bluuebunny/crossref_metadata_2025_split huggingface dataset:
Orthobunyavirus Entry into Neurons and Other Mammalian Cells Occurs via Clathrin-Mediated Endocytosis and Requires Trafficking into Early Endosomes
Authors: Hollidge Bradley S. , Nedelsky Natalia B. , Salzano Mary-Virginia , Fraser Jonathan W. , González-Scarano Francisco , Soldan Samantha S. 
Published: May 2012

ABSTRACT
La Crosse virus (LACV) is a leading cause of pediatric encephalitis and aseptic meningitis in the midwestern and southern United States, where it is considered an emerging human pathogen. No specific therapies or vaccines are available for LACV or any other orthobunyaviruses. Inhibition of LACV entry into cells is a potential target for therapeutic intervention, but this approach is limited by our current knowledge of the entry process. Here, we determined that clathrin-mediated endocytosis is the primary mechanism of orthobunyavirus entry and identified key cellular factors in this process. First, we demonstrated that LACV colocalized with clathrin shortly after infection in HeLa cells; we then confirmed the functional requirement of dynamin- and clathrin-mediated endocytosis for orthobunyavirus entry using several independent assays and, importantly, extended these findings to primary neuronal cultures. We also determined that macropinocytosis and caveolar endocytosis, both established routes of virus entry, are not critical for cellular entry of LACV. Moreover, we demonstrated that LACV infection is dependent on Rab5, which plays an important regulatory role in early endosomes, but not on Rab7, which is associated with late endosomes. These findings provide the first description of bunyavirus entry into cells of the central nervous system, where infection can cause severe neurological disease, and will aid in the design and development of antivirals and therapeutics that may be useful in the treatment of LACV and, more broadly, arboviral infections of the central nervous system.
Human Respiratory Syncytial Virus Nucleoprotein and Inclusion Bodies Antagonize the Innate Immune Response Mediated by MDA5 and MAVS
Authors: Lifland Aaron W. , Jung Jeenah , Alonas Eric , Zurla Chiara , Crowe James E. , Santangelo Philip J. 
Published: May 2012

ABSTRACT
Currently, the spatial distribution of human respiratory syncytial virus (hRSV) proteins and RNAs in infected cells is still under investigation, with many unanswered questions regarding the interaction of virus-induced structures and the innate immune system. Very few studies of hRSV have used subcellular imaging as a means to explore the changes in localization of retinoic-acid-inducible gene-I (RIG-I)-like receptors or the mitochondrial antiviral signaling (MAVS) protein, in response to the infection and formation of viral structures. In this investigation, we found that both RIG-I and melanoma differentiation-associated gene 5 (MDA5) colocalized with viral genomic RNA and the nucleoprotein (N) as early as 6 h postinfection (hpi). By 12 hpi, MDA5 and MAVS were observed within large viral inclusion bodies (IB). We used a proximity ligation assay (PLA) and determined that the N protein was in close proximity to MDA5 and MAVS in IBs throughout the course of the infection. Similar results were found with the transient coexpression of N and the phosphoprotein (P). Additionally, we demonstrated that the localization of MDA5 and MAVS in IBs inhibited the expression of interferon β mRNA 27-fold following Newcastle disease virus infection. From these data, we concluded that the N likely interacts with MDA5, is in close proximity to MAVS, and localizes these molecules within IBs in order to attenuate the interferon response. To our knowledge, this is the first report of a specific function for hRSV IBs and of the hRSV N protein as a modulator of the innate immune response.
Shutoff of BZLF1 Gene Expression Is Necessary for Immortalization of Primary B Cells by Epstein-Barr Virus
Authors: Yu Xianming , McCarthy Patrick J. , Wang Zhenxun , Gorlen Daniel A. , Mertz Janet E. 
Published: May 2012

