bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Improved Whole-Blood Gamma Interferon Assay Based on the CFP21-MPT64 Fusion Protein
Authors: Fu Ruiling , Wang Chun , Shi Chunwei , Lu Mengji , Fang Zhengming , Lu Jia , Wang Fang , Fan Xionglin 
Published: March 2009

ABSTRACT

Differentiation of latent tuberculosis infection (LTBI) from a healthy, unexposed population plays a vital role in the strategy of controlling and eliminating tuberculosis (TB). Both CFP21 and MPT64, antigens encoded by the RD2 region which are restricted in the
Mycobacterium tuberculosis
complex, are TB-specific diagnostic candidate antigens. In this study, we designed a fusion protein by linking both CFP21 and MPT64 with a 15-amino-acid peptide, (G
4
S
1
)
3
, and overexpressed the fusion protein in
Escherichia coli
. A new whole-blood gamma interferon assay based on the recombinant fusion protein, CFP21-MPT64 (rCM-WBIA), was developed and compared with the tuberculin skin test (TST) for screening of LTBI in household contacts of patients with sputum-positive TB. rCM-WBIA had a slightly higher sensitivity (66.7%; 24/36 contacts) than that of the TST (61.1%; 22/36 contacts) for household contacts. We found that rCM-WBIA had a very high sensitivity (90.9%) and specificity (71.4%) for LTBI detection compared with TST. The overall agreement between rCM-WBIA and TST was 83.3% (
k
= 0.64); rCM-WBIA positivity was associated with a larger TST induration. These results suggest that rCM-WBIA, based on the recombinant fusion protein CFP21-MPT64, is a promising alternative diagnostic tool for detection of LTBI.
Universal Detection and Identification of Avian Influenza Virus by Use of Resequencing Microarrays
Authors: Lin Baochuan , Malanoski Anthony P. , Wang Zheng , Blaney Kate M. , Long Nina C. , Meador Carolyn E. , Metzgar David , Myers Christopher A. , Yingst Samuel L. , Monteville Marshall R. , Saad Magdi D. , Schnur Joel M. , Tibbetts Clark , Stenger David A. 
Published: March 2009

ABSTRACT
Zoonotic microbes have historically been, and continue to emerge as, threats to human health. The recent outbreaks of highly pathogenic avian influenza virus in bird populations and the appearance of some human infections have increased the concern of a possible new influenza pandemic, which highlights the need for broad-spectrum detection methods for rapidly identifying the spread or outbreak of all variants of avian influenza virus. In this study, we demonstrate that high-density resequencing pathogen microarrays (RPM) can be such a tool. The results from 37 influenza virus isolates show that the RPM platform is an effective means for detecting and subtyping influenza virus, while simultaneously providing sequence information for strain resolution, pathogenicity, and drug resistance without additional analysis. This study establishes that the RPM platform is a broad-spectrum pathogen detection and surveillance tool for monitoring the circulation of prevalent influenza viruses in the poultry industry and in wild birds or incidental exposures and infections in humans.
PCR Diagnosis of
Opisthorchis viverrini
and
Haplorchis taichui
Infections in a Lao Community in an Area of Endemicity and Comparison of Diagnostic Methods for Parasitological Field Surveys
Authors: Lovis Leonore , Mak Tippi K. , Phongluxa Khampheng , Soukhathammavong Phonepasong , Sayasone Somphou , Akkhavong Kongsap , Odermatt Peter , Keiser Jennifer , Felger Ingrid 
Published: March 2009

