bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inosine-Mediated Modulation of RNA Sensing by Toll-Like Receptor 7 (TLR7) and TLR8
Authors: Sarvestani Soroush T. , Tate Michelle D. , Moffat Jessica M. , Jacobi Ashley M. , Behlke Mark A. , Miller Alistair R. , Beckham Simone A. , McCoy Claire E. , Chen Weisan , Mintern Justine D. , O'Keeffe Meredith , John Matthias , Williams Bryan R. G. , Gantier Michael P. 
Published: November 2013

ABSTRACT

RNA-specific adenosine deaminase (ADAR)-mediated adenosine-to-inosine (A-to-I) editing is a critical arm of the antiviral response. However, mechanistic insights into how A-to-I RNA editing affects viral infection are lacking. We posited that inosine incorporation into RNA facilitates sensing of nonself RNA by innate immune sensors and accordingly investigated the impact of inosine-modified RNA on Toll-like receptor 7 and 8 (TLR7/8) sensing. Inosine incorporation into synthetic single-stranded RNA (ssRNA) potentiated tumor necrosis factor alpha (TNF-α) or alpha interferon (IFN-α) production in human peripheral blood mononuclear cells (PBMCs) in a sequence-dependent manner, indicative of TLR7/8 recruitment. The effect of inosine incorporation on TLR7/8 sensing was restricted to immunostimulatory ssRNAs and was not seen with inosine-containing short double-stranded RNAs or with a deoxy-inosine-modified ssRNA. Inosine-mediated increase of self-secondary structure of an ssRNA resulted in potentiated IFN-α production in human PBMCs through TLR7 recruitment, as established through the use of a TLR7 antagonist and
Tlr7
-deficient cells. There was a correlation between hyperediting of influenza A viral ssRNA and its ability to stimulate TNF-α, independent of 5′-triphosphate residues, and involving Adar-1. Furthermore, A-to-I editing of viral ssRNA directly enhanced mouse Tlr7 sensing, when present in proportions reproducing biologically relevant levels of RNA editing. Thus, we demonstrate for the first time that inosine incorporation into immunostimulatory ssRNA can potentiate TLR7/8 activation. Our results suggest a novel function of A-to-I RNA editing, which is to facilitate TLR7/8 sensing of phagocytosed viral RNA.
Inhibition of Bim Enhances Replication of Varicella-Zoster Virus and Delays Plaque Formation in Virus-Infected Cells
Authors: Liu XueQiao , Cohen Jeffrey I. 
Published: November 2013

ABSTRACT
Programmed cell death (apoptosis) is an important host defense mechanism against intracellular pathogens, such as viruses. Accordingly, viruses have evolved multiple mechanisms to modulate apoptosis to enhance replication. Varicella-zoster virus (VZV) induces apoptosis in human fibroblasts and melanoma cells. We found that VZV triggered the phosphorylation of the proapoptotic proteins Bim and BAD but had little or no effect on other Bcl-2 family members. Since phosphorylation of Bim and BAD reduces their proapoptotic activity, this may prevent or delay apoptosis in VZV-infected cells. Phosphorylation of Bim but not BAD in VZV-infected cells was dependent on activation of the MEK/extracellular signal-regulated kinase (ERK) pathway. Cells knocked down for Bim showed delayed VZV plaque formation, resulting in longer survival of VZV-infected cells and increased replication of virus, compared with wild-type cells infected with virus. Conversely, overexpression of Bim resulted in earlier plaque formation, smaller plaques, reduced virus replication, and increased caspase 3 activity. Inhibition of caspase activity in VZV-infected cells overexpressing Bim restored levels of virus production similar to those seen with virus-infected wild-type cells. Previously we showed that VZV ORF12 activates ERK and inhibits apoptosis in virus-infected cells. Here we found that VZV ORF12 contributes to Bim and BAD phosphorylation. In summary, VZV triggers Bim phosphorylation; reduction of Bim levels results in longer survival of VZV-infected cells and increased VZV replication.
Novel Neuroprotective GSK-3β Inhibitor Restricts Tat-Mediated HIV-1 Replication
Authors: Guendel Irene , Iordanskiy Sergey , Van Duyne Rachel , Kehn-Hall Kylene , Saifuddin Mohammed , Das Ravi , Jaworski Elizabeth , Sampey Gavin C. , Senina Svetlana , Shultz Leonard , Narayanan Aarthi , Chen Hao , Lepene Benjamin , Zeng Chen , Kashanchi Fatah 
Published: November 2013

