bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of a Varicella-Zoster Virus Replication Inhibitor That Blocks Capsid Assembly by Interacting with the Floor Domain of the Major Capsid Protein
Authors: Inoue Naoki , Matsushita Misato , Fukui Yoshiko , Yamada Souichi , Tsuda Mihoko , Higashi Chizuka , Kaneko Keiko , Hasegawa Hideki , Yamaguchi Toyofumi 
Published: August 2012

ABSTRACT

A novel anti-varicella-zoster virus compound, a derivative of pyrazolo[1,5-
c
]1,3,5-triazin-4-one (coded as 35B2), was identified from a library of 9,600 random compounds. This compound inhibited both acyclovir (ACV)-resistant and -sensitive strains. In a plaque reduction assay under conditions in which the 50% effective concentration of ACV against the vaccine Oka strain (V-Oka) in human fibroblasts was 4.25 μM, the 50% effective concentration of 35B2 was 0.75 μM. The selective index of the compound was more than 200. Treatment with 35B2 inhibited neither immediate-early gene expression nor viral DNA synthesis. Twenty-four virus clones resistant to 35B2 were isolated, all of which had a mutation(s) in the amino acid sequence of open reading frame 40 (ORF40), which encodes the major capsid protein (MCP). Most of the mutations were located in the regions corresponding to the “floor” domain of the MCP of herpes simplex virus 1. Treatment with 35B2 changed the localization of MCP in the fibroblasts infected with V-Oka but not in the fibroblasts infected with the resistant clones, although it did not affect steady-state levels of MCP. Overexpression of the scaffold proteins restored the normal MCP localization in the 35B2-treated infected cells. The compound did not inhibit the scaffold protein-mediated translocation of MCP from the cytoplasm to the nucleus. Electron microscopic analysis demonstrated the lack of capsid formation in the 35B2-treated infected cells. These data indicate the feasibility of developing a new class of antivirals that target the herpesvirus MCPs and inhibit normal capsid formation by a mechanism that differs from those of the known protease and encapsidation inhibitors. Further biochemical studies are required to clarify the precise antiviral mechanism.
Recent Transmission of a Novel Alphacoronavirus, Bat Coronavirus HKU10, from Leschenault's Rousettes to Pomona Leaf-Nosed Bats: First Evidence of Interspecies Transmission of Coronavirus between Bats of Different Suborders
Authors: Lau Susanna K. P. , Li Kenneth S. M. , Tsang Alan K. L. , Shek Chung-Tong , Wang Ming , Choi Garnet K. Y. , Guo Rongtong , Wong Beatrice H. L. , Poon Rosana W. S. , Lam Carol S. F. , Wang Sylvia Y. H. , Fan Rachel Y. Y. , Chan Kwok-Hung , Zheng Bo-Jian , Woo Patrick C. Y. , Yuen Kwok-Yung 
Published: August 2012

ABSTRACT

Although coronaviruses are known to infect various animals by adapting to new hosts, interspecies transmission events are still poorly understood. During a surveillance study from 2005 to 2010, a novel alphacoronavirus, BatCoV HKU10, was detected in two very different bat species, Ro-BatCoV HKU10 in Leschenault's rousettes (
Rousettus leschenaulti
) (fruit bats in the suborder Megachiroptera) in Guangdong and Hi-BatCoV HKU10 in Pomona leaf-nosed bats (
Hipposideros pomona
) (insectivorous bats in the suborder Microchiroptera) in Hong Kong. Although infected bats appeared to be healthy, Pomona leaf-nosed bats carrying Hi-BatCoV HKU10 had lower body weights than uninfected bats. To investigate possible interspecies transmission between the two bat species, the complete genomes of two Ro-BatCoV HKU10 and six Hi-BatCoV HKU10 strains were sequenced. Genome and phylogenetic analyses showed that Ro-BatCoV HKU10 and Hi-BatCoV HKU10 represented a novel alphacoronavirus species, sharing highly similar genomes except in the genes encoding spike proteins, which had only 60.5% amino acid identities. Evolution of the spike protein was also rapid in Hi-BatCoV HKU10 strains from 2005 to 2006 but stabilized thereafter. Molecular-clock analysis dated the most recent common ancestor of all BatCoV HKU10 strains to 1959 (highest posterior density regions at 95% [HPDs], 1886 to 2002) and that of Hi-BatCoV HKU10 to 1986 (HPDs, 1956 to 2004). The data suggested recent interspecies transmission from Leschenault's rousettes to Pomona leaf-nosed bats in southern China. Notably, the rapid adaptive genetic change in BatCoV HKU10 spike protein by ∼40% amino acid divergence after recent interspecies transmission was even greater than the ∼20% amino acid divergence between spike proteins of severe acute respiratory syndrome-related
Rhinolophus
bat coronavirus (SARSr-CoV) in bats and civets. This study provided the first evidence for interspecies transmission of coronavirus between bats of different suborders.
Sequences in Glycoprotein gp41, the CD4 Binding Site, and the V2 Domain Regulate Sensitivity and Resistance of HIV-1 to Broadly Neutralizing Antibodies
Authors: O'Rourke Sara M. , Schweighardt Becky , Phung Pham , Mesa Kathryn A. , Vollrath Aaron L. , Tatsuno Gwen P. , To Briana , Sinangil Faruk , Limoli Kay , Wrin Terri , Berman Phillip W. 
Published: August 2012

