bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proinflammatory innate cytokines and metabolomic signatures shape the T cell response in active COVID-19
Authors: Binayke Akshay , Zaheer Aymaan , Dandotiya Jyotsna , Gupta Sonu K , Mani Shailendra , Tripathi Manas , Madan Upasna , Shrivastava Tripti , Kumar Yashwant , Pandey Anil K , Rathore Deepak K , Awasthi Amit 
Published: March 2022

AbstractThe underlying factors contributing to the evolution of SARS-CoV-2-specific T cell responses during COVID-19 infection remain unidentified. To address this, we characterized innate and adaptive immune responses with metabolomic profiling longitudinally at three different time points (0-3, 7-9, and 14-16 days post-COVID-19 positivity) from young mildly symptomatic active COVID-19 patients infected during the first wave in mid-2020. We observed that anti-RBD IgG and viral neutralization are significantly reduced against the Delta variant compared to the ancestral strain. In contrast, compared to the ancestral strain, T cell responses remain preserved against the delta and omicron variants. We determined innate immune responses during the early stage of active infection in response to TLR 3/7/8 mediated activation in PBMCs and serum metabolomic profiling. Correlation analysis indicated PBMCs-derived proinflammatory cytokines, IL-18, IL-1β, and IL-23, and the abundance of plasma metabolites involved in arginine biosynthesis were predictive of a robust SARS-CoV-2-specific Th1 response at a later stage (two weeks after PCR positivity). These observations may contribute to designing effective vaccines and adjuvants that promote innate immune responses and metabolites to induce long-lasting anti-SARS-CoV-2 specific T cells response.
Syntaxin-1A modulates vesicle fusion in mammalian neurons via juxtamembrane domain dependent palmitoylation of its transmembrane domain
Authors: Vardar Gülçin , Salazar-Lázaro Andrea , Zobel Sina , Trimbuch Thorsten , Rosenmund Christian 
Published: March 2022

AbstractSNAREs are undoubtedly one of the core elements of synaptic transmission. On the contrary to the well characterized function of their SNARE domains bringing the plasma and vesicular membranes together, the level of contribution of their juxtamembrane domain (JMD) and the transmembrane domain (TMD) to the vesicle fusion is still under debate. To elucidate this issue, we analyzed three groups of STX1A mutations: 1) elongation of STX1A’s JMD by three amino acid insertions in the junction of SNARE-JMD or JMD-TMD; 2) charge reversal mutations in STX1A’s JMD; and 3) palmitoylation deficiency mutations in STX1A’s TMD. We found that both JMD elongations and charge reversal mutations have position dependent differential effects on Ca2+-evoked and spontaneous neurotransmitter release in cultured murine hippocampal neurons. Importantly, we show that STX1A’s JMD regulates the palmitoylation of STX1A’s TMD and loss of STX1A palmitoylation either through charge reversal mutation K260E or by loss of TMD cysteines particularly inhibits spontaneous vesicle fusion. Interestingly, the retinal ribbon specific STX3B has a glutamate in the position corresponding to the K260E mutation in STX1A and mutating it with E259K acts as a molecular on-switch. Furthermore, palmitoylation of post-synaptic STX3A can be induced by the exchange of its JMD with STX1A’s JMD together with the incorporation of two cysteines into its TMD. Forced palmitoylation of STX3A dramatically enhances spontaneous vesicle fusion suggesting that STX1A regulates spontaneous release through two distinct mechanisms: one through the C-terminal half of its SNARE domain and the other through the palmitoylation of its TMD.
Neurons in inferior temporal cortex are sensitive to motion trajectory during degraded object recognition
Authors: Burk Diana C. , Sheinberg David L. 
Published: March 2022