ABSTRACTThe implementation of new antiretroviral therapies targeting transcription of early viral proteins in postintegrated HIV-1 can aid in overcoming current therapy limitations. Using high-throughput screening assays, we have previously described a novel Tat-dependent HIV-1 transcriptional inhibitor named 6-bromoindirubin-3′-oxime (6BIO). The screening of 6BIO derivatives yielded unique compounds that show potent inhibition of HIV-1 transcription. We have identified a second-generation derivative called 18BIOder as an inhibitor of HIV-1 Tat-dependent transcription in TZM-bl cells and a potent inhibitor of GSK-3β kinasein vitro. Structurally, 18BIOder is half the molecular weight and structure of its parental compound, 6BIO. More importantly, we also have found a different GSK-3β complex present only in HIV-1-infected cells. 18BIOder preferentially inhibits this novel kinase complex from infected cells at nanomolar concentrations. Finally, we observed that neuronal cultures treated with Tat protein are protected from Tat-mediated cytotoxicity when treated with 18BIOder. Overall, our data suggest that HIV-1 Tat-dependent transcription is sensitive to small-molecule inhibition of GSK-3β.
Evolution and Diversity in Human Herpes Simplex Virus Genomes
Authors: Szpara Moriah L. , Gatherer Derek , Ochoa Alejandro , Greenbaum Benjamin , Dolan Aidan , Bowden Rory J. , Enquist Lynn W. , Legendre Matthieu , Davison Andrew J. 
Published: November 2013

ABSTRACT
Herpes simplex virus 1 (HSV-1) causes a chronic, lifelong infection in >60% of adults. Multiple recent vaccine trials have failed, with viral diversity likely contributing to these failures. To understand HSV-1 diversity better, we comprehensively compared 20 newly sequenced viral genomes from China, Japan, Kenya, and South Korea with six previously sequenced genomes from the United States, Europe, and Japan. In this diverse collection of passaged strains, we found that one-fifth of the newly sequenced members share a gene deletion and one-third exhibit homopolymeric frameshift mutations (HFMs). Individual strains exhibit genotypic and potential phenotypic variation via HFMs, deletions, short sequence repeats, and single-nucleotide polymorphisms, although the protein sequence identity between strains exceeds 90% on average. In the first genome-scale analysis of positive selection in HSV-1, we found signs of selection in specific proteins and residues, including the fusion protein glycoprotein H. We also confirmed previous results suggesting that recombination has occurred with high frequency throughout the HSV-1 genome. Despite this, the HSV-1 strains analyzed clustered by geographic origin during whole-genome distance analysis. These data shed light on likely routes of HSV-1 adaptation to changing environments and will aid in the selection of vaccine antigens that are invariant worldwide.
TMPRSS2 and ADAM17 Cleave ACE2 Differentially and Only Proteolysis by TMPRSS2 Augments Entry Driven by the Severe Acute Respiratory Syndrome Coronavirus Spike Protein
Authors: Heurich Adeline , Hofmann-Winkler Heike , Gierer Stefanie , Liepold Thomas , Jahn Olaf , Pöhlmann Stefan 
Published: November 2013

