bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single Nucleotide Polymorphisms on the Road to Strain Differentiation in
Mycobacterium ulcerans
Authors: Käser Michael , Hauser Julia , Pluschke Gerd 
Published: September 2009

ABSTRACT

The genomic fine-typing of strains of
Mycobacterium ulcerans
, the causative agent of the emerging human disease Buruli ulcer, is difficult due to the clonal population structure of geographical lineages. Although large sequence polymorphisms (LSPs) resulted in the clustering of patient isolates originating from across the globe, differentiation of strains within continents using conventional typing methods is very limited. In this study, we analyzed
M. ulcerans
LSP haplotype-specific insertion sequence elements among 83
M. ulcerans
strains and identified single nucleotide polymorphisms (SNPs) that differentiate between regional strains. This is the first genetic discrimination based on SNPs of
M. ulcerans
strains from African countries where Buruli ulcer is endemic, resulting in the highest geographic resolution of genotyping so far. The findings support the concept of genome-wide SNP analyses as tools to study the epidemiology and evolution of
M. ulcerans
at a local level.
Role of Deletion Located between the Intermediate and Middle Regions of the
Helicobacter pylori vacA
Gene in Cases of Gastroduodenal Diseases
Authors: Ogiwara Hiroaki , Sugimoto Mitsushige , Ohno Tomoyuki , Vilaichone Ratha-Korn , Mahachai Varocha , Graham David Y. , Yamaoka Yoshio 
Published: September 2009

ABSTRACT

The vacuolating cytotoxin gene of
Helicobacter pylori
,
vacA
, induces cytoplasmic vacuolation in gastric epithelial cells. Recently, the
vacA
intermediate (i) region, which is located between the signal (s) and middle (m) regions, was identified as a third polymorphic determinant of
vacA
activity. In
vacA
, there are approximately 81-bp deletions between the
vacA
i and m regions (denoted the d region). The aim was to clarify the roles of the
vacA
d region in relation to
H. pylori
-related diseases and histopathological gastric mucosal changes. We assessed the
vacA
signal s-, m-, i-, and d-region genotypes and
cagA
status in
H. pylori
isolates recovered from Western countries (
n
= 266) and East Asian countries (
n
= 244) by PCR. In East Asian countries, there were no relationships between the
vacA
genotypes and the clinical outcomes and histopathological changes. In Western countries, strains with the
vacA
s1, m1, i1, or d1 (no deletion) genotype significantly increased the risk for the development of gastric cancer compared with the risk from strains with the s2, m2, i2, or d2 genotype (adjusted odd ratios, 3.17 [95% confidence interval {CI}, 1.07 to 9.45] for s1, 10.65 [95% CI, 3.36 to 31.35] for m1, 8.57 [95% CI, 2.85 to 25.81] for i1, and 8.04 [95% CI, 2.67 to 24.16] for d1). The highly virulent
vacA
genotypes significantly enhanced neutrophil infiltration and gastric atrophy in univariant analysis, whereas only the
vacA
d-region genotype was significantly associated with neutrophil infiltration and gastric atrophy in both the antrum and the corpus by multiple linear regression analysis. The presence of the
vacA
d1 genotype in
H. pylori
strains could be an improved predictor of histological inflammation and the potential for atrophy compared with the presence of the
vacA
s-, m-, and i-region genotypes in Western countries.
Design and Validation of Real-Time Reverse Transcription-PCR Assays for Detection of Pandemic (H1N1) 2009 Virus
Authors: Pabbaraju Kanti , Wong Sallene , Wong Anita A. , Appleyard Greg D. , Chui Linda , Pang Xiao-Li , Yanow Stephanie K. , Fonseca Kevin , Lee Bonita E. , Fox Julie D. , Preiksaitis Jutta K. 
Published: September 2009

