bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Six-Helix Bundle of Human Immunodeficiency Virus Env Controls Pore Formation and Enlargement and Is Initiated at Residues Proximal to the Hairpin Turn
Authors: Markosyan Ruben M. , Leung Michael Y. , Cohen Fredric S. 
Published: July 2009

ABSTRACT
Residues that create the grooves of the human immunodeficiency virus type 1 (HIV-1) Env triple-stranded coiled coil (HR1) and the residues that pack into the grooves (HR2) to complete the formation of the six-helix bundle (6HB) were mutated. The extent and kinetics of fusion as well as pore enlargement were measured for each mutant. Mutations near the hairpin turns of each monomer of the 6HB were more important than those far from the turn, for both HR1 and HR2. This result is consistent with the idea that binding of HR2 to the HR1 grooves is initiated near the hairpin turn of each monomer. Mutations at the distal portions also reduced fusion, albeit to a smaller extent. An intermediate of fusion (temperature-arrested state [TAS]) was formed, and the consequences of mutation were compared; a mutant that exhibited less fusion also showed slower kinetics from TAS. This suggests that formation of the bundle is a rate-limiting step downstream of the intermediate state. The rate of enlargement of a fusion pore also correlated with the extent and kinetics of fusion. The rate of pore enlargement was severely reduced by mutation. This supports our prior conclusion that formation of the 6HB occurs after pore creation and strongly suggests that the free energy released by bundle formation is directly used to promote pore growth.
Development of a Human Immunodeficiency Virus Type 1-Based Lentiviral Vector That Allows Efficient Transduction of both Human and Rhesus Blood Cells
Authors: Uchida Naoya , Washington Kareem N. , Hayakawa Jun , Hsieh Matthew M. , Bonifacino Aylin C. , Krouse Allen E. , Metzger Mark E. , Donahue Robert E. , Tisdale John F. 
Published: July 2009

ABSTRACT

Human immunodeficiency virus type 1 (HIV-1) vectors transduce rhesus blood cells poorly due to a species-specific block by TRIM5α and APOBEC3G, which target HIV-1 capsid and viral infectivity factor (Vif), respectively. We sought to develop a lentiviral vector capable of transducing both human and rhesus blood cells by combining components of both HIV-1 and simian immunodeficiency virus (SIV), including SIV capsid (sCA) and SIV Vif. A chimeric HIV-1 vector including sCA (χHIV) was superior to the conventional SIV in transducing a human blood cell line and superior to the conventional HIV-1 vector in transducing a rhesus blood cell line. Among human CD34
+
hematopoietic stem cells (HSCs), the χHIV and HIV-1 vectors showed similar transduction efficiencies; in rhesus CD34
+
HSCs, the χHIV vector yielded superior transduction rates. In in vivo competitive repopulation experiments with two rhesus macaques, the χHIV vector demonstrated superior marking levels over the conventional HIV-1 vector in all blood lineages (first rhesus, 15 to 30% versus 1 to 5%; second rhesus, 7 to 15% versus 0.5 to 2%, respectively) 3 to 7 months postinfusion. In summary, we have developed an HIV-1-based lentiviral vector system that should allow comprehensive preclinical testing of HIV-1-based therapeutic vectors in the rhesus macaque model with eventual clinical application.
Prime-Boost Vaccination with Recombinant Mumps Virus and Recombinant Vesicular Stomatitis Virus Vectors Elicits an Enhanced Human Immunodeficiency Virus Type 1 Gag-Specific Cellular Immune Response in Rhesus Macaques
Authors: Xu R. , Nasar F. , Megati S. , Luckay A. , Lee M. , Udem S. A. , Eldridge J. H. , Egan M. A. , Emini E. , Clarke D. K. 
Published: July 2009