ABSTRACT

The
BZLF1
gene controls the switch between latent and lytic infection by Epstein-Barr virus (EBV). We previously reported that both the ZV and ZIIR elements within the
BZLF1
promoter, Zp, are potent transcription silencers within the context of an intact EBV genome. We report here identification of another sequence element, ZV′, which synergized with ZV in repressing Zp via binding ZEB1 or ZEB2. We then determined the phenotype of a variant of EBV strain B95.8 in which the ZV, ZV′, and ZIIR elements were concurrently mutated. HEK293 cell lines infected with this triple mutant (tmt) virus spontaneously synthesized 6- to 10-fold more viral
BZLF1
,
BRLF1
,
BMRF1
, and
BLLF1
RNAs, 3- to 6-fold more viral Zta, Rta, and EAD proteins, 3- to 5-fold more viral DNA, and 7- to 9-fold more infectious virus than did 293 cell lines latently infected with either the ZV ZV′ double mutant (dmt) or ZIIR mutant (mt) virus. While ZV ZV′ ZIIR tmt EBV efficiently infected human primary blood B cells
in vitro
, it was highly defective in immortalizing them. Instead of the nearly complete silencing of
BZLF1
gene expression that occurs within 4 days after primary infection with wild-type EBV, the ZV ZV′ ZIIR tmt-infected cells continued to synthesize
BZLF1
RNA, with 90% of them dying within 9 days postinfection. BL41 cells infected with this “superlytic” virus also exhibited increased synthesis of
BZLF1
and
BMRF1
RNAs. Thus, we conclude that the ZV, ZV′, and ZIIR silencing elements act synergistically to repress transcription from Zp, thereby tightly controlling
BZLF1
gene expression, which is crucial for establishing and maintaining EBV latency.
Epstein-Barr Virus BPLF1 Deubiquitinates PCNA and Attenuates Polymerase η Recruitment to DNA Damage Sites
Authors: Whitehurst Christopher B. , Vaziri Cyrus , Shackelford Julia , Pagano Joseph S. 
Published: May 2012

ABSTRACT

PCNA is monoubiquitinated in response to DNA damage and fork stalling and then initiates recruitment of specialized polymerases in the DNA damage tolerance pathway, translesion synthesis (TLS). Since PCNA is reported to associate with Epstein-Barr virus (EBV) DNA during its replication, we investigated whether the EBV deubiquitinating (DUB) enzyme encoded by BPLF1 targets ubiquitinated PCNA and disrupts TLS. An N-terminal BPLF1 fragment (a BPLF1 construct containing the first 246 amino acids [BPLF1 1-246]) associated with PCNA and attenuated its ubiquitination in response to fork-stalling agents UV and hydroxyurea in cultured cells. Moreover, monoubiquitinated PCNA was deubiquitinated after incubation with purified BPLF1 1-246
in vitro
. BPLF1 1-246 dysregulated TLS by reducing recruitment of the specialized repair polymerase polymerase η (Polη) to the detergent-resistant chromatin compartment and virtually abolished localization of Polη to nuclear repair foci, both hallmarks of TLS. Expression of BPLF1 1-246 decreased viability of UV-treated cells and led to cell death, presumably through deubiquitination of PCNA and the inability to repair damaged DNA. Importantly, deubiquitination of PCNA could be detected endogenously in EBV-infected cells in comparison with samples expressing short hairpin RNA (shRNA) against BPLF1. Further, the specificity of the interaction between BPLF1 and PCNA was dependent upon a PCNA-interacting peptide (PIP) domain within the N-terminal region of BPLF1. Both DUB activity and PIP sequence are conserved in the members of the family
Herpesviridae
. Thus, deubiquitination of PCNA, normally deubiquitinated by cellular USP1, by the viral DUB can disrupt repair of DNA damage by compromising recruitment of TLS polymerase to stalled replication forks. PCNA is the first cellular target identified for BPLF1 and its deubiquitinating activity.
Cofilin 1-Mediated Biphasic F-Actin Dynamics of Neuronal Cells Affect Herpes Simplex Virus 1 Infection and Replication
Authors: Xiang Yangfei , Zheng Kai , Ju Huaiqiang , Wang Shaoxiang , Pei Ying , Ding Weichao , Chen Zhenping , Wang Qiaoli , Qiu Xianxiu , Zhong Meigong , Zeng Fanli , Ren Zhe , Qian Chuiwen , Liu Ge , Kitazato Kaio , Wang Yifei 
Published: May 2012