ABSTRACT

Tracking novel influenza viruses which have the potential to cause pandemics, such as the pandemic (H1N1) 2009 virus, is a public health priority. Pandemic (H1N1) 2009 virus was first identified in Mexico in April 2009 and spread worldwide over a short period of time. Well-validated diagnostic tools that are rapid, sensitive, and specific for the detection and tracking of this virus are needed. Three real-time reverse transcription PCR (RT-PCR) assays for the amplification and detection of pandemic (H1N1) 2009 virus were developed, and their performance characteristics were compared with those of other published diagnostic assays. Thirty-nine samples confirmed to be positive for pandemic (H1N1) 2009 virus from Alberta, Canada, and six additional samples that were positive for influenza A virus but that were not typeable by using published seasonal influenza H1/H3 virus assays were available for this validation. Amplification and direct sequencing of the products was considered the “gold standard” for case identification. The new assays were sensitive and able to reproducibly detect virus in a 10
−6
dilution of 4 × 10
6
50% tissue culture infective doses/ml when 5 μl was used as the template. They showed 100% specificity and did not cross-react with other respiratory viruses or seasonal influenza A virus subtypes. The coefficient of variation in crossing cycle threshold values for the detection of different template concentrations of pandemic (H1N1) 2009 virus was ≤3.13%, showing good reproducibility. The assays had a wide dynamic range for the detection of pandemic (H1N1) 2009 virus and utilized testing platforms appropriate for high diagnostic throughput with rapid turnaround times. We developed and validated these real-time PCR procedures with the goal that they will be useful for diagnosis and surveillance of pandemic (H1N1) 2009 virus. These findings will contribute to the informed management of this novel virus.
Use of Boronic Acid Disk Tests To Detect Extended- Spectrum β-Lactamases in Clinical Isolates of KPC Carbapenemase-Possessing
Enterobacteriaceae
Authors: Tsakris Athanassios , Poulou Aggeliki , Themeli-Digalaki Katerina , Voulgari Evangelia , Pittaras Theodore , Sofianou Danai , Pournaras Spyros , Petropoulou Dimitra 
Published: September 2009

ABSTRACT

We evaluated boronic acid (BA)-based methods for their ability to detect extended-spectrum β-lactamases (ESBLs) among clinical isolates of KPC-producing members of the
Enterobacteriaceae
family. A total of 155 isolates of
Klebsiella pneumoniae
(
n
= 141),
Escherichia coli
(
n
= 6),
Enterobacter aerogenes
(
n
= 6), and
Klebsiella oxytoca
(
n
= 2) genotypically confirmed to be KPC producers were analyzed. As many as 118 isolates harbored ESBLs (103 harbored SHV-type ESBLs, 13 harbored CTX-M-type ESBLs, and 2 harbored both SHV- and CTX-M-type ESBLs); the remaining 37 isolates were genotypically negative for ESBL production. The CLSI ESBL confirmatory test was positive for 79 of the 118 ESBL producers (sensitivity, 66.9%), while all 37 non-ESBL producers were negative (specificity, 100%). When a ≥5-mm increase in the zone diameter of either the cefotaxime (CTX)-clavulanate (CA) or the ceftazidime (CAZ)-CA disks containing BA compared with the zone diameter of the CTX or CAZ disks containing BA was considered to be a positive result for ESBL production, the method detected all 118 ESBL producers (sensitivity, 100%) and showed no false-positive results for non-ESBL producers (specificity, 100%). Double-disk synergy tests, in which disks of CTX, CAZ, aztreonam, or cefepime in combination with BA were placed at distances of 20, 25, and 30 mm (center to center) from a disk containing amoxicillin (amoxicilline)-clavulanate-BA, were able to detect 116 (98.3%), 101 (85.6%), and 28 (23.7%) of the ESBL-positive isolates, respectively; no false-positive results for non-ESBL-producing isolates were detected. Our results demonstrate that the modified CLSI ESBL confirmatory test with antibiotic disks containing BA is the most accurate phenotypic method for the detection of ESBLs in
Enterobacteriaceae
producing KPC carbapenemases.
FAT10: a Novel Mediator of Vpr-Induced Apoptosis in Human Immunodeficiency Virus-Associated Nephropathy
Authors: Snyder Alexandra , Alsauskas Zygimantas , Gong Pengfei , Rosenstiel Paul E. , Klotman Mary E. , Klotman Paul E. , Ross Michael J. 
Published: September 2009

