bluuebunny/crossref_metadata_2025_split huggingface dataset:
The HIV-1 Tat Protein Has a Versatile Role in Activating Viral Transcription
Authors: Das Atze T. , Harwig Alex , Berkhout Ben 
Published: July 2011

ABSTRACT
It is generally acknowledged that the Tat protein has a pivotal role in HIV-1 replication because it stimulates transcription from the viral long terminal repeat (LTR) promoter by binding to the TAR hairpin in the nascent RNA transcript. However, a multitude of additional Tat functions have been suggested. The importance of these functions is difficult to assess in replication studies with Tat-mutated HIV-1 variants because of the dominant negative effect on viral gene expression. We therefore used an HIV-1 construct that does not depend on the Tat-TAR interaction for transcription to reevaluate whether or not Tat has a second essential function in HIV-1 replication. This HIV-rtTA variant uses the incorporated Tet-On gene expression system for activation of transcription and replicates efficiently upon complete TAR deletion. Here we demonstrated that Tat inactivation does nevertheless severely inhibit replication. Upon long-term culturing, the Tat-minus HIV-rtTA variant acquired mutations in the U3 region that improved promoter activity and reestablished replication. We showed that in the absence of a functional TAR, Tat remains important for viral transcription via Sp1 sequence elements in the U3 promoter region. Substitution of these U3 sequences with nonrelated promoter elements created a virus that replicates efficiently without Tat in SupT1 T cells. These results indicate that Tat has a versatile role in transcription via TAR and U3 elements. The results also imply that Tat has no other essential function in viral replication in cultured T cells.
Hepatitis C Virus Infection Is Blocked by HMGB1 Released from Virus-Infected Cells
Authors: Jung Jong Ha , Park Ji Hoon , Jee Min Hyeok , Keum Sun Ju , Cho Min-Sun , Yoon Seung Kew , Jang Sung Key 
Published: July 2011

ABSTRACTHigh-mobility group box 1 (HMGB1), an abundant nuclear protein that triggers host immune responses, is an endogenous danger signal involved in the pathogenesis of various infectious agents. However, its role in hepatitis C virus (HCV) infection is not known. Here, we show that HMGB1 protein is translocated from the nucleus to cytoplasm and subsequently is released into the extracellular milieu by HCV infection. Secreted HMGB1 triggers antiviral responses and blocks HCV infection, a mechanism that may limit HCV propagation in HCV patients. Secreted HMGB1 also may have a role in liver cirrhosis, which is a common comorbidity in HCV patients. Further investigations into the roles of HMGB1 in the diseases caused by HCV infection will shed light on and potentially help prevent these serious and prevalent HCV-related diseases.
Role of Calpain in the Formation of Human Papillomavirus Type 16 E1^E4 Amyloid Fibers and Reorganization of the Keratin Network
Authors: Khan Jameela , Davy Clare E. , McIntosh Pauline B. , Jackson Deborah J. , Hinz Steven , Wang Qian , Doorbar John 
Published: July 2011

ABSTRACT
The human papillomavirus (HPV) type 16 E1^E4 (16E1^E4) protein is expressed in the middle to upper layers of infected epithelium and has several roles within the virus life cycle. It is apparent that within the epithelium there are multiple species of 16E1^E4 that differ in length and/or degree of phosphorylation and that some or all of these can associate with the cellular keratin networks, leading to network disruption. We show here that the cellular cysteine protease calpain cleaves the 16E1^E4 protein after amino acid 17 to generate species that lack the N terminus. These C-terminal fragments are able to multimerize and form amyloid-like fibers. This can lead to accumulation of 16E1^E4 and disruption of the normal dynamics of the keratin networks. The cleavage of E1^E4 proteins by calpain may be a common strategy used by α-group viruses, since we show that cleavage of type 18 E1^E4 in raft culture is also dependent on calpain. Interestingly, the cleavage of 16E1^E4 by calpain appears to be highly regulated as differentiation of HPV genome-containing cells by methylcellulose is insufficient to induce cleavage. We hypothesize that this is important since it ensures that the formation of the amyloid fibers is not prematurely triggered in the lower layers and is restricted to the upper layers, where calpain is active and where disruption of the keratin networks may aid virus release.
A High Level of Mutation Tolerance in the Multifunctional Sequence Encoding the RNA Encapsidation Signal of an Avian Hepatitis B Virus and Slow Evolution Rate Revealed by
In Vivo
Infection
Authors: Schmid Bernadette , Rösler Christine , Nassal Michael 
Published: July 2011

