bluuebunny/crossref_metadata_2025_split huggingface dataset:
Barcoding aphids (Hemiptera: Aphididae) of the Korean Peninsula: updating the global data set
Authors: LEE WONHOON , KIM HYOJOONG , LIM JONGOK , CHOI HWAL‐RAN , KIM YEYEUN , KIM YANG‐SU , JI JEONG‐YEON , FOOTTIT ROBERT G. , LEE SEUNGHWAN 
Published: May 2010

AbstractDNA barcode (mitochondrial COI) sequences are provided for species identification of aphids from the Korean Peninsula. Most (98%) of the 154 species had distinct COI sequences (average 0.05% intraspecific pairwise divergence) relative to the degree of sequence divergence among species (average value 5.84%). For species in common with other regions, barcodes for Korean samples fell near or within known levels of variation. Based on these results, we conclude that DNA barcodes can provide an effective tool for identifying aphid species in such applications as pest management, monitoring and plant quarantine.
Combining Background Knowledge and Learned Topics
Authors: Steyvers Mark , Smyth Padhraic , Chemuduganta Chaitanya 
Published: May 2010

AbstractStatistical topic models provide a general data‐driven framework for automated discovery of high‐level knowledge from large collections of text documents. Although topic models can potentially discover a broad range of themes in a data set, the interpretability of the learned topics is not always ideal. Human‐defined concepts, however, tend to be semantically richer due to careful selection of words that define the concepts, but they may not span the themes in a data set exhaustively. In this study, we review a new probabilistic framework for combining a hierarchy of human‐defined semantic concepts with a statistical topic model to seek the best of both worlds. Results indicate that this combination leads to systematic improvements in generalization performance as well as enabling new techniques for inferring and visualizing the content of a document.
Genetic Fusions of Heat-Labile Toxoid (LT) and Heat-Stable Toxin b (STb) of Porcine EnterotoxigenicEscherichia coliElicit Protective Anti-LT and Anti-STb Antibodies
Authors: Zhang Weiping , Francis David H. 
Published: May 2010

ABSTRACTEnterotoxigenicEscherichia coli(ETEC)-associated diarrhea causes a substantial economic loss to swine producers worldwide. The majority of ETEC strains causing porcine diarrhea, especially postweaning diarrhea (PWD), produce heat-labile toxin (LT) and heat-stable toxin b (STb). LT is commonly used in vaccine development, but STb has not been included because of its poor immunogenicity. As a virulence factor in porcine diarrhea, STb needs to be included as an antigen for development of broad-spectrum vaccines. In this study, we used an LT toxoid (LTR192G[hereafter, LT192]) derived from porcine ETEC to carry a mature STb peptide for LT192-STb fusions to enhance STb immunogenicity for potential vaccine application. Anti-LT and anti-STb antibodies were detected in immunized rabbits and pigs. In addition, when challenged with an STb-positive ETEC strain, all 10 suckling piglets borne by immunized gilts remained healthy, whereas 7 out 9 piglets borne by unimmunized gilts developed moderate diarrhea. This study indicates that the LT192-STb fusion enhanced anti-STb immunogenicity and suggests the LT192-STb fusion antigen can be used in future vaccine development against porcine ETEC diarrhea.
Erythema Multiforme Caused byTreponema pallidumin a Young Patient with Human Immunodeficiency Virus Infection
Authors: Chiang Mei-Chun , Chiang Fu-Chiang , Chang Yun-Ting , Chen Te-Li , Fung Chang-Phone 
Published: May 2010

ABSTRACTErythema multiforme (EM) is usually caused by drug reactions or virus infection. We report a case of secondary syphilis presenting as EM in an HIV-infected patient, proved by immunohistochemical staining, which is rare in the literature. It is valuable to determine the etiology of EM to optimize treatment.
Detection of All Species of the Genus
Alphavirus
by Reverse Transcription-PCR with Diagnostic Sensitivity
Authors: Grywna Klaus , Kupfer Bernd , Panning Marcus , Drexler Jan Felix , Emmerich Petra , Drosten Christian , Kümmerer Beate M. 
Published: May 2010