ABSTRACT

The swarm of quasispecies that evolves in each HIV-1-infected individual represents a source of closely related Env protein variants that can be used to explore various aspects of HIV-1 biology. In this study, we made use of these variants to identify mutations that confer sensitivity and resistance to the broadly neutralizing antibodies found in the sera of selected HIV-1-infected individuals. For these studies, libraries of Env proteins were cloned from infected subjects and screened for infectivity and neutralization sensitivity. The nucleotide sequences of the Env proteins were then compared for pairs of neutralization-sensitive and -resistant viruses.
In vitro
mutagenesis was used to identify the specific amino acids responsible for the neutralization phenotype. All of the mutations altering neutralization sensitivity/resistance appeared to induce conformational changes that simultaneously enhanced the exposure of two or more epitopes located in different regions of gp160. These mutations appeared to occur at unique positions required to maintain the quaternary structure of the gp160 trimer, as well as conformational masking of epitopes targeted by neutralizing antibodies. Our results show that sequences in gp41, the CD4 binding site, and the V2 domain all have the ability to act as global regulators of neutralization sensitivity. Our results also suggest that neutralization assays designed to support the development of vaccines and therapeutics targeting the HIV-1 Env protein should consider virus variation within individuals as well as virus variation between individuals.
Probing, by Self-Assembly, the Number of Potential Binding Sites for Minor Protein Subunits in the Procapsid of Double-Stranded RNA Bacteriophage φ6
Authors: Sun Xiaoyu , Bamford Dennis H. , Poranen Minna M. 
Published: August 2012

ABSTRACT

The double-stranded RNA bacteriophage ϕ6 is an extensively studied prokaryotic model system for virus assembly. There are established
in vitro
assembly protocols available for the ϕ6 system for obtaining infectious particles from purified protein and RNA constituents. The polymerase complex is a multifunctional nanomachine that replicates, transcribes, and translocates viral RNA molecules in a highly specific manner. The complex is composed of (i) the major structural protein (P1), forming a T=1 icosahedral lattice with two protein subunits in the icosahedral asymmetric unit; (ii) the RNA-dependent RNA polymerase (P2); (iii) the hexameric packaging nucleoside triphosphatase (NTPase) (P4); and (iv) the assembly cofactor (P7). In this study, we analyzed several ϕ6 virions and recombinant polymerase complexes to investigate the relative copy numbers of P2, P4, and P7, and we applied saturated concentrations of these proteins in the self-assembly system to probe their maximal numbers of binding sites in the P1 shell. Biochemical quantitation confirmed that the composition of the recombinant particles was similar to that of the virion cores. By including a high concentration of P2 or P7 in the self-assembly reaction mix, we observed that the numbers of these proteins in the resulting particles could be increased beyond those observed in the virion. Our results also suggest a previously unidentified P2-P7 dependency in the assembly reaction. Furthermore, it appeared that P4 must initially be incorporated at each, or a majority, of the 5-fold symmetry positions of the P1 shell for particle assembly. Although required for nucleation, excess P4 resulted in slower assembly kinetics.
Differential Roles of Hsp70 and Hsp90 in the Assembly of the Replicase Complex of a Positive-Strand RNA Plant Virus
Authors: Mine Akira , Hyodo Kiwamu , Tajima Yuri , Kusumanegara Kusumawaty , Taniguchi Takako , Kaido Masanori , Mise Kazuyuki , Taniguchi Hisaaki , Okuno Tetsuro 
Published: August 2012

