bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of Immune Responses to Capsid Protein p24 of Human Immunodeficiency Virus Type 1 and Implications for Detection
Authors: Tang Shixing , Zhao Jiangqin , Wang Aifeng , Viswanath Ragupathy , Harma Harri , Little Richard F. , Yarchoan Robert , Stramer Susan L. , Nyambi Phillipe N. , Lee Sherwin , Wood Owen , Wong Eric Y. , Wang Xue , Hewlett Indira K. 
Published: June 2010

ABSTRACT
To further refine our current nanoparticle-based HIV-1 p24 antigen assay, we investigated immune responses to p24 to identify diagnostically significant immune dominant epitopes (IDEs) in HIV-infected human sera, to address cross-reactivity of anti-p24 antibodies to different subtypes, and to identify new biomarkers that distinguish acute from chronic HIV infection for more accurate incidence estimation. We identified two major linear epitope regions, located in the CypA binding loop and adjacent helices and at the end of the C-terminal domain. Most sera (86%) from acutely HIV-1-infected individuals reacted with multiple peptides, while 60% and 30% of AIDS patient samples reacted with multiple and single peptides, respectively. In contrast, 46% and 43% of chronically HIV-1-infected individuals reacted with one and none of the peptides, respectively, and only 11% reacted with multiple p24 peptides, indicating a progression of immune responses from polyclone-like during acute infection to monoclone-like or a nonresponse to linear epitopes during chronic infection. Anti-p24 antibodies (subtype B) show broad cross-reactivity to different HIV-1 subtypes, and the synergistic action of different combinations of anti-HIV antibodies improves capture and detection of divergent HIV-1 subtypes. Our results indicate that the modified peptide immunoassay is sensitive and specific for the rapid identification of HIV-1 p24 IDEs and for investigation of immune responses to p24 during natural HIV-1 infection. The data provide the foundation for development and refinement of new assays for improved p24 antigen testing as future tools for rapid and accurate diagnosis as part of early intervention strategies and estimations of incidence.
Establishment of an Aerosol Challenge Model of Tuberculosis in Rhesus Macaques and an Evaluation of Endpoints for Vaccine Testing
Authors: Sharpe S. A. , McShane H. , Dennis M. J. , Basaraba R. J. , Gleeson F. , Hall G. , McIntyre A. , Gooch K. , Clark S. , Beveridge N. E. R. , Nuth E. , White A. , Marriott A. , Dowall S. , Hill A. V. S. , Williams A. , Marsh P. D. 
Published: June 2010

ABSTRACT

The establishment of an aerosol challenge model in nonhuman primates (NHPs) for the testing of vaccines against
Mycobacterium tuberculosis
would assist the global effort to optimize novel vaccination strategies. The endpoints used in preclinical challenge studies to identify measures of disease burden need to be accurate and sensitive enough to distinguish subtle differences and benefits afforded by different tuberculosis (TB) vaccine regimens when group sizes are inevitably small. This study sought to assess clinical and nonclinical endpoints as potentially sensitive measures of disease burden in a challenge study with rhesus macaques by using a new protocol of aerosol administration of
M. tuberculosis
. Immunological and clinical readouts were assessed for utility in vaccine evaluation studies. This is the first example of TB vaccine evaluation with rhesus macaques where long-term survival was one of the primary endpoints. However, we found that in NHP vaccine efficacy studies with maximum group sizes of six animals, survival did not provide a valuable endpoint. Two approaches used in human clinical trials for the evaluation of the gamma interferon (IFN-γ) response to vaccination (enzyme-linked immunospot [ELISpot] assay and enzyme-linked immunosorbent assay [ELISA]) were included in this study. The IFN-γ profiles induced following vaccination were found not to correlate with protection, nor did the level of purified protein derivative (PPD)-specific proliferation. The only readout to reliably distinguish vaccinated and unvaccinated NHPs was the determination of lung lesion burden using magnetic resonance (MR) imaging combined with stereology at the end of the study. Therefore, the currently proposed key markers were not shown to correlate with protection, and only imaging offered a potentially reliable correlate.
Identification of
Mycoplasma mycoides
subsp.
mycoides
Small Colony Genes Coding for T-Cell Antigens
Authors: Totté Philippe , Mather Arshad , Reslan Lina , Boublik Yvan , Niang Mamadou , Du Plessis Dion , Dedieu Laurence 
Published: June 2010