ABSTRACT
Herpes simplex virus 1 (HSV-1) invades the nervous system and causes pathological changes. In this study, we defined the remodeling of F-actin and its possible mechanisms during HSV-1 infection of neuronal cells. HSV-1 infection enhanced the formation of F-actin-based structures in the early stage of infection, which was followed by a continuous decrease in F-actin during the later stages of infection. The disruption of F-actin dynamics by chemical inhibitors significantly reduced the efficiency of viral infection and intracellular HSV-1 replication. The active form of the actin-depolymerizing factor cofilin 1 was found to increase at an early stage of infection and then to continuously decrease in a manner that corresponded to the remodeling pattern of F-actin, suggesting that cofilin 1 may be involved in the biphasic F-actin dynamics induced by HSV-1 infection. Knockdown of cofilin 1 impaired HSV-1-induced F-actin assembly during early infection and inhibited viral entry; however, overexpression of cofilin 1 did not affect F-actin assembly or viral entry during early infection but decreased intracellular viral reproduction efficiently. Our results, for the first time, demonstrated the biphasic F-actin dynamics in HSV-1 neuronal infection and confirmed the association of F-actin with the changes in the expression and activity of cofilin 1. These results may provide insight into the mechanism by which HSV-1 productively infects neuronal cells and causes pathogenesis.
Complete Genome Sequence of a Novel Porcine Enterovirus Strain in China
Authors: Zhang Wen , Yang Shixing , Shen Quan , Ren Liping , Shan Tongling , Wei Jianzhong , Cui Li , Hua Xiuguo 
Published: May 2012

ABSTRACT

The porcine enteroviruses (PEVs) belong to the family
Picornaviridae
. We report a complete genome sequence of a novel PEV strain that is widely prevalent in pigs at least in central and eastern China. The complete genome consists of 7,390 nucleotides, excluding the 3′ poly(A) tail, and has an open reading frame that maps between nucleotide positions 812 and 7318 and encodes a 2,168-amino-acid polyprotein. Phylogenetic analysis based on the 3CD and VP1 regions reveals that this PEV strain belongs to a species of PEV9 but may represent a novel sero-/genotype in CPE group III. We also report the major findings from bootscan analysis based on the whole genomes of PEVs in the present study and those available in GenBank.
Human T-Cell Leukemia Virus Type 2 Antisense Viral Protein 2 Is Dispensable for
In Vitro
Immortalization but Functions To Repress Early Virus Replication
In Vivo
Authors: Yin Han , Kannian Priya , Dissinger Nathan , Haines Robyn , Niewiesk Stefan , Green Patrick L. 
Published: May 2012

ABSTRACT

Human T-cell leukemia virus type 1 (HTLV-1) and HTLV-2 are closely related but pathogenically distinct human retroviruses. The antisense strand of the HTLV-1 genome encodes HTLV-1 basic leucine zipper (b-ZIP) protein (HBZ), a protein that inhibits Tax-mediated viral transcription, enhances T-cell proliferation, and promotes viral persistence. Recently, an HTLV-2 antisense viral protein (APH-2) was identified. Despite its lack of a typical b-ZIP domain, APH-2, like HBZ, interacts with cyclic AMP response element binding protein (CREB) and downregulates Tax-mediated viral transcription. Here, we provide evidence that the APH-2 C-terminal LXXLL motif is important for CREB binding and Tax repression. In order to investigate the functional role of APH-2 in the HTLV-2-mediated immortalization of primary T lymphocytes
in vitro
and in HTLV-2 infection
in vivo
, we generated APH-2 mutant viruses. In cell cultures, the immortalization capacities of APH-2 mutant viruses were indistinguishable from that of wild-type HTLV-2 (wtHTLV-2), indicating that, like HBZ, APH-2 is dispensable for viral infection and cellular transformation.
In vivo
, rabbits inoculated with either wtHTLV-2 or APH-2 mutant viruses established a persistent infection. However, the APH-2 knockout virus displayed an increased replication rate, as measured by an increased viral antibody response and a higher proviral load. In contrast to HTLV-1 HBZ, we show that APH-2 is dispensable for the establishment of an efficient infection and persistence in a rabbit animal model. Therefore, antisense proteins of HTLV-1 and HTLV-2 have evolved different functions
in vivo
, and further comparative studies will provide fundamental insights into the distinct pathobiologies of these two viruses.
Complete Genome Sequence of Porcine Kobuvirus Strain WUH1
Authors: Lin Yuchen , Xiao Shaobo , Zeng Yuqing , Song Tao , Zeng Songlin , Chen Huanchun , Fang Liurong 
Published: May 2012

ABSTRACT
Porcine kobuvirus, an emerging virus, was first identified in Hungary in 2007. We report here the complete genome sequence of porcine kobuvirus strain WUH1 isolated from piglets with severe diarrhea, which will help toward understanding the molecular and evolutionary characteristics of the porcine kobuvirus.
Complete Genome Sequence of a New-Genotype Porcine Norovirus Isolated from Piglets with Diarrhea
Authors: Shen Quan , Zhang Wen , Yang Shixing , Cui Li , Hua Xiuguo 
Published: May 2012

ABSTRACT

Noroviruses (NoVs) are members of the family
Caliciviridae
and are emerging enteric pathogens of humans and animals. So far, porcine NoVs have been detected exclusively in fecal samples from adult swine without clinical signs. Here we report the genome sequence of a NoV strain isolated from piglets with diarrhea. Experimental infection of miniature pigs with this porcine NoV-positive fecal sample confirmed that this strain can cause diarrhea in piglets. A phylogenetic tree based on the predicted amino acid sequence of the complete capsid region showed that this strain is separate from known porcine GII strains (GII-11, GII-18, and GII-19), constituting the sole member of a new branch.
A Novel Porcine Circovirus Type 2a Strain, 10JS-2, with Eleven-Nucleotide Insertions in the Origin of Genome Replication
Authors: Cai Lin , Han Xue , Hu Dongmei , Li Xiaoxia , Wang Baoyue , Ni Jianqiang , Zhou Zhi , Yu Xiuling , Zhai Xinyan , Tian Kegong 
Published: May 2012

ABSTRACT
Here, we report a novel porcine circovirus type 2a (PCV2a) strain with 11 nucleotides (nt) inserted in the origin of genome replication (Ori). This is the first report of a PCV2a strain with nucleotide insertion in Ori. Our study will help further epidemiological studies and extend our knowledge of evolutionary characteristics of PCV2.
Complete Genome Sequence of Avian Bornavirus Genotype 1 from a Macaw with Proventricular Dilatation Disease
Authors: Mirhosseini Negin , Gray Patricia L. , Tizard Ian , Payne Susan 
Published: May 2012

ABSTRACT
Avian bornaviruses (ABV) were first detected and described in 2008. They are the etiologic agents of proventricular dilatation disease (PDD), a frequently fatal neurologic disease of captive parrots. Seven ABV genogroups have been identified worldwide from a variety of sources, and that number may increase as surveillance for novel bornaviruses continues. Here, we report the first complete sequence of a genogroup 1 avian bornavirus (ABV1).
Organization of the Ambisense Genome of the Helicoverpa armigera Densovirus
Authors: El-Far Mohamed , Szelei Jozsef , Yu Qian , Fédière Gilles , Bergoin Max , Tijssen Peter 
Published: May 2012