ABSTRACT

Clinical arbovirus screening requires exclusion of a broad range of viruses with as few assays as possible. We present a reverse transcription-PCR (RT-PCR) for the detection of all species of the genus
Alphavirus
qualified for exclusion screening (limit of detection [LOD], 5 to 100 RNA copies per reaction across all
Alphavirus
species; detection of viremia down to ca. 10,000 copies per ml).
Patterns of Human Immunodeficiency Virus Type 1 Recombination
Ex Vivo
Provide Evidence for Coadaptation of Distant Sites, Resulting in Purifying Selection for Intersubtype Recombinants during Replication
Authors: Galli Andrea , Kearney Mary , Nikolaitchik Olga A. , Yu Sloane , Chin Mario P. S. , Maldarelli Frank , Coffin John M. , Pathak Vinay K. , Hu Wei-Shau 
Published: May 2010

ABSTRACT

High-frequency recombination is a hallmark of HIV-1 replication. Recombination can occur between two members of the same subtype or between viruses from two different subtypes, generating intra- or intersubtype recombinants, respectively. Many intersubtype recombinants have been shown to circulate in human populations. We hypothesize that sequence diversity affects the emergence of viable recombinants by decreasing recombination events and reducing the ability of the recombinants to replicate. To test our hypothesis, we compared recombination between two viruses containing subtype B
pol
genes (B/B) and between viruses with
pol
genes from subtype B or F (B/F). Recombination events generated during a single cycle of infection without selection pressure on
pol
gene function were analyzed by single-genome sequencing. We found that recombination occurred slightly (∼30%) less frequently in B/F than in B/B viruses, and the overall distribution of crossover junctions in
pol
was similar for the two classes of recombinants. We then examined the emergence of recombinants in a multiple cycle assay, so that functional
pol
gene products were selected. We found that the emerging B/B recombinants had complex patterns, and the crossover junctions were distributed throughout the
pol
gene. In contrast, selected B/F recombinants had limited recombination patterns and restricted crossover junction distribution. These results provide evidence for the evolved coadapted sites in variants from different subtypes; these sites may be segregated by recombination events, causing the newly generated intersubtype recombinants to undergo purifying selection. Therefore, the ability of the recombinants to replicate is the major barrier for many of these viruses.
The Capsid Protein Encoded by U
L
17 of Herpes Simplex Virus 1 Interacts with Tegument Protein VP13/14
Authors: Scholtes Luella D. , Yang Kui , Li Lucy X. , Baines Joel D. 
Published: May 2010

ABSTRACT

The U
L
17 protein (pU
L
17) of herpes simplex virus 1 (HSV-1) likely associates with the surfaces of DNA-containing capsids in a heterodimer with pU
L
25. pU
L
17 is also associated with viral light particles that lack capsid proteins, suggesting its presence in the tegument of the HSV-1 virion. To help determine how pU
L
17 becomes incorporated into virions and its functions therein, we identified pU
L
17-interacting proteins by immunoprecipitation with pU
L
17-specific IgY at 16 h postinfection, followed by mass spectrometry. Coimmunoprecipitated proteins included cellular histone proteins H2A, H3, and H4; the intermediate filament protein vimentin; the major HSV-1 capsid protein VP5; and the HSV tegument proteins VP11/12 (pU
L
46) and VP13/14 (pU
L
47). The pU
L
17-VP13/14 interaction was confirmed by coimmunoprecipitation in the presence and absence of intact capsids and by affinity copurification of pU
L
17 and VP13/14 from lysates of cells infected with a recombinant virus encoding His-tagged pU
L
17. pU
L
17 and VP13/14-HA colocalized in the nuclear replication compartment, in the cytoplasm, and at the plasma membrane between 9 and 18 h postinfection. One possible explanation of these data is that pU
L
17 links the external face of the capsid to VP13/14 and associated tegument components.
Impaired Replication Capacity of Acute/Early Viruses in Persons Who Become HIV Controllers
Authors: Miura Toshiyuki , Brumme Zabrina L. , Brockman Mark A. , Rosato Pamela , Sela Jennifer , Brumme Chanson J. , Pereyra Florencia , Kaufmann Daniel E. , Trocha Alicja , Block Brian L. , Daar Eric S. , Connick Elizabeth , Jessen Heiko , Kelleher Anthony D. , Rosenberg Eric , Markowitz Martin , Schafer Kim , Vaida Florin , Iwamoto Aikichi , Little Susan , Walker Bruce D. 
Published: May 2010

ABSTRACT

Human immunodeficiency virus type 1 (HIV-1) controllers maintain viremia at <2,000 RNA copies/ml without antiretroviral therapy. Viruses from controllers with chronic infection were shown to exhibit impaired replication capacities, in part associated with escape mutations from cytotoxic-T-lymphocyte (CTL) responses. In contrast, little is known about viruses during acute/early infection in individuals who subsequently become HIV controllers. Here, we examine the viral replication capacities, HLA types, and virus sequences from 18 HIV-1 controllers identified during primary infection.
g
ag-protease
chimeric viruses constructed using the earliest postinfection samples displayed significantly lower replication capacities than isolates from persons who failed to control viremia (
P
= 0.0003). Protective HLA class I alleles were not enriched in these early HIV controllers, but viral sequencing revealed a significantly higher prevalence of drug resistance mutations associated with impaired viral fitness in controllers than in noncontrollers (6/15 [40.0%] versus 10/80 [12.5%],
P
= 0.018). Moreover, of two HLA-B57-positive (B57
+
) controllers identified, both harbored, at the earliest time point tested, signature escape mutations within Gag that likewise impair viral replication capacity. Only five controllers did not express “protective” alleles or harbor viruses with drug resistance mutations; intriguingly, two of them displayed typical B57 signature mutations (T242N), suggesting the acquisition of attenuated viruses from B57
+
donors. These data indicate that acute/early stage viruses from persons who become controllers have evidence of reduced replication capacity during the initial stages of infection which is likely associated with transmitted or acquired CTL escape mutations or transmitted drug resistance mutations. These data suggest that viral dynamics during acute infection have a major impact on HIV disease outcome.
Ten Years of Global Evolution of the Human Respiratory Syncytial Virus BA Genotype with a 60-Nucleotide Duplication in the G Protein Gene
Authors: Trento Alfonsina , Casas Inmaculada , Calderón Ana , Garcia-Garcia Maria L. , Calvo Cristina , Perez-Breña Pilar , Melero José A. 
Published: May 2010

ABSTRACT
The emergence of natural isolates of human respiratory syncytial virus group B (HRSV-B) with a 60-nucleotide (nt) duplication in the G protein gene in Buenos Aires, Argentina, in 1999 (A. Trento et al., J. Gen. Virol. 84:3115-3120, 2003) and their dissemination worldwide allowed us to use the duplicated segment as a natural tag to examine in detail the evolution of HRSV during propagation in its natural host. Viruses with the duplicated segment were all clustered in a new genotype, named BA (A. Trento et al., J. Virol. 80:975-984, 2006). To obtain information about the prevalence of these viruses in Spain, we tested for the presence of the duplicated segment in positive HRSV-B clinical samples collected at the Severo Ochoa Hospital (Madrid) during 12 consecutive epidemics (1996-1997 to 2007-2008). Viruses with the 60-nt duplication were found in 61 samples, with a high prevalence relative to the rest of B genotypes in the most recent seasons. Global phylogenetic and demographic analysis of all G sequences containing the duplication, collected across five continents up until April 2009, revealed that the prevalence of the BA genotype increased gradually until 2004-2005, despite its rapid dissemination worldwide. After that date and coinciding with a bottleneck effect on the population size, a relatively new BA lineage (BA-IV) replaced all other group B viruses, suggesting further adaptation of the BA genotype to its natural host.
Acutely Transforming Retrovirus Expressing Nras Generated from HT-1080 Fibrosarcoma Cells Infected with the Human Retrovirus XMRV
Authors: Metzger Michael J. , Miller A. Dusty 
Published: May 2010

ABSTRACT
Virus from HT-1080 fibrosarcoma cells infected with the human retrovirus XMRV (xenotropic murine leukemia virus-related virus) can induce rare foci of transformation in rat 208F fibroblasts. Characterization of three such foci revealed that one produced an acutely transforming virus at a high titer. The virus consists of a mutant Nras cDNA from the HT-1080 cells inserted into a retroviral vector (added to the HT-1080 cells as a marker for infection) in place of internal vector sequences. These results show that XMRV can generate acutely transforming viruses at a low rate, as is typical of other replication-competent retroviruses, and reveal the potential for transforming virus contamination of retroviral vectors made from transformed cell lines.
Role of Phosphatidylinositol 3-Kinase in Friend Spleen Focus-Forming Virus-Induced Erythroid Disease
Authors: Umehara Daigo , Watanabe Shinya , Ochi Haruyo , Anai Yukari , Ahmed Nursarat , Kannagi Mari , Hanson Charlotte , Ruscetti Sandra , Nishigaki Kazuo 
Published: May 2010

