bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reevaluating Herpes Simplex Virus Hemifusion
Authors: Jackson Julia O. , Longnecker Richard 
Published: September 2010

ABSTRACT
Membrane fusion induced by enveloped viruses proceeds through the actions of viral fusion proteins. Once activated, viral fusion proteins undergo large protein conformational changes to execute membrane fusion. Fusion is thought to proceed through a “hemifusion” intermediate in which the outer membrane leaflets of target and viral membranes mix (lipid mixing) prior to fusion pore formation, enlargement, and completion of fusion. Herpes simplex virus type 1 (HSV-1) requires four glycoproteins—glycoprotein D (gD), glycoprotein B (gB), and a heterodimer of glycoprotein H and L (gH/gL)—to accomplish fusion. gD is primarily thought of as a receptor-binding protein and gB as a fusion protein. The role of gH/gL in fusion has remained enigmatic. Despite experimental evidence that gH/gL may be a fusion protein capable of inducing hemifusion in the absence of gB, the recently solved crystal structure of HSV-2 gH/gL has no structural homology to any known viral fusion protein. We found that in our hands, all HSV entry proteins—gD, gB, and gH/gL—were required to observe lipid mixing in both cell-cell- and virus-cell-based hemifusion assays. To verify that our hemifusion assay was capable of detecting hemifusion, we used glycosylphosphatidylinositol (GPI)-linked hemagglutinin (HA), a variant of the influenza virus fusion protein, HA, known to stall the fusion process before productive fusion pores are formed. Additionally, we found that a mutant carrying an insertion within the short gH cytoplasmic tail, 824L gH, is incapable of executing hemifusion despite normal cell surface expression. Collectively, our findings suggest that HSV gH/gL may not function as a fusion protein and that all HSV entry glycoproteins are required for both hemifusion and fusion. The previously described gH 824L mutation blocks gH/gL function prior to HSV-induced lipid mixing.
Andes Virus Regulation of Cellular MicroRNAs Contributes to Hantavirus-Induced Endothelial Cell Permeability
Authors: Pepini Timothy , Gorbunova Elena E. , Gavrilovskaya Irina N. , Mackow Jonathan E. , Mackow Erich R. 
Published: September 2010

ABSTRACT
Hantaviruses infect human endothelial cells (ECs) and cause two diseases marked by vascular permeability defects, hemorrhagic fever with renal syndrome (HFRS) and hantavirus pulmonary syndrome (HPS). Vascular permeability occurs in the absence of EC lysis, suggesting that hantaviruses alter normal EC fluid barrier functions. ECs infected by pathogenic hantaviruses are hyperresponsive to vascular endothelial growth factor (VEGF), and this alters the fluid barrier function of EC adherens junctions, resulting in enhanced paracellular permeability. Vascular permeability and VEGF-directed responses are determined by EC-specific microRNAs (miRNAs), which regulate cellular mRNA transcriptional responses. miRNAs mature within cytoplasmic processing bodies (P bodies), and the hantavirus nucleocapsid (N) protein binds RNA and localizes to P bodies, suggesting that hantaviruses may modify miRNA functions within infected ECs. Here we assessed changes in EC miRNAs following infection by the HPS-causing Andes hantavirus (ANDV). We analyzed 352 human miRNAs within ANDV-infected ECs using quantitative real-time (RT)-PCR arrays. Fourteen miRNAs, including six miRNAs that are associated with regulating vascular integrity, were upregulated >4-fold following infection by ANDV. Nine miRNAs were downregulated 3- to 3,400-fold following ANDV infection; these included miR-410, involved in regulating secretion, and miR-218, which is linked to the regulation of EC migration and vascular permeability. We further analyzed changes in miR-126, an EC-specific miRNA that regulates vascular integrity by suppressing SPRED1 and PIK3R2 mRNAs. While miR-126 levels were only slightly altered, we found that SPRED1 and PIK3R2 mRNA levels were increased 10- and 7-fold, respectively, in ANDV-infected ECs but were unaltered in ECs infected by the nonpathogenic Tula hantavirus (TULV). Consistent with increased SPRED1 expression, we found that the level of phospho-cofilin was decreased within ANDV-infected ECs. Moreover, small interfering RNA (siRNA) knockdown of SPRED1 dramatically decreased the permeability of ANDV-infected ECs in response to VEGF, suggesting that increased SPRED1 contributes to EC permeability following ANDV infection. These findings suggest that interference with normal miRNA functions contributes to the enhanced paracellular permeability of ANDV-infected ECs and that hantavirus regulation of miRNA functions is an additional determinant of hantavirus pathogenesis.
Low frequency of extra-pair paternity in Savi's Warblers (Locustella luscinioides)
Authors: Hasselquist Dennis , Hansson Bengt , Neto Júlio 
Published: September 2010