ABSTRACT

A natural densovirus (DNV) of a serious phytophagous pest,
Helicoverpa armigera
, was isolated. The genome of HaDNV contained 6,039 nucleotides (nt) and included inverted terminal repeats (ITRs) of 545 nt with terminal Y-shaped hairpins of 126 nt. Its DNA sequence and ambisense organization with four typical open reading frames (ORFs) demonstrated that it belonged to the genus
Densovirus
in the subfamily
Densovirinae
of the family
Parvoviridae
.
Characterization of
Magnaporthe oryzae
Chrysovirus 1 Structural Proteins and Their Expression in
Saccharomyces cerevisiae
Authors: Urayama Syunichi , Ohta Tomoko , Onozuka Nobuya , Sakoda Hirofumi , Fukuhara Toshiyuki , Arie Tsutomu , Teraoka Tohru , Moriyama Hiromitsu 
Published: May 2012

ABSTRACT

Magnaporthe oryzae chrysovirus
1 (MoCV1), which is associated with an impaired growth phenotype of its host fungus, harbors four major proteins: P130 (130 kDa), P70 (70 kDa), P65 (65 kDa), and P58 (58 kDa). N-terminal sequence analysis of each protein revealed that P130 was encoded by double-stranded RNA1 (dsRNA1) (open reading frame 1 [ORF1] 1,127 amino acids [aa]), P70 by dsRNA4 (ORF4; 812 aa), and P58 by dsRNA3 (ORF3; 799 aa), although the molecular masses of P58 and P70 were significantly smaller than those deduced for ORF3 and ORF4, respectively. P65 was a degraded form of P70. Full-size proteins of ORF3 (84 kDa) and ORF4 (85 kDa) were produced in
Escherichia coli
. Antisera against these recombinant proteins detected full-size proteins encoded by ORF3 and ORF4 in mycelia cultured for 9, 15, and 28 days, and the antisera also detected smaller degraded proteins, namely, P58, P70, and P65, in mycelia cultured for 28 days. These full-size proteins and P58 and P70 were also components of viral particles, indicating that MoCV1 particles might have at least two forms during vegetative growth of the host fungus. Expression of the ORF4 protein in
Saccharomyces cerevisiae
resulted in cytological changes, with a large central vacuole associated with these growth defects. MoCV1 has five dsRNA segments, as do two
Fusarium graminearum
viruses (FgV-ch9 and FgV2), and forms a separate clade with FgV-ch9, FgV2,
Aspergillus
mycovirus 1816 (AsV1816), and
Agaricus bisporus
virus 1 (AbV1) in the
Chrysoviridae
family on the basis of their RdRp protein sequences.
Equine Herpesvirus Type 4 UL56 and UL49.5 Proteins Downregulate Cell Surface Major Histocompatibility Complex Class I Expression Independently of Each Other
Authors: Said Abdelrahman , Azab Walid , Damiani Armando , Osterrieder Nikolaus 
Published: May 2012

ABSTRACT
Major histocompatibility complex class I (MHC-I) molecules are critically important in the host defense against various pathogens through presentation of viral peptides to cytotoxic T lymphocytes (CTLs), a process resulting in the destruction of virus-infected cells. Herpesviruses interfere with CTL-mediated elimination of infected cells by various mechanisms, including inhibition of peptide transport and loading, perturbation of MHC-I trafficking, and rerouting and proteolysis of cell surface MHC-I. In this study, we show that equine herpesvirus type 4 (EHV-4) modulates MHC-I cell surface expression through two different mechanisms. First, EHV-4 can lead to a significant downregulation of MHC-I expression at the cell surface through the product of ORF1, a protein expressed with early kinetics from a gene that is homologous to herpes simplex virus 1 UL56. The EHV-4 UL56 protein reduces cell surface MHC-I as early as 4 h after infection. Second, EHV-4 can interfere with MHC-I antigen presentation, starting at 6 h after infection, by inhibition of the transporter associated with antigen processing (TAP) through its UL49.5 protein. Although pUL49.5 has no immediate effect on overall surface MHC-I levels in infected cells, it blocks the supply of antigenic peptides to the endoplasmic reticulum (ER) and transport of peptide-loaded MHC-I to the cell surface. Taken together, our results show that EHV-4 encodes at least two viral immune evasion proteins: pUL56 reduces MHC-I molecules on the cell surface at early times after infection, and pUL49.5 interferes with MHC-I antigen presentation by blocking peptide transport in the ER.
Challenges of making a diagnosis in the outpatient setting: a multi-site survey of primary care physicians
Authors: Sarkar Urmimala , Bonacum Doug , Strull William , Spitzmueller Christiane , Jin Nancy , López Andrea , Giardina Traber Davis , Meyer Ashley N D , Singh Hardeep 
Published: May 2012

