bluuebunny/crossref_metadata_2025_split huggingface dataset:
All small things considered: the diversity of fungi, bacteria and oomycota isolated from the seagrass,Zostera marina
Authors: Ettinger Cassandra L. , Eisen Jonathan A. 
Published: March 2020

AbstractFungi in the marine environment are often neglected as a research topic, despite that fungi having critical roles on land as decomposers, pathogens or beneficial endophytes. Here we used culture-dependent methods to survey the fungi associated with the seagrass,Zostera marina, also obtaining bacteria and oomycete isolates in the process. A total of 108 fungi, 41 bacteria and 2 oomycetes were isolated. These isolates were then taxonomically identified using a combination of molecular and phylogenetic methods. The majority of the fungal isolates were classified as belonging to the classes Eurotiomycetes, Dothideomycetes, and Sordariomycetes. Most fungal isolates were habitat generalists likePenicillium sp.andCladosporium sp., but we also cultured a diverse set of rare taxa including possible habitat specialists likeColletotrichum sp.which may preferentially associate withZ. marinaleaf tissue. Although the bulk of bacterial isolates were identified as being from known ubiquitous marine lineages, we also obtained several Actinomycetes isolates which might produce interesting secondary metabolites and aPhyllobacterium sp. which may be involved in nitrogen cycling in the seagrass ecosystem. We identified two oomycetes, another understudied group of marine microbial eukaryotes, asHalophytophthora sp. which may be opportunistic pathogens ofZ. marina. Overall, this study generates a culture collection of fungi, bacteria and oomycetes which expands knowledge of the diversity ofZ. marinaassociated microbes and highlights a need for more investigation into the functional and evolutionary roles of microbial eukaryotes associated with seagrasses.
Increased Ethanol Intake is Associated with Social Anxiety in Offspring Exposed to Ethanol on Gestational Day 12
Authors: Diaz Marvin R. , Johnson Julia M. , Varlinskaya Elena I. 
Published: March 2020

AbstractPrenatal alcohol exposure (PAE) can result in physical, cognitive, and neurological deficits termed Fetal Alcohol Spectrum Disorder (FASD). Deficits in social functioning associated with PAE are frequently observed and persist throughout the lifespan. Social impairments, such as social anxiety, are associated with increased alcohol abuse, which is also highly pervasive following PAE. Yet, the relationship between PAE-induced social alterations and alcohol intake later in life is not well understood. In order to test this relationship, we exposed pregnant female Sprague Dawley rats to a single instance of PAE on gestational day 12 and tested offspring in adulthood (postnatal day 63) in a modified social interaction test followed by alternating alone and social ethanol intake sessions. Consistent with our previous findings, we found that, in general, PAE reduced social preference (measure of social anxiety-like behavior) in female but not male adults. However, ethanol intake was significantly higher in the PAE group regardless of sex. When dividing subjects according to level of social anxiety-like behavior (low, medium, or high), PAE males (under both drinking contexts) and control females (under the social drinking context) with a high social anxiety phenotype showed the highest level of ethanol intake. Taken together, these data indicate that PAE differentially affects the interactions between social anxiety, ethanol intake, and drinking context in males and females. These findings extend our understanding of the complexity and persistence of PAE’s sex-dependent effects into adulthood.
A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV
Authors: Yuan Meng , Wu Nicholas C. , Zhu Xueyong , Lee Chang-Chun D. , So Ray T. Y. , Lv Huibin , Mok Chris K. P. , Wilson Ian A. 
Published: March 2020

ABSTRACTThe outbreak of COVID-19, which is caused by SARS-CoV-2 virus, continues to spread globally, but there is currently very little understanding of the epitopes on the virus. In this study, we have determined the crystal structure of the receptor-binding domain (RBD) of the SARS-CoV-2 spike (S) protein in complex with CR3022, a neutralizing antibody previously isolated from a convalescent SARS patient. CR3022 targets a highly conserved epitope that enables cross-reactive binding between SARS-CoV-2 and SARS-CoV. Structural modeling further demonstrates that the binding site can only be accessed when at least two RBDs on the trimeric S protein are in the “up” conformation. Overall, this study provides structural and molecular insight into the antigenicity of SARS-CoV-2.ONE SENTENCE SUMMARYStructural study of a cross-reactive SARS antibody reveals a conserved epitope on the SARS-CoV-2 receptor-binding domain.
A molecular map of lymph node blood vascular endothelium at single cell resolution
Authors: Brulois Kevin , Rajaraman Anusha , Szade Agata , Nordling Sofia , Bogoslowski Ania , Dermadi Denis , Rahman Milladur , Kiefel Helena , O’Hara Edward , Koning Jasper J , Kawashima Hiroto , Zhou Bin , Vestweber Dietmar , Red-Horse Kristy , Mebius Reina , Adams Ralf H. , Kubes Paul , Pan Junliang , Butcher Eugene C 
Published: March 2020

AbstractBlood vascular endothelial cells (BECs) control the immune response by regulating immune cell recruitment, metabolite exchange and blood flow in lymphoid tissues. However, the diversity of BEC and their origins during immune angiogenesis remain poorly understood. Here we profile transcriptomes of BEC from mouse peripheral lymph nodes and map key phenotypes to the vasculature. Our analysis identifies multiple novel subsets including a venous population whose gene signature predicts an unexpectedly selective role in myeloid cell (vs lymphocyte) recruitment to the medulla, confirmed by 2 photon videomicroscopy. We define five phenotypes of capillary lining BEC including a capillary resident regenerative population (CRP) that displays stem cell and migratory gene signatures and contributes to homeostatic BEC turnover and to vascular neogenesis after immunization. Trajectory analyses reveal retention of developmental programs along a progression of cellular phenotypes from CRP to mature venous and arterial BEC subsets. Overall, our single cell atlas provides a molecular blueprint of the lymph node blood vasculature and defines subset specialization for immune cell recruitment and vascular homeostasis.
HCFC1R1 Deficiency Blocks Herpes Simplex Virus-1 Infection by Inhibiting Nuclear Translocation of HCFC1 and VP16
Authors: Shen Yangkun , Ye Zhoujie , Zhao Xiangqian , Feng Zhihua , Chen Jinfeng , Yang Lei , Chen Qi 
Published: March 2020

ABSTRACTUpon HSV-1 infection, viral protein 16 (VP16), supported by Host Cell Factor C1 (HCFC1), is rapidly transported into the nucleus, and help to express a series of HSV-1 immediate-early proteins to begin its lytic replication. However, no direct evidence has shown if the HCFC1 deficiency can affect the proliferation of HSV-1 so far. Here, we showed that the HCFC1 deficiency led to a strong resistance to HSV-1 infection. Moreover, we identified Host Cell Factor C1 Regulator 1 (HCFC1R1) as a new host factor acting early in HSV infection for the transport of the HSV-1 capsid to the nucleus. The HCFC1R1 deficiency also led to a strong resistance to HSV-1 infection. The HCFC1R1 deficiency did not affect the attachment of HSV-1 to host cells but act early in HSV-1 infection by perturbing the formation of HCFC1/VP16 complex. Remarkably, in addition to wild-type HSV-1 infection, the host cells in the absence of either HCFC1 or HCFC1R1 showed strong resistant to the infection of TK-deficient HSV-1, which strain can course severe symptoms and tolerate to the current anti-HSV drug Acyclovir. Our data suggest that HCFC1 or HCFC1R1 may be used as the novel target for developing anti-HSV-1 therapies.IMPORTANCEHerpes simplex virus-1 (HSV-1) is widely spread in the human population and can cause a variety of herpetic diseases. Acyclovir, a guanosine analogue that targets the TK protein of HSV-1, is the first specific and selective anti-HSV-1 drug. However, the rapid emergence of resistant HSV-1 strains is occurring worldwide, endangering the efficacy of Acyclovir. Alternatively, targeting host factors is another strategy to stop HSV-1 infection. Unfortunately, although the HSV-1’s receptor, Nectin-1, was discovered in 1998, no effective antiviral drug to date has been developed by targeting Nectin-1. Targeting multiple pathways is the ultimate choice to prevent HSV-1 infection. Here we demonstrated that the deletion of HCFC1 or HCFC1R1 exhibits a strong inhibitory effect on both wild-type and TK-deficient HSV-1. Overall, we present evidence that HCFC1 or HCFC1R1 may be used as the novel target for developing anti-HSV-1 therapies with a defined mechanism of action.
Cell Type Development inChlamydia trachomatisFollows a Program Intrinsic to the Reticulate Body
Authors: Chiarelli Travis J , Grieshaber Nicole A , Omsland Anders , Remien Christopher H , Grieshaber Scott S 
Published: March 2020

AbstractThe obligate intracellular bacterial pathogenChlamydia trachomatis(Ctr) is reliant on an unusual developmental cycle consisting of two cell forms termed the elementary body (EB) and the reticulate body (RB). The EB is infectious and utilizes a type III secretion system and preformed effector proteins during invasion, but does not replicate. The RB replicates in the host cell but is non-infectious. This developmental cycle is central to chlamydial pathogenesis. In this study we developed mathematical models of the chlamydial developmental cycle that account for potential factors influencing the timing of RB to EB cell type switching during infection. Our models predicted that two broad categories of regulatory signals for RB to EB development could be differentiated experimentally; an “intrinsic” cell autonomous program inherent to each RB or an “extrinsic” environmental signal to which RBs respond. To experimentally differentiate between these hypotheses, we tracked the expression ofCtrdevelopmental specific promoters using fluorescent reporters and live cell imaging. These experiments indicated that EB production was not influenced by increased MOI or by superinfection, suggesting the cycle follows an intrinsic program that is not influenced by environmental factors. Additionally, live cell imaging of these promoter constructs revealed that EB development is a multistep process linked to RB growth rate and cell division. The formation of EBs followed a cell type gene expression progression with the promoters foreuoandihtAactive in RBs, while the promoter forhctAwas active in early EBs/intermediate cells and finally the promoters for the true late genes,hctB, scc2, andtarpactive in the maturing EB.ImportanceChlamydia trachomatisis an obligate intracellular bacteria that can cause trachoma, cervicitis, urethritis, salpingitis, and pelvic inflammatory disease. To establish infection in host cellsChlamydiamust complete a multi cell type developmental cycle. The developmental cycle consists of two specialized cells; the EB which mediates infection of new cells and the RB which replicates and eventually produces more EB cells to mediate the next round of infection. By developing and testing mathematical models to discriminate between two competing hypotheses for the nature of the signal controlling RB to EB cell type switching. We demonstrate that RB to EB development follows a cell autonomous program that does not respond to environmental cues. Additionally, we show that RB to EB development is a function of cell growth and cell division. This study serves to further our understanding of the chlamydial developmental cycle that is central to the bacterium’s pathogenesis.
Highly accurate and sensitive diagnostic detection of SARS-CoV-2 by digital PCR
Authors: Dong Lianhua , Zhou Junbo , Niu Chunyan , Wang Quanyi , Pan Yang , Sheng Sitong , Wang Xia , Zhang Yongzhuo , Yang Jiayi , Liu Manqing , Zhao Yang , Zhang Xiaoying , Zhu Tao , Peng Tao , Xie Jie , Gao Yunhua , Wang Di , Zhao Yun , Dai Xinhua , Fang Xiang 
Published: March 2020

BACKGROUNDThe outbreak of COVID-19 caused by a novel Coronavirus (termed SARS-CoV-2) has spread to over 140 countries around the world. Currently, reverse transcription quantitative qPCR (RT-qPCR) is used as the gold standard for diagnostics of SARS-CoV-2. However, the positive rate of RT-qPCR assay of pharyngeal swab samples are reported to vary from 30∼60%. More accurate and sensitive methods are urgently needed to support the quality assurance of the RT-qPCR or as an alternative diagnostic approach.METHODSWe established a reverse transcription digital PCR (RT-dPCR) protocol to detect SARS-CoV-2 on 194 clinical pharyngeal swab samples, including 103 suspected patients, 75 close contacts and 16 supposed convalescents.RESULTSThe limit of blanks (LoBs) of the RT-dPCR assays were ∼1.6, ∼1.6 and ∼0.8 copies/reaction for ORF 1ab, N and E genes, respectively. The limit of detection (LoD) was 2 copies/reaction. For the 103 fever suspected patients, the sensitivity of SARS-CoV-2 detection was significantly improved from 28.2% by RT-qPCR to 87.4% by RT-dPCR. For close contacts, the suspect rate was greatly decreased from 21% down to 1%. The overall sensitivity, specificity and diagnostic accuracy of RT-dPCR were 90%, 100% and 93 %, respectively. In addition, quantification of the viral load for convalescents by RT-dPCR showed that a longer observation period was needed in the hospital for elderly patients.CONCLUSIONRT-dPCR could be a confirmatory method for suspected patients diagnosed by RT-qPCR. Furthermore, RT-dPCR was more sensitive and suitable for low viral load specimens from the both patients under isolation and those under observation who may not be exhibiting clinical symptoms.
ATM-mediated DNA damage response in macrophages primes phagocytosis and immune checkpoint regulation
Authors: Bansal Aakanksha , Neuhaus René , Izquierdo-Alvarez Elena , Vorholt Daniela , Feldkötter Henning , Nolte Hendrik , Lohneis Philipp , Büttner Reinhard , Krüger Markus , Pallasch Christian P. , Schumacher Björn 
Published: March 2020

AbstractGenotoxin-based cancer therapies trigger a DNA damage response (DDR) to eliminate cancer cells but similarly exert profound alterations to the immune cell compartment. Macrophages in the tumor microenvironment are important and multifaceted components in actively sustaining tumor progression but also in clearance of tumor cells and play an important role in the outcome of chemotherapy. Here, we report that post neo-adjuvant chemotherapy macrophages in tumor samples display elevated expression of the immune checkpoint PD-L1. We determined that chemotherapy or direct application of DNA damage to macrophagesin vitrotriggers a specific MDDRpolarization phenotype characterized by increased phagocytic activity, elevated PD-L1 expression, and induction of endotoxin tolerance. Phospho-proteomics analysis revealed epigenetic alterations and ATM-dependent induction of senescence in macrophages upon DNA damage. We propose that ATM-induced senescence and PD-L1 immune checkpoint induction mediate a specific MDDRmacrophage polarization that might contribute to chemotherapy responses. Furthermore, our results clarify the functional role of tumor associated macrophages in the context of DNA damage and combination therapies including checkpoint inhibition.
SARS-CoV-2 invades host cells via a novel route: CD147-spike protein
Authors: Wang Ke , Chen Wei , Zhou Yu-Sen , Lian Jian-Qi , Zhang Zheng , Du Peng , Gong Li , Zhang Yang , Cui Hong-Yong , Geng Jie-Jie , Wang Bin , Sun Xiu-Xuan , Wang Chun-Fu , Yang Xu , Lin Peng , Deng Yong-Qiang , Wei Ding , Yang Xiang-Min , Zhu Yu-Meng , Zhang Kui , Zheng Zhao-Hui , Miao Jin-Lin , Guo Ting , Shi Ying , Zhang Jun , Fu Ling , Wang Qing-Yi , Bian Huijie , Zhu Ping , Chen Zhi-Nan 
Published: March 2020

SUMMARYCurrently, COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been widely spread around the world; nevertheless, so far there exist no specific antiviral drugs for treatment of the disease, which poses great challenge to control and contain the virus. Here, we reported a research finding that SARS-CoV-2 invaded host cells via a novel route of CD147-spike protein (SP). SP bound to CD147, a receptor on the host cells, thereby mediating the viral invasion. Our further research confirmed this finding. First, in vitro antiviral tests indicated Meplazumab, an anti-CD147 humanized antibody, significantly inhibited the viruses from invading host cells, with an EC50of 24.86 μg/mL and IC50of 15.16 μg/mL. Second, we validated the interaction between CD147 and SP, with an affinity constant of 1.85×10−7M. Co-Immunoprecipitation and ELISA also confirmed the binding of the two proteins. Finally, the localization of CD147 and SP was observed in SARS-CoV-2 infected Vero E6 cells by immuno-electron microscope. Therefore, the discovery of the new route CD147-SP for SARS-CoV-2 invading host cells provides a critical target for development of specific antiviral drugs.
Self-antigen driven affinity maturation is required for pathogenic monovalent IgG4 autoantibody development
Authors: Fichtner Miriam L. , Vieni Casey , Redler Rachel L. , Kolich Ljuvica , Jiang Ruoyi , Takata Kazushiro , Stathopoulos Panos , Suarez Pablo , Nowak Richard J. , Burden Steven J. , Ekiert Damian C. , O’Connor Kevin C. 
Published: March 2020

AbstractPathogenic IgG4 autoantibodies in autoimmune myasthenia gravis (MG) are functionally monovalent as a result of Fab-arm exchange. The origin and development of these unique autoantibodies are not well understood. We examined MG patient-derived monoclonal autoantibodies (mAbs), their corresponding germline-encoded unmutated common ancestors (UCA) and monovalent antigen-binding fragments (Fabs) to investigate how antigen-driven affinity maturation contributes to both binding and immunopathology. Mature mAbs, their UCA counterparts and mature monovalent Fabs bound to the autoantigen and retained their pathogenic capacity. However, monovalent UCA Fabs still bound the autoantigen but lost their pathogenic capacity. The mature Fabs were characterized by very high affinity (sub-nanomolar) driven by a rapid on-rate and slow off-rate. However, the UCA affinity was approximately 100-fold less than that of the mature Fabs, which was driven by a rapid off-rate. Crystal structures of two Fabs shed light on how mutations acquired during affinity maturation may contribute to increased MuSK binding affinity. These collective findings indicate that the autoantigen initiates the autoimmune response in MuSK MG and drives autoimmunity through the accumulation of somatic hypermutation such that monovalent IgG4 Fab-arm exchanged MG autoantibodies reach a high affinity threshold required for pathogenic capacity.SummaryIgG4 autoantibodies in autoimmune myasthenia gravis are functionally monovalent, requiring a high affinity threshold featuring fast on/slow off rates, to reach pathogenic capacity. This capacity is dependent on self-antigen initiated and driven maturation, which includes the accumulation of indispensable somatic hypermutations that may alter electrostatic interactions with the antigen.
Differential encoding in prefrontal cortex projection neuron classes across cognitive tasks
Authors: Lui Jan H. , Nguyen Nghia D. , Grutzner Sophie M. , Darmanis Spyros , Peixoto Diogo , Wagner Mark J. , Allen William E. , Kebschull Justus M. , Richman Ethan B. , Ren Jing , Newsome William T. , Quake Stephen R. , Luo Liqun 
Published: March 2020

SUMMARYSingle-cell transcriptomics has been widely applied to classify neurons in the mammalian brain, while systems neuroscience has historically analyzed the encoding properties of cortical neurons without considering cell types. Here we examine how specific transcriptomic types of mouse prefrontal cortex (PFC) projection neurons relate to axonal projections and encoding properties across multiple cognitive tasks. We found that most types projected to multiple targets, and most targets received projections from multiple types, except PFC→PAG (periaqueductal gray). By comparing Ca2+-activity of the molecularly homogeneous PFC→PAG type against two heterogeneous classes in several two-alternative choice tasks in freely-moving mice, we found that all task-related signals assayed were qualitatively present in all examined classes. However, PAG-projecting neurons most potently encoded choice in cued tasks, whereas contralateral PFC-projecting neurons most potently encoded reward context in an uncued task. Thus, task signals are organized redundantly, but with clear quantitative biases across cells of specific molecular-anatomical characteristics.
Dynamic changes in tRNA modifications and abundance during T-cell activation
Authors: Rak Roni , Polonsky Michal , Eizenberg-Magar Inbal , Mo Yufeng , Sakaguchi Yuriko , Mizrahi Orel , Nachshon Aharon , Reich-Zeliger Shlomit , Stern-Ginossar Noam , Dahan Orna , Suzuki Tsutomu , Friedman Nir , Pilpel Yitzhak 
Published: March 2020

AbstractThe tRNA pool determines the efficiency, throughput, and accuracy of translation. Previous studies have identified dynamic changes in the tRNA supply and mRNA demand during cancerous proliferation. Yet, dynamic changes may occur also during physiologically normal proliferation, and these are less characterized. We examined the tRNA and mRNA pools of T-cells during their vigorous proliferation and differentiation upon triggering their antigen receptor. We observe a global signature of switch in demand for codons at the early proliferation phase of the response, accompanied by corresponding changes in tRNA expression levels. In the later phase, upon differentiation, the response of the tRNA pool is relaxed back to basal level, potentially restraining excessive proliferation. Sequencing of tRNAs allowed us to also evaluate their diverse base-modifications. We found that two types of tRNA modifications, wybutosine and ms2t6A, are reduced dramatically during T-cell activation. These modifications occur in the anti-codon loops of two tRNAs that decode “slippery codons”, that are prone to ribosomal frameshifting. Attenuation of these frameshift-protective modifications is expected to increase the potential for proteome-wide frameshifting during T-cell proliferation. Indeed, human cell lines deleted of a wybutosine writer showed increased ribosomal frameshifting, as detected with a HIV gag-pol frameshifting site reporter. These results may explain HIV’s specific tropism towards proliferating T-Cells since it requires ribosomal frameshift exactly on the corresponding codon for infection. The changes in tRNA expression and modifications uncover a new layer of translation regulation during T-cell proliferation and exposes a potential trade-off between cellular growth and translation fidelity.Significance statementThe tRNA pool decodes genetic information during translation. As such, it is subject to intricate physiological regulation in all species, across different physiological conditions. Here we show for the first time a program that governs the tRNA pool and its interaction with the transcriptome upon a physiological cellular proliferation- T-cells activation. We found that upon antigenic activation of T-cells, their tRNA and mRNA pools undergo coordinated and complementary changes, which are relaxed when cells reduce back their proliferation rate and differentiate into memory cells. We found a reduction in two particular tRNA modifications that have a role in governing translation fidelity and frameshift prevention. This exposes a vulnerability in activated T-cells that may be utilized by HIV for its replication.ClassificationBIOLOGICAL SCIENCES; cell biology