ABSTRACT

Genes of the
Mycoplasma mycoides
subsp
. mycoides
small colony biotype (
Mmm
SC) coding for proteins capable of eliciting protective T-cell memory responses have potential for incorporation into a recombinant subunit vaccine against contagious bovine pleuropneumonia (CBPP). Here we used lymphocytes from cattle that had completely recovered from infection to screen products of
Mmm
SC genes for recognition by CD4
+
effector memory (Tem) and central memory (Tcm) T lymphocytes. Six
Mmm
SC genes (
abc
,
gapN
,
glpO
,
lppA
,
lppB
, and
ptsG
) were expressed as histidine-tagged recombinant polypeptides, or synthetic overlapping peptides, before inclusion in proliferation and gamma interferon (IFN-γ) assays. Only two
Mmm
SC antigens, LppA and PtsG, consistently induced recall proliferation from immune CD4
+
T cells and IFN-γ production in all animals tested. Moreover, LppA and PtsG were shown to possess epitopes recognized by both short-lived CD4
+
Tem and long-lived CD4
+
Tcm cells.
Diagnosis of Amebic Liver Abscess and Amebic Colitis by Detection of
Entamoeba histolytica
DNA in Blood, Urine, and Saliva by a Real-Time PCR Assay
Authors: Haque Rashidul , Kabir Mamun , Noor Zannatun , Rahman S. M. Mazidur , Mondal Dinesh , Alam Faisal , Rahman Intekhab , Al Mahmood Abdullh , Ahmed Nooruddin , Petri William A. 
Published: June 2010

ABSTRACT

The noninvasive diagnosis of amebic liver abscess is challenging, as most patients at the time of diagnosis do not have a concurrent intestinal infection with
Entamoeba histolytica
. Fecal testing for
E. histolytica
parasite antigen or DNA is negative in most patients. A real-time PCR assay was evaluated for detection of
E. histolytica
DNA in blood, urine, and saliva samples from amebic liver abscess as well as amebic colitis patients in Bangladesh. A total of 98 amebic liver abscess and 28 amebic colitis patients and 43 control subjects were examined. The real-time PCR assay detected
E. histolytica
DNA in 49%, 77%, and 69% of blood, urine, and saliva specimens from the amebic liver abscess patients. For amebic colitis the sensitivity of the real-time PCR assay for detection of
E. histolytica
DNA in blood, urine, and saliva was 36%, 61%, and 64%, respectively. All blood, urine, and saliva samples from control subjects were negative by the real-time PCR assay for
E. histolytica
DNA. When the real-time PCR assay results of the urine and saliva specimens were taken together (positive either in urine or saliva), the real-time PCR assay was 97% and 89% sensitive for detection of
E. histolytica
DNA in liver abscess and intestinal infection, respectively. We conclude that the detection of
E. histolytica
DNA in saliva and urine could be used as a diagnostic tool for amebic liver abscess.
Potency of Anidulafungin Compared to Nine Other Antifungal Agents Tested against
Candida
spp.,
Cryptococcus
spp., and
Aspergillus
spp.: Results from the Global SENTRY Antimicrobial Surveillance Program (2008)
Authors: Messer Shawn A. , Jones Ronald N. , Moet Gary J. , Kirby Jeffrey T. , Castanheira Mariana 
Published: June 2010

ABSTRACT

The SENTRY Antimicrobial Surveillance Program regularly monitors global susceptibility rates for a spectrum of both novel and established antifungal agents. Anidulafungin and the other echinocandins displayed sustained, excellent activity against
Candida
spp. and
Aspergillus fumigatus
, with ≥98% of MIC results at ≤2 μg/ml. Six yeast isolates (all
Candida glabrata
) showing caspofungin MIC values of ≥0.5 μg/ml were further analyzed for potential
fks
hot spot (HS) mutations; three isolates had confirmed mutations in the
fks1
HS1 region (S645P), and three exhibited mutations in the
fks2
HS1 region (S645F and S645P).
Quantitative Analysis of a Urine-Based Assay for Detection of Lipoarabinomannan in Patients with Tuberculosis
Authors: Shah Maunank , Martinson Neil A. , Chaisson Richard E. , Martin Desmond J. , Variava Ebrahim , Dorman Susan E. 
Published: June 2010

ABSTRACT
Urinary lipoarabinomannan (LAM) detection is a promising approach for rapid diagnosis of active tuberculosis (TB). In microbiologically confirmed TB patients, quantitative LAM detection results increased progressively with bacillary burden and immunosuppression. Patients with disseminated TB and/or advanced HIV are target populations for whom urine LAM detection may be particularly useful.
Helcococcus kunzii
Isolated from a Sow with Purulent Urocystitis
Authors: Grattarola Carla , Bellino Claudio , Tursi Massimiliano , Maggi Elisa , D'Angelo Antonio , Gianella Paola , Dondo Alessandro , Cagnasso Aurelio 
Published: June 2010