ABSTRACT
The type II transmembrane serine proteases TMPRSS2 and HAT can cleave and activate the spike protein (S) of the severe acute respiratory syndrome coronavirus (SARS-CoV) for membrane fusion. In addition, these proteases cleave the viral receptor, the carboxypeptidase angiotensin-converting enzyme 2 (ACE2), and it was proposed that ACE2 cleavage augments viral infectivity. However, no mechanistic insights into this process were obtained and the relevance of ACE2 cleavage for SARS-CoV S protein (SARS-S) activation has not been determined. Here, we show that arginine and lysine residues within ACE2 amino acids 697 to 716 are essential for cleavage by TMPRSS2 and HAT and that ACE2 processing is required for augmentation of SARS-S-driven entry by these proteases. In contrast, ACE2 cleavage was dispensable for activation of the viral S protein. Expression of TMPRSS2 increased cellular uptake of soluble SARS-S, suggesting that protease-dependent augmentation of viral entry might be due to increased uptake of virions into target cells. Finally, TMPRSS2 was found to compete with the metalloprotease ADAM17 for ACE2 processing, but only cleavage by TMPRSS2 resulted in augmented SARS-S-driven entry. Collectively, our results in conjunction with those of previous studies indicate that TMPRSS2 and potentially related proteases promote SARS-CoV entry by two separate mechanisms: ACE2 cleavage, which might promote viral uptake, and SARS-S cleavage, which activates the S protein for membrane fusion. These observations have interesting implications for the development of novel therapeutics. In addition, they should spur efforts to determine whether receptor cleavage promotes entry of other coronaviruses, which use peptidases as entry receptors.
Discovery of a Novel Bottlenose Dolphin Coronavirus Reveals a Distinct Species of Marine Mammal Coronavirus in Gammacoronavirus
Authors: Woo Patrick C. Y. , Lau Susanna K. P. , Lam Carol S. F. , Tsang Alan K. L. , Hui Suk-Wai , Fan Rachel Y. Y. , Martelli Paolo , Yuen Kwok-Yung 
Published: November 2013

ABSTRACT

While gammacoronaviruses mainly comprise infectious bronchitis virus (IBV) and its closely related bird coronaviruses (CoVs), the only mammalian gammacoronavirus was discovered from a white beluga whale (beluga whale CoV [BWCoV] SW1) in 2008. In this study, we discovered a novel gammacoronavirus from fecal samples from three Indo-Pacific bottlenose dolphins (
Tursiops aduncus
), which we named bottlenose dolphin CoV (BdCoV) HKU22. All the three BdCoV HKU22-positive samples were collected on the same date, suggesting a cluster of infection, with viral loads of 1 × 10
3
to 1 × 10
5
copies per ml. Clearance of virus was associated with a specific antibody response against the nucleocapsid of BdCoV HKU22. Complete genome sequencing and comparative genome analysis showed that BdCoV HKU22 and BWCoV SW1 have similar genome characteristics and structures. Their genome size is about 32,000 nucleotides, the largest among all CoVs, as a result of multiple unique open reading frames (NS5a, NS5b, NS5c, NS6, NS7, NS8, NS9, and NS10) between their membrane (M) and nucleocapsid (N) protein genes. Although comparative genome analysis showed that BdCoV HKU22 and BWCoV SW1 should belong to the same species, a major difference was observed in the proteins encoded by their spike (S) genes, which showed only 74.3 to 74.7% amino acid identities. The high ratios of the number of synonymous substitutions per synonymous site (

K
s

) to the number of nonsynonymous substitutions per nonsynonymous site (

K
a

) in multiple regions of the genome, especially the S gene (

K
a

/

K
s

ratio, 2.5), indicated that BdCoV HKU22 may be evolving rapidly, supporting a recent transmission event to the bottlenose dolphins. We propose a distinct species,
Cetacean coronavirus
, in
Gammacoronavirus
, to include BdCoV HKU22 and BWCoV SW1, whereas IBV and its closely related bird CoVs represent another species,
Avian coronavirus
, in
Gammacoronavirus
.
Histone Deacetylase Classes I and II Regulate Kaposi's Sarcoma-Associated Herpesvirus Reactivation
Authors: Shin Hye Jin , DeCotiis Jennifer , Giron Mario , Palmeri Diana , Lukac David M. 
Published: November 2013