AbstractOur brains continuously acquire sensory information and make judgments even when visual information is limited. In some circumstances, an ambiguous object can be recognized from how it moves, such as an animal hopping or a plane flying overhead. Yet it remains unclear how movement is processed by brain areas involved in visual object recognition. Here we investigate whether inferior temporal cortex, an area traditionally known for shape processing, has access to motion information during degraded shape recognition. We developed a matching task that required monkeys to recognize moving shapes with variable levels of shape degradation. Neural recordings in area IT showed that, surprisingly, some IT neurons preferred blurry shapes over clear ones. Further, many of the neurons exhibited motion sensitivity at different times during the presentation of the blurry target. Population decoding analyses showed that motion pattern could be decoded from IT neuron pseudo-populations. Contrary to previous findings, these results suggest that neurons in IT can integrate visual motion and shape information, particularly when shape information is degraded, in a way that has been previously overlooked. Our results highlight the importance of using challenging multi-feature recognition tasks to understand the role of area IT in naturalistic visual object recognition. (Word count: 199)
Comparative analysis of total alpha-synuclein (αSYN) immunoassays reveals that they do not capture the diversity of modified αSYN proteoforms
Authors: Petricca Lara , Chiki Nour , Hanna-El-Daher Layane , Aeschbach Lorène , Burai Ritwik , Stoops Erik , Fares Mohamed-Bilal , Lashuel Hilal A. 
Published: March 2022

AbstractBackgroundThe development of therapeutics for Parkinson’s disease (PD) requires the establishment of biomarker assays to enable stratifying patients, monitoring disease progression and assessing target engagement. Attempts to develop diagnostic assays based on detecting levels of the α-synuclein (αSYN) protein, a central player in the pathogenesis of PD, have yielded inconsistent results.ObjectiveTo determine whether the three commercial kits that have been extensively used for total αSYN quantification in human biological fluids (from Euroimmun, MSD, and Biolegend) are capable of capturing the diversity and complexity of relevant αSYN proteoforms.MethodsWe investigated and compared the ability of the different assays to detect the diversity of αSYN proteoform using a library of αSYN proteins that compromise the majority of disease-relevant αSYN variants and post-translational modification.ResultsOur findings showed that none of the three tested immunoassays accurately capture the totality of relevant αSYN species and are unable to recognize most disease-associated C-terminally truncated variants of αSYN. Moreover, several N-terminal truncations and phosphorylation/nitration differentially modify the level of αSYN detection and recovery by different immunoassays, and a CSF matrix effect was observed for most of the αSYN proteoforms analyzed by the three immunoassays.ConclusionsOur results showed that these immunoassays do not capture the totality of the relevant αSYN species and therefore may not be appropriate tools to provide an accurate measure of total αSYN levels in samples containing modified forms of the protein. This highlights the need for next-generation αSYN immunoassays that capture the diversity of αSYN proteoforms.
Cortical interneuron loss and seizure generation as novel clinically relevant disease phenotypes in Cln2R207X mice
Authors: Takahashi Keigo , Eultgen Elizabeth M. , Wang Sophie H. , Rensing Nicholas R. , Nelvagal Hemanth R. , Dearborn Joshua T. , Sands Mark S. , Wong Michael , Cooper Jonathan D. 
Published: March 2022

AbstractAimsCLN2 disease is a fatal inherited childhood neurodegenerative disorder. Although a disease-modifying therapy now exists, a fundamental lack of understanding of disease pathogenesis has hampered development of more effective therapies. To better understand the cellular pathophysiology of CLN2 disease, we investigated the nature and progression of neuropathological and neurological changes in the recently generated Cln2R207X mouse.MethodsWe have detailed microglial activation, astrogliosis, cytokine and chemokine expression, and neuron loss across the forebrain and spinal cords of Cln2R207X mice, along with quantitative gait analysis. We also performed long-term electroencephalography (EEG) recordings to characterize seizure activity, a clinically-relevant phenotype yet to be defined in any CLN2 disease model.ResultsHistology revealed early localized microglial activation months before neuron loss in the thalamocortical system and spinal cord, which was accompanied by astrogliosis. These pathological changes were more pronounced and occurred in the cortex before the thalamus or spinal cord. There were early-onset and progressive changes in the expression of specific chemokines and cytokines including IL-33, IP-10, and MIP-1α. Gait analysis revealed impaired performance only at disease end stage. EEG recordings revealed robust and progressive epileptiform activity from disease mid-stage including spontaneous seizures, which were accompanied by a profound loss of cortical GABAergic interneurons.ConclusionsOur data reveal novel phenotypes in Cln2R207X mice that differ markedly in their timing and progression through the CNS from other NCL mouse models. Our findings provide new insights on CLN2 disease pathogenesis and clinically-relevant readouts for future therapeutic studies.
Functional convergence in slow-growing microbial communities arises from thermodynamic constraints
Authors: George Ashish B. , Wang Tong , Maslov Sergei 
Published: March 2022