ABSTRACT

Helcococcus kunzii
has never been reported in veterinary medicine. The isolation of
H. kunzii
from a sow with purulent urocystitis is described, suggesting this organism's potential pathogenic role in swine.
Development and Evaluation of a Novel Single-Nucleotide-Polymorphism Real-Time PCR Assay for Rapid Detection of Fluoroquinolone-Resistant
Mycoplasma bovis
Authors: Ben Shabat M. , Mikula I. , Gerchman I. , Lysnyansky I. 
Published: June 2010

ABSTRACT

Monitoring of the susceptibility of
Mycoplasma bovis
field isolates to antibiotics is important for the appropriate choice of treatment. However,
in vitro
susceptibility testing of mycoplasmas is technically demanding and time-consuming, especially for clinical isolates, and is rarely performed in mycoplasma diagnostic laboratories. Thus, the development of methods allowing rapid real-time detection of resistant strains of
M. bovis
in clinical samples is a high priority for successful treatment. In this study, a novel TaqMan single-nucleotide-polymorphism (SNP) real-time PCR assay, which enables the rapid identification of
M. bovis
strains with different susceptibilities to fluoroquinolones, was developed and evaluated. The TaqMan SNP real-time PCR assay is based on the amplification of a 97-bp fragment of the
parC
quinolone resistance-determining region (QRDR) and allows the specific detection of four possible genotypes: GAC or GAT (susceptible to fluoroquinolones) and AAC or AAT (resistant to fluoroquinolones). Four TaqMan minor groove binder (MGB) probes identifying 1-base mismatches were designed and applied in a dual-probe assay with two reaction tubes. The TaqMan SNP real-time PCRs developed are highly specific for
M. bovis
, with a detection limit of 5 fg/μl (about 5
M. bovis
genomes). In addition, all four SNP real-time PCR tests have almost the same efficiency (97.7% [GAC], 94% [AAC], 99.99% [GAT], and 98% [AAT]). Taken together, the data suggest that this SNP real-time PCR assay has potential as a routine diagnostic test for the detection of decreased susceptibility of
M. bovis
to fluoroquinolones.
Ancestral Lineages of Human Enterotoxigenic
Escherichia coli
Authors: Steinsland Hans , Lacher David W. , Sommerfelt Halvor , Whittam Thomas S. 
Published: June 2010

ABSTRACT

Enterotoxigenic
Escherichia coli
(ETEC) is a common cause of diarrhea among children living in and among travelers visiting developing countries. Human ETEC strains represent an epidemiologically and phenotypically diverse group of pathogens, and there is a need to identify natural groupings of these organisms that may help to explain this diversity. Here, we sought to identify most of the important human ETEC lineages that exist in the
E. coli
population, because strains that originate from the same lineage may also have inherited many of the same epidemiological and phenotypic traits. We performed multilocus sequence typing (MLST) on 1,019 ETEC isolates obtained from humans in different countries and analyzed the data against a backdrop of MLST data from 1,250 non-ETEC
E. coli
and eight ETEC isolates from pigs. A total of 42 different lineages were identified, 15 of which, representing 792 (78%) of the strains, were estimated to have emerged >900 years ago. Twenty of the lineages were represented in more than one country. There was evidence of extensive exchange of enterotoxin and colonization factor genes between different lineages. Human and porcine ETEC have probably emerged from the same ancestral ETEC lineage on at least three occasions. Our findings suggest that most ETEC strains circulating in the human population today originate from well-established, globally widespread ETEC lineages. Some of the more important lineages identified here may represent a smaller and more manageable target for the ongoing efforts to develop effective ETEC vaccines.
The Lytic Transcriptome of Kaposi's Sarcoma-Associated Herpesvirus Reveals Extensive Transcription of Noncoding Regions, Including Regions Antisense to Important Genes
Authors: Chandriani Sanjay , Xu Yiyang , Ganem Don 
Published: June 2010

