bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intermolecular Complementation between Two Varicella-Zoster Virus pORF30 Terminase Domains Essential for DNA Encapsidation
Authors: Visalli Melissa A. , House Brittany L. , Lahrman Frances J. , Visalli Robert J. 
Published: July 2015

ABSTRACTThe herpesviral terminase complex is part of the intricate machinery that delivers a single viral genome into empty preformed capsids (encapsidation). The varicella-zoster virus (VZV) terminase components (pORF25, pORF30, and pORF45/42) have not been studied as extensively as those of herpes simplex virus 1 and human cytomegalovirus (HCMV). In this study, VZV bacterial artificial chromosomes (BACs) were generated with small (Δ30S), medium (Δ30M), and large (Δ30L) ORF30 internal deletions. In addition, we isolated recombinant viruses with specific alanine substitutions in the putative zinc finger motif (30-ZF3A) or in a conserved region (region IX) with predicted structural similarity to the human topoisomerase I core subdomains I and II (30-IXAla, 30-620A, and 30-622A). Recombinant viruses replicated in an ORF30-complementing cell line (ARPE30) but failed to replicate in noncomplementing ARPE19 and MeWo cells. Transmission electron microscopy of 30-IXAla-, 30-620A-, and 30-622A-infected ARPE19 cells revealed only empty VZV capsids. Southern analysis showed that cells infected with parental VZV (VZVLUC) or a repaired virus (30R) contained DNA termini, whereas cells infected with Δ30L, 30-IXAla, 30-620A, or 30-622A contained little or no processed viral DNA. These results demonstrated that pORF30, specifically amino acids 619 to 624 (region IX), was required for DNA encapsidation. A luciferase-based assay was employed to assess potential intermolecular complementation between the zinc finger domain and conserved region IX. Complementation between 30-ZF3A and 30-IXAla provided evidence that distinct pORF30 domains can function independently. The results suggest that pORF30 may exist as a multimer or participate in higher-order assemblies during viral DNA encapsidation.IMPORTANCEAntivirals with novel mechanisms of action are sought as additional therapeutic options to treat human herpesvirus infections. Proteins involved in the viral DNA encapsidation process have become promising antiviral targets. For example, letermovir is a small-molecule drug targeting HCMV terminase that is currently in phase III clinical trials. It is important to define the structural and functional characteristics of proteins that make up viral terminase complexes to identify or design additional terminase-specific compounds. The VZV ORF30 mutants described in this study represent the first VZV terminase mutants reported to date. Targeted mutations confirmed the importance of a conserved zinc finger domain found in all herpesvirus ORF30 terminase homologs but also identified a novel, highly conserved region (region IX) essential for terminase function. Homology modeling suggested that the structure of region IX is present in all human herpesviruses and thus represents a potential structurally conserved antiviral target.
Inhibition of Ebola and Marburg Virus Entry by G Protein-Coupled Receptor Antagonists
Authors: Cheng Han , Lear-Rooney Calli M. , Johansen Lisa , Varhegyi Elizabeth , Chen Zheng W. , Olinger Gene G. , Rong Lijun 
Published: July 2015

ABSTRACT
Filoviruses, consisting of Ebola virus (EBOV) and Marburg virus (MARV), are among the most lethal infectious threats to mankind. Infections by these viruses can cause severe hemorrhagic fevers in humans and nonhuman primates with high mortality rates. Since there is currently no vaccine or antiviral therapy approved for humans, there is an urgent need to develop prophylactic and therapeutic options for use during filoviral outbreaks and bioterrorist attacks. One of the ideal targets against filoviral infection and diseases is at the entry step, which is mediated by the filoviral glycoprotein (GP). In this report, we screened a chemical library of small molecules and identified numerous inhibitors, which are known G protein-coupled receptor (GPCR) antagonists targeting different GPCRs, including histamine receptors, 5-HT (serotonin) receptors, muscarinic acetylcholine receptor, and adrenergic receptor. These inhibitors can effectively block replication of both infectious EBOV and MARV, indicating a broad antiviral activity of the GPCR antagonists. The time-of-addition experiment and microscopic studies suggest that GPCR antagonists block filoviral entry at a step following the initial attachment but prior to viral/cell membrane fusion. These results strongly suggest that GPCRs play a critical role in filoviral entry and GPCR antagonists can be developed as an effective anti-EBOV/MARV therapy.

IMPORTANCE
Infection of Ebola virus and Marburg virus can cause severe illness in humans with a high mortality rate, and currently there is no FDA-approved vaccine or therapeutic treatment available. The 2013-2015 epidemic in West Africa underscores a lack of our understanding in the infection and pathogenesis of these viruses and the urgency of drug discovery and development. In this study, we have identified numerous inhibitors that are known G protein-coupled receptor (GPCR) antagonists targeting different GPCRs. These inhibitors can effectively block replication of both infectious EBOV and MARV, indicating a broad antiviral activity of the GPCR antagonists. Our results strongly suggest that GPCRs play a critical role in filoviral entry and GPCR antagonists can be developed as an effective anti-EBOV/MARV therapy.
Polyphenols Inhibit Hepatitis C Virus Entry by a New Mechanism of Action
Authors: Calland Noémie , Sahuc Marie-Emmanuelle , Belouzard Sandrine , Pène Véronique , Bonnafous Pierre , Mesalam Ahmed Atef , Deloison Gaspard , Descamps Véronique , Sahpaz Sevser , Wychowski Czeslaw , Lambert Olivier , Brodin Priscille , Duverlie Gilles , Meuleman Philip , Rosenberg Arielle R. , Dubuisson Jean , Rouillé Yves , Séron Karin 
Published: July 2015

ABSTRACT
Despite the validation of direct-acting antivirals for hepatitis C treatment, the discovery of new compounds with different modes of action may still be of importance for the treatment of special patient populations. We recently identified a natural molecule, epigallocatechin-3-gallate (EGCG), as an inhibitor of hepatitis C virus (HCV) targeting the viral particle. The aim of this work was to discover new natural compounds with higher anti-HCV activity than that of EGCG and determine their mode of action. Eight natural molecules with structure similarity to EGCG were selected. HCV JFH1 in cell culture and HCV pseudoparticle systems were used to determine the antiviral activity and mechanism of action of the compounds. We identified delphinidin, a polyphenol belonging to the anthocyanidin family, as a new inhibitor of HCV entry. Delphinidin inhibits HCV entry in a pangenotypic manner by acting directly on the viral particle and impairing its attachment to the cell surface. Importantly, it is also active against HCV in primary human hepatocytes, with no apparent cytotoxicity and in combination with interferon and boceprevir in cell culture. Different approaches showed that neither aggregation nor destruction of the particle occurred. Cryo-transmission electron microscopy observations of HCV pseudoparticles treated with delphinidin or EGCG showed a bulge on particles that was not observed under control conditions. In conclusion, EGCG and delphinidin inhibit HCV entry by a new mechanism, i.e., alteration of the viral particle structure that impairs its attachment to the cell surface.

IMPORTANCE
In this article, we identify a new inhibitor of hepatitis C virus (HCV) infection, delphinidin, that prevents HCV entry. This natural compound, a plant pigment responsible for the blue-purple color of flowers and berries, belongs to the flavonoid family, like the catechin EGCG, the major component present in green tea extract, which is also an inhibitor of HCV entry. We studied the mode of action of these two compounds against HCV and demonstrated that they both act directly on the virus, inducing a bulging of the viral envelope. This deformation might be responsible for the observed inhibition of virus attachment to the cell surface. The discovery of such HCV inhibitors with an unusual mode of action is important to better characterize the mechanism of HCV entry into hepatocytes and to help develop a new class of HCV entry inhibitors.
Going Viral with Fluorescent Proteins
Authors: Costantini Lindsey M. , Snapp Erik L. 
Published: July 2015

ABSTRACT
Many longstanding questions about dynamics of virus-cell interactions can be answered by combining fluorescence imaging techniques with fluorescent protein (FP) tagging strategies. Successfully creating a FP fusion with a cellular or viral protein of interest first requires selecting the appropriate FP. However, while viral architecture and cellular localization often dictate the suitability of a FP, a FP's chemical and physical properties must also be considered. Here, we discuss the challenges of and offer suggestions for identifying the optimal FPs for studying the cell biology of viruses.
Thermotolerant Yeast Strains Adapted by Laboratory Evolution Show Trade-Off at Ancestral Temperatures and Preadaptation to Other Stresses
Authors: Caspeta Luis , Nielsen Jens 
Published: July 2015

ABSTRACTA major challenge for the production of ethanol from biomass-derived feedstocks is to develop yeasts that can sustain growth under the variety of inhibitory conditions present in the production process, e.g., high osmolality, high ethanol titers, and/or elevated temperatures (≥40°C). Using adaptive laboratory evolution, we previously isolated sevenSaccharomyces cerevisiaestrains with improved growth at 40°C. Here, we show that genetic adaptations to high temperature caused a growth trade-off at ancestral temperatures, reduced cellular functions, and improved tolerance of other stresses. Thermotolerant yeast strains showed horizontal displacement of their thermal reaction norms to higher temperatures. Hence, their optimal and maximum growth temperatures increased by about 3°C, whereas they showed a growth trade-off at temperatures below 34°C. Computational analysis of the physical properties of proteins showed that the lethal temperature for yeast is around 49°C, as a large fraction of the yeast proteins denature above this temperature. Our analysis also indicated that the number of functions involved in controlling the growth rate decreased in the thermotolerant strains compared with the number in the ancestral strain. The latter is an advantageous attribute for acquiring thermotolerance and correlates with the reduction of yeast functions associated with loss of respiration capacity. This trait caused glycerol overproduction that was associated with the growth trade-off at ancestral temperatures. In combination with altered sterol composition of cellular membranes, glycerol overproduction was also associated with yeast osmotolerance and improved tolerance of high concentrations of glucose and ethanol. Our study shows that thermal adaptation of yeast is suitable for improving yeast resistance to inhibitory conditions found in industrial ethanol production processes.IMPORTANCEYeast thermotolerance can significantly reduce the production costs of biomass conversion to ethanol. However, little information is available about the underlying genetic changes and physiological functions required for yeast thermotolerance. We recently revealed the genetic changes of thermotolerance in thermotolerant yeast strains (TTSs) generated through adaptive laboratory evolution. Here, we examined these TTSs’ physiology and computed their proteome stability over the entire thermal niche, as well as their preadaptation to other stresses. Using this approach, we showed that TTSs exhibited evolutionary trade-offs in the ancestral thermal niche, as well as reduced numbers of growth functions and preadaptation to other stresses found in ethanol production processes. This information will be useful for rational engineering of yeast thermotolerance for the production of biofuels and chemicals.
Mapping the Evolution of Hypervirulent Klebsiella pneumoniae
Authors: Struve Carsten , Roe Chandler C. , Stegger Marc , Stahlhut Steen G. , Hansen Dennis S. , Engelthaler David M. , Andersen Paal S. , Driebe Elizabeth M. , Keim Paul , Krogfelt Karen A. 
Published: July 2015

ABSTRACT

Highly invasive, community-acquired
Klebsiella pneumoniae
infections have recently emerged, resulting in pyogenic liver abscesses. These infections are caused by hypervirulent
K. pneumoniae
(hvKP) isolates primarily of capsule serotype K1 or K2. Hypervirulent K1 isolates belong to clonal complex 23 (CC23), indicating that this clonal lineage has a specific genetic background conferring hypervirulence. Here, we apply whole-genome sequencing to a collection of
K. pneumoniae
isolates to characterize the phylogenetic background of hvKP isolates with an emphasis on CC23. Most of the hvKP isolates belonged to CC23 and grouped into a distinct monophyletic clade, revealing that CC23 is a unique clonal lineage, clearly distinct from nonhypervirulent strains. Separate phylogenetic analyses of the CC23 isolates indicated that the CC23 lineage evolved recently by clonal expansion from a single common ancestor. Limited grouping according to geographical origin was observed, suggesting that CC23 has spread globally through multiple international transmissions. Conversely, hypervirulent K2 strains clustered in genetically unrelated groups. Strikingly, homologues of a large virulence plasmid were detected in all hvKP clonal lineages, indicating a key role in
K. pneumoniae
hypervirulence. The plasmid encodes two siderophores, aerobactin and salmochelin, and RmpA (regulator of the mucoid phenotype); all these factors were found to be restricted to hvKP isolates. Genomic comparisons revealed additional factors specifically associated with CC23. These included a distinct variant of a genomic island encoding yersiniabactin, colibactin, and microcin E492. Furthermore, additional novel genomic regions unique to CC23 were revealed which may also be involved in the increased virulence of this important clonal lineage.

IMPORTANCE
During the last 3 decades, hypervirulent
Klebsiella pneumoniae
(hvKP) isolates have emerged, causing severe community-acquired infections primarily in the form of pyogenic liver abscesses. This syndrome has so far primarily been found in Southeast Asia, but increasing numbers of cases are being reported worldwide, indicating that the syndrome is turning into a globally emerging disease. We applied whole-genome sequencing to a collection of
K. pneumoniae
clinical isolates to reveal the phylogenetic background of hvKP and to identify genetic factors associated with the increased virulence. The hvKP isolates primarily belonged to clonal complex 23 (CC23), and this clonal lineage was revealed to be clearly distinct from nonhypervirulent strains. A specific virulence plasmid was found to be associated with hypervirulence, and novel genetic determinants uniquely associated with CC23 were identified. Our findings extend the understanding of the genetic background of the emergence of hvKP clones.
An Intranasal Virus-Like Particle Vaccine Broadly Protects Mice from Multiple Subtypes of Influenza A Virus
Authors: Schwartzman Louis M. , Cathcart Andrea L. , Pujanauski Lindsey M. , Qi Li , Kash John C. , Taubenberger Jeffery K. 
Published: July 2015

ABSTRACTInfluenza virus infections are a global public health problem, with a significant impact of morbidity and mortality from both annual epidemics and pandemics. The current strategy for preventing annual influenza is to develop a new vaccine each year against specific circulating virus strains. Because these vaccines are unlikely to protect against an antigenically divergent strain or a new pandemic virus with a novel hemagglutinin (HA) subtype, there is a critical need for vaccines that protect against all influenza A viruses, a so-called “universal” vaccine. Here we show that mice were broadly protected against challenge with a wide variety of lethal influenza A virus infections (94% aggregate survival following vaccination) with a virus-like particle (VLP) vaccine cocktail. The vaccine consisted of a mixture of VLPs individually displaying H1, H3, H5, or H7 HAs, and vaccinated mice showed significant protection following challenge with influenza viruses expressing 1918 H1, 1957 H2, and avian H5, H6, H7, H10, and H11 hemagglutinin subtypes. These experiments suggest a promising and practical strategy for developing a broadly protective “universal” influenza vaccine.IMPORTANCEThe rapid and unpredictable nature of influenza A virus evolution requires new vaccines to be produced annually to match circulating strains. Human infections with influenza viruses derived from animals can cause outbreaks that may be associated with high mortality, and such strains may also adapt to humans to cause a future pandemic. Thus, there is a large public health need to create broadly protective, or “universal,” influenza vaccines that could prevent disease from a wide variety of human and animal influenza A viruses. In this study, a noninfectious virus-like particle (VLP) vaccine was shown to offer significant protection against a variety of influenza A viruses in mice, suggesting a practical strategy to develop a universal influenza vaccine.
Barriers and facilitators related to the implementation of surgical safety checklists: a systematic review of the qualitative evidence
Authors: Bergs Jochen , Lambrechts Frank , Simons Pascale , Vlayen Annemie , Marneffe Wim , Hellings Johan , Cleemput Irina , Vandijck Dominique 
Published: July 2015

ObjectiveThe objective of this review is to obtain a better understanding of the user-related barriers against, and facilitators for, the implementation of surgical safety checklists.MethodsWe searched MEDLINE for articles describing stakeholders’ perspectives regarding, and experiences with, the implementation of surgical safety checklists. The quality of the papers was assessed by means of the Qualitative Assessment and Review Instrument. Thematic synthesis was used to integrate the emergent descriptive themes into overall analytical themes.ResultsThe synthesis of 18 qualitative studies indicated that implementation requires change in the workflow of healthcare professionals as well as in their perception of the checklist and the perception of patient safety in general. The factors impeding or advancing the required change concentrated around the checklist, the implementation process and the local context. We found that the required safety checks disrupt operating theatre staffs’ routines. Furthermore, conflicting priorities and different perspectives and motives of stakeholders complicate checklist implementation. When approaching the checklist as a simple technical intervention, the expectation of cooperation between surgeons, anaesthetists and nurses is often not addressed, reducing the checklist to a tick-off exercise.ConclusionsThe complex reality in which the checklist needs to be implemented requires an approach that includes more than eliminating barriers and supporting facilitating factors. Implementation leaders must facilitate team learning to foster the mutual understanding of perspectives and motivations, and the realignment of routines. This paper provides a pragmatic overview of the user-related barriers and facilitators upon which theories, hypothesising potential change strategies and interactions, can be developed and tested empirically.
Transport and magnetic properties of cobalt disulfide prepared by solid state hybrid microwave heating and hot pressing
Authors: Ouyang Ting , Xie Mianyu , Shi Yunfeng , Chen Bing , Lan Yu , Yue Song 
Published: July 2015

In this study, single phase cobalt disulfide [Formula: see text] was synthesized by temperature-controlled solid state hybrid microwave heating. The structure, composition and morphology of the obtained samples were studied using X-ray diffraction (XRD), scanning electron spectroscopy (SEM), energy dispersive X-ray spectroscopy (EDX) and high resolution transmission electron microscopy (HRTEM), respectively. The loose [Formula: see text] polycrystalline precursor was then hot pressed to dense bulk sample. The subsequent transport and magnetic properties measurements reveal the ferromagnetic Curie temperature at the magnetic transition near 128 K. These results suggest that the magnetic transition in [Formula: see text] is susceptible to the preparation conditions and the microstructure of the samples.
Crustal-scale structure of South Tien Shan: implications for subduction polarity and Cenozoic reactivation
Authors: Loury C. , Rolland Y. , Guillot S. , Mikolaichuk A. V. , Lanari P. , Bruguier O. , Bosch D. 
Published: July 2015

Abstract

Based on new structural and petrological investigations, we present two crustal-scale cross-sections of the Kyrgyz South Tien Shan, and correlations of main faults and units between Kyrgyzstan and China. The overall structure corresponds to a doubly-vergent mountain belt. The Kyrgyz and Chinese areas exhibit identical structural and metamorphic histories. To the west, the Atbashi Range comprises high-pressure oceanic and continental units stacked by north-verging thrusts above a low metamorphic accretionary prism. High-pressure (HP) gneisses are bound to their south by a south-dipping detachment exhibiting mantle relicts. The high-pressure oceanic and continental units underwent similar pressure–temperature (
P
–
T
) paths with peak conditions of around 500 °C–20 kbar, followed by rapid exhumation. The overall south-dipping structure and kinematics indicate a south-dipping subduction of the Central Tien Shan Ocean at 320–310 Ma, ending with the docking of the Tarim block to the Kazakh continent. To the east, the Pobeda Massif shows a narrow push-up structure. A major north-vergent thrust exhumes deep-crustal-level granulites, constituting the highest summits, which were thrust towards the north onto low-grade Devonian–Carboniferous schists. The southern part of South Tien Shan is made up of a south-verging thrust stack that formed later during ongoing convergence, reactivated throughout post-30 Ma phases.
Systems Approaches to Tackling Configuration Errors
Authors: Xu Tianyin , Zhou Yuanyuan 
Published: July 2015

In recent years, configuration errors (i.e., misconfigurations) have become one of the dominant causes of system failures, resulting in many severe service outages and downtime. Unfortunately, it is notoriously difficult for system users (e.g., administrators and operators) to prevent, detect, and troubleshoot configuration errors due to the complexity of the configurations as well as the systems under configuration. As a result, the cost of resolving configuration errors is often tremendous from the aspects of both compensating the service disruptions and diagnosing, recovering from the failures. The prevalence, severity, and cost have made configuration errors one of the most thorny system problems that desire to be addressed.
This survey article provides a holistic and structured overview of the systems approaches that tackle configuration errors. To understand the problem fundamentally, we first discuss the characteristics of configuration errors and the challenges of tackling such errors. Then, we discuss the state-of-the-art systems approaches that address different types of configuration errors in different scenarios. Our primary goal is to equip the stakeholder with a better understanding of configuration errors and the potential solutions for resolving configuration errors in the spectrum of system development and management. To inspire follow-up research, we further discuss the open problems with regard to system configuration. To the best of our knowledge, this is the first survey on the topic of tackling configuration errors.