ABSTRACT

Intramuscular inoculation of rhesus macaques with one or more doses of recombinant vesicular stomatitis virus (rVSV) expressing human immunodeficiency virus type 1 (HIV-1) Gag (rVSVgag) typically elicits peak cellular immune responses of 500 to 1,000 gamma interferon (IFN-γ) enzyme-linked immunospots (ELISPOTS)/10
6
peripheral blood lymphocytes (PBL). Here, we describe the generation of a novel recombinant mumps virus (rMuV) expressing HIV-1 Gag (rMuVgag) and measure the Gag-specific cellular immune responses detected in rhesus macaques following vaccination with a highly attenuated form of rVSV expressing HIV-1 Gag (rVSVN4CT1gag1) and rMuVgag in various prime-boost combinations. Notably, peak Gag-specific cellular immune responses of 3,000 to 3,500 ELISPOTS/10
6
PBL were detected in macaques that were primed with rMuVgag and boosted with rVSVN4CT1gag1. Lower peak cellular immune responses were detected in macaques that were primed with rVSVN4CT1gag1 and boosted with rMuVgag, although longer-term gag-specific responses appeared to remain higher in this group of macaques. These findings indicate that rMuVgag may significantly enhance Gag-specific cellular immune responses when administered with rVSVN4CT1gag1 in heterologous prime-boost regimens.
Detection of Mammalian Virulence Determinants in Highly Pathogenic Avian Influenza H5N1 Viruses: Multivariate Analysis of Published Data
Authors: Lycett S. J. , Ward M. J. , Lewis F. I. , Poon A. F. Y. , Kosakovsky Pond S. L. , Brown A. J. Leigh 
Published: July 2009

ABSTRACT
Highly pathogenic avian influenza (HPAI) virus H5N1 infects water and land fowl and can infect and cause mortality in mammals, including humans. However, HPAI H5N1 strains are not equally virulent in mammals, and some strains have been shown to cause only mild symptoms in experimental infections. Since most experimental studies of the basis of virulence in mammals have been small in scale, we undertook a meta-analysis of available experimental studies and used Bayesian graphical models (BGM) to increase the power of inference. We applied text-mining techniques to identify 27 individual studies that experimentally determined pathogenicity in HPAI H5N1 strains comprising 69 complete genome sequences. Amino acid sequence data in all 11 genes were coded as binary data for the presence or absence of mutations related to virulence in mammals or nonconsensus residues. Sites previously implicated as virulence determinants were examined for association with virulence in mammals in this data set, and the sites with the most significant association were selected for further BGM analysis. The analyses show that virulence in mammals is a complex genetic trait directly influenced by mutations in polymerase basic 1 (PB1) and PB2, nonstructural 1 (NS1), and hemagglutinin (HA) genes. Several intra- and intersegment correlations were also found, and we postulate that there may be two separate virulence mechanisms involving particular combinations of polymerase and NS1 mutations or of NS1 and HA mutations.
Bypass Suppression of Small-Plaque Phenotypes by a Mutation in Poliovirus 2A That Enhances Apoptosis
Authors: Burgon Trever B. , Jenkins Jomaquai A. , Deitz Stephen B. , Spagnolo Jeannie F. , Kirkegaard Karla 
Published: July 2009

ABSTRACT

The rate of protein secretion in host cells is inhibited during infection with several different picornaviruses, with consequences likely to have significant effects on viral growth, spread, and pathogenesis. This
Sin

+

(secretion inhibition) phenotype has been documented for poliovirus, foot-and-mouth disease virus, and coxsackievirus B3 and can lead to reduced cell surface expression of major histocompatibility complex class I and tumor necrosis factor receptor as well as reduced extracellular secretion of induced cytokines such as interleukin-6 (IL-6), IL-8, and beta interferon. The inhibition of protein secretion is global, affecting the movement of all tested cargo proteins through the cellular secretion apparatus. To test the physiological significance of the
Sin
−
and
Sin

+

phenotypes in animal models,
Sin
−
mutant viruses are needed that fail to inhibit host protein secretion and also exhibit robust growth properties. To identify such
Sin
−
mutant polioviruses, we devised a fluorescence-activated cell sorter-based screen to select virus-infected cells that nevertheless expressed newly synthesized surface proteins. After multiple rounds of selection, candidate
Sin
−
mutant viruses were screened for genetic stability, increased secretion of cargo molecules and wild-type translation and growth properties. A newly identified
Sin
−
mutant poliovirus that contained coding changes in nonstructural proteins 2A (N32D) and 2C (E253G) was characterized. In this virus, the 2C mutation is responsible for the
Sin
−
phenotype and the 2A mutation suppresses a resulting growth defect by increasing the rate of cell death and therefore the rate of viral spread. The 2A-N32D suppressor mutation was not allele specific and, by increasing the rate of cellular apoptosis, affected a completely different pathway than the 2C-E253G
Sin
−
mutation. Therefore, the 2A mutation suppresses the 2C-E253G mutant phenotype by a bypass suppression mechanism.
Cellular Restriction Targeting Viral Capsids Perturbs Human Immunodeficiency Virus Type 1 Infection of Nondividing Cells
Authors: Yamashita Masahiro , Emerman Michael 
Published: July 2009