AbstractAlthough the frequency of extra-pair paternity (EPP) has been described for many species, the relative importance of the various contemporary and historical factors explaining EPP variation is still the subject of debate. In this study, we found 11 polymorphic microsatellite loci in the Savi's Warbler (Locustella luscinioides), and used eight loci to analyze the paternity of 392 nestlings belonging to 102 broods of this little-known species. The frequency of EPP was 4.1% of nestlings and 5.9% of broods, which is surprisingly low given what is known about Savi's Warbler's life history and ecology, and among the lowest found of any socially-monogamous passerine bird. Comparisons with similar species indicate that this low frequency is unlikely to have been determined by the ancient evolution of life history strategies. Our observations suggest that the costs of engaging in extra-pair copulations might be high for the females. Larger males, particularly those with longer bill and tarsus, are more likely to be cuckolded; and the few possible comparisons between cuckolded males and extrapair sires reveal a similar pattern. We further show that bill and tarsus lengths correlate with arrival date, which is associated with individual quality in many migratory bird species.
John Calvin: Catholic Theologian
Authors: Lane Anthony 
Published: September 2010

AbstractCalvin began by affirming the Catholicity of the Church, but such positive affirmations become rarer as he grew older. By contrast, he more and more frequently rejects the claims of the Roman Church to Catholicity. The change is provoked by the barrage of claims to Catholicity that Calvin faced from his opponents, together with the claim that the Reformers had abandoned it. This made Calvin less enthusiastic about using the word for himself, thus pointing the way towards the eventual development where Catholic came to mean Roman Catholic. Calvin accepted the Catholic canon of the New Testament, though without ever explaining the basis for this. He appealed to the early Catholic tradition (most especially Augustine) for support, though he was not uncritical of it. The Church had declined from the truth during the Middle Ages and the true Church remained but had lost outward form.
The First Yiddish Book Printed in Amsterdam: Śefer Mismor Lethode
Authors: Neuberg Simon 
Published: September 2010

This is a first approach to the text of Mismor-lethode a strophic retelling of parts of the Bible, first printed in Amsterdam 1644 (which has so far only been the object of short bibliographical notices), highlighting some of its specific typographical, literary and linguistic aspects:
• It is a very nice piece of work and inaugurates the renowned tradition of Amsterdam Yiddish typographical works; it is also presented within the output of Amsterdam typesetters whose career is reflected in many later books.
• It is remarkable as a late specimen of biblical strophic poetry that makes no use of midrashic elements (perhaps in keeping with the Sephardic influence prevalent in Amsterdam).
• Linguistically it is an important document—among other idiosyncrasies— for its use of the all-purpose relative pronoun s2o and for the free usage of final unstressed vowels for reasons of euphony, rhythm and rhyme.
Tipifarnib sensitizes cells to proteasome inhibition by blocking degradation of bortezomib-induced aggresomes
Authors: David Ebenezer , Kaufman Jonathan L. , Flowers Christopher R. , Schafer-Hales Katherine , Torre Claire , Chen Jing , Marcus Adam I. , Sun Shi-Yong , Boise Lawrence H. , Lonial Sagar 
Published: September 2010

AbstractIn this report, we investigated the mechanism responsible for synergistic induction of myeloma cell apoptosis induced by the combination of tipifarnib and bortezomib. Immunofluorescence studies revealed that bortezomib alone resulted in an accumulation of puncta of ubiquitinated proteins that was further enhanced by the addition of tipifarnib. These data suggest inhibition of the degradation of bortezomib-induced aggresomes; and consistent with this possibility, we also observed an increase in p62SQSTM1 in cells treated with the combination. However, autophagy in these cells appears to be normal as LC3BII is present, and autophagic flux appears to be unaffected as demonstrated by the addition of bafilomycin A1. Together, these data demonstrate that tipifarnib synergizes with bortezomib by inducing protein accumulation as a result of the uncoupling of the aggresome and autophagy pathways.
HGAL, a germinal center specific protein, decreases lymphoma cell motility by modulation of the RhoA signaling pathway
Authors: Jiang Xiaoyu , Lu Xiaoqing , McNamara George , Liu Xiaofei , Cubedo Elena , Sarosiek Kristopher A. , Sánchez-García Isidro , Helfman David M. , Lossos Izidore S. 
Published: September 2010