ABSTRACT

Opisthorchiasis is a major public health problem in Southeast Asia. Affected individuals often have mixed infections with the liver fluke
Opisthorchis viverrini
and minute intestinal flukes such as
Haplorchis taichui
. The usual methods of diagnosing these infections involve the demonstration of fluke eggs in stool samples under light microscopy, but sensitivity and specificity are low. We developed two PCR tests that detect and discriminate between
O. viverrini
and
H. taichui
infections. PCR tests were validated by stool samples from purged individuals. We then applied the PCR tests to estimate the prevalence of
O. viverrini
and
H. taichui
infections from a random sample of individuals selected from a community in an area of endemicity in Khong District, Laos. PCR results were compared with those from the Kato-Katz (KK) method and the formalin-ether concentration technique (FECT). When validated with purge results, PCR tests of
O. viverrini
and
H. taichui
had sensitivities of 93.7% (95% confidence interval [CI], 85.8 to 97.9%) and 73.3% (95% CI, 60.3 to 83.9%) and could detect as little as 0.75 pg DNA and 1.32 ng DNA, respectively. The PCR-determined community prevalences of
O. viverrini
and
H. taichui
infections were 63.9% (95% CI, 54.1 to 72.9%) and 30.6% (95% CI, 22.1 to 40.2%), respectively. Using PCR as the gold standard to detect
O. viverrini
, three KK thick smears performed comparably well, whereas one KK smear and FECT were poorer (sensitivities of 91.4% [95% CI, 81.0 to 97.1%,], 62.3% [95% CI, 49.8 to 73.7%], and 49.3% [95% CI, 37.0 to 61.6%], respectively). PCR may be a valuable and sensitive diagnostic tool, particularly for low-intensity
O. viverrini
and
H. taichui
infections.
Rapid and Accurate Diagnosis of Human Intestinal Spirochetosis by Fluorescence In Situ Hybridization
Authors: Schmiedel Dinah , Epple Hans-Jörg , Loddenkemper Christoph , Ignatius Ralf , Wagner Jutta , Hammer Bettina , Petrich Annett , Stein Harald , Göbel Ulf B. , Schneider Thomas , Moter Annette 
Published: March 2009

ABSTRACT

Human intestinal spirochetosis (HIS) is associated with overgrowth of the large intestine by spirochetes of the genus
Brachyspira
. The microbiological diagnosis of HIS is hampered by the fastidious nature and slow growth of
Brachyspira
spp. In clinical practice, HIS is diagnosed histopathologically, and a significant portion of cases may be missed. Fluorescence in situ hybridization (FISH) is a molecular method that allows the visualization and identification of single bacteria within tissue sections. In this study, we analyzed intestinal biopsy samples from five patients with possible HIS. All specimens yielded positive results by histopathological techniques. PCR amplification and sequencing of the 16S rRNA gene were performed. Sequences of two isolates clustered in the group of
Brachyspira aalborgi
, whereas in three cases, the sequences were highly similar to that of
Brachyspira pilosicoli
. Three phylotypes showed mismatches at distinct nucleotide positions with
Brachyspira
sp. sequences published previously. In addition, culture for
Brachyspira
was successful in three cases. On the basis of these data, we designed and evaluated a
Brachyspira
genus-specific 16S rRNA-directed FISH probe that detects all of the
Brachyspira
spp. published to date. FISH of biopsy samples resulted in strong, unequivocal signals of brush-like formations at the crypt surfaces. This technique allowed simultaneous visualization of single spirochetes and their identification as
Brachyspira
spp. In conclusion, FISH provides a fast and accurate technique for the visualization and identification of intestinal spirochetes in tissue sections. It therefore represents a valuable tool for routine diagnosis of HIS.
Epstein-Barr Virus-Related Diarrhea or Exacerbation of Inflammatory Bowel Disease: Diagnostic Dilemma
Authors: Weinberg Ido , Neuman Tzahi , Margalit Maya , Ayman Fadeela , Wolf Dana G. , Ben-Yehuda Arie 
Published: March 2009

ABSTRACT
While the presence of Epstein-Barr virus (EBV) in colonic specimens from patients with inflammatory bowel disease (IBD) has been documented, diarrhea secondary to gastrointestinal involvement by EBV in the context of primary EBV infection in patients with IBD has not been reported. We describe a patient with IBD who presented with diarrhea and primary EBV infection and propose a role for colonic involvement by EBV in the pathogenesis of his symptoms.
Comparison of Routine Bench and Molecular Diagnostic Methods in Identification of
Burkholderia pseudomallei
Authors: Hodgson Kelly , Engler Cathy , Govan Brenda , Ketheesan Natkunam , Norton Robert 
Published: March 2009