ABSTRACT

In all hepadnaviruses, protein-primed reverse transcription of the pregenomic RNA (pgRNA) is initiated by binding of the viral polymerase, P protein, to the ε RNA element. Universally, ε consists of a lower stem and an upper stem, separated by a bulge, and an apical loop. Complex formation triggers pgRNA encapsidation and the ε-templated synthesis of a DNA oligonucleotide (priming) that serves to generate minus-strand DNA.
In vitro
systems for duck hepatitis B virus (DHBV) yielded important insights into the priming mechanism, yet their relevance in infection is largely unexplored. Moreover, additional functions encoded in the DHBV ε (Dε) sequence could affect
in vivo
fitness. We therefore assessed the
in vivo
performances of five recombinant DHBVs bearing multiple mutations in the upper Dε stem. Three variants with only modestly reduced
in vitro
replication competence established chronic infection in ducks. From one variant but not another, three adapted new variants emerged upon passaging, as demonstrated by increased relative fitness in coinfections with wild-type DHBV. All three showed enhanced priming and replication competence
in vitro
, and in one, DHBV e antigen (DHBeAg) production was restored. Pronounced impacts on other Dε functions were not detected; however, gradual, synergistic contributions to overall performance are suggested by the fact of none of the variants reaching the
in vivo
fitness of wild-type virus. These data shed more light on the P-Dε interaction, define important criteria for the design of future
in vivo
evolution experiments, and suggest that the upper Dε stem sequences provided an evolutionary playground for DHBV to optimize
in vivo
fitness.
The Structure of Barmah Forest Virus as Revealed by Cryo-Electron Microscopy at a 6-Angstrom Resolution Has Detailed Transmembrane Protein Architecture and Interactions
Authors: Kostyuchenko Victor A. , Jakana Joanita , Liu Xiangan , Haddow Andrew D. , Aung Myint , Weaver Scott C. , Chiu Wah , Lok Shee-Mei 
Published: July 2011

ABSTRACT
Barmah Forest virus (BFV) is a mosquito-borne alphavirus that infects humans. A 6-Å-resolution cryo-electron microscopy three-dimensional structure of BFV exhibits a typical alphavirus organization, with RNA-containing nucleocapsid surrounded by a bilipid membrane anchored with the surface proteins E1 and E2. The map allows details of the transmembrane regions of E1 and E2 to be seen. The C-terminal end of the E2 transmembrane helix binds to the capsid protein. Following the E2 transmembrane helix, a short α-helical endodomain lies on the inner surface of the lipid envelope. The E2 endodomain interacts with E1 transmembrane helix from a neighboring E1-E2 trimeric spike, thereby acting as a spacer and a linker between spikes. In agreement with previous mutagenesis studies, the endodomain plays an important role in recruiting other E1-E2 spikes to the budding site during virus assembly. The E2 endodomain may thus serve as a target for antiviral drug design.
Human Immunodeficiency Virus Rev-Binding Protein Is Essential for Influenza A Virus Replication and Promotes Genome Trafficking in Late-Stage Infection
Authors: Eisfeld Amie J. , Neumann Gabriele , Kawaoka Yoshihiro 
Published: July 2011

ABSTRACT
Influenza A virus uses cellular protein transport systems (e.g., CRM1-mediated nuclear export and Rab11-dependent recycling endosomes) for genome trafficking from the nucleus to the plasma membrane, where new virions are assembled. However, the detailed mechanisms of these events have not been completely resolved, and additional cellular factors are probably required. Here, we investigated the role of the cellular human immunodeficiency virus (HIV) Rev-binding protein (HRB), which interacts with influenza virus nuclear export protein (NEP), during the influenza virus life cycle. By using small interfering RNAs (siRNAs) and overexpression of a dominant negative HRB protein fragment, we show that cells lacking functional HRB have significantly reduced production of influenza virus progeny and that this defect results from impaired viral ribonucleoprotein (vRNP) delivery to the plasma membrane in late-stage infection. Since HRB colocalizes with influenza vRNPs early after their delivery to the cytoplasm, it may mediate a connection between the nucleocytoplasmic transport machinery and the endosomal system, thus facilitating the transfer of vRNPs from nuclear export to cytoplasmic trafficking complexes. We also found an association between NEP and HRB in the perinuclear region, suggesting that NEP may contribute to this process. Our results identify HRB as a second endosomal factor with a crucial role in influenza virus genome trafficking, suggest cooperation between unique endosomal compartments in the late steps of the influenza virus life cycle, and provide a common link between the cytoplasmic trafficking mechanisms of influenza virus and HIV.
Cell-Type-Specific Type I Interferon Antagonism Influences Organ Tropism of Murine Coronavirus
Authors: Zhao Ling , Rose Kristine M. , Elliott Ruth , Van Rooijen Nico , Weiss Susan R. 
Published: July 2011