Abstract
HGAL is a germinal center (GC)–specific gene that negatively regulates lymphocyte motility and whose expression predicts improved survival of patients with diffuse large B-cell lymphoma (DLBCL) and classical Hodgkin lymphoma (cHL). We demonstrate that HGAL serves as a regulator of the RhoA signaling pathway. HGAL enhances activation of RhoA and its down-stream effectors by a novel mechanism – direct binding to the catalytic DH-domain of the RhoA-specific guanine nucleotide exchange factors (RhoGEFs) PDZ-RhoGEF and LARG that stimulate the GDP-GTP exchange rate of RhoA. We delineate the structural domain of HGAL that mediates its interaction with the PDZ-RhoGEF protein. These observations reveal a novel molecular mechanism underlying the inhibitory effects of GC-specific HGAL protein on the motility of GC-derived lymphoma cells. This mechanism may underlie the limited dissemination and better outcome of patients with HGAL-expressing DLBCL and cHL.
Erythropoietin stimulates spleen BMP4-dependent stress erythropoiesis and partially corrects anemia in a mouse model of generalized inflammation
Authors: Millot Sarah , Andrieu Valérie , Letteron Philippe , Lyoumi Saïd , Hurtado-Nedelec Margarita , Karim Zoubida , Thibaudeau Olivier , Bennada Samira , Charrier Jean-Luc , Lasocki Sigismond , Beaumont Carole 
Published: September 2010

AbstractMouse bone marrow erythropoiesis is homeostatic, whereas after acute anemia, bone morphogenetic protein 4 (BMP4)–dependent stress erythropoiesis develops in the spleen. The aim of this work was to compare spleen stress erythropoiesis and bone marrow erythropoiesis in a mouse model of zymosan-induced generalized inflammation, which induces long-lasting anemia and to evaluate the ability of erythropoietin (Epo) injections to correct anemia in this setting. The effects of zymosan and/or Epo injections on erythroid precursor maturation and apoptosis, serum interferon-γ levels, hematologic parameters, and spleen BMP4 expression were analyzed, as well as the effect of zymosan on red blood cell half-life. We found that bone marrow erythropoiesis is suppressed by inflammation and does not respond to Epo administration, despite repression of erythroblast apoptosis. On the contrary, a robust erythropoietic response takes place in the spleen after Epo injections in both control and zymosan-induced generalized inflammation mice. This specific response implies Epo-mediated induction of BMP4 expression by F4/80+ spleen macrophages, proliferation of stress burst-forming units-erythroid, and increased number of spleen erythroblasts. It allows only partial recovery of anemia, probably because of peripheral destruction of mature red cells. It is not clear whether similar BMP4-dependent stress erythropoiesis can occur in human bone marrow after Epo injections.
Mapping Quantitative Trait Loci (QTL) in sheep. III. QTL for carcass composition traits derived from CT scans and aligned with a meta-assembly for sheep and cattle carcass QTL
Authors: Cavanagh Colin R , Jonas Elisabeth , Hobbs Matthew , Thomson Peter C , Tammen Imke , Raadsma Herman W 
Published: September 2010

Abstract
An (Awassi × Merino) × Merino single-sire backcross family with 165 male offspring was used to map quantitative trait loci (QTL) for body composition traits on a framework map of 189 microsatellite loci across all autosomes. Two cohorts were created from the experimental progeny to represent alternative maturity classes for body composition assessment. Animals were raised under paddock conditions prior to entering the feedlot for a 90-day fattening phase. Body composition traits were derived in vivo at the end of the experiment prior to slaughter at 2 (cohort 1) and 3.5 (cohort 2) years of age, using computed tomography. Image analysis was used to gain accurate predictions for 13 traits describing major fat depots, lean muscle, bone, body proportions and body weight which were used for single- and two-QTL mapping analysis. Using a maximum-likelihood approach, three highly significant (LOD ≥ 3), 15 significant (LOD ≥ 2), and 11 suggestive QTL (1.7 ≤ LOD < 2) were detected on eleven chromosomes. Regression analysis confirmed 28 of these QTL and an additional 17 suggestive (P < 0.1) and two significant (P < 0.05) QTL were identified using this method. QTL with pleiotropic effects for two or more tissues were identified on chromosomes 1, 6, 10, 14, 16 and 23. No tissue-specific QTL were identified.
A meta-assembly of ovine QTL for carcass traits from this study and public domain sources was performed and compared with a corresponding bovine meta-assembly. The assembly demonstrated QTL with effects on carcass composition in homologous regions on OAR1, 2, 6 and 21.
Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions
Authors: Laing Chad , Buchanan Cody , Taboada Eduardo N , Zhang Yongxiang , Kropinski Andrew , Villegas Andre , Thomas James E , Gannon Victor PJ 
Published: September 2010

AbstractBackgroundThe pan-genome of a bacterial species consists of a core and an accessory gene pool. The accessory genome is thought to be an important source of genetic variability in bacterial populations and is gained through lateral gene transfer, allowing subpopulations of bacteria to better adapt to specific niches. Low-cost and high-throughput sequencing platforms have created an exponential increase in genome sequence data and an opportunity to study the pan-genomes of many bacterial species. In this study, we describe a new online pan-genome sequence analysis program, Panseq.ResultsPanseq was used to identifyEscherichia coliO157:H7 andE. coliK-12 genomic islands. Within a population of 60E. coliO157:H7 strains, the existence of 65 accessory genomic regions identified by Panseq analysis was confirmed by PCR. The accessory genome and binary presence/absence data, and core genome and single nucleotide polymorphisms (SNPs) of sixL. monocytogenesstrains were extracted with Panseq and hierarchically clustered and visualized. The nucleotide core and binary accessory data were also used to construct maximum parsimony (MP) trees, which were compared to the MP tree generated by multi-locus sequence typing (MLST). The topology of the accessory and core trees was identical but differed from the tree produced using seven MLST loci. The Loci Selector module found the most variable and discriminatory combinations of four loci within a 100 loci set among 10 strains in 1 s, compared to the 449 s required to exhaustively search for all possible combinations; it also found the most discriminatory 20 loci from a 96 lociE. coliO157:H7 SNP dataset.ConclusionPanseq determines the core and accessory regions among a collection of genomic sequences based on user-defined parameters. It readily extracts regions unique to a genome or group of genomes, identifies SNPs within shared core genomic regions, constructs files for use in phylogeny programs based on both the presence/absence of accessory regions and SNPs within core regions and produces a graphical overview of the output. Panseq also includes a loci selector that calculates the most variable and discriminatory loci among sets of accessory loci or core gene SNPs.AvailabilityPanseq is freely available online athttp://76.70.11.198/panseq. Panseq is written in Perl.
Context dependent substitution biases vary within the human genome
Authors: Nevarez P Andrew , DeBoever Christopher M , Freeland Benjamin J , Quitt Marissa A , Bush Eliot C 
Published: September 2010

AbstractBackgroundModels of sequence evolution typically assume that different nucleotide positions evolve independently. This assumption is widely appreciated to be an over-simplification. The best known violations involve biases due to adjacent nucleotides. There have also been suggestions that biases exist at larger scales, however this possibility has not been systematically explored.ResultsTo address this we have developed a method which identifies over- and under-represented substitution patterns and assesses their overall impact on the evolution of genome composition. Our method is designed to account for biases at smaller pattern sizes, removing their effects. We used this method to investigate context bias in the human lineage after the divergence from chimpanzee. We examined bias effects in substitution patterns between 2 and 5 bp long and found significant effects at all sizes. This included some individual three and four base pair patterns with relatively large biases. We also found that bias effects vary across the genome, differing between transposons and non-transposons, between different classes of transposons, and also near and far from genes.ConclusionsWe found that nucleotides beyond the immediately adjacent one are responsible for substantial context effects, and that these biases vary across the genome.
Intracellular localization and interaction of mRNA binding proteins as detected by FRET
Authors: David Gerecht Pamela S , Taylor Molly A , Port J David 
Published: September 2010