ABSTRACT

The ability of human immunodeficiency virus (HIV) to infect nondividing cells is a fundamental property by which HIV replicates in critical target cells, such as macrophages and resting CD4
+
T cells. Recent studies have revealed that the capsid (CA) protein is a dominant factor that determines retrovirus infectivity in nondividing cells, and several mutations in HIV type 1 (HIV-1) CA abrogate the ability of HIV-1 to infect nondividing cells. We present evidence for a connection between cellular restriction against viral capsids and the resistance of nondividing cells to retrovirus infection. TRIM proteins that are able to target incoming viral capsids restrict HIV-1 more potently in nondividing cells than in dividing cells, thus rendering HIV-1 infection dependent on cell division. Moreover, cyclophilin A, another cellular protein that binds to HIV-1 CA, regulates HIV-1 infection of nondividing cells. Together, these data demonstrate the importance of capsid-binding cellular proteins in the control of the cell cycle independence of HIV-1. We propose that cellular restrictions to retroviral infections are themselves cell cycle dependent.
Human Immunodeficiency Virus Type 1 Vpr Modulates Cellular Expression of UNG2 via a Negative Transcriptional Effect
Authors: Langevin Christelle , Maidou-Peindara Priscilla , Aas Per Arne , Jacquot Guillaume , Otterlei Marit , Slupphaug Geir , Benichou Serge 
Published: July 2009

ABSTRACT

It was recently reported that human immunodeficiency virus type 1 (HIV-1) Vpr induced the proteasomal degradation of the nuclear UNG2 enzyme for efficient virus replication. We confirm here that HIV-1 infection and Vpr expression reduce the level of endogenous UNG2, but this effect is not reverted by treatment with the proteasome inhibitor MG132. Moreover, this reduction is not mediated by Vpr binding to UNG2 and is independent of the Vpr-induced G
2
arrest. Finally, we show that Vpr influences the
UNG2
promoter without affecting
UNG1
gene expression. These data indicate that the Vpr-induced decrease of UNG2 level is mainly related to a transcriptional effect.
Clinical evaluation of NucliSENS magnetic extraction and NucliSENS analytical specific reagents for the real-time detection of respiratory syncytial virus (RSV) in paediatric respiratory specimens
Authors: Manji R , Lotlikar M , Zhang F , Ginocchio C C 
Published: July 2009

Aims:To evaluate the combination of NucliSENS magnetic extraction and NucliSENS analytical specific reagents (bioMérieux, Marcy L’Etoile, France) for the detection of respiratory syncytial virus (RSV) from a variety of respiratory samples.Methods:Nucleic acids (NA) from paediatric samples (n = 603) and an RSV-specific inhibition control (R-IC) were coextracted using the miniMAG and/or the easyMAG. Nucleic-acid-sequence-based amplification (NASBA) and molecular beacon detection of RSV and R-IC were performed using NucliSENS analyte-specific reagents (NRSVA) and the NucliSENS EasyQ Analyzer. NRSVA results were compared with R-Mix culture and direct fluorescent antibody detection (DFA).Results:The NRSVA analytical specificity was 100%, and the NRSVA limit of detection was 5–20 RNA copies/reaction. The prediscordant analysis, sensitivity, specificity, PPV and NPV were, respectively, for R-Mix (64.7%, 100%, 100%, 94.5%); DFA (98.8%, 99.0%, 94.4%, 99.8%); NRSVA (94.1%, 95%, 75.5%, 99%). After discordant analysis, sensitivity, specificity, PPV and NPV were, respectively, for R-Mix (56.7%, 100%, 100%, 92.3%); DFA (87.6%, 99.2%, 95.5%, 97.7%); NRSVA (93.8%, 97%, 85.9%, 99%). RSV was detected in 17.8% of the samples and in seven coinfections. Children with proven RSV infection, compared with children without a pathogen identified, had shorter median hospitalisation stays (2 days vs 3 days, p = 0.035), used fewer antibiotics (54% vs 69%) and had shorter durations of antibiotic therapy (6.2 days vs 9.3 days, p = 0.021), respectively.Conclusions:NRSVA is sensitive and specific for RSV detection in respiratory samples. The R-IC monitored the test process, including NA extraction, target amplification and detection. The rapid detection of respiratory pathogens can foster appropriate patient management.
Occupational risk of lung cancer among lifetime non-smoking women in Shanghai, China
Authors: Pronk A , Coble J , Ji B-T , Shu X-O , Rothman N , Yang G , Gao Y-T , Zheng W , Chow W-H 
Published: July 2009