ABSTRACTPrevious studies have demonstrated that mouse hepatitis virus (MHV) hepatotropism is determined largely by postentry events rather than by availability of the viral receptor. In addition, mutation of MHV nonstructural protein 2 (ns2) abrogates the ability of the virus to replicate in the liver and induce hepatitis but does not affect replication in the central nervous system (CNS). Here we show that replication of ns2 mutant viruses is attenuated in bone marrow-derived macrophages (BMM) generated from wild-type (wt) mice but not in L2 fibroblasts, primary astrocytes, or BMM generated from type I interferon receptor-deficient (IFNAR−/−) mice. In addition, ns2 mutants are more sensitive than wt virus to pretreatment of BMM, but not L2 fibroblasts or primary astrocytes, with alpha/beta interferon (IFN-α/β). The ns2 mutants induced similar levels of IFN-α/β in wt and IFNAR−/−BMM, indicating that ns2 expression has no effect on the induction of IFN but rather that it antagonizes a later step in IFN signaling. Consistent with thesein vitrodata, the virulence of ns2 mutants increased to near that of wt virus after depletion of macrophagesin vivo. These data imply that the ability of MHV to replicate in macrophages is a prerequisite for replication in the liver and induction of hepatitis but not for replication or disease in the CNS, underscoring the importance of IFN signaling in macrophagesin vivofor protection of the host from hepatitis. Our results further support the notion that viral tissue tropism is determined in part by postentry events, including the early type I interferon response.
Antagonistic Effects of Cellular Poly(C) Binding Proteins on Vesicular Stomatitis Virus Gene Expression
Authors: Dinh Phat X. , Beura Lalit K. , Panda Debasis , Das Anshuman , Pattnaik Asit K. 
Published: July 2011

ABSTRACTImmunoprecipitation and subsequent mass spectrometry analysis of the cellular proteins from cells expressing the vesicular stomatitis virus (VSV) P protein identified the poly(C) binding protein 2 (PCBP2) as one of the P protein-interacting proteins. To investigate the role of PCBP2 in the viral life cycle, we examined the effects of depletion or overexpression of this protein on VSV growth. Small interfering RNA-mediated silencing of PCBP2 promoted VSV replication. Conversely, overexpression of PCBP2 in transfected cells suppressed VSV growth. Further studies revealed that PCBP2 negatively regulates overall viral mRNA accumulation and subsequent genome replication. Coimmunoprecipitation and immunofluorescence microscopic studies showed that PCBP2 interacts and colocalizes with VSV P protein in virus-infected cells. The P-PCBP2 interaction did not result in reduced levels of protein complex formation with the viral N and L proteins, nor did it induce degradation of the P protein. In addition, PCBP1, another member of the poly(C) binding protein family with homology to PCBP2, was also found to interact with the P protein and inhibit the viral mRNA synthesis at the level of primary transcription without affecting secondary transcription or genome replication. The inhibitory effects of PCBP1 on VSV replication were less pronounced than those of PCBP2. Overall, the results presented here suggest that cellular PCBP2 and PCBP1 antagonize VSV growth by affecting viral gene expression and highlight the importance of these two cellular proteins in restricting virus infections.
Malignant ovarian germ cell tumours in gonadal Y chromosome mosaicism
Authors: Shahsiah Reza , Jahanbin Behnaz , Rabiei Reza , Ardalan Farid Azmoudeh , Sarhadi Behnaz , Izadi-Mood Narges 
Published: July 2011

AimsPrevious studies have shown that two partially overlapping mechanisms are responsible for the development of malignant ovarian germ cell tumours (MOGCT): either spontaneous mutations, mostly in KIT gene, or the presence of Y chromosome material, in dysgenetic gonads. While unilateral oophorectomy and preservation of fertility is favourable in most cases, presence of whole or part of Y chromosome in dysgenetic ovaries is associated with a risk of bilateral germ cell tumour development. The aim of this study was to evaluate the frequency of Y chromosome material in these tumours.MethodsA total of 47 cases with histopathologic diagnosis of malignant germ cell tumour were selected in a period of 9 years. A relative quantitative PCR (RQ-PCR) method was designed and validated to detect testis-specific protein Y-encoded (TSPY) gene on Y chromosome. After DNA extraction, TSPY gene was sought as a surrogate of Y chromosome.ResultsSignificant amounts of TSPY gene were found in seven cases, two of which had gonadoblastoma and one had cytogenetic proof of Y chromosome presence.ConclusionsSome MOGCTs develop on the background of gonadal mosaicism and gonadal dysgenesis. Bilateral oophorectomy may be indicated in patients with these disorders because they are at risk of developing an MOGCT on the contralateral gonad. Moreover, this chromosomal abnormality is hardly found by routine methods, and the abnormality is more easily sought in MOGCT cells by means of RQ-PCR.
Young adult smokers' perceptions of plain packaging: a pilot naturalistic study
Authors: Moodie Crawford , Mackintosh Anne Marie , Hastings Gerard , Ford Allison 
Published: July 2011