ABSTRACT
Human immunodeficiency virus (HIV)-associated nephropathy is a significant cause of morbidity and mortality in HIV-infected persons. Vpr-induced cell cycle dysregulation and apoptosis of renal tubular epithelial cells are important components of the pathogenesis of HIV-associated nephropathy (HIVAN). FAT10 is a ubiquitin-like protein that is upregulated in renal tubular epithelial cells in HIVAN. In these studies, we report that Vpr induces increased expression of FAT10 in tubular cells and that inhibition of FAT10 expression prevents Vpr-induced apoptosis in human and murine tubular cells. Moreover, we found that Vpr interacts with FAT10 and that these proteins colocalize at mitochondria. These studies establish FAT10 as a novel mediator of Vpr-induced cell death.
Induction of Therapeutic Antibodies by Vaccination against External Loops of Tumor-Associated Viral Latent Membrane Protein
Authors: Delbende Catherine , Verwaerde Claudie , Mougel Alexandra , Tranchand Bunel Denis 
Published: September 2009

ABSTRACT
Some human herpesviruses (HHV) are etiological contributors to a wide range of malignant diseases. These HHV express latent membrane proteins (LMPs), which are type III membrane proteins consistently exposed at the cell surface in these malignancies. These LMPs have relatively large cytoplasmic domains but only short extracellular loops connecting transmembrane segments that are accessible at the surface of infected cells, but they do not elicit antibodies in the course of natural infection and tumorigenesis. We report here that conformational peptides mimicking two adjacent loops of the Epstein-Barr virus (EBV) LMP1 (2LS peptides) induce high-affinity antibodies with remarkable antitumor activities in mice. In active immunization experiments, LMP1-targeting 2LS vaccine conferred tumor protection in BALB/c mice. Moreover, this tumor protection is dependent upon a humoral anti-2LS immune response as demonstrated in DO11.10 (TCR-OVA) mice challenged with LMP1-expressing tumor and in SCID mice xenografted with human EBV-positive lymphoma cells. These data provide a proof of concept for 2LS immunization against short external loops of viral LMPs. This approach might possibly be extended to other infectious agents expressing type III membrane proteins.
The Heptad Repeat 2 Domain Is a Major Determinant for Enhanced Human Immunodeficiency Virus Type 1 (HIV-1) Fusion and Pathogenicity of a Highly Pathogenic HIV-1 Env
Authors: Sivaraman Vijay , Zhang Liguo , Meissner Eric G. , Jeffrey Jerry L. , Su Lishan 
Published: September 2009

ABSTRACT

Human immunodeficiency virus type 1 (HIV-1)-mediated depletion of CD4
+
lymphocytes in an infected individual is the hallmark of progression to AIDS. However, the mechanism for this depletion remains unclear. To identify mechanisms of HIV-1-mediated CD4 T-cell death, two similar viral isolates obtained from a rapid progressor patient with significantly different pathogenic phenotypes were studied. One isolate (R3A) demonstrates enhanced pathogenesis in both in vivo models and relevant ex vivo lymphoid organ model systems compared to another isolate, R3B. The pathogenic determinants were previously mapped to the V5-gp41 envelope region, correlating functionally with enhanced fusion activity and elevated CXCR4 binding affinity. To further elucidate specific differences between R3A and R3B within the V5-gp41 domains that enhance CD4 depletion, R3A-R3B chimeras to study the V5-gp41 region were developed. Our data demonstrate that six residues in the ectodomain of R3A provide the major determinant for both enhanced Env-cell fusion and pathogenicity. Furthermore, three amino acid differences in the heptad repeat 2 (HR-2) domain of R3A determined its fusion activity and significantly elevated its pathogenic activity. The chimeric viruses with enhanced fusion activity, but not elevated CXCR4 affinity, correlated with high pathogenicity in the thymus organ. We conclude that the functional domain of a highly pathogenic HIV-1 Env is determined by mutations in the HR-2 region that contribute to enhanced fusion and CD4 T-cell depletion.
Loss of the Brm-Type SWI/SNF Chromatin Remodeling Complex Is a Strong Barrier to the Tat-Independent Transcriptional Elongation of Human Immunodeficