bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diagnostic Value of Galactomannan Antigen Test in Serum and Bronchoalveolar Lavage Fluid Samples from Patients with Nonneutropenic Invasive Pulmonary Aspergillosis
Authors: Zhou Wei , Li Hongxing , Zhang Yan , Huang Mei , He Qian , Li Pei , Zhang Fang , Shi Yi , Su Xin 
Published: April 2017

ABSTRACT

The objective of this study was to compare the diagnostic value of galactomannan (GM) detection in bronchoalveolar lavage fluid (BALF) and serum samples from nonneutropenic patients with invasive pulmonary aspergillosis (IPA) and determine the optimal BALF GM cutoff value for pulmonary aspergillosis. GM detection in BALF and serum samples was performed by enzyme-linked immunosorbent assay (ELISA) in 128 patients with clinically suspected nonneutropenic pulmonary aspergillosis between June 2014 and June 2016. On the basis of the clinical and pathological diagnoses, 8 patients were excluded because their diagnosis was uncertain. The remaining 120 patients were diagnosed with either IPA (
n
= 37), community-acquired pneumonia (CAP;
n
= 59), noninfectious diseases (
n
= 19), or tuberculosis (
n
= 5). At a cutoff optical density index (ODI) value of ≥0.5, the sensitivity of BALF GM detection was much higher than that of serum GM detection (75.68% versus 37.84%;
P
= 0.001), but there was no significant difference between their specificities (80.72% versus 87.14%;
P
= 0.286). At a cutoff value of ≥1.0, the sensitivity of BALF GM detection was still much higher than that of serum GM detection (64.86% versus 24.32%;
P
< 0.001), and their specificities were similar (90.36% versus 95.71%;
P
= 0.202). Receiver operating characteristic (ROC) curve analysis showed that when the BALF GM detection cutoff value was 0.7, its diagnostic value for pulmonary aspergillosis was optimized, and the sensitivity and specificity reached 72.97% and 89.16%, respectively. BALF GM detection was valuable for the diagnosis of IPA in nonneutropenic patients, and its diagnostic value was superior to that of serum GM detection. The optimal BALF GM cutoff value was 0.7.
Serine 235 Is the Primary NS5A Hyperphosphorylation Site Responsible for Hepatitis C Virus Replication
Authors: Hsu Shih-Chin , Lo Chieh-Wen , Pan Ting-Chun , Lee Kuan-Ying , Yu Ming-Jiun 
Published: April 2017

ABSTRACTThe nonstructural protein 5A (NS5A) of the hepatitis C virus (HCV) is a phosphoprotein with two phosphorylation states: hypo- and hyperphosphorylation. Genetic mutation studies have demonstrated a cluster of serine residues responsible for NS5A hyperphosphorylation and functions in viral replication and assembly; however, the phosphorylation levels and potential interactions among the serine residues are unclear. We used three specific antibodies to measure NS5A phosphorylation at S222, S235, and S238 that were identified in our previous proteomics study. In the HCV (J6/JFH-1)-infected Huh7.5.1 cells, S222 phosphorylation was barely detected, whereas S235 phosphorylation and S238 phosphorylation were always detected in parallel in time and intracellular spaces. S235A mutation eliminated S238 phosphorylation whereas S238A mutation did not affect S235 phosphorylation, indicating that S235 phosphorylation occurs independently of S238 phosphorylation while S238 phosphorylation depends on S235 phosphorylation. In line with this, immunoprecipitation coupled with immunoblotting showed that S235 phosphorylation existed alone without S238 phosphorylation, whereas S238 phosphorylation existed only when S235 was phosphorylated on the same NS5A molecule. S235-phosphorylated NS5A constituted the primary hyperphosphorylated NS5A species. S235A mutation blunted viral replication, whereas S238A mutation did not affect replication. We concluded that S235 is the primary NS5A hyperphosphorylation site required for HCV replication. S238 is likely phosphorylated by casein kinase Iα, which requires a priming phosphorylation at S235.IMPORTANCEIt has been known for years that the hepatitis C virus nonstructural protein 5A (NS5A) undergoes transition between two phosphorylation states: hypo- and hyperphosphorylation. It is also known that a cluster of serine residues is responsible for NS5A hyperphosphorylation and functions; however, the primary serine residue responsible for NS5A hyperphosphorylation is not clear. Here, we show for the first time that serine 235-phosphorylated NS5A constitutes the primary hyperphosphorylated NS5A species required for viral replication. We also show that NS5A phosphorylation among the serine residues is interdependent and occurs in a directional manner, i.e., phosphorylation at serine 235 leads to phosphorylation at serine 238. Our data provide the first proof-of-principle evidence that NS5A undergoes a sequential phosphorylation cascade.
Pacmanvirus, a New Giant Icosahedral Virus at the Crossroads between Asfarviridae and Faustoviruses
Authors: Andreani Julien , Khalil Jacques Yaacoub Bou , Sevvana Madhumati , Benamar Samia , Di Pinto Fabrizio , Bitam Idir , Colson Philippe , Klose Thomas , Rossmann Michael G. , Raoult Didier , La Scola Bernard 
Published: April 2017

ABSTRACT

African swine fever virus
, a double-stranded DNA virus that infects pigs, is the only known member of the
Asfarviridae
family. Nevertheless, during our isolation and sequencing of the complete genome of faustovirus, followed by the description of kaumoebavirus, carried out over the past 2 years, we observed the emergence of previously unknown related viruses within this group of viruses. Here we describe the isolation of pacmanvirus, a fourth member in this group, which is capable of infecting
Acanthamoeba castellanii
. Pacmanvirus A23 has a linear compact genome of 395,405 bp, with a 33.62% G+C content. The pacmanvirus genome harbors 465 genes, with a high coding density. An analysis of reciprocal best hits shows that 31 genes are conserved between
African swine fever virus
, pacmanvirus, faustovirus, and kaumoebavirus. Moreover, the major capsid protein locus of pacmanvirus appears to be different from those of kaumoebavirus and faustovirus. Overall, comparative and genomic analyses reveal the emergence of a new group or cluster of viruses encompassing
African swine fever virus
, faustovirus, pacmanvirus, and kaumoebavirus.

IMPORTANCE
Pacmanvirus is a newly discovered icosahedral double-stranded DNA virus that was isolated from an environmental sample by amoeba coculture. We describe herein its structure and replicative cycle, along with genomic analysis and genomic comparisons with previously known viruses. This virus represents the third virus, after faustovirus and kaumoebavirus, that is most closely related to classical representatives of the
Asfarviridae
family. These results highlight the emergence of previously unknown double-stranded DNA viruses which delineate and extend the diversity of a group around the asfarvirus members.
Disparate Contributions of Human Retrovirus Capsid Subdomains to Gag-Gag Oligomerization, Virus Morphology, and Particle Biogenesis
Authors: Martin Jessica L. , Mendonça Luiza M. , Angert Isaac , Mueller Joachim D. , Zhang Wei , Mansky Louis M. 
Published: April 2017

ABSTRACT
The capsid domain (CA) of the retroviral Gag protein is a primary determinant of Gag oligomerization, which is a critical step for immature Gag lattice formation and virus particle budding. Although the human immunodeficiency virus type 1 (HIV-1) CA carboxy-terminal domain (CTD) is essential for CA-CA interactions, the CA CTD has been suggested to be largely dispensable for human T-cell leukemia virus type 1 (HTLV-1) particle biogenesis. To more clearly define the roles of the HTLV-1 CA amino-terminal domain (NTD) and CA CTD in particle biogenesis, we generated and analyzed a panel of Gag proteins with chimeric HIV-1/HTLV-1 CA domains. Subcellular distribution and protein expression levels indicated that Gag proteins with a chimeric HIV-1 CA NTD/HTLV-1 CA CTD did not result in Gag oligomerization regardless of the parent Gag background. Furthermore, chimeric Gag proteins with the HTLV-1 CA NTD produced particles phenotypically similar to HTLV-1 immature particles, highlighting the importance of the HTLV-1 CA NTD in HTLV-1 immature particle morphology. Taken together, these observations support the conclusion that the HTLV-1 CA NTD can functionally replace the HIV-1 CA CTD, but the HIV-1 CA NTD cannot replace the HTLV-1 CA CTD, indicating that the HTLV-1 CA subdomains provide distinct contributions to Gag-Gag oligomerization, particle morphology, and biogenesis. Furthermore, we have shown for the first time that HIV-1 and HTLV-1 Gag domains outside the CA (e.g., matrix and nucleocapsid) impact Gag oligomerization as well as immature particle size and morphology.

IMPORTANCE
A key aspect in virus replication is virus particle assembly, which is a poorly understood process for most viruses. For retroviruses, the Gag structural protein is the primary driver of virus particle biogenesis, and the CA CTD is the primary determinant of Gag-Gag interactions for HIV-1. In this study, the HTLV-1 capsid amino-terminal domain was found to provide distinct contributions to Gag-Gag oligomerization, particle morphology, and biogenesis. This study provides information that will aid efforts for discovery of therapeutic targets for intervention.
Analysis of Competing HIV-1 Splice Donor Sites Uncovers a Tight Cluster of Splicing Regulatory Elements within Exon 2/2b
Authors: Brillen Anna-Lena , Walotka Lara , Hillebrand Frank , Müller Lisa , Widera Marek , Theiss Stephan , Schaal Heiner 
Published: April 2017

ABSTRACT

The HIV-1 accessory protein Vif is essential for viral replication by counteracting the host restriction factor APOBEC3G (A3G), and balanced levels of both proteins are required for efficient viral replication. Noncoding exons 2/2b contain the Vif start codon between their alternatively used splice donors 2 and 2b (D2 and D2b). For
vif
mRNA, intron 1 must be removed while intron 2 must be retained. Thus, splice acceptor 1 (A1) must be activated by U1 snRNP binding to either D2 or D2b, while splicing at D2 or D2b must be prevented. Here, we unravel the complex interactions between previously known and novel components of the splicing regulatory network regulating HIV-1 exon 2/2b inclusion in viral mRNAs. In particular, using RNA pulldown experiments and mass spectrometry analysis, we found members of the heterogeneous nuclear ribonucleoparticle (hnRNP) A/B family binding to a novel splicing regulatory element (SRE), the exonic splicing silencer ESS2b, and the splicing regulatory proteins Tra2/SRSF10 binding to the nearby exonic splicing enhancer ESE2b. Using a minigene reporter, we performed bioinformatics HEXplorer-guided mutational analysis to narrow down SRE motifs affecting splice site selection between D2 and D2b. Eventually, the impacts of these SREs on the viral splicing pattern and protein expression were exhaustively analyzed in viral particle production and replication experiments. Masking of these protein binding sites by use of locked nucleic acids (LNAs) impaired Vif expression and viral replication.

IMPORTANCE
Based on our results, we propose a model in which a dense network of SREs regulates
vif
mRNA and protein expression, crucial to maintain viral replication within host cells with varying A3G levels and at different stages of infection. This regulation is maintained by several serine/arginine-rich splicing factors (SRSF) and hnRNPs binding to those elements. Targeting this cluster of SREs with LNAs may lead to the development of novel effective therapeutic strategies.
Dense Array of Spikes on HIV-1 Virion Particles
Authors: Stano Armando , Leaman Daniel P. , Kim Arthur S. , Zhang Lei , Autin Ludovic , Ingale Jidnyasa , Gift Syna K. , Truong Jared , Wyatt Richard T. , Olson Arthur J. , Zwick Michael B. 
Published: April 2017

ABSTRACTHIV-1 is rare among viruses for having a low number of envelope glycoprotein (Env) spikes per virion, i.e., ∼7 to 14. This exceptional feature has been associated with avoidance of humoral immunity, i.e., B cell activation and antibody neutralization. Virus-like particles (VLPs) with increased density of Env are being pursued for vaccine development; however, these typically require protein engineering that alters Env structure. Here, we used instead a strategy that targets the producer cell. We employed fluorescence-activated cell sorting (FACS) to sort for cells that are recognized by trimer cross-reactive broadly neutralizing antibody (bnAb) and not by nonneutralizing antibodies. Following multiple iterations of FACS, cells and progeny virions were shown to display higher levels of antigenically correct Env in a manner that correlated between cells and cognate virions (P= 0.027). High-Env VLPs, or hVLPs, were shown to be monodisperse and to display more than a 10-fold increase in spikes per particle by electron microscopy (average, 127 spikes; range, 90 to 214 spikes). Sequencing revealed a partial truncation in the C-terminal tail of Env that had emerged in the sort; however, iterative rounds of “cell factory” selection were required for the high-Env phenotype. hVLPs showed greater infectivity than standard pseudovirions but largely similar neutralization sensitivity. Importantly, hVLPs also showed superior activation of Env-specific B cells. Hence, high-Env HIV-1 virions, obtained through selection of producer cells, represent an adaptable platform for vaccine design and should aid in the study of native Env.IMPORTANCEThe paucity of spikes on HIV is a unique feature that has been associated with evasion of the immune system, while increasing spike density has been a goal of vaccine design. Increasing the density of Env by modifying it in various ways has met with limited success. Here, we focused instead on the producer cell. Cells that stably express HIV spikes were screened on the basis of high binding by bnAbs and low binding by nonneutralizing antibodies. Levels of spikes on cells correlated well with those on progeny virions. Importantly, high-Env virus-like particles (hVLPs) were produced with a manifest array of well-defined spikes, and these were shown to be superior in activating desirable B cells. Our study describes HIV particles that are densely coated with functional spikes, which should facilitate the study of HIV spikes and their development as immunogens.
Minute Virus of Mice Inhibits Transcription of the Cyclin B1 Gene during Infection
Authors: Fuller Matthew S. , Majumder Kinjal , Pintel David J. 
Published: April 2017

ABSTRACT
Replication of minute virus of mice (MVM) induces a sustained cellular DNA damage response (DDR) which the virus then exploits to prepare the nuclear environment for effective parvovirus takeover. An essential aspect of the MVM-induced DDR is the establishment of a potent premitotic block, which we previously found to be independent of activated p21 and ATR/Chk1 signaling. This arrest, unlike others reported previously, depends upon a significant, specific depletion of cyclin B1 and its encoding RNA, which precludes cyclin B1/CDK1 complex function, thus preventing mitotic entry. We show here that while the stability of cyclin B1 RNA was not affected by MVM infection, the production of nascent cyclin B1 RNA was substantially diminished at late times postinfection. Ectopic expression of NS1 alone did not reduce cyclin B1 expression. MVM infection also reduced the levels of cyclin B1 protein, and RNA levels normally increased in response to DNA-damaging reagents. We demonstrated that at times of reduced cyclin B1 expression during infection, there was a significantly reduced occupancy of RNA polymerase II and the essential mitotic transcription factor FoxM1 on the cyclin B1 gene promoter. Additionally, while total FoxM1 levels remained constant, there was a significant decrease of the phosphorylated, likely active, forms of FoxM1. Targeting of a constitutively active FoxM1 construct or the activation domain of FoxM1 to the cyclin B1 gene promoter via clustered regularly interspaced short palindromic repeats (CRISPR)-enzymatically inactive Cas9 in MVM-infected cells increased both cyclin B1 protein and RNA levels, implicating FoxM1 as a critical target for cyclin B1 inhibition during MVM infection.

IMPORTANCE
Replication of the parvovirus minute virus of mice (MVM) induces a sustained cellular DNA damage response (DDR) which the virus exploits to prepare the nuclear environment for effective takeover. An essential aspect of the MVM-induced DDR is establishment of a potent premitotic block. This block depends upon a significant, specific depletion of cyclin B1 and its encoding RNA that precludes cyclin B1/CDK1 complex functions necessary for mitotic entry. We show that reduced cyclin B1 expression is controlled primarily at the level of transcription initiation. Additionally, the essential mitotic transcription factor FoxM1 and RNA polymerase II were found to occupy the cyclin B1 gene promoter at reduced levels during infection. Recruiting a constitutively active FoxM1 construct or the activation domain of FoxM1 to the cyclin B1 gene promoter via CRISPR-catalytically inactive Cas9 (dCas9) in MVM-infected cells increased expression of both cyclin B1 protein and RNA, implicating FoxM1 as a critical target mediating MVM-induced cyclin B1 inhibition.
Acupuncture Upregulates G Protein Coupled Activity in Samp8 Mice
Authors: Luo Benhua , Zhao Lan , Zhang Xuezhu , Kan Bohong , Liu Yunhe , Jia Yujie , Han Jingxian , Yu Jianchun 
Published: April 2017

Background Transmembrane and intracellular signal transduction of G protein is closely related to the pathophysiology of Alzheimer's disease (AD). Objective To explore the effects of Sanjiao acupuncture on G protein signal transduction pathways in the pathogenesis of AD. Methods 36 senescence-accelerated (SAM) prone 8 mice were divided into three groups that remained untreated (SAMP8, n=12) or received Sanjiao acupuncture (SAMP8+SA, n=12) or control acupuncture (SAMP8+CA, n=12). An additional control group of SAM resistant 1 mice was included (SAMR1 group, n=12). Morris water maze tests were used to investigate learning and memory abilities. Immunoprecipitation and Western blotting were used to study expression of G protein subunits and their activities in the cortex/hippocampus. Results Behavioural analysis showed that acupuncture attenuated the severe cognitive deficits observed in untreated/CA-treated SAMP8 mice. The findings of the G protein activation assays via immunoprecipitation and Western blots were that the physiologically coupled activation rate (PCAR) and maximal coupled activation rate (MCAR) of Gαs and Gαi were decreased in the cortex of SAMP8 vs SAMR1 mice. Sanjiao acupuncture induced an upregulation in the PCAR of Gαs and Gαi. In the hippocampus of untreated SAMP8 mice, the PCAR of Gαs and MCAR of both Gαs and Gαi declined, and Sanjiao acupuncture was associated with an upregulation in the MCAR of Gαs and Gαi. There were no significant differences in Gαs and Gαi expression between the groups. Conclusions Sanjiao acupuncture attenuates cognitive deficits in a mouse model of AD via upregulation of G protein activity and stabilisation of the cellular signal.
Injuries impair the chance of successful performance by sportspeople: a systematic review
Authors: Drew Michael K , Raysmith Ben P , Charlton Paula C 
Published: April 2017