ABSTRACT

Assembly of viral replicase complexes of eukaryotic positive-strand RNA viruses is a regulated process: multiple viral and host components must be assembled on intracellular membranes and ordered into quaternary complexes capable of synthesizing viral RNAs. However, the molecular mechanisms underlying this process are poorly understood. In this study, we used a model virus,
Red clover necrotic mosaic virus
(RCNMV), whose replicase complex can be detected readily as the 480-kDa functional protein complex. We found that host heat shock proteins Hsp70 and Hsp90 are required for RCNMV RNA replication and that they interact with p27, a virus-encoded component of the 480-kDa replicase complex, on the endoplasmic reticulum membrane. Using a cell-free viral translation/replication system in combination with specific inhibitors of Hsp70 and Hsp90, we found that inhibition of p27-Hsp70 interaction inhibits the formation of the 480-kDa complex but instead induces the accumulation of large complexes that are nonfunctional in viral RNA synthesis. In contrast, inhibition of p27-Hsp90 interaction did not induce such large complexes but rendered p27 incapable of binding to a specific viral RNA element, which is a critical step for the assembly of the 480-kDa replicase complex and viral RNA replication. Together, our results suggest that Hsp70 and Hsp90 regulate different steps in the assembly of the RCNMV replicase complex.
The
ac53
,
ac78
,
ac101
, and
ac103
Genes Are Newly Discovered Core Genes in the Family Baculoviridae
Authors: Garavaglia Matías Javier , Miele Solange Ana Belén , Iserte Javier Alonso , Belaich Mariano Nicolás , Ghiringhelli Pablo Daniel 
Published: August 2012

ABSTRACT

The family
Baculoviridae
is a large group of insect viruses containing circular double-stranded DNA genomes of 80 to 180 kbp, which have broad biotechnological applications. A key feature to understand and manipulate them is the recognition of orthology. However, the differences in gene contents and evolutionary distances among the known members of this family make it difficult to assign sequence orthology. In this study, the genome sequences of 58 baculoviruses were analyzed, with the aim to detect previously undescribed core genes because of their remote homology. A routine based on Multi PSI-Blast/tBlastN and Multi HaMStR allowed us to detect 31 of 33 accepted core genes and 4 orthologous sequences in the
Baculoviridae
which were not described previously. Our results show that the
ac53
,
ac78
,
ac101
(
p40
), and
ac103
(
p48
) genes have orthologs in all genomes and should be considered core genes. Accordingly, there are 37 orthologous genes in the family
Baculoviridae
.
Epstein-Barr Virus BGLF4 Kinase Downregulates NF-κB Transactivation through Phosphorylation of Coactivator UXT
Authors: Chang Ling-Shih , Wang Jiin-Tarng , Doong Shin-Lian , Lee Chung-Pei , Chang Chou-Wei , Tsai Ching-Hwa , Yeh Sheng-Wen , Hsieh Ching-Yueh , Chen Mei-Ru 
Published: August 2012

ABSTRACT

Epstein-Barr virus (EBV) BGLF4 is a member of the conserved herpesvirus kinases that regulate multiple cellular and viral substrates and play an important role in the viral lytic cycles. BGLF4 has been found to phosphorylate several cellular and viral transcription factors, modulate their activities, and regulate downstream events. In this study, we identify an NF-κB coactivator, UXT, as a substrate of BGLF4. BGLF4 downregulates not only NF-κB transactivation in reporter assays in response to tumor necrosis factor alpha (TNF-α) and poly(I·C) stimulation, but also NF-κB-regulated cellular gene expression. Furthermore, BGLF4 attenuates NF-κB-mediated repression of the EBV lytic transactivators, Zta and Rta. In EBV-positive NA cells, knockdown of BGLF4 during lytic progression elevates NF-κB activity and downregulates the activity of the EBV oriLyt
BHLF1
promoter, which is the first promoter activated upon lytic switch. We show that BGLF4 phosphorylates UXT at the Thr3 residue. This modification interferes with the interaction between UXT and NF-κB. The data also indicate that BGLF4 reduces the interaction between UXT and NF-κB and attenuates NF-κB enhanceosome activity. Upon infection with short hairpin RNA (shRNA) lentivirus to knock down UXT, a spontaneous lytic cycle was observed in NA cells, suggesting UXT is required for maintenance of EBV latency. Overexpression of wild-type, but not phosphorylation-deficient, UXT enhances the expression of lytic proteins both in control and UXT knockdown cells. Taking the data together, transcription involving UXT may also be important for EBV lytic protein expression, whereas BGLF4-mediated phosphorylation of UXT at Thr3 plays a critical role in promoting the lytic cycle.
Ultrasensitive Allele-Specific PCR Reveals Rare Preexisting Drug-Resistant Variants and a Large Replicating Virus Population in Macaques Infected with a Simian Immunodeficiency Virus Containing Human Immunodeficiency Virus Reverse Transcriptase
Authors: Boltz Valerie F. , Ambrose Zandrea , Kearney Mary F. , Shao Wei , KewalRamani Vineet N. , Maldarelli Frank , Mellors John W. , Coffin John M. 
Published: August 2012

ABSTRACT

It has been proposed that most drug-resistant mutants, resulting from a single-nucleotide change, exist at low frequency in human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus (SIV) populations
in vivo
prior to the initiation of antiretroviral therapy (ART). To test this hypothesis and to investigate the emergence of resistant mutants with drug selection, we developed a new ultrasensitive allele-specific PCR (UsASP) assay, which can detect drug resistance mutations at a frequency of ≥0.001% of the virus population. We applied this assay to plasma samples obtained from macaques infected with an SIV variant containing HIV-1 reverse transcriptase (RT) (RT-simian-human immunodeficiency [SHIV]
mne
), before and after they were exposed to a short course of efavirenz (EFV) monotherapy. We detected RT inhibitor (RTI) resistance mutations K65R and M184I but not K103N in 2 of 2 RT-SHIV-infected macaques prior to EFV exposure. After three doses over 4 days of EFV monotherapy, 103N mutations (AAC and AAT) rapidly emerged and increased in the population to levels of ∼20%, indicating that they were present prior to EFV exposure. The rapid increase of 103N mutations from <0.001% to 20% of the viral population indicates that the replicating virus population size in RT-SHIV-infected macaques must be 10
6
or more infected cells per replication cycle.
Role of ambient light in structuring north-temperate fish communities: potential effects of increasing dissolved organic carbon concentration with a changing climate
Authors: Stasko Ashley D. , Gunn John M. , Johnston Tom A. 
Published: August 2012

The vertical light environment in freshwater lakes is sensitive to changes in dissolved organic carbon (DOC) concentrations, and DOC concentrations in most boreal lakes appear to be increasing as the climate changes. Understanding how DOC dynamics in lakes and watersheds are then linked to fish habitat is therefore critical to assessing the effects of climate change on fish communities. This paper reviews the evidence for climate-induced alterations to DOC in north-temperate watersheds and assesses the potential consequences of the resultant decreases in water clarity on fish production and community structure in small boreal lakes (<500 ha). Although DOC increases are forecast for most boreal lakes, complex interactions between local climate, rates of terrestrial organic matter decomposition and runoff, existing water quality, species shifts in forest communities, and changing season lengths can all combine to affect the magnitude of water clarity declines that will occur in individual lakes. Elevated DOC concentrations will affect the availability of coldwater versus warmwater habitat and niche characteristics that are dependent on lake depth, water clarity, and the preferences and physiological tolerances of the individual species. The shifts in availability of suitable thermal habitat will in turn affect fish growth, production, and community composition. Range expansions for warmwater species and range reductions for coldwater species will likely occur in warmer, darker environments, with adverse consequences for some native species and likely advantages for invasive species such as smallmouth bass. Likewise, major shifts in trophic dynamics would accompany the darkening of boreal lakes as species-specific feeding efficiencies change and primary and secondary production are altered. From a beneficial perspective, elevated DOC concentrations will likely relieve some physiological stress in biota via protection against contaminant toxicity and ultraviolet radiation (UVR) exposure. As with many other disturbances, we need to view climate change impacts on fish communities as a multiple stressor problem and the potential impacts of the changing light environment needs to be given as much prominence as the study of stressors such as eutrophication and trace contaminants.
The CXCL12–CXCR4 Chemokine Pathway: A Novel Axis Regulates Lymphangiogenesis
Authors: Zhuo Wei , Jia Lin , Song Nan , Lu Xin-an , Ding Yanping , Wang Xiaofeng , Song Xiaomin , Fu Yan , Luo Yongzhang 
Published: August 2012