ABSTRACT

This study compared the identification of
Burkholderia pseudomallei
with that of related organisms. Bench tests and latex agglutination were compared with molecular identification. Using bench tests and latex agglutination alone, 100% (30/30) of
B. pseudomallei
isolates were correctly identified. Amoxicillin-clavulanate susceptibility testing was also a good and simple discriminatory test.
Regulation of Episomal Gene Expression by KRAB/KAP1-Mediated Histone Modifications
Authors: Barde Isabelle , Laurenti Elisa , Verp Sonia , Groner Anna Claire , Towne Christopher , Padrun Viviane , Aebischer Patrick , Trumpp Andreas , Trono Didier 
Published: March 2009

ABSTRACT
KAP1 is an essential cofactor of KRAB zinc finger proteins, a family of vertebrate-specific epigenetic repressors of largely unknown functions encoded in the hundreds by the mouse and human genomes. So far, KRAB/KAP1-mediated gene regulation has been studied within the environment of chromosomal DNA. Here we demonstrate that KRAB/KAP1 regulation is fully functional within the context of episomal DNA, such as adeno-associated viral and nonintegrated lentiviral vectors, and is correlated with histone modifications typically associated with this epigenetic regulator.
The Marmoset Model of GB Virus B Infections: Adaptation to Host Phenotypic Variation
Authors: Weatherford Trudie , Chavez Deborah , Brasky Kathleen M. , Lanford Robert E. 
Published: March 2009

ABSTRACT

Worldwide, approximately 170 million people are chronically infected with hepatitis C virus (HCV), and chronic infection frequently progresses to serious liver disease, including cirrhosis and hepatocellular carcinoma. GB virus B (GBV-B), the virus phylogenetically most closely related to HCV, causes hepatitis in tamarins. We have demonstrated the suitability of the tamarin as a host for GBV-B and as a surrogate nonhuman primate model for HCV infection, and we have initiated studies of GBV-B infection in a closely related species, the common marmoset (
Callithrix jacchus
). Here, we demonstrate that marmosets exhibit two phenotypes upon infection with GBV-B: the susceptible phenotype and the partially resistant phenotype. In addition, we identify changes that may correlate with adaptation of the virus to the partially resistant host. GBV-B was serially passaged five times through 14 marmosets as one lineage and two times through 6 marmosets as a second lineage. Virus adapted to the marmosets and eventually exhibited robust infections in two separate lineages, lineages 1 and 2. A third lineage was initiated with a molecular clone, and again, susceptible and partially resistant phenotypes were observed. Three isolates were fully sequenced (from lineage 1), and 21 nucleotide changes were observed, with six amino acid changes. We speculate that the marmoset partially resistant phenotype may be due to a polymorphism in the marmoset population that affects critical virus-host interactions and that wild-type GBV-B is capable of rapidly adapting to this altered host.
Selection of a Simian-Human Immunodeficiency Virus Strain Resistant to a Vaginal Microbicide in Macaques
Authors: Dudley Dawn M. , Wentzel Jennifer L. , Lalonde Matthew S. , Veazey Ronald S. , Arts Eric J. 
Published: March 2009

ABSTRACT

PSC-RANTES binds to CCR5, inhibits human immunodeficiency virus type 1 (HIV-1) entry, and has been shown as a vaginal microbicide to protect rhesus macaques from a simian-human immunodeficiency virus chimera (SHIV
SF162-p3
) infection in a dose-dependent manner. In this study,
env
gene sequences from SHIV
SF162-p3
-infected rhesus macaques treated with PSC-RANTES were analyzed for possible drug escape variants. Two specific mutations located in the V3 region of gp120 (K315R) and C-helical domain of gp41 (N640D) were identified in a macaque (m584) pretreated with a 100 μM dose of PSC-RANTES. These two
env
mutations were found throughout infection (through week 77) but were found at only low frequencies in the inoculating SHIV
SF162-p3
stock and in the other SHIV
SF162-p3
-infected macaques. HIV-1
env
genes from macaque m584 (
env
m584
) and from inoculating SHIV
SF162-p3
(
env
p3
) were cloned into an HIV-1 backbone. Increases in 50% inhibitory concentrations to PSC-RANTES with
env
m584
were modest (sevenfold) and most pronounced in cells expressing rhesus macaque CCR5 as compared to human CCR5. Nonetheless, virus harboring
env
m584
, unlike inoculating virus
env
p3
, could replicate even at the highest tissue culture PSC-RANTES concentrations (100 nM). Dual-virus competitions revealed a dramatic increase in fitness of chimeric virus containing
env
m584
(K315R/N640D) over that containing
env
p3
, but again, only in rhesus CCR5-expressing cells. This study is the first to describe the immediate selection and infection of a drug-resistant SHIV variant in the face of a protective vaginal microbicide, PSC-RANTES. This rhesus CCR5-specific/PSC- RANTES resistance selection is particularly alarming given the relative homogeneity of the SHIV
SF162-p3
stock compared to the potential exposure to a heterogeneous HIV-1 population in human transmission.
Virion Incorporation of the Herpes Simplex Virus Type 1 Tegument Protein VP22 Occurs via Glycoprotein E-Specific Recruitment to the Late Secretory Pathway
Authors: Stylianou Julianna , Maringer Kevin , Cook Rachelle , Bernard Emmanuelle , Elliott Gillian 
Published: March 2009

ABSTRACT

The mechanism by which herpesviruses acquire their tegument is not yet clear. One model is that outer tegument proteins are recruited by the cytoplasmic tails of viral glycoproteins. In the case of herpes simplex virus tegument protein VP22, interactions with the glycoproteins gE and gD have been shown. We have previously shown that the C-terminal half of VP22 contains the necessary signal for assembly into the virus. Here, we show that during infection VP22 interacts with gE and gM, as well as its tegument partner VP16. However, by using a range of techniques we were unable to demonstrate VP22 binding to gD. By using pulldown assays, we show that while the cytoplasmic tails of both gE and gM interact with VP22, only gE interacts efficiently with the C-terminal packaging domain of VP22. Furthermore, gE but not gM can recruit VP22 to the Golgi/
trans
-Golgi network region of the cell in the absence of other virus proteins. To examine the role of the gE-VP22 interaction in infection, we constructed a recombinant virus expressing a mutant VP22 protein with a 14-residue deletion that is unable to bind gE (ΔgEbind). Coimmunoprecipitation assays confirmed that this variant of VP22 was unable to complex with gE. Moreover, VP22 was no longer recruited to its characteristic cytoplasmic trafficking complexes but exhibited a diffuse localization. Importantly, packaging of this variant into virions was abrogated. The mutant virus exhibited poor growth in epithelial cells, similar to the defect we have observed for a VP22 knockout virus. These results suggest that deletion of just 14 residues from the VP22 protein is sufficient to inhibit binding to gE and hence recruitment to the viral envelope and assembly into the virus, resulting in a growth phenotype equivalent to that produced by deleting the entire reading frame.
Phosphorylation of the U
L
31 Protein of Herpes Simplex Virus 1 by the U
S
3-Encoded Kinase Regulates Localization of the Nuclear Envelopment Complex and Egress of Nucleocapsids
Authors: Mou Fan , Wills Elizabeth , Baines Joel D. 
Published: March 2009