ABSTRACT
Genomewide analyses of the mammalian transcriptome have revealed that large tracts of sequence previously annotated as noncoding are frequently transcribed and give rise to stable RNA. Although the transcription of individual genes of the Kaposi's sarcoma-associated herpesvirus (KSHV) has been well studied, little is known of the architecture of the viral transcriptome on a genomewide scale. Here we have employed a genomewide tiling array to examine the lytic transcriptome of the Kaposi's sarcoma-associated herpesvirus, KSHV. Our results reveal that during lytic growth (but not during latency), there is extensive transcription from noncoding regions, including both intergenic regions and, especially, noncoding regions antisense to known open reading frames (ORFs). Several of these transcripts have been characterized in more detail, including (i) a 10-kb RNA antisense to the major latency locus, including many of its microRNAs as well as its ORFs; (ii) a 17-kb RNA antisense to numerous ORFs at the left-hand end of the genome; and (iii) a 0.7-kb RNA antisense to the viral homolog of interleukin-6 (vIL-6). These studies indicate that the lytic herpesviral transcriptome resembles a microcosm of the host transcriptome and provides a useful system for the study of noncoding RNAs.
Selective Induction of Host Genes by MVA-B, a Candidate Vaccine against HIV/AIDS
Authors: Guerra Susana , González José Manuel , Climent Núria , Reyburn Hugh , López-Fernández Luis A. , Nájera José L. , Gómez Carmen E. , García Felipe , Gatell José M. , Gallart Teresa , Esteban Mariano 
Published: June 2010

ABSTRACTThe aim of this study was to define the effects on antigen-presenting cells of the expression of HIV antigens from an attenuated poxvirus vector. We have analyzed the transcriptional changes in gene expression following infection of human immature monocyte-derived dendritic cells (DC) with recombinant modified vaccinia virus Ankara (MVA) expressing the genes encoding the gp120 and Gag-Pol-Nef antigens of HIV type 1 clade B (referred to as MVA-B) versus parental MVA infection. Using microarray technology and real-time reverse transcription-PCR, we demonstrated that the HIV proteins induced the expression of cytokines, cytokine receptors, chemokines, chemokine receptors, and molecules involved in antigen uptake and processing, including major histocompatibility complex (MHC) genes. Levels of mRNAs for interleukin-1, beta interferon, CCR8, and SCYA20 were higher after HIV antigen production. MVA-B infection also modulated the expression of antigen processing and presentation genes: the gene for MICA was upregulated, whereas those for HLA-DRA and HSPA5 were downregulated. Indeed, the increased expression of the gene for MICA, a glycoprotein related to major histocompatibility complex class I molecules, was shown to enhance the interaction between MVA-B-infected target cells and cytotoxic lymphocytes. The expression profiles of the genes for protein kinases such as JAK1 and IRAK2 were activated after HIV antigen expression. Several genes included in the JAK-STAT and mitogen-activated protein kinase signaling pathways were regulated after HIV antigen expression. Our findings provide the first gene signatures in DC of a candidate MVA-B vaccine expressing four HIV antigens and identified the biological roles of some of the regulatory genes, like that for MICA, which will help in the design of more effective MVA-derived vaccines.
Role of the Kaposi's Sarcoma-Associated Herpesvirus K15 SH3 Binding Site in Inflammatory Signaling and B-Cell Activation
Authors: Pietrek Marcel , Brinkmann Melanie M. , Glowacka Ilona , Enlund Anette , Hävemeier Anika , Dittrich-Breiholz Oliver , Kracht Michael , Lewitzky Marc , Saksela Kalle , Feller Stephan M. , Schulz Thomas F. 
Published: June 2010

ABSTRACT
The Kaposi's sarcoma-associated herpesvirus (KSHV) contains several open reading frames (ORFs) that encode proteins capable of initiating and modulating cellular signaling pathways. Among them is ORF K15, encoding a 12-transmembrane-spanning protein with a cytoplasmic C-terminal domain. Through conserved binding motifs, such as Src homology 2 (SH2) and SH3 binding sites, K15 interacts with cellular proteins, activates the NF-κB, MEK/Erk, and Jun N-terminal protein kinase (JNK) pathways, and induces the expression of several inflammatory and angiogenic genes. In this study, we investigated the role of an SH3 domain binding site centered on a PPLP motif in K15. We screened libraries of cellular SH3 domains to identify signaling molecules interacting with the KSHV PPLP motif. We found its affinities for two Src kinase family members, Lyn and Hck, to exceed those of other viral proteins. While the SH2 binding motif YEEV is essential for the inflammatory response induced by KSHV K15, recruitment of Lyn and Hck to the K15 PPLP motif seems to be dispensable for this inflammatory response. However, the PPLP motif is essential for the decrease in B-cell receptor-mediated signaling induced by K15, as measured by calcium mobilization assays.
Divergent Evolution of Norovirus GII/4 by Genome Recombination from May 2006 to February 2009 in Japan
Authors: Motomura Kazushi , Yokoyama Masaru , Ode Hirotaka , Nakamura Hiromi , Mori Hiromi , Kanda Tadahito , Oka Tomoichiro , Katayama Kazuhiko , Noda Mamoru , Tanaka Tomoyuki , Takeda Naokazu , Sato Hironori 
Published: June 2010