Abstract
Purpose: Lymphangiogenesis, the growth of lymphatic vessels, contributes to lymphatic metastasis. However, the precise mechanism underlying lymphangiogenesis remains poorly understood. This study aimed to examine chemokine/chemokine receptors that directly contribute to chemoattraction of activated lymphatic endothelial cells (LEC) and tumor lymphangiogenesis.
Experimental Design: We used quantitative RT-PCR to analyze specifically expressed chemokine receptors in activated LECs upon stimulation of vascular endothelial growth factor-C (VEGF-C). Subsequently, we established in vitro and in vivo models to show lymphangiogenic functions of the chemokine axis. Effects of targeting the chemokine axis on tumor lymphangiogenesis and lymphatic metastasis were determined in an orthotopic breast cancer model.
Results: VEGF-C specifically upregulates CXCR4 expression on lymphangiogenic endothelial cells. Moreover, hypoxia-inducible factor-1α (HIF-1α) mediates the CXCR4 expression induced by VEGF-C. Subsequent analyses identify the ligand CXCL12 as a chemoattractant for LECs. CXCL12 induces migration, tubule formation of LECs in vitro, and lymphangiogenesis in vivo. CXCL12 also stimulates the phosphorylation of intracellular signaling Akt and Erk, and their specific antagonists impede CXCL12-induced chemotaxis. In addition, its level is correlated with lymphatic vessel density in multiple cancer tissues microarray. Furthermore, the CXCL12–CXCR4 axis is independent of the VEGFR-3 pathway in promoting lymphangiogenesis. Intriguingly, combined treatment with anti-CXCL12 and anti-VEGF-C antibodies results in additive inhibiting effects on tumor lymphangiogenesis and lymphatic metastasis.
Conclusions: These results show the role of the CXCL12–CXCR4 axis as a novel chemoattractant for LECs in promoting lymphangiogenesis, and support the potential application of combined targeting of both chemokines and lymphangiogenic factors in inhibiting lymphatic metastasis. Clin Cancer Res; 18(19); 5387–98. ©2012 AACR.
Clinical and Functional Correlates of Early Microvascular Dysfunction After Heart Transplantation
Authors: Haddad François , Khazanie Prateeti , Deuse Tobias , Weisshaar Dana , Zhou Jessica , Nam Chang Wook , Vu Thu A. , Gomari Fatemeh A. , Skhiri Mehdi , Simos Ana , Schnittger Ingela , Vrotvec Bojan , Hunt Sharon A. , Fearon William F. 
Published: August 2012

Background—
Microvascular dysfunction is emerging as a strong predictor of outcome in heart transplant recipients. At this time, the determinants and consequences of early microvascular dysfunction are not well established. The objective of the study was to determine the risk factors and functional correlates associated with early microvascular dysfunction in heart transplant recipients.

Methods and Results—

Sixty-three heart transplant recipients who had coronary physiology assessment, right heart catheterization, and echocardiography performed at the time of their first annual evaluation were included in the study. Microvascular dysfunction was assessed using the recently described index of microcirculatory resistance. The presence of microvascular dysfunction, predefined by an index of microcirculatory resistance >20, was observed in 46% of patients at 1 year. A history of acute rejection and undersized donor hearts were associated with microvascular dysfunction at 1 year, with odds ratio of 4.0 (1.3–12.8) and 3.6 (1.2–11.1), respectively. Patients with microvascular dysfunction had lower cardiac index (3.1±0.7 versus 3.5±0.7 L/min per m
2
;
P
=0.02) and mild graft dysfunction measured by echocardiography-derived left and right myocardial performance indices ([0.54±0.09 versus 0.43±0.09;
P
<0.01] and [0.47±0.14 versus 0.32±0.05;
P
<0.01], respectively). Microvascular dysfunction was also associated with a higher likelihood of death, graft failure, or allograft vasculopathy at 5 years after transplant (hazard ratio, 2.52 [95% CI, 1.04–5.91]).

Conclusions—
A history of acute rejection during the first year and smaller donor hearts were identified as risk factors for early microvascular dysfunction. Microvascular dysfunction assessed using index of microcirculatory resistances at 1 year was also associated with worse graft function and possibly worse clinical outcomes.