bluuebunny/crossref_metadata_2025_split huggingface dataset:
HIV-1 Vpu promotes phagocytosis of infected CD4+T cells by macrophages through downregulation of CD47
Authors: Cong Lijun , Sugden Scott M. , Leclair Pascal , Lim Chinten James , Pham Tram NQ. , Cohen Éric A. 
Published: March 2021

ABSTRACTHuman immunodeficiency virus (HIV) remodels the cell surface of infected cells to facilitate viral dissemination and promote immune evasion. The membrane-associated Vpu accessory protein encoded by HIV-1 plays a key role in this process by altering cell surface levels of multiple host proteins. Using an unbiased quantitative plasma membrane profiling approach, we previously identified CD47 as a putative host target downregulated by Vpu. CD47 is a ubiquitously-expressed cell surface protein that interacts with the myeloid cell inhibitory receptor SIRPα to deliver a “don’t-eat-me” signal, thus protecting cells from phagocytosis. In this study, we investigate whether CD47 modulation by HIV-1 Vpu might promote the susceptibility of macrophages to viral infection via phagocytosis of infected CD4+T cells. Indeed, we find that Vpu downregulates CD47 expression on infected CD4+T cells leading to an enhanced capture and phagocytosis by macrophages. Interestingly, it is through this process that a CCR5-tropic transmitted/founder (T/F) virus, which otherwise poorly infects macrophages in its cell-free form, becomes infectious in macrophages. Importantly, we show that HIV-1-infected cells expressing a Vpu-resistant CD47 mutant are less prone to infect macrophages through phagocytosis. Mechanistically, Vpu forms a physical complex with CD47 through its transmembrane domain and targets the latter for lysosomal degradation. These results reveal a novel role of Vpu in modulating macrophage infection, which has important implications for HIV-1 transmission in early stages of infection and the establishment of viral reservoir.IMPORTANCEMacrophages play critical roles in HIV transmission, viral spread early in infection, and as a reservoir of virus. Selective capture and engulfment of HIV-1 infected T cells was shown to drive efficient macrophage infection suggesting that this mechanism represents an important mode of infection notably for weakly macrophage-tropic T/F viruses. In this study, we provide insight into the signals that regulate this process. We show that the HIV-1 accessory protein Vpu downregulates cell surface levels of CD47, a host protein that interacts with the inhibitory receptor SIRPα to deliver a “don’t-eat-me” signal to macrophages. This allows for enhanced capture and phagocytosis of infected T cells by macrophages, ultimately leading to their productive infection even with T/F virus. These findings provide new insights into the mechanisms governing the intercellular transmission of HIV-1 to macrophages with implications for the establishment of the macrophage reservoir and early HIV-1 disseminationin vivo.
Longitudinal characterization of humoral and cellular immunity in hospitalized COVID-19 patients reveal immune persistence up to 9 months after infection
Authors: Sandberg John Tyler , Varnaitė Renata , Christ Wanda , Chen Puran , Muvva Jagadeeswara R. , Maleki Kimia T. , García Marina , Dzidic Majda , Folkesson Elin , Skagerberg Magdalena , Ahlén Gustaf , Frelin Lars , Sällberg Matti ,   The Karolinska COVID-19 Study Group, Eriksson Lars I. , Rooyackers Olav , Sönnerborg Anders , Buggert Marcus , Björkström Niklas K. , Aleman Soo , Strålin Kristoffer , Klingström Jonas , Ljunggren Hans-Gustaf , Blom Kim , Gredmark-Russ Sara 
Published: March 2021

AbstractBackgroundInsights into early, specific humoral and cellular responses to infection with SARS-CoV-2, as well as the persistence and magnitude of resulting immune memory is important amidst the ongoing pandemic. The combination of humoral and cellular immunity will most likely contribute to protection from reinfection or severe disease.MethodsHere, we conducted a longitudinal study on hospitalized moderate and severe COVID-19 patients from the acute phase of disease into convalescence at five- and nine-months post symptom onset. Utilizing flow cytometry, serological assays as well as B cell and T cell FluoroSpot assays, we assessed the magnitude and specificity of humoral and cellular immune memory during and after human SARS-CoV-2 infection.FindingsDuring acute COVID-19, we observed an increase in germinal center activity, a substantial expansion of antibodysecreting cells, and the generation of SARS-CoV-2-neutralizing antibodies. Despite gradually decreasing antibody levels, we show persistent, neutralizing antibody titers as well as robust specific memory B cell responses and polyfunctional T cell responses at five- and nine-months after symptom onset in both moderate and severe COVID-19 patients. Long-term SARS-CoV-2 specific responses were marked by preferential targeting of spike over nucleocapsid protein.ConclusionsOur findings describe the initiation and, importantly, persistence of cellular and humoral SARS-CoV-2 specific immunological memory in hospitalized COVID-19 patients long after recovery, likely contributing towards protection against reinfection.
3’-Sulfated Lewis A is a Biomarker for Metaplastic and Oncogenic Transformation of Several Gastrointestinal Epithelia
Authors: Brown Jeffrey W. , Das Koushik K. , Kalas Vasilios , Das Kiron M. , Mills Jason C. 
Published: March 2021

ABSTRACTIntroductionMultiple previous studies have shown the monoclonal antibody Das-1 (formerly called 7E12H12) specifically recognizes metaplastic and carcinomatous lesions in multiple organs of the gastrointestinal system (e.g. Barrett’s esophagus, intestinal-type metaplasia of the stomach, gastric adenocarcinoma, high-grade pancreatic intraepithelial neoplasm, and pancreatic ductal adenocarcinoma) as well as in other organs (bladder and lung carcinomas). Beyond being a useful biomarker in tissue, mAb Das-1 has recently proven to be more accurate than current paradigms for identifying cysts harboring advanced neoplasia. Though this antibody has been used extensively for clinical, basic science, and translational applications for decades, its epitope has remained elusive.MethodsIn this study, we chemically deglycosylated a standard source of antigen, which resulted in near complete loss of the signal as measured by western blot analysis. The epitope recognized by mAb Das-1 was determined by affinity to a comprehensive glycan array and validated by inhibition of a direct ELISA.ResultsThe epitope recognized by mAb Das-1 is 3’-Sulfo-Lewis A (3’-Sulfo-LeA). 3’-Sulfo-LeAis broadly reexpressed across numerous GI epithelia and elsewhere only after metaplastic and carcinomatous transformation.Discussion3’-Sulfo-LeAis a clinically important antigen that can be detected both intracellularly in tissue using immunohistochemistry and extracellularly in cyst fluid and serum by ELISA. The results open new avenues for tumorigenic risk stratification of various gastrointestinal lesions.
RABL6A promotes pancreatic neuroendocrine tumor angiogenesis and progressionin vivo
Authors: Maharjan Chandra K. , Kaemmer Courtney A. , Muniz Viviane P. , Bauchle Casey , Mott Sarah L. , Zamba K.D. , Breheny Patrick , Leidinger Mariah R. , Darbro Benjamin W. , Stephens Samuel B. , Meyerholz David K. , Quelle Dawn E. 
Published: March 2021

AbstractPancreatic neuroendocrine tumors (pNETs) are difficult-to-treat neoplasms whose incidence is rising. Greater understanding of pNET pathogenesis is needed to identify new biomarkers and targets for improved therapy. RABL6A, a novel oncogenic GTPase, is highly expressed in patient pNETs and required for pNET cell proliferation and survivalin vitro. Here, we investigated the role of RABL6A in pNET progressionin vivousing a well-established model of the disease. RIP-Tag2 (RT2) mice develop functional pNETs (insulinomas) due to SV40 large T-antigen expression in pancreatic islet β cells. RABL6A loss in RT2 mice significantly delayed pancreatic tumor formation, reduced tumor angiogenesis and mitoses, and extended survival. Those effects correlated with upregulation of anti-angiogenic p19ARF and downregulation of proangiogenicc-Mycin RABL6A-deficient islets and tumors. Our findings demonstrate that RABL6A is a bona fide oncogenic driver of pNET angiogenesis and developmentin vivo.
Histone sample preparation for bottom-up mass spectrometry: a roadmap to informed decisions
Authors: Daled Simon , Willems Sander , Van Puyvelde Bart , Corveleyn Laura , Verhelst Sigrid , De Clerck Laura , Deforce Dieter , Dhaenens Maarten 
Published: March 2021

AbstractHistone-based chromatin organization enabled eukaryotic genome complexity. This epigenetic control mechanism allowed for the differentiation of stable gene-expression and thus the very existence of multicellular organisms. This existential role in biology makes histones one of the most complexly modified molecules in the biotic world, which makes these key regulators notoriously hard to analyze. We here provide a roadmap to enable fast and informed selection of a bottom-up mass spectrometry sample preparation protocol that matches a specific research question. We therefore propose a two-step assessment procedure: (i) visualization of the coverage that is attained for a given workflow and (ii) direct alignment-between-runs to assess potential pitfalls at the ion level. To illustrate the applicability, we compare four different sample preparation protocols, while adding a new enzyme to the toolbox, i.e., RgpB (GingisREX®, Genovis), an endoproteinase that selectively and efficiently cleaves at the c-terminal end of arginine residues.Raw data is available via ProteomeXchange with identifier PXD024423.
A distinct assembly pathway of the human 39S late pre-mitoribosome
Authors: Cheng Jingdong , Berninghausen Otto , Beckmann Roland 
Published: March 2021

AbstractAssembly of the mitoribosome is largely enigmatic and involves numerous assembly factors. However, little is known about their function and the architectural transitions of the pre-ribosomal intermediates. Here, we solved cryo-EM structures of the human 39S large subunit pre-ribosomes, representing four distinct late state intermediates. Besides the MALSU1 complex, we identified several assembly factors, including the DDX28 helicase, MRM3, GTPBP10 and the NSUN4-mTERF4 complex, all of which keep the 16S rRNA in immature conformations. The late transitions mainly involved rRNA domains IV and V, which form the central protuberance, the intersubunit side and the peptidyltransferase center of the 39S subunit. Unexpectedly, we found deacylated tRNA in the ribosomal E-site, suggesting a role in 39S assembly. Taken together, our study provides an architectural inventory of the distinct late assembly phase of the human 39S mitoribosome.
Single-stranded nucleic acid sensing and coacervation by linker histone H1
Authors: Leicher Rachel , Osunsade Adewola , Latham Andrew P. , Chua Gabriella N. L. , Watters John W. , Christodoulou-Rubalcava Sophia , Zhang Bin , David Yael , Liu Shixin 
Published: March 2021

ABSTRACTThe linker histone H1 is the most abundant group of eukaryotic chromatin-binding proteins. The mechanism underlying the diverse physiological functions of H1 remains unclear. Here we used single-molecule fluorescence and force microscopy to observe the behavior of H1 on DNA under different tensions. Unexpectedly, we found that H1 coalesces around nascent ssDNA. Molecular dynamics simulations revealed that multivalent and transient interactions between H1 and ssDNA mediate their phase separation. We further showed that longer and unpaired nucleic acids result in more viscous, gel-like H1 droplets. Finally, we imaged H1 puncta in cells under normal and stressed conditions and observed that RPA and H1 occupy separate nuclear regions. Overall, our results provide a new perspective to understanding the role of H1 in genome organization and maintenance.
Identification of guanylyltransferase activity in the SARS-CoV-2 RNA polymerase
Authors: Walker Alexander P , Fan Haitian , Keown Jeremy R , Grimes Jonathan M , Fodor Ervin 
Published: March 2021

AbstractSARS-CoV-2 is a positive-sense RNA virus that is responsible for the ongoing Coronavirus Disease 2019 (COVID-19) pandemic, which continues to cause significant morbidity, mortality and economic strain. SARS-CoV-2 can cause severe respiratory disease and death in humans, highlighting the need for effective antiviral therapies. The RNA synthesis machinery of SARS-CoV-2 is an ideal drug target and consists of non-structural protein 12 (nsp12), which is directly responsible for RNA synthesis, and numerous co-factors that are involved in RNA proofreading and 5’ capping of viral mRNAs. The formation of the 5’ cap-1 structure is known to require a guanylyltransferase (GTase) as well as 5’ triphosphatase and methyltransferase activities. However, the mechanism of SARS-CoV-2 mRNA capping remains poorly understood. Here we show that the SARS-CoV-2 RNA polymerase nsp12 functions as a GTase. We characterise this GTase activity and find that the nsp12 NiRAN (nidovirus RdRP-associated nucleotidyltransferase) domain is responsible for carrying out the addition of a GTP nucleotide to the 5’ end of viral RNA via a 5’ to 5’ triphosphate linkage. We also show that remdesivir triphosphate, the active form of the antiviral drug remdesivir, inhibits the SARS-CoV-2 GTase reaction as efficiently as RNA polymerase activity. These data improve understanding of coronavirus mRNA cap synthesis and highlight a new target for novel or repurposed antiviral drugs against SARS-CoV-2.ImportanceSARS-CoV-2 is a respiratory RNA virus responsible for the Coronavirus Disease 2019 (COVID-19) pandemic. Coronaviruses encode an RNA polymerase which, in combination with other viral proteins, is responsible for synthesising capped viral mRNA. mRNA cap synthesis requires a guanylyltransferase enzyme; here we show that the SARS-CoV-2 guanylyltransferase is located in the viral RNA polymerase, and we identify the protein domain responsible for guanylyltransferase activity. Furthermore we demonstrate that remdesivir triphosphate, the active metabolite of remdesivir, inhibits both the guanylyltransferase and RNA polymerase functions of the SARS-CoV-2 RNA polymerase. These findings improve understanding of the coronavirus mRNA cap synthesis mechanism, in addition to highlighting a new target for the development of therapeutics to treat SARS-CoV-2 infection.
The ConservedColletotrichumspp. Effector CEC3 Induces Nuclear Expansion and Cell Death in Plants
Authors: Tsushima Ayako , Narusaka Mari , Gan Pamela , Kumakura Naoyoshi , Hiroyama Ryoko , Kato Naoki , Takahashi Shunji , Takano Yoshitaka , Narusaka Yoshihiro , Shirasu Ken 
Published: March 2021