ABSTRACT

Infection of erythroid cells by Friend spleen focus-forming virus (SFFV) leads to acute erythroid hyperplasia in mice due to expression of its unique envelope glycoprotein, gp55. Erythroid cells expressing SFFV gp55 proliferate in the absence of their normal regulator, erythropoietin (Epo), because of interaction of the viral envelope protein with the erythropoietin receptor and a short form of the receptor tyrosine kinase Stk (sf-Stk), leading to constitutive activation of several signal transduction pathways. Our previous
in vitro
studies showed that phosphatidylinositol 3-kinase (PI3-kinase) is activated in SFFV-infected cells and is important in mediating the biological effects of the virus. To determine the role of PI3-kinase in SFFV-induced disease, mice deficient in the p85α regulatory subunit of class IA PI3-kinase were inoculated with different strains of SFFV. We observed that p85α status determined the extent of erythroid hyperplasia induced by the sf-Stk-dependent viruses SFFV-P (polycythemia-inducing strain of SFFV) and SFFV-A (anemia-inducing strain of SFFV) but not by the sf-Stk-independent SFFV variant BB6. Our data also indicate that p85α status determines the response of mice to stress erythropoiesis, consistent with a previous report showing that SFFV uses a stress erythropoiesis pathway to induce erythroleukemia. We further showed that sf-Stk interacts with p85α and that this interaction depends upon sf-Stk kinase activity and tyrosine 436 in the multifunctional docking site. Pharmacological inhibition of PI3-kinase blocked proliferation of primary erythroleukemia cells from SFFV-infected mice and the erythroleukemia cell lines derived from them. These results indicate that p85α may regulate sf-Stk-dependent erythroid proliferation induced by SFFV as well as stress-induced erythroid hyperplasia.
Human Staufen1 Protein Interacts with Influenza Virus Ribonucleoproteins and Is Required for Efficient Virus Multiplication
Authors: de Lucas Susana , Peredo Joan , Marión Rosa María , Sánchez Carmen , Ortín Juan 
Published: May 2010

ABSTRACT
The influenza A virus genome consists of 8 negative-stranded RNA segments. NS1 is a nonstructural protein that participates in different steps of the virus infectious cycle, including transcription, replication, and morphogenesis, and acts as a virulence factor. Human Staufen1 (hStau1), a protein involved in the transport and regulated translation of cellular mRNAs, was previously identified as a NS1-interacting factor. To investigate the possible role of hStau1 in the influenza virus infection, we characterized the composition of hStau1-containing granules isolated from virus-infected cells. Viral NS1 protein and ribonucleoproteins (RNPs) were identified in these complexes by Western blotting, and viral mRNAs and viral RNAs (vRNAs) were detected by reverse transcription (RT)-PCR. Also, colocalization of hStau1 with NS1, nucleoprotein (NP), and PA in the cytosol of virus-infected cells was shown by immunofluorescence. To analyze the role of hStau1 in the infection, we downregulated its expression by gene silencing. Human HEK293T cells or A549 cells were silenced using either short hairpin RNAs (shRNAs) or small interfering RNAs (siRNAs) targeting four independent sites in the hStau1 mRNA. The yield of influenza virus was reduced 5 to 10 times in the various hStau1-silenced cells compared to that in control silenced cells. The expression levels of viral proteins and their nucleocytoplasmic localization were not affected upon hStau1 silencing, but virus particle production, as determined by purification of virions from supernatants, was reduced. These results indicate a role for hStau1 in late events of the influenza virus infection, possibly during virus morphogenesis.
Evidence for a Premature Termination Mechanism of Subgenomic mRNA Transcription in a Carmovirus
Authors: Wu Baodong , Oliveri Stefanie , Mandic Jana , White K. Andrew 
Published: May 2010

ABSTRACT

The transcriptional mechanism utilized by turnip crinkle carmovirus to synthesize subgenomic (sg) mRNAs was investigated by analyzing viral RNAs and their associated regulatory RNA elements.
In vivo
analyses revealed the following: (i) that minus-strand sg RNAs are detectable in infections, (ii) that minus-strand sg RNA accumulation can be partially uncoupled from that of their plus-strand sg mRNA counterparts, and (iii) that an RNA secondary structure located upstream of the sg mRNA start site mediates transcription by functioning in the plus strand of the viral genome. Collectively, these observations are consistent with this carmovirus using a premature termination mechanism for sg mRNA transcription.
The Capsid Protein of
Turnip Crinkle Virus
Overcomes Two Separate Defense Barriers To Facilitate Systemic Movement of the Virus in
Arabidopsis
Authors: Cao Mingxia , Ye Xiaohong , Willie Kristen , Lin Junyan , Zhang Xiuchun , Redinbaugh Margaret G. , Simon Anne E. , Morris T. Jack , Qu Feng 
Published: May 2010

