTD-directed antibodies have been studied structurally, and all target a single antigenic supersite in NTD (site 1). Here we report the 3.7 Å resolution cryo-EM structure of a potent NTD-directed neutralizing antibody 5-7, which recognizes a site distinct from other potently neutralizing antibodies, inserting a binding loop into an exposed hydrophobic pocket between the two sheets of the NTD β-sandwich. Interestingly, this pocket has been previously identified as the binding site for hydrophobic molecules including heme metabolites, but we observe their presence to not substantially impede 5-7 recognition. Mirroring its distinctive binding, antibody 5-7 retains a distinctive neutralization potency with variants of concern (VOC). Overall, we reveal a hydrophobic pocket in NTD proposed for immune evasion can actually be used by the immune system for recognition.HighlightsCryo-EM structure of neutralizing antibody 5-7 in complex with SARS CoV-2 spike5-7 recognizes NTD outside of the previously identified antigenic supersite5-7 binds to a site known to accommodate numerous hydrophobic ligandsStructural basis of 5-7 neutralization tolerance to some variants of concern
AUTS2 controls neuronal lineage choice through a novel PRC1-independent complex and BMP inhibition
Authors: Geng Zhuangzhuang , Wang Qiang , Miao Weili , Wolf Trevor , Chavez Jessenia , Giddings Emily , Hobbs Ryan , DeGraff David J. , Wang Yinsheng , Stafford James , Gao Zhonghua 
Published: June 2021

SummaryDespite a prominent risk factor for Neurodevelopmental disorders (NDD), it remains unclear how Autism Susceptibility Candidate 2 (AUTS2) controls the neurodevelopmental program. Our studies investigated the role of AUTS2 in neuronal differentiation and discovered that AUTS2, together with WDR68 and SKI, forms a novel protein complex (AWS) specifically in neuronal progenitors and promotes neuronal differentiation through inhibiting BMP signaling. Genomic and biochemical analyses demonstrated that the AWS complex achieves this effect by recruiting the CUL4 E3 ubiquitin ligase complex to mediate poly-ubiquitination and subsequent proteasomal degradation of phosphorylated SMAD1/5/9. Furthermore, using primary cortical neurons, we observed aberrant BMP signaling and dysregulated expression of neuronal genes upon manipulating the AWS complex, indicating that the AWS-CUL4-BMP axis plays a role in regulating neuronal lineage specification in vivo. Thus, our findings uncover a sophisticated cellular signaling network mobilized by a prominent NDD risk factor, presenting multiple potential therapeutic targets for NDD.