AbstractThe dynamics of microbial communities is complex, determined by competition for metabolic substrates and cross-feeding of byproducts. Species in the community grow by harvesting energy from chemical reactions that transform substrates to products. In many anoxic environments, these reactions are close to thermodynamic equilibrium and growth is slow. To understand the community structure in these energy-limited environments, we developed a microbial community consumer-resource model incorporating energetic and thermodynamic constraints on an intercon-nected metabolic network. The central element of the model is product inhibition, meaning that microbial growth may be limited not only by depletion of metabolic substrates but also by accu-mulation of products. We demonstrate that these additional constraints on microbial growth cause a convergence in the structure and function of the community metabolic network—independent of species composition and biochemical details—providing a possible explanation for convergence of community function despite taxonomic variation observed in many natural and industrial en-vironments. Furthermore, we discovered that the structure of community metabolic network is governed by the thermodynamic principle of maximum free energy dissipation. Our results predict the decrease of functional convergence in faster growing communities, which we validate by ana-lyzing experimental data from anaerobic digesters. Overall, the work demonstrates how universal thermodynamic principles may constrain community metabolism and explain observed functional convergence in microbial communities.
High throughput screen in a co-culture model to uncover therapeutic strategies to potentiate the cancer-inhibiting properties of the tumor-stroma in pancreatic cancer
Authors: Mason James , Cumming Joshua , Eriksson Anna U. , Binder Carina , Dongre Mitesh , Patthey Cedric , Espona-Fiedler Margarita , Chorell Erik , Öhlund Daniel 
Published: March 2022

AbstractPancreatic stellate cells (PSCs) differentiate into multiple subtypes of cancer associated fibroblasts (CAFs) that modulate disease progression in pancreatic ductal adenocarcinoma (PDAC). CAF subtypes demonstrate functional heterogeneity in tumor development, with conflicting consequences for disease progression. Here, we show that myofibroblastic CAFs (myCAFs), but not inflammatory CAFs (iCAFs), can act to restrain tumor cell growth in an in vitro PDAC model of tumor organoids co-cultured with PSCs. Inhibiting myCAF formation by TGF-β pathway inhibition improved tumor organoid growth, indicating that manipulating the balance of CAF subtypes may be exploited as a therapeutic approach. We therefore conducted a high throughput screen of approximately 36,000 compounds on the co-culture model to find novel compounds to inhibit PDAC tumor cell growth via CAF manipulation. We identify a new role for GNF-5, a known Abelson tyrosine kinase (Abl) inhibitor, in the context of PDAC as a compound that inhibits tumor cell growth in co-culture; an effect that was accompanied by an induction of the myCAF phenotype around tumor organoids. This highlights the therapeutic potential of novel therapies targeting specific CAF subtypes in PDAC.
Interspecies isobaric labeling-based quantitative proteomics reveals protein changes in the ovary of Aedes aegypti co-infected with ZIKV and Wolbachia
Authors: Ramos Luis Felipe Costa , Martins Michele , Murillo Jimmy Rodriguez , Domont Gilberto Barbosa , de Oliveira Danielle Maria Perpétua , Nogueira Fábio César Sousa , Maciel-de-Freitas Rafael , Junqueira Magno 
Published: March 2022