ABSTRACT

The capsid protein (CP) of
Turnip crinkle virus
(TCV) is a multifunctional protein needed for virus assembly, suppression of RNA silencing-based antiviral defense, and long-distance movement in infected plants. In this report, we have examined genetic requirements for the different functions of TCV CP and evaluated the interdependence of these functions. A series of TCV mutants containing alterations in the CP coding region were generated. These alterations range from single-amino-acid substitutions and domain truncations to knockouts of CP translation. The latter category also contained two constructs in which the CP coding region was replaced by either the cDNA of a silencing suppressor of a different virus or that of green fluorescent protein. These mutants were used to infect
Arabidopsis
plants with diminished antiviral silencing capability (
dcl2 dcl3 dcl4
plants). There was a strong correlation between the ability of mutants to reach systemic leaves and the silencing suppressor activity of mutant CP. Virus particles were not essential for entry of the viral genome into vascular bundles in the inoculated leaves in the absence of antiviral silencing. However, virus particles were necessary for egress of the viral genome from the vasculature of systemic leaves. Our experiments demonstrate that TCV CP not only allows the viral genome to access the systemic movement channel through silencing suppression but also ensures its smooth egress by way of assembled virus particles. These results illustrate that efficient long-distance movement of TCV requires both functions afforded by the CP.
Nitroaromatic Compounds, from Synthesis to Biodegradation
Authors: Ju Kou-San , Parales Rebecca E. 
Published: May 2010

SUMMARYNitroaromatic compounds are relatively rare in nature and have been introduced into the environment mainly by human activities. This important class of industrial chemicals is widely used in the synthesis of many diverse products, including dyes, polymers, pesticides, and explosives. Unfortunately, their extensive use has led to environmental contamination of soil and groundwater. The nitro group, which provides chemical and functional diversity in these molecules, also contributes to the recalcitrance of these compounds to biodegradation. The electron-withdrawing nature of the nitro group, in concert with the stability of the benzene ring, makes nitroaromatic compounds resistant to oxidative degradation. Recalcitrance is further compounded by their acute toxicity, mutagenicity, and easy reduction into carcinogenic aromatic amines. Nitroaromatic compounds are hazardous to human health and are registered on the U.S. Environmental Protection Agency's list of priority pollutants for environmental remediation. Although the majority of these compounds are synthetic in nature, microorganisms in contaminated environments have rapidly adapted to their presence by evolving new biodegradation pathways that take advantage of them as sources of carbon, nitrogen, and energy. This review provides an overview of the synthesis of both man-made and biogenic nitroaromatic compounds, the bacteria that have been identified to grow on and completely mineralize nitroaromatic compounds, and the pathways that are present in these strains. The possible evolutionary origins of the newly evolved pathways are also discussed.
Coverage of Related Pathogenic Species by Multivalent and Cross-Protective Vaccine Design: Arenaviruses as a Model System
Authors: Botten Jason , Sidney John , Mothé Bianca R. , Peters Bjoern , Sette Alessandro , Kotturi Maya F. 
Published: May 2010

SUMMARYThe arenaviruses are a family of negative-sense RNA viruses that cause severe human disease ranging from aseptic meningitis to hemorrhagic fever syndromes. There are currently no FDA-approved vaccines for the prevention of arenavirus disease, and therapeutic treatment is limited to the use of ribavirin and/or immune plasma for a subset of the pathogenic arenaviruses. The considerable genetic variability observed among the seven arenaviruses that are pathogenic for humans illustrates one of the major challenges for vaccine development today, namely, to overcome pathogen heterogeneity. Over the past 5 years, our group has tested several strategies to overcome pathogen heterogeneity, utilizing the pathogenic arenaviruses as a model system. Because T cells play a prominent role in protective immunity following arenavirus infection, we specifically focused on the development of human vaccines that would induce multivalent and cross-protective cell-mediated immune responses. To facilitate our vaccine development and testing, we conducted large-scale major histocompatibility complex (MHC) class I and class II epitope discovery on murine, nonhuman primate, and human backgrounds for each of the pathogenic arenaviruses, including the identification of protective HLA-restricted epitopes. Finally, using the murine model of lymphocytic choriomeningitis virus infection, we studied the phenotypic characteristics associated with immunodominant and protective T cell epitopes. This review summarizes the findings from our studies and discusses their application to future vaccine design.