ABSTRACT

Norovirus GII/4 is a leading cause of acute viral gastroenteritis in humans. We examined here how the GII/4 virus evolves to generate and sustain new epidemics in humans, using 199 near-full-length GII/4 genome sequences and 11 genome segment clones from human stool specimens collected at 19 sites in Japan between May 2006 and February 2009. Phylogenetic studies demonstrated outbreaks of 7 monophyletic GII/4 subtypes, among which a single subtype, termed 2006b, had continually predominated. Phylogenetic-tree, bootscanning-plot, and informative-site analyses revealed that 4 of the 7 GII/4 subtypes were mosaics of recently prevalent GII/4 subtypes and 1 was made up of the GII/4 and GII/12 genotypes. Notably, single putative recombination breakpoints with the highest statistical significance were constantly located around the border of open reading frame 1 (ORF1) and ORF2 (
P
≤ 0.000001), suggesting outgrowth of specific recombinant viruses in the outbreaks. The GII/4 subtypes had many unique amino acids at the time of their outbreaks, especially in the N-term, 3A-like, and capsid proteins. Unique amino acids in the capsids were preferentially positioned on the outer surface loops of the protruding P2 domain and more abundant in the dominant subtypes. These findings suggest that intersubtype genome recombination at the ORF1/2 boundary region is a common mechanism that realizes independent and concurrent changes on the virion surface and in viral replication proteins for the persistence of norovirus GII/4 in human populations.
Poliovirus Polymerase Residue 5 Plays a Critical Role in Elongation Complex Stability
Authors: Hobdey Sarah E. , Kempf Brian J. , Steil Benjamin P. , Barton David J. , Peersen Olve B. 
Published: June 2010

ABSTRACT

The structures of polio-, coxsackie-, and rhinovirus polymerases have revealed a conserved yet unusual protein conformation surrounding their buried N termini where a β-strand distortion results in a solvent-exposed hydrophobic amino acid at residue 5. In a previous study, we found that coxsackievirus polymerase activity increased or decreased depending on the size of the amino acid at residue 5 and proposed that this residue becomes buried during the catalytic cycle. In this work, we extend our studies to show that poliovirus polymerase activity is also dependent on the nature of residue 5 and further elucidate which aspects of polymerase function are affected. Poliovirus polymerases with mutations of tryptophan 5 retain wild-type elongation rates, RNA binding affinities, and elongation complex formation rates but form unstable elongation complexes. A large hydrophobic residue is required to maintain the polymerase in an elongation-competent conformation, and smaller hydrophobic residues at position 5 progressively decrease the stability of elongation complexes and their processivity on genome-length templates. Consistent with this, the mutations also reduced viral RNA production in a cell-free replication system.
In vivo
, viruses containing residue 5 mutants produce viable virus, and an aromatic phenylalanine was maintained with only a slightly decreased virus growth rate. However, nonaromatic amino acids resulted in slow-growing viruses that reverted to wild type. The structural basis for this polymerase phenotype is yet to be determined, and we speculate that amino acid residue 5 interacts directly with template RNA or is involved in a protein structural interaction that stabilizes the elongation complex.
Identification of Five Interferon-Induced Cellular Proteins That Inhibit West Nile Virus and Dengue Virus Infections
Authors: Jiang Dong , Weidner Jessica M. , Qing Min , Pan Xiao-Ben , Guo Haitao , Xu Chunxiao , Zhang Xianchao , Birk Alex , Chang Jinhong , Shi Pei-Yong , Block Timothy M. , Guo Ju-Tao 
Published: June 2010

ABSTRACT
Interferons (IFNs) are key mediators of the host innate antiviral immune response. To identify IFN-stimulated genes (ISGs) that instigate an antiviral state against two medically important flaviviruses, West Nile virus (WNV) and dengue virus (DENV), we tested 36 ISGs that are commonly induced by IFN-α for antiviral activity against the two viruses. We discovered that five ISGs efficiently suppressed WNV and/or DENV infection when they were individually expressed in HEK293 cells. Mechanistic analyses revealed that two structurally related cell plasma membrane proteins, IFITM2 and IFITM3, disrupted early steps (entry and/or uncoating) of the viral infection. In contrast, three IFN-induced cellular enzymes, viperin, ISG20, and double-stranded-RNA-activated protein kinase, inhibited steps in viral proteins and/or RNA biosynthesis. Our results thus imply that the antiviral activity of IFN-α is collectively mediated by a panel of ISGs that disrupt multiple steps of the DENV and WNV life cycles.