AimsTo explore the impact, if any, that using plain (non-branded) cigarette packs in real-life settings has on young adult smokers.MethodsNaturalistic-type research was employed, where smokers used brown ‘plain’ packs for 2 weeks and their regular packs for 2 weeks, in real-life settings. Participants were recruited in Glasgow, Scotland. Of the 140 smokers aged 18–35 years who participated in the naturalistic study, 48 correctly completed and returned all questionnaires. Over the 4-week study period, participants completed a questionnaire twice a week assessing pack perceptions and feelings, feelings about smoking, salience of health warnings and smoking-related behaviours. A subsample of 18 participated in a post-study interview, which employed a semistructured topic guide to assess perceptions and experiences of using plain packs.ResultsTrends in the data show that in comparison with branded packaging, plain packaging increased negative perceptions and feelings about the pack and about smoking. Plain packaging also increased avoidant behaviour (hiding the pack, covering the pack), certain smoking cessation behaviours, such as smoking less around others and forgoing cigarettes, and thinking about quitting. Almost half (n=8) of those in the post-study interview, predominantly women (n=6), reported that the use of plain packs had either increased avoidant behaviour or reduced consumption.ConclusionsThis pilot naturalistic study suggests that plain packaging could potentially help reduce tobacco consumption among some young adult smokers, and women in particular. Employing an innovative research methodology, the findings of this study are consistent with, and indeed support, past plain packaging research.
Smokers' self-reported responses to the introduction of reduced ignition propensity (RIP) cigarettes: Table 1
Authors: Seidenberg Andrew B , Rees Vaughan W , Alpert Hillel R , O'Connor Richard J , Giovino Gary A , Hyland Andrew , Connolly Gregory N 
Published: July 2011

BackgroundChanges in cigarette design to meet mandated fire safety standards may have unintended effects on smoker responses by diminishing the consumer's perceptions of product acceptability, smoking and increasing fire-risk behaviours. To address these concerns, population-level data are needed from a jurisdiction where reduced ignition propensity (RIP) cigarettes have been introduced.MethodsA cohort of adult smokers was recruited in Massachusetts, USA using a random-digit-dialled telephone survey. The cohort was contacted prior to, and 8 months following, the state-mandated introduction of RIP cigarettes on 1 January 2008. Changes in self-reported subjective cigarette characteristics, smoking topography, fire-risk behaviours, fire events and quitting intentions were assessed.ResultsA total of 620 Massachusetts smokers completed the baseline survey conducted prior to implementation of the law, and 353 (57%) completed the follow-up survey conducted after implementation. No significant changes were found in self-reported fire-risk behaviour or quitting intentions. In addition, smokers were less likely to report smoking greater than 20 cigarettes per day and inhaling deeply into the chest after the law.ConclusionsThe introduction of RIP cigarettes in Massachusetts yielded little change, and no adverse effect, on self-reported smoker response, among a sample of mostly Caucasian smokers.
Telomere Attrition and Decreased Fetuin-A Levels Indicate Accelerated Biological Aging and Are Implicated in the Pathogenesis of Colorectal Cancer
Authors: Maxwell Fraser , McGlynn Liane M. , Muir Hannah C. , Talwar Dinesh , Benzeval Michaela , Robertson Tony , Roxburgh Campbell S. , McMillan Donald C. , Horgan Paul G. , Shiels Paul G. 
Published: July 2011