BackgroundCost–benefit analyses have been proposed for determining acceptable risk of injury regarding training and competition participation. Currently, there is no best evidence synthesis of the literature evaluating the relationship between injury/illness and chance of success or failure.ObjectiveTo evaluate the relationship between injury and/or illness and success and/or failure in athletic populations (individual and team sports).MethodsThis review was prospectively registered (PROSPERO CRD42016036729) and a systematic electronic search was conducted in May 2016. Inclusion criterion was any study design describing the association between injury and/or illness and success or failure in athletic performance. Two independent authors screened search results, performed data extraction and assessed methodological quality and strength of evidence using a modified Downs and Black appraisal tool and a modified van Tulder method, respectively.ResultsOf 10 546 titles identified, 14 satisfied the inclusion criteria and 7 had low risk of bias. Outcome measures associated with success and/or failure included: (1) availability of team members, (2) injury incidence, (3) injury burden, (4) squad utilisation and (5, 6) precompetition and in-competition injury. There was strong evidence that (1) increased availability of team members/athletes decreased the risk of failure and (2) precompetition and in-competition injuries were associated with increased risk of failure.ConclusionsInjuries have a detrimental impact on team and individual athletic success. Increased player availability improves chances of success. Conversely, injuries sustained both prior to and during competition may increase risk of failure. Injury prevention should therefore be a priority for maximising athletic performance.
MerTK expressing hepatic macrophages promote the resolution of inflammation in acute liver failure
Authors: Triantafyllou Evangelos , Pop Oltin T , Possamai Lucia A , Wilhelm Annika , Liaskou Evaggelia , Singanayagam Arjuna , Bernsmeier Christine , Khamri Wafa , Petts Gemma , Dargue Rebecca , Davies Scott P , Tickle Joseph , Yuksel Muhammed , Patel Vishal C , Abeles Robin D , Stamataki Zania , Curbishley Stuart M , Ma Yun , Wilson Ian D , Coen Muireann , Woollard Kevin J , Quaglia Alberto , Wendon Julia , Thursz Mark R , Adams David H , Weston Chris J , Antoniades Charalambos G 
Published: April 2017

ObjectiveAcute liver failure (ALF) is characterised by overwhelming hepatocyte death and liver inflammation with massive infiltration of myeloid cells in necrotic areas. The mechanisms underlying resolution of acute hepatic inflammation are largely unknown. Here, we aimed to investigate the impact of Mer tyrosine kinase (MerTK) during ALF and also examine how the microenvironmental mediator, secretory leucocyte protease inhibitor (SLPI), governs this response.DesignFlow cytometry, immunohistochemistry, confocal imaging and gene expression analyses determined the phenotype, functional/transcriptomic profile and tissue topography of MerTK+ monocytes/macrophages in ALF, healthy and disease controls. The temporal evolution of macrophage MerTK expression and its impact on resolution was examined in APAP-induced acute liver injury using wild-type (WT) and Mer-deficient (Mer−/−) mice. SLPI effects on hepatic myeloid cells were determined in vitro and in vivo using APAP-treated WT mice.ResultsWe demonstrate a significant expansion of resolution-like MerTK+HLA-DRhigh cells in circulatory and tissue compartments of patients with ALF. Compared with WT mice which show an increase of MerTK+MHCIIhigh macrophages during the resolution phase in ALF, APAP-treated Mer−/− mice exhibit persistent liver injury and inflammation, characterised by a decreased proportion of resident Kupffer cells and increased number of neutrophils. Both in vitro and in APAP-treated mice, SLPI reprogrammes myeloid cells towards resolution responses through induction of a MerTK+HLA-DRhigh phenotype which promotes neutrophil apoptosis and their subsequent clearance.ConclusionsWe identify a hepatoprotective, MerTK+, macrophage phenotype that evolves during the resolution phase following ALF and represents a novel immunotherapeutic target to promote resolution responses following acute liver injury.