Objectives:Occupational lung carcinogens have been primarily studied in men. The aim of this study was to investigate occupational lung cancer risk in a cohort of Chinese non-smoking women.Methods:In 1996–2000, 71 067 non-smoking women who had held a job outside the home were interviewed for the prospective Shanghai Women’s Health Study in China. Exposure to lung carcinogens was assessed by matching occupation and industry titles from lifetime occupational histories with lists of jobs identified by the International Agency for Research on Cancer to have potential exposure to: (1) known (A-list); or (2) suspected (B-list) carcinogens. In addition, similar occupational titles were grouped independent of the a priori defined lists. Relative risks (RRs) were calculated using Cox proportional hazards regression.Results:During follow-up through 2005, 219 incident lung cancer cases were diagnosed. Jobs on the A-list and B-list were held by 0.8–6.7% and 2.7–9.4% of the cohort, respectively. Overall, ever holding any job on the A-list or B-list was not associated with lung cancer incidence. Indications of excess risk were found for two subgroups: painters (A-list) and rubber workers (B-list) (RR  =  2.0 and 1.7, respectively, p⩽0.1). An exploratory analysis of 35 occupational categories independent of the lists showed significantly increased risks for leather products/shoes, wood/paper products and miscellaneous production/transportation. The former two of these categories were similar to subgroups of the B-list, but broader than the specific a priori defined jobs.Conclusions:Significantly elevated lung cancer risk was associated with employment in some broad occupational categories that also included jobs with potential exposure to suspected carcinogens (B-list). The results suggest that although similar exposures to those described on the B-list may play a role in this cohort of Chinese women, carcinogenic exposure may not be restricted only to the jobs on the B-list.
Turning Access TM into a web-enabled secure information system for clinical trials
Authors: Dongquan Chen  , Chen Wei-Bang , Soong Mayhue , Soong Seng-Jaw , Orthner Helmuth F. 
Published: July 2009

Background Organizations that have limited resources need to conduct clinical studies in a cost-effective, but secure way. Clinical data residing in various individual databases need to be easily accessed and secured. Although widely available, digital certification, encryption, and secure web server, have not been implemented as widely, partly due to a lack of understanding of needs and concerns over issues such as cost and difficulty in implementation. Purpose The objective of this study was to test the possibility of centralizing various databases and to demonstrate ways of offering an alternative to a large-scale comprehensive and costly commercial product, especially for simple phase I and II trials, with reasonable convenience and security. Methods We report a working procedure to transform and develop a standalone AccessTM database into a secure Web-based secure information system. Results For data collection and reporting purposes, we centralized several individual databases; developed, and tested a web-based secure server using self-issued digital certificates. Limitations The system lacks audit trails. The cost of development and maintenance may hinder its wide application. Conclusions The clinical trial databases scattered in various departments of an institution could be centralized into a web-enabled secure information system. The limitations such as the lack of a calendar and audit trail can be partially addressed with additional programming. The centralized Web system may provide an alternative to a comprehensive clinical trial management system.
Development and Implementation of Clinical Trial Protocol Templates at the National Institute of Allergy and Infectious Diseases
Authors: Bridge Heather , Smolskis Mary , Bianchine Peter , Dixon Dennis O. , Kelly Grace , Herpin Betsey , Tavel Jorge ,   Protocol Template Working Group of the NIAID Clinical Research Subcommittee
Published: July 2009