AbstractBackgroundA number of RNA binding proteins (BPs) bind to A+U rich elements (AREs), commonly present within 3'UTRs of highly regulated RNAs. Individual RNA-BPs proteins can modulate RNA stability, RNA localization, and/or translational efficiency. Although biochemical studies have demonstrated selectivity of ARE-BPs for individual RNAs, less certain is thein vivocomposition of RNA-BP multiprotein complexes and how their composition is affected by signaling events and intracellular localization. Using FRET, we previously demonstrated that two ARE-BPs, HuR and AUF1, form stable homomeric and heteromeric associations in the nucleus and cytoplasm. In the current study, we use immuno-FRET of endogenous proteins to examine the intracellular localization and interactions of HuR and AUF1 as well as KSRP, TIA-1, and Hedls. These results were compared to those obtained with their exogenously expressed, fluorescently labeled counterparts.ResultsAll ARE-BPs examined were found to colocalize and to form stable associations with selected other RNA-BPs in one or more cellular locations variably including the nucleus, cytoplasm (in general), or in stress granules or P bodies. Interestingly, FRET based interaction of the translational suppressor, TIA-1, and the decapping protein, Hedls, was found to occur at the interface of stress granules and P bodies, dynamic sites of intracellular RNA storage and/or turnover. To explore the physical interactions of RNA-BPs with ARE containing RNAs,in vitrotranscribed Cy3-labeled RNA was transfected into cells. Interestingly, Cy3-RNA was found to coalesce in P body like punctate structures and, by FRET, was found to interact with the RNA decapping proteins, Hedls and Dcp1.ConclusionsBiochemical methodologies, such as co-immunoprecipitation, and cell biological approaches such as standard confocal microscopy are useful in demonstrating the possibility of proteins and/or proteins and RNAs interacting. However, as demonstrated herein, colocalization of proteins and proteins and RNA is not always indicative of interaction. To this point, using FRET and immuno-FRET, we have demonstrated that RNA-BPs can visually colocalize without producing a FRET signal. In contrast, proteins that appear to be delimited to one or another intracellular compartment can be shown to interact when those compartments are juxtaposed.
Extracellular Paracoccidioides brasiliensis phospholipase B involvement in alveolar macrophage interaction
Authors: Soares Deyze Alencar , de Andrade Rosângela Vieira , Silva Simoneide Sousa , Bocca Anamélia Lorenzetti , Soares Felipe Sueli Maria , Petrofeza Silvana 
Published: September 2010

Abstract

Background
Phospholipase B (PLB) has been reported to be one of the virulence factors for human pathogenic fungi and has also been described as necessary for the early events in infection. Based on these data, we investigated the role of PLB in virulence and modulation of the alveolar pulmonary immune response during infection using an in-vitro model of host-pathogen interaction, i.e. Paracoccidioides brasiliensis yeast cells infecting alveolar macrophage (MH-S) cells.

Results
The effect of PLB was analyzed using the specific inhibitor alexidine dihydrochloride (0.25 μM), and pulmonary surfactant (100 μg mL-1), during 6 hours of co-cultivation of P. brasiliensis and MH-S cells. Alexidine dihydrochloride inhibited PLB activity by 66% and significantly decreased the adhesion and internalization of yeast cells by MH-S cells. Genes involved in phagocytosis (trl2, cd14) and the inflammatory response (nfkb, tnf-α, il-1β) were down-regulated in the presence of this PLB inhibitor. In contrast, PLB activity and internalization of yeast cells significantly increased in the presence of pulmonary surfactant; under this condition, genes such as clec 2 and the pro-inflammatory inhibitor (nkrf) were up-regulated. Also, the pulmonary surfactant did not alter cytokine production, while alexidine dihydrochloride decreased the levels of interleukin-10 (IL-10) and increased the levels of IL-12 and tumor necrosis factor-α (TNF-α). In addition, gene expression analysis of plb1, sod3 and icl1 suggests that P. brasiliensis gene re-programming is effective in facilitating adaptation to this inhospitable environment, which mimics the lung-environment interaction.

Conclusion

P. brasiliensis PLB activity is involved in the process of adhesion and internalization of yeast cells at the MH-S cell surface and may enhance virulence and subsequent down-regulation of macrophage activation.