Abstract
Purpose: Increasing chronological age is a risk factor for many types of cancer including colorectal. An understanding of the biology of aging and factors which regulate it may provide insight into cancer pathogenesis. The role of telomere biology in both the cancer and aging process could prove useful in this regard.
Experimental Design: Using quantitative PCR, we determined telomere length in the peripheral blood leukocytes of 64 colorectal cancer (CRC) patients and 1,348 controls. We also measured telomere length in 32 colorectal tumor samples and matched normal tissue. We aimed to assess whether telomere lengths were reflected in circulating mediators of inflammation and redox control factors, including fetuin-A, a circulating modulator of calcium homeostasis.
Results: CRC patients had shorter telomeres [adjusted mean ratio of relative telomere repeat copy number to single-copy gene number (RelT/S) = 0.61] compared with chronologically older controls (mean age = 75, adjusted mean RelT/S = 0.70; ANCOVA, P = 0.004). Telomere length in tumor tissue [median = 0.43, interquartile range (IQR) = 0.40] was significantly shorter than adjacent normal tissue (median = 0.65, IQR = 0.28; P = 0.004). Patients with low fetuin-A levels were shown to have significantly shorter telomeres (P = 0.041). Patients with rectal tumors had significantly higher levels of fetuin-A than those with colonic tumors (P = 0.045).
Conclusions: We have observed that patients with CRC display clear evidence of telomere attrition compared with controls. This is congruent with accelerated biological aging in the pathogenesis of CRC. An imbalance in redox control mechanisms and calcium homeostasis may be a contributing factor to telomere dynamics in our patients. Furthermore, fetuin-A levels can be used to distinguish between colon and rectal cancers. Clin Cancer Res; 17(17); 5573–81. ©2011 AACR.
Cell Surface Delivery of TRAIL Strongly Augments the Tumoricidal Activity of T Cells
Authors: de Bruyn Marco , Wei Yunwei , Wiersma Valerie R. , Samplonius Douwe F. , Klip Harry G. , van der Zee Ate G.J. , Yang Baofeng , Helfrich Wijnand , Bremer Edwin 
Published: July 2011

Abstract
Purpose: Adoptive T-cell therapy generally fails to induce meaningful anticancer responses in patients with solid tumors. Here, we present a novel strategy designed to selectively enhance the tumoricidal activity of T cells by targeted delivery of TNF-related apoptosis-inducing ligand (TRAIL) to the T-cell surface.
Experimental Design: We constructed two recombinant fusion proteins, anti-CD3:TRAIL and K12:TRAIL. Tumoricidal activity of T cells in the presence of these fusion proteins was assessed in solid tumor cell lines, primary patient-derived malignant cells, and in a murine xenograft model.
Results: When added to T cells, K12:TRAIL and anti-CD3:TRAIL selectively bind to the T-cell surface antigens CD3 and CD7, respectively, leading to cell surface accretion of TRAIL. Subsequently, anti-CD3:TRAIL and K12:TRAIL increased the tumoricidal activity of T cells toward cancer cell lines and primary patient-derived malignant cells by more than 500-fold. Furthermore, T-cell surface delivery of TRAIL strongly inhibited tumor growth and increased survival time of xenografted mice more than 6-fold.
Conclusions: Targeted delivery of TRAIL to cell surface antigens of T cells potently enhances the tumoricidal activity of T cells. This approach may be generally applicable to enhance the efficacy of adoptive T-cell therapy. Clin Cancer Res; 17(17); 5626–37. ©2011 AACR.
Salvage Surgery following Radiation Failure for Laryngeal Cancer in Elderly Patients
Authors: Lusardi Jonathan J. , Buchanan Paula M. , Christopher Kara M. , Varvares Mark A. 
Published: July 2011

ObjectiveTo find the survival rate of patients ≥80 years old who undergo salvage surgery for squamous cell carcinoma of the larynx.Study DesignNational data registry analysis.SettingSeventeen population‐based registries comprising the National Cancer Institute’s Surveillance, Epidemiology, and End Results database.Subjects and MethodsOverall, cancer‐specific, and relative survival rates were calculated from 1418 patients, stratified into 3 age cohorts, who underwent surgery following radiation therapy for treatment of laryngeal cancer.ResultsThe 1‐year overall survival of patients ≥80 years old (n = 57) was 76.1%. The cancer‐specific survival at 1 year was 86.4%. These survival rates were significantly less than those of patients <65 years old (n = 869), who had a 1‐year overall survival of 88.1% (P =. 006) and cancer‐specific survival of 90.5% (P =. 029). Patients aged between 65 and 79 years old (n = 492) displayed 1‐year overall survival of 80.7% (P =. 426) and cancer‐specific survival of 85.1% (P =. 711), which were not significantly different from the ≥80 year cohort. When comparing relative survival at 5 years, the ≥80‐year‐old cohort’s survival trended the highest (≥80 years, 62.8%; 65‐79 years, 51.3%; 20‐64 years, 56.2%).ConclusionWhile patients ≥80 years old have a less favorable prognosis than patients <65 years old, the survival rates of patients ≥80 years old are not significantly different from the 65‐ to 79‐year‐old cohort. After controlling for non‐cancer‐related death, patients ≥80 years old appear to have similar 5‐year survival outcomes compared with other patients.