ABSTRACTZika is a vector-borne disease caused by an arbovirus (ZIKV) and overwhelmingly transmitted by Ae. aegypti. This disease is linked to adverse fetal outcomes, mostly microcephaly in newborns, and other clinical aspects such as acute febrile illness and neurologic complications, for example, Guillain-Barré syndrome. One of the actual most promising strategies to mitigate arbovirus transmission involves releasing Ae. aegypti mosquitoes carrying the maternally inherited endosymbiont bacteria Wolbachia pipientis. The presence of Wolbachia is associated with a reduced susceptibility to arboviruses and a fitness cost in mosquito life-history traits as fecundity and fertility. However, the mechanisms by which Wolbachia influences metabolic pathways leading to differences in egg production remains poorly known. To investigate the impact of co-infections on the reproductive tract of the mosquito, we applied an isobaric labeling-based quantitative proteomic strategy to investigate the influence of Wolbachia wMel and ZIKV infection in Ae. aegypti ovaries. To the best of our knowledge, this is the most complete proteome of Ae. aegypti ovaries reported so far, with a total of 3,913 proteins identified, also,were able to quantify a total of 1,044 Wolbachia proteins in complex sample tissue of Ae. aegypti ovary.. Furthermore, we discuss proteins and pathways altered in Ae. aegypti during ZIKV infections, Wolbachia infections, co-infection Wolbachia/ZIKV, and compared with no infection, focusing on immune and reproductive aspects of Ae. aegypti. The modified aspects were mostly related to the immune priming enhancement by Wolbachia presence and the modulation of the Juvenile Hormone pathway caused by both microorganisms infection.HighlightsProteome changes in Ae. aegypti, Wolbachia, and ZIKV interactionsA great diversity of Wolbachia proteins were quantified in Ae. aegypti ovaryJuvenile Hormone pathway is modulated by both infectionsWolbachia enhances Ae. aegypti immune priming mechanismZIKV unsettles host immune response by reducing antimicrobial peptides productionCoinfection triggers oxidative stress and a lack of vitellogenin precursors
Dual inhibition of vacuolar ATPase and TMPRSS2 is required for complete blockade of SARS-CoV-2 entry into cells
Authors: Icho Simoun , Rujas Edurne , Muthuraman Krithika , Tam John , Liang Huazhu , Harms Shelby , Liao Mingmin , Falzarano Darryl , Julien Jean-Philippe , Melnyk Roman A. 
Published: March 2022

AbstractAn essential step in the infection life cycle of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the proteolytic activation of the viral spike (S) protein, which enables membrane fusion and entry into the host cell. Two distinct classes of host proteases have been implicated in the S protein activation step: cell-surface serine proteases, such as the cell-surface transmembrane protease, serine 2 (TMPRSS2), and endosomal cathepsins, leading to entry through either the cell-surface route or the endosomal route, respectively. In cells expressing TMPRSS2, inhibiting endosomal proteases using non-specific cathepsin inhibitors such as E64d or lysosomotropic compounds such as hydroxychloroquine fails to prevent viral entry, suggesting that the endosomal route of entry is unimportant; however, mechanism-based toxicities and poor efficacy of these compounds confound our understanding of the importance of the endosomal route of entry. Here, to identify better pharmacological agents to elucidate the role of the endosomal route of entry, we profiled a panel of molecules identified through a high throughput screen that inhibit endosomal pH and/or maturation through different mechanisms. Among the three distinct classes of inhibitors, we found that inhibiting vacuolar-ATPase using the macrolide bafilomycin A1 was the only agent able to potently block viral entry without associated cellular toxicity. Using both pseudotyped and authentic virus, we showed that bafilomycin A1 inhibits SARS-CoV-2 infection both in the absence and presence of TMPRSS2. Moreover, synergy was observed upon combining bafilomycin A1 with Camostat, a TMPRSS2 inhibitor, in neutralizing SARS-CoV-2 entry into TMPRSS2-expressing cells. Overall, this study highlights the importance of the endosomal route of entry for SARS-CoV-2 and provides a rationale for the generation of successful intervention strategies against this virus that combine inhibitors of both entry pathways.
Is Melanopsin Activation Affecting Large Field Color Matching Functions?
Authors: Barrionuevo Pablo , Filgueira Clemente Paz , Cao Dingcai 
Published: March 2022

AbstractColor theory is based on the exclusive activation of cones. However, since the discovery of melanopsin expressing cells in the human retina, evidence of its intrusion in brightness and color vision is increasing. We aimed to assess if differences between peripheral or large field and foveal color matches can be accounted for melanopsin activation or rod intrusion. Photopic color matches by young observers showed that differences between extrafoveal and foveal results cannot be explained by rod intrusion. Furthermore, statistical analyses on existing color matching functions suggest a role of melanopsin activation, particularly, in Large Field S Fundamentals.
The Balbiani body is formed by microtubule-controlled molecular condensation of Buc in early oogenesis
Authors: Kar Swastik , Deis Rachael , Ahmad Adam , Bogoch Yoel , Dominitz Avichai , Shvaizer Gal , Sasson Esther , Mytlis Avishag , Ben-Zvi Ayal , Elkouby Yaniv M. 
Published: March 2022

SummaryVertebrate oocyte polarity has been observed for two centuries and is essential for embryonic axis formation and germline specification, yet its underlying mechanisms remain unknown. In oocyte polarization, critical RNA-protein (RNP) granules delivered to the oocyte’s vegetal pole, are stored by the Balbiani body (Bb), a membraneless organelle conserved across species from insects to humans. However, the mechanisms of Bb formation are still unclear. Here, we elucidate mechanisms of Bb formation in zebrafish through developmental biomolecular condensation. Using super-resolution microscopy, live imaging, biochemical, and genetic analysesin-vivo, we demonstrate that Bb formation is driven by molecular condensation through phase-separation of the essential intrinsically disordered protein Bucky ball (Buc). Live imaging, molecular analyses, and FRAP experimentsin-vivoreveal Buc-dependent changes in the Bb condensate’s dynamics and apparent material properties, transitioning from liquid-like condensates to a solid-like stable compartment. Furthermore, we identify a multi-step regulation by microtubules that controls Bb condensation: first through dynein-mediated trafficking of early condensing Buc granules, then by scaffolding condensed granules, likely through molecular crowding, and finally by caging the mature Bb to prevent overgrowth and maintain shape. These regulatory steps ensure the formation of a single intact Bb, which is considered essential for oocyte polarization and embryonic development. Our work offers insight into the long-standing question of the origins of embryonic polarity in non-mammalian vertebrates, support a paradigm of cellular control over molecular condensation by microtubules, and highlight biomolecular condensation as a key process in female reproduction.
Structure of the human RAD17-RFC clamp loader and 9-1-1 checkpoint clamp bound to a dsDNA-ssDNA junction
Authors: Day Matthew , Oliver Antony W. , Pearl Laurence H. 
Published: March 2022

ABSTRACTThe RAD9-RAD1-HUS1 (9-1-1) clamp forms one half of the DNA damage checkpoint system that signals the presence of substantial regions of single-stranded DNA arising from replication fork collapse or resection of DNA double strand breaks. Loaded at the 5’-recessed end of a dsDNA-ssDNA junction by the RAD17-RFC clamp loader complex, the phosphorylated C-terminal tail of the RAD9 subunit of 9-1-1 engages with the mediator scaffold TOPBP1 which in turn activates the ATR kinase, localised through the interaction of its constitutive partner ATRIP with RPA-coated ssDNA.Using cryogenic electron microscopy (cryoEM) we have determined the structure of a complex of the human RAD17-RFC clamp loader bound to human 9-1-1, engaged with a dsDNA-ssDNA junction. The structure answers the key questions of how RAD17 confers specificity for 9-1-1 over PCNA, and how the clamp loader specifically recognises the recessed 5’ DNA end and fixes the orientation of 9-1-1 on the ssDNA.
Structural and biochemical insights into lipid transport by VPS13 proteins
Authors: Adlakha Jyoti , Hong Zhouping , Li PeiQi , Reinisch Karin M. 
Published: March 2022

AbstractVPS13 proteins are proposed to function at contact sites between organelles as bridges for lipids to move directionally and in bulk between organellar membranes. VPS13s are anchored between membranes via interactions with receptors, including both peripheral or integral membrane proteins. Here we present the crystal structure of VPS13s adaptor binding domain (VAB) complexed with a Pro-X-Pro peptide recognition motif present in one such receptor, the integral membrane protein Mcp1p, and show biochemically that other Pro-X-Pro motifs bind the VAB in the same site. We further demonstrate that Mcp1p and another integral membrane protein that interacts directly with human VPS13A, XK, are scramblases. This finding supports an emerging paradigm of a partnership between bulk lipid transport proteins and scramblases. Scramblases can re-equilibrate lipids between membrane leaflets as lipids are removed from or inserted into, respectively, the cytosolic leaflet of donor and acceptor organelles in the course of protein-mediated transport.