ABSTRACT

Herpes simplex virus 1 nucleocapsids bud through the inner nuclear membrane (INM) into the perinuclear space to obtain a primary viral envelope. This process requires a protein complex at the INM composed of the U
L
31 and U
L
34 gene products. While it is clear that the viral kinase encoded by the U
S
3 gene regulates the localization of pU
L
31/pU
L
34 within the INM, the molecular mechanism by which this is accomplished remains enigmatic. Here, we have determined the following. (i) The N terminus of pU
L
31 is indispensable for the protein's normal function and contains up to six serines that are phosphorylated by the U
S
3 kinase during infection. (ii) Phosphorylation at these six serines was not essential for a productive infection but was required for optimal viral growth kinetics. (iii) In the presence of active U
S
3 kinase, changing the serines to alanine caused the pU
L
31/pU
L
34 complex to aggregate at the nuclear rim and caused some virions to accumulate aberrantly in herniations of the nuclear membrane, much as in cells infected with a U
S
3 kinase-dead mutant. (iv) The replacement of the six serines of pU
L
31 with glutamic acid largely restored the smooth distribution of pU
L
34/pU
L
31 at the nuclear membrane and precluded the accumulation of virions in herniations whether or not U
S
3 kinase was active but also precluded the optimal primary envelopment of nucleocapsids. These observations indicate that the phosphorylation of pU
L
31 by pU
S
3 represents an important regulatory event in the virion egress pathway that can account for much of pU
S
3's role in nuclear egress. The data also suggest that the dynamics of pU
L
31 phosphorylation modulate both the primary envelopment and the subsequent fusion of the nascent virion envelope with the outer nuclear membrane.
Region Required for Protein Expression from the Stop-Start Pentanucleotide in the M Gene of Influenza B Virus
Authors: Hatta Masato , Kohlmeier Candice K. , Hatta Yasuko , Ozawa Makoto , Kawaoka Yoshihiro 
Published: March 2009

ABSTRACT
Segment 7 of influenza B virus encodes two proteins, M1 and BM2. BM2 is expressed from a stop-start pentanucleotide, in which the BM2 initiation codon overlaps with the M1 stop codon. Here, we demonstrate that 45 nucleotides of the 3′ end of the M1 coding region, but not the 5′ end of the BM2 coding region, are sufficient for the efficient expression of the downstream protein. Placing these 45 nucleotides and the stop-start pentanucleotide in between the coding sequences induced the expression of at least three noninfluenza proteins, suggesting the utility of this system for expressing multiple proteins from one mRNA.
Geminivirus AL2 and L2 Proteins Suppress Transcriptional Gene Silencing and Cause Genome-Wide Reductions in Cytosine Methylation
Authors: Buchmann R. Cody , Asad Shaheen , Wolf Jamie N. , Mohannath Gireesha , Bisaro David M. 
Published: March 2009

ABSTRACT

Geminiviruses replicate single-stranded DNA genomes through double-stranded intermediates that associate with cellular histone proteins. Unlike RNA viruses, they are subject to RNA-directed methylation pathways that target viral chromatin and likely lead to transcriptional gene silencing (TGS). Here we present evidence that the related geminivirus proteins AL2 and L2 are able to suppress this aspect of host defense. AL2 and L2 interact with and inactivate adenosine kinase (ADK), which is required for efficient production of
S
-adenosyl methionine, an essential methyltransferase cofactor. We demonstrate that the viral proteins can reverse TGS of a green fluorescent protein (GFP) transgene in
Nicotiana benthamiana
when overexpressed from a
Potato virus X
vector and that reversal of TGS by geminiviruses requires L2 function. We also show that AL2 and L2 cause ectopic expression of endogenous
Arabidopsis thaliana
loci silenced by methylation in a manner that correlates with ADK inhibition. However, at one exceptional locus, ADK inhibition was insufficient and TGS reversal required the transcriptional activation domain of AL2. Using restriction-sensitive PCR and bisulfite sequencing, we showed that AL2-mediated TGS suppression is accompanied by reduced cytosine methylation. Finally, using a methylation-sensitive single-nucleotide extension assay, we showed that transgenic expression of AL2 or L2 causes global reduction in cytosine methylation. Our results provide further evidence that viral chromatin methylation is an important host defense and allow us to propose that as a countermeasure, geminivirus proteins reverse TGS by nonspecifically inhibiting cellular transmethylation reactions. To our knowledge, this is the first report that viral proteins can inhibit TGS.
Human T-Cell Leukemia Virus Type 2 Rex Carboxy Terminus Is an Inhibitory/Stability Domain That Regulates Rex Functional Activity and Viral Replication
Authors: Xie Li , Kesic Matthew , Yamamoto Brenda , Li Min , Younis Ihab , Lairmore Michael D. , Green Patrick L. 
Published: March 2009