ABSTRACT
In primary effusion lymphoma (PEL) cells infected with latent Kaposi's sarcoma-associated herpesvirus (KSHV), the promoter of the viral lytic switch gene, Rta, is organized into bivalent chromatin, similar to cellular developmental switch genes. Histone deacetylase (HDAC) inhibitors (HDACis) reactivate latent KSHV and dramatically remodel the viral genome topology and chromatin architecture. However, reactivation is not uniform across a population of infected cells. We sought to identify an HDACi cocktail that would uniformly reactivate KSHV and reveal the regulatory HDACs. Using HDACis with various specificities, we found that class I HDACis were sufficient to reactivate the virus but differed in potency. Valproic acid (VPA) was the most effective HDACi, inducing lytic cycle gene expression in 75% of cells, while trichostatin A (TSA) induced less widespread lytic gene expression and inhibited VPA-stimulated reactivation. VPA was only slightly superior to TSA in inducing histone acetylation of Rta's promoter, but only VPA induced significant production of infectious virus, suggesting that HDAC regulation after Rta expression has a dramatic effect on reactivation progression. Ectopic HDACs 1, 3, and 6 inhibited TPA-stimulated KSHV reactivation. Surprisingly, ectopic HDACs 1 and 6 stimulated reactivation independently, suggesting that the stoichiometries of HDAC complexes are critical for the switch. Tubacin, a specific inhibitor of the ubiquitin-binding, proautophagic HDAC6, also inhibited VPA-stimulated reactivation. Immunofluorescence indicated that HDAC6 is expressed diffusely throughout latently infected cells, but its expression level and nuclear localization is increased during reactivation. Overall, our data suggest that inhibition of HDAC classes I and IIa and maintenance of HDAC6 (IIb) activity are required for optimal KSHV reactivation.
A Novel Strategy To Develop a Robust Infectious Hepatitis C Virus Cell Culture System Directly from a Clinical Isolate
Authors: Lu Jie , Xiang Yu , Tao Wanyin , Li Qingchao , Wang Na , Gao Yongfeng , Xiang Xiaogang , Xie Qing , Zhong Jin 
Published: November 2013

ABSTRACT

Hepatitis C virus (HCV) infection is a leading cause of chronic liver diseases. Progress in the HCV field was greatly enhanced by constructing infectious cDNA clone of JFH-1. Since then, JFH-1-based intra- and intergenotypic recombinants have been developed, and this permitted the study of vaccines and antiviral inhibitors for all genotypes. Recently, highly efficient HCV culture systems have been established by using consensus sequence-based clones. We developed a novel strategy to construct infectious HCV cDNA clone by combining functional screening of sequences directly from a genotype 2a clinical isolate (PR63) and cell culture adaptation. Using JFH-1 cDNA as the starting backbone, we sequentially replaced the JFH-1 fragments with a sequence from the pools of PR63 sequences. Through engineering adaptive mutations that improve HCV infectivity, we finally established a full-length cell culture-derived infectious clone of PR63, named PR63cc, that could efficiently produce virus particles in Huh7-derived cells, with peak titers of 1.6 × 10
5
focus-forming units/ml. The PR63cc could be neutralized by an anti-E2 antibody and inhibited by antiviral agents but appeared more resistant to an NS5A inhibitor than JFH-1. In summary, we developed a new approach to construct an infectious HCV cDNA clone that can produce viruses efficiently in cell culture. This approach could be applied to other viral isolates, with potential implications for individualized treatments of HCV patients.
Tectonomagmatic evolution of the Early Ordovician suprasubduction-zone ophiolites of the Trondheim Region, Mid-Norwegian Caledonides
Authors: Slagstad Trond , Pin Christian , Roberts David , Kirkland Christopher L. , Grenne Tor , Dunning Greg , Sauer Simone , Andersen Tom 
Published: November 2013

Abstract

The Trondheim Region ophiolites in the Mid-Norwegian Caledonides represent variably tectonized ophiolite fragments. We present high-precision thermal-ionization mass spectrometry and secondary-ion mass spectrometry (SIMS) U–Pb zircon dates, whole-rock geochemical and Sm–Nd data and Lu–Hf zircon analyses that permit the timing and nature of various stages in the evolution of the ophiolite to be elucidated. Plagiogranite intrusions dated at 487 and 480 Ma have relatively juvenile Nd and Hf isotopic compositions (ε

Nd(
t
)

=6.3, ε

Hf(
t
)

=8.2–12.4). Geochemical data indicate a subduction-zone influence, suggesting formation in an oceanic back-arc setting. At 481 Ma, a granitoid body with a relatively strong unradiogenic Nd and Hf isotopic composition (ε

Nd(
t
)

=−2.6 to −4.0, ε

Hf(
t
)

=3.8–6.4) and subduction-zone geochemical signature intruded the ophiolite. We interpret this stage to reflect the formation or migration of an oceanic arc above a subduction zone influenced by continentally derived sediments. At
c.
475–465 Ma, a greenstone-dominated conglomerate and volcaniclastic sequence was deposited on the eroded ophiolite, indicating obduction between about 480 and 475 Ma. At
c.
468–467 Ma, the deformed ophiolite and its sedimentary cover was intruded by trondhjemite dykes and shoshonitic volcanic rocks with intermediate Nd and Hf isotopic compositions (ε

Nd(
t
)

=3.0–3.9, ε

Hf(
t
)

=4.4–10.2). We interpret this magmatism to reflect subduction-polarity reversal and establishment of a magmatic arc at the continental margin shortly after obduction.

Supplementary material:

Whole-rock geochemistry, Sm–Nd isotopic data, SHRIMP U–Pb zircon, TIMS U–Pb zircon and Lu–Hf isotopic data are available at
http://www.geolsoc.org.uk/SUP18689
.
Association Between Insomnia Symptoms and Mortality
Authors: Li Yanping , Zhang Xuehong , Winkelman John W. , Redline Susan , Hu Frank B. , Stampfer Meir , Ma Jing , Gao Xiang 
Published: November 2013

Background—
Insomnia complaints are common in older adults and may be associated with mortality risk. However, evidence regarding this association is mixed. Thus, we prospectively examined whether men with insomnia symptoms had an increased risk of mortality during 6 years of follow-up.

Methods and Results—

A prospective cohort study of 23 447 US men participating in the Health Professionals Follow-Up Study and free of cancer, reported on insomnia symptoms in 2004, were followed through 2010. Deaths were identified from state vital statistic records, the National Death Index, family reports, and the postal system. We documented 2025 deaths during 6 years of follow-up (2004–2010). The multivariable-adjusted hazard ratios of total mortality were 1.25 (95% confidence interval [CI], 1.04–1.50) for difficulty initiating sleep, 1.09 (95% CI, 0.97–1.24) for difficulty maintaining sleep, 1.04 (95% CI, 0.88–1.22) for early-morning awakenings, and 1.24 (95% CI, 1.05–1.46) for nonrestorative sleep, comparing men with those symptoms most of the time with men without those symptoms, after adjusting for age, lifestyle factors, and presence of common chronic conditions. Men with difficulty initiating sleep and nonrestorative sleep most of the time had a 55% (hazard ratio, 1.55; 95% CI, 1.19–2.04;
P
-trend=0.01) and 32% (hazard ratio, 1.32; 95% CI, 1.02–1.72;
P
-trend=0.002) increased risk of cardiovascular disease mortality, respectively, relative to men without those symptoms.

Conclusion—
Some insomnia symptoms, especially difficulty initiating asleep and nonrestorative sleep, are associated with a modestly higher risk of mortality.
Knowledge, attitudes and practices of clinicians in promoting physical activity to prostate cancer survivors
Authors: Spellman Claire , Craike Melinda , Livingston Patricia 
Published: November 2013

Objectives: This study examined the knowledge, attitudes and practices of clinicians in promoting physical activity to prostate cancer survivors. Design: A purposeful sample was used and cross-sectional data were collected using an anonymous, self-reported online questionnaire or an identical paper-based questionnaire. Settings: Health services and online questionnaire. Methods: Clinicians were invited to complete the questionnaire which measured their knowledge, attitudes and practices relating to physical activity for their patients. Results: Thirty-one clinicians completed a questionnaire. Most participants were men (71%), aged 30–40 years (45.2%), and radiation oncologists (35.5%). Although clinicians recognized the benefits of physical activity for their patients, few always gave advice about physical activity. Advice was verbal in nature, very few provided written material and none referred patients to an exercise specialist. Older age, a belief that physical activity reduces side effects of treatment, higher confidence and disagreement that physical activity has risks were associated with higher frequency of providing physical activity advice. Over half of the clinicians (55%) reported that advising patients on physical activity was not part of their role. Conclusions: This study provides preliminary evidence that physical activity advice may not be provided routinely to prostate cancer survivors. It is important for future research to address the involvement of clinicians in physical activity promotion so that holistic care is provided.
Alliances in the Dutch BeweegKuur lifestyle intervention
Authors: den Hartog Franciska , Wagemakers Annemarie , Vaandrager Lenneke , van Dijk Marieke , Koelen Maria A 
Published: November 2013

Objective: BeweegKuur (Exercise Therapy) is a Dutch lifestyle programme in which participants are referred by a general practitioner (GP) to a lifestyle advisor. To support participants, regional and local alliances are established. The present study explored the successes and challenges associated with collaboration processes in local BeweegKuur alliances. Design: A qualitative explorative study. Setting: The Netherlands Institute for Sports and Physical Activity (NISB) initiated the Building BeweegKuur Alliances project to support local alliances. The BeweegKuur intervention is implemented by over 30 regional and about 150 local alliances throughout the Netherlands. Method: 12 in-depth interviews were held with coordinators of the alliances, and four focus groups were held with regional and local alliance partners. Results: Collaboration within the alliances is perceived as successful in integrating prevention and care. Challenges include the participation of sectors such as the local municipality and the sports sector, and the transition of BeweegKuur participants to local sports facilities. Conclusion: This study identifies three general conditions for successful coordinated action: (a) flexible protocols and management that allow for contextual adaptations; (b) making successes and challenges visible using facilitating methods and tools; and (c) time and funding to overcome differences of culture between different sectors, and to build trust.
Prosthetic reconstruction of bicuspid pulmonary valve in tetralogy of Fallot
Authors: Sasikumar Navaneetha , Ramanan Sowmya , Rema Krishna Manohar Soman , Kumar Raghavannair Suresh , Subramanyan Raghavan , Cherian Kootturathu Mammen 
Published: November 2013

Background Various techniques have been described for preserving pulmonary valve function in tetralogy of Fallot repair. In selected substrates, the pulmonary valve can be bicuspidized and preserved using polytetrafluoroethylene pericardial membrane. Methods This study was a retrospective review of 20 patients aged 11 months to 31 years with tetralogy of Fallot and a bicuspid pulmonary valve (with anteroposterior cusps) who underwent intracardiac repair from August 2010 to January 2013. The anterior cusp was augmented using polytetrafluoroethylene pericardial membrane to preserve the valve hinge. A transannular patch was used in all cases. Data relating to surgical outcome, intensive care unit course, pulmonary regurgitation, and right ventricular outflow tract gradient were collected. Results There was no mortality. Predischarge pulmonary regurgitation was ≤grade 2 in 18 (90%) patients. One patient had an outflow gradient >40 mm Hg. On follow-up of 3–24 months, there was no increase in outflow gradient; 18.7% had progression of pulmonary regurgitation. Conclusion In selected substrates, this technique is associated with minimization of pulmonary regurgitation and an excellent functional outcome. The utility of this technique needs to be validated over a longer time scale in a larger series.