BackgroundAlthough misdiagnosis in the outpatient setting leads to significant patient harm and wasted resources, it is not well studied. The authors surveyed primary care physicians (PCPs) about barriers to timely diagnosis in the outpatient setting and assessed their perceptions of diagnostic difficulty.MethodsSurveys of PCPs practicing in an integrated health system across 10 geographically dispersed states in 2005. The survey elicited information on key cognitive failures (including in clinical knowledge or judgement) for a specific case, and solicited strategies for reducing diagnostic delays. Content analysis was used to categorise cognitive failures and strategies for improvement. The authors examined the extent and predictors of diagnostic difficulty, defined as reporting >5% patients difficult to diagnose.ResultsOf 1817 physicians surveyed, 1054 (58%) responded; 848 (80%) respondents primarily practiced in outpatient settings and had an assigned patient panel (inclusion sample). Inadequate knowledge (19.9%) was the most commonly reported cognitive factor. Half reported >5% of their patients were difficult to diagnose; more experienced physicians reported less diagnostic difficulty. In adjusted analyses, problems with information processing (information availability and time to review it) and the referral process were associated with greater diagnostic difficulty. Strategies for improvement most commonly involved workload issues (panel size, non-visit tasks).ConclusionsPCPs report a variety of reasons for diagnostic difficulties in primary care practice. In this study, knowledge gaps appear to be a prominent concern. Interventions that address these gaps as well as practice level issues such as time to process diagnostic information and better subspecialty input may reduce diagnostic difficulties in primary care.
Signal and noise: applying a laboratory trigger tool to identify adverse drug events among primary care patients
Authors: Brenner Stacey , Detz Alissa , López Andrea , Horton Claire , Sarkar Urmimala 
Published: May 2012

BackgroundThe extent of outpatient adverse drug events (ADEs) remains unclear. Trigger tools are used as a screening method to identify care episodes that may be ADEs, but their value in a population with high chronic-illness burden remains unclear.MethodsThe authors used six abnormal laboratory triggers for detecting ADEs among adults in outpatient care. Eligible patients were included if they were >18 years, sought primary or urgent care between November 2008 and November 2009 and were prescribed at least one medication. The authors then used the clinical / administrative database to identity patients with these triggers. Two physicians conducted in-depth chart review of any medical records with identified triggers.ResultsThe authors reviewed 1342 triggers representing 622 unique episodes among 516 patients. The trigger tool identified 91 (15%) ADEs. Of the 91 ADEs included in the analysis, 49 (54%) occurred during medication monitoring, 41 (45%) during patient self-administration, and one could not be determined. 96% of abnormal international normalised ratio triggers were ADEs, followed by 12% of abnormal blood urea nitrogen triggers, 9% of abnormal alanine aminotransferase triggers, 8% of abnormal serum creatinine triggers and 3% of aspartate aminotransferase triggers.ConclusionsThe findings imply that other tools such as text triggers or more complex automated screening rules, which combine data hierarchically are needed to effectively screen for ADEs in chronically ill adults seen in primary care.