ABSTRACT

Human T-cell leukemia virus (HTLV) regulatory protein, Rex, functions to increase the expression of the viral structural and enzymatic gene products. The phosphorylation of two serine residues (S151 and S153) at the C terminus is important for the function of HTLV-2 Rex (Rex-2). The Rex-2 phosphomimetic double mutant (S151D, S153D) is locked in a functionally active conformation. Since
rex
and
tax
genes overlap, Rex S151D and S153D mutants were found to alter the Tax oncoprotein coding sequence and transactivation activities. Therefore, additional Rex-2 mutants including P152D, A157D, S151Term, and S158Term were generated and characterized (“Term” indicates termination codon). All Rex-2 mutants and wild-type (wt) Rex-2 localized predominantly to the nucleus/nucleolus, but in contrast to the detection of phosphorylated and unphosphorylated forms of wt Rex-2 (p26 and p24), mutant proteins were detected as a single phosphoprotein species. We found that Rex P152D, A157D, and S158Term mutants are more functionally active than wt Rex-2 and that the Rex-2 C terminus and its specific phosphorylation state are required for stability and optimal expression. In the context of the provirus, the more active Rex mutants (A157D or S158Term) promoted increased viral protein production, increased viral infectious spread, and enhanced HTLV-2-mediated cellular proliferation. Moreover, these Rex mutant viruses replicated and persisted in inoculated rabbits despite higher antiviral antibody responses. Thus, we identified in Rex-2 a novel C-terminal inhibitory domain that regulates functional activity and is positively regulated through phosphorylation. The ability of this domain to modulate viral replication likely plays a key role in the infectious spread of the virus and in virus-induced cellular proliferation.
The Receptor Complex Associated with Human T-Cell Lymphotropic Virus Type 3 (HTLV-3) Env-Mediated Binding and Entry Is Distinct from, but Overlaps with, the Receptor Complexes of HTLV-1 and HTLV-2
Authors: Jones Kathryn S. , Huang Ying K. , Chevalier Sébastien A. , Afonso Philippe V. , Petrow-Sadowski Cari , Bertolette Daniel C. , Gessain Antoine , Ruscetti Francis W. , Mahieux Renaud 
Published: March 2009

ABSTRACT

Little is known about the transmission or tropism of the newly discovered human retrovirus, human T-cell lymphotropic virus type 3 (HTLV-3). Here, we examine the entry requirements of HTLV-3 using independently expressed Env proteins. We observed that HTLV-3 surface glycoprotein (SU) binds efficiently to both activated CD4
+
and CD8
+
T cells. This contrasts with both HTLV-1 SU, which primarily binds to activated CD4
+
T cells, and HTLV-2 SU, which primarily binds to activated CD8
+
T cells. Binding studies with heparan sulfate proteoglycans (HSPGs) and neuropilin-1 (NRP-1), two molecules important for HTLV-1 entry, revealed that these molecules also enhance HTLV-3 SU binding. However, unlike HTLV-1 SU, HTLV-3 SU can bind efficiently in the absence of both HSPGs and NRP-1. Studies of entry performed with HTLV-3 Env-pseudotyped viruses together with SU binding studies revealed that, for HTLV-1, glucose transporter 1 (GLUT-1) functions at a postbinding step during HTLV-3 Env-mediated entry. Further studies revealed that HTLV-3 SU binds efficiently to naïve CD4
+
T cells, which do not bind either HTLV-1 or HTLV-2 SU and do not express detectable levels of HSPGs, NRP-1, and GLUT-1. These results indicate that the complex of receptor molecules used by HTLV-3 to bind to primary T lymphocytes differs from that of both HTLV-1 and HTLV-2.