Background A clinical research protocol document must reflect both sound scientific rationale as well as local, national and, when applicable, international regulatory and human subject protections requirements. These requirements originate from a variety of sources, undergo frequent revision and are subject to interpretation. Tools to assist clinical investigators in the production of clinical protocols could facilitate navigating these requirements and ultimately increase the efficiency of clinical research. Purpose The National Institute of Allergy and Infectious Diseases (NIAID) developed templates for investigators to serve as the foundation for protocol development. These protocol templates are designed as tools to support investigators in developing clinical protocols. Methods NIAID established a series of working groups to determine how to improve its capacity to conduct clinical research more efficiently and effectively. The Protocol Template Working Group was convened to determine what protocol templates currently existed within NIAID and whether standard NIAID protocol templates should be produced. After review and assessment of existing protocol documents and requirements, the group reached consensus about required and optional content, determined the format and identified methods for distribution as well as education of investigators in the use of these templates. Results The templates were approved by the NIAID Executive Committee in 2006 and posted as part of the NIAID Clinical Research Toolkit [1] website for broad access. These documents require scheduled revisions to stay current with regulatory and policy changes. Limitations The structure of any clinical protocol template, whether comprehensive or specific to a particular study phase, setting or design, affects how it is used by investigators. Each structure presents its own set of advantages and disadvantages. While useful, protocol templates are not stand-alone tools for creating an optimal protocol document, but must be complemented by institutional resources and support. Education and guidance of investigators in the appropriate use of templates is necessary to ensure a complete yet concise protocol document. Due to changing regulatory requirements, clinical protocol templates cannot become static, but require frequent revisions.
Nicked β2-glycoprotein I binds angiostatin 4.5 (plasminogen kringle 1-5) and attenuates its antiangiogenic property
Authors: Nakagawa Hisako , Yasuda Shinsuke , Matsuura Eiji , Kobayashi Kazuko , Ieko Masahiro , Kataoka Hiroshi , Horita Tetsuya , Atsumi Tatsuya , Koike Takao 
Published: July 2009

AbstractAngiostatin was first discovered as a plasminogen fragment with antitumor/antiangiogenic property. One of the angiostatin isoforms, that is, angiostatin 4.5 (AS4.5), consisting of plasminogen kringle 1 to 4 and a most part of kringle 5, is produced by autoproteolysis and present in human plasma. β2-glycoprotein I (β2GPI) is proteolytically cleaved by plasmin in its domain V (nicked β2GPI), resulting in binding to plasminogen. Antiangiogenic properties have been recently reported in nicked β2GPI as well as in intact β2GPI at higher concentrations. In the present study, we found significant binding of nicked β2GPI to AS4.5 (KD = 3.27 × 106 M−1). Via this binding, nicked β2GPI attenuates the antiangiogenic functions of AS4.5 in the proliferation of arterial/venous endothelial cells, in the extracellular matrix invasion and the tube formation of venous endothelial cells, and in vivo angiogenesis. In contrast, intact β2GPI does not bind to AS4.5 or inhibit its antiangiogenic activity. Thus, nicked β2GPI exerts dual effects on angiogenesis, that is, nicked β2GPI promotes angiogenesis in the presence of AS4.5, whereas nicked β2GPI inhibits angiogenesis at concentrations high enough to neutralize AS4.5. Our data suggest that plasmin-nicked β2GPI promotes angiogenesis by interacting with plasmin-generated AS4.5 in sites of increased fibrinolysis such as thrombus.
Interferon-γ–triggered indoleamine 2,3-dioxygenase competence in human monocyte-derived dendritic cells induces regulatory activity in allogeneic T cells
Authors: Jürgens Birgit , Hainz Ursula , Fuchs Dietmar , Felzmann Thomas , Heitger Andreas 
Published: July 2009

AbstractThe role of the tryptophan-metabolizing enzyme indoleamine 2,3-dioxygenase (IDO) in down-regulating human alloresponses has recently been controversially debated. We here demonstrate that human monocyte-derived dendritic cells (mDCs) can be endowed with sustained IDO competence in vitro by 48-hour activation with lipopolysaccharide (LPS) and interferon-gamma (IFN-γ). IFN-γ also amplified proinflammatory cytokine secretion during activation. Yet, on reculture after activation cytokine production ceased, whereas IDO enzymatic activity continued. Manipulation of tryptophan metabolism did not affect proinflammatory cytokine release, suggesting that IFN-γ triggers IDO activity and proinflammatory cytokine release as distinct cellular programs. IDO-competent DCs down-regulated allogeneic T-cell responses, but this IDO-mediated effect was overcome by slightly modifying cell culture conditions. Nevertheless, the CD4+CD25+ T-cell fraction stimulated by IDO-competent DCs displayed substantial suppressor activity. This suppressive activity (1) required allogeneic stimulation for its induction, (2) affected third-party T cells, and (3) was reduced by the IDO inhibitor methyl-thiohydantoin-tryptophan. It became also manifest when DC/T-cell cocultures were initiated with naive (CD4+CD25−CD45RA+) T cells, indicating the differentiation of adaptive regulatory T cells. Together, these findings suggest that IFN-γ triggered IDO competence in human mDCs constitutes a critical factor for endowing allogeneic T cells with regulatory activity.