AbstractPlant pathogens secrete small proteins, known as effectors, that promote infection by manipulating host cells. Members of the phytopathogenic fungal genusColletotrichumcollectively have a broad host range and generally adopt a hemibiotrophic lifestyle that includes an initial biotrophic phase and a later necrotrophic phase. We hypothesized thatColletotrichumfungi use a set of conserved effectors during infection to support the two phases of their hemibiotrophic lifestyle. This study aimed to examine this hypothesis by identifying and characterizing conserved effectors amongColletotrichumfungi. Comparative genomic analyses using genomes of ascomycete fungi with different lifestyles identified seven effector candidates that are conserved across the genusColletotrichum. Transient expression assays showed that one of these conserved effectors, CEC3, induces nuclear expansion and cell death inNicotiana benthamiana, suggesting that CEC3 is involved in promoting host cell death during infection. Nuclear expansion and cell death induction were commonly observed in CEC3 homologs from four differentColletotrichumspecies that vary in host specificity. Thus, CEC3 proteins could represent a novel class of core effectors with functional conservation in the genus Colletotrichum.
The fungal root endophyteSerendipita vermiferadisplays inter-kingdom synergistic beneficial effects with the microbiota inArabidopsis thalianaand barley
Authors: Mahdi Lisa K. , Miyauchi Shingo , Uhlmann Charles , Garrido-Oter Ruben , Langen Gregor , Wawra Stephan , Niu Yulong , Robertson-Albertyn Senga , Bulgarelli Davide , Parker Jane E. , Zuccaro Alga 
Published: March 2021

AbstractPlant root-associated bacteria can confer protection against pathogen infection. By contrast, the beneficial effects of root endophytic fungi and their synergistic interactions with bacteria remain poorly defined. We demonstrate that the combined action of a fungal root endophyte from a widespread taxon with core bacterial microbiota members provides synergistic protection against an aggressive soil-borne pathogen inArabidopsis thalianaand barley. We additionally show early inter-kingdom growth promotion benefits which are host and microbiota composition dependent.HighlightsThe root endophytic fungusSerendipita vermiferacan functionally replace core bacterial microbiota members in mitigating pathogen infection and disease symptoms.S. vermiferaadditionally stabilizes and potentiates the protective activities of root-associated bacteria and mitigates the negative effects of a non-native bacterial community inA. thaliana.Inter-kingdom synergistic beneficial effects do not require extensive host transcriptional reprogramming nor high levels ofS. vermiferacolonisation.Inter-kingdom protective benefits are largely independent of the host while synergism leading to early inter-kingdom growth promotion is driven by host species and microbiota composition.
C-Jun N-terminal kinase post-translational regulation of pain-related Acid-Sensing Ion Channels 1b and 3
Authors: Verkest Clément , Diochot Sylvie , Lingueglia Eric , Baron Anne 
Published: March 2021

AbstractNeuronal proton-gated Acid-Sensing Ion Channels (ASICs) participate in the detection of tissue acidosis, a phenomenon often encountered in painful pathological diseases. Such conditions often involve in parallel the activation of various signaling pathways such as the Mitogen Activated Protein Kinases (MAPKs) that ultimately leads to phenotype modifications of sensory neurons. Here, we identify one member of the MAPKs, c-Jun N-terminal Kinase (JNK), as a new post-translational positive regulator of ASIC channels in rodent sensory neurons. Recombinant H+-induced ASIC currents in HEK293 cells are potently inhibited within minutes by the JNK inhibitor SP600125 in a subunit and species dependent manner, targeting both rat and human ASIC1b and ASIC3 subunits but only mouse ASIC1b subunit. The regulation by JNK of recombinant ASIC1b- and ASIC3-containing channels (homomers and heteromers) is lost upon mutation of a putative phosphorylation site within the intracellular N- and the C-terminal domain of the ASIC1b and ASIC3 subunit, respectively. Moreover, short-term JNK activation regulates the activity of native ASIC1b- and ASIC3-containing channels in rodent sensory neurons and is involved in the rapid potentiation of ASIC activity by the proinflammatory cytokine TNFα. Local JNK activationin vivoin mice induces a short-term potentiation of the acid-induced cutaneous pain in inflammatory conditions that is partially blocked by the ASIC1-specific inhibitor mambalgin-1. Collectively, our data identify pain-related channels as novel physiological JNK substrates in nociceptive neurons, and propose JNK-dependent phosphorylation as a fast post-translational mechanism of regulation of sensory neuron-expressed ASIC1b- and ASIC3-containing channels that may contribute to peripheral sensitization and pain hypersensitivity.
Comprehensive mouse gut metagenome catalog reveals major difference to the human counterpart
Authors: Kieser Silas , Zdobnov Evgeny M. , Trajkovski Mirko 
Published: March 2021

AbstractMouse is the most used model for studying the impact of microbiota on its host, but the repertoire of species from the mouse gut microbiome remains largely unknown. Here, we construct a Comprehensive Mouse Gut Metagenome (CMGM) catalog by assembling all currently available mouse gut metagenomes and combining them with published reference and metagenome-assembled genomes. The 50’011 genomes cluster into 1’699 species, of which 78.1% are uncultured, and we discovered 226 new genera, 7 new families, and 1 new order. Rarefaction analysis indicates comprehensive sampling of the species from the mouse gut. CMGM enables an unprecedented coverage of the mouse gut microbiome exceeding 90%. Comparing CMGM to the human gut microbiota shows an overlap 64% at the genus, but only 16% at the species level, demonstrating that human and mouse gut microbiota are largely distinct.
Geographic Confounding in Genome-Wide Association Studies
Authors: Abdellaoui Abdel , Verweij Karin J.H. , Nivard Michel G. 
Published: March 2021

AbstractGene-environment correlations can bias associations between genetic variants and complex traits in genome-wide association studies (GWASs). Here, we control for geographic sources of gene-environment correlation in GWASs on 56 complex traits (N=69,772–271,457). Controlling for geographic region significantly decreases heritability signals for SES-related traits, most strongly for educational attainment and income, indicating that socio-economic differences between regions induce gene-environment correlations that become part of the polygenic signal. For most other complex traits investigated, genetic correlations with educational attainment and income are significantly reduced, most significantly for traits related to BMI, sedentary behavior, and substance use. Controlling for current address has greater impact on the polygenic signal than birth place, suggesting both active and passive sources of gene-environment correlations. Our results show that societal sources of social stratification that extend beyond families introduce regional-level gene-environment correlations that affect GWAS results.
Mixed emotional appeal enhances advertising effectiveness of pro-environmental luxury brands: the mediating role of cognitive flexibility
Authors: Nallaperuma Kaushalya , Septianto Felix , Bandyopadhyay Argho 
Published: March 2021

PurposeThe concepts of luxury and pro-environment may be viewed as being in contradiction with each other. Consequently, it is unclear how to promote pro-environmental luxury brands. The present research seeks to develop effective advertising strategies for pro-environmental luxury brands by employing mixed emotional appeals.Design/methodology/approachTwo experimental studies were conducted to test two hypotheses. Study 1 examines the effects of mixed emotions (happiness and sadness vs. happiness alone) on intentions to purchase a pro-environmental luxury product. Study 2 replicates the findings of Study 1 using a different product and extends it by establishing the underlying mechanism.FindingsThe results reveal that an advertisement featuring mixed emotions of happiness and sadness (vs. happiness alone) enhances intentions to purchase a pro-environmental luxury product. Further, the effect is mediated by cognitive flexibility.Originality/valueThe present research tests a novel perspective on how mixed emotional appeals can leverage the advertising effectiveness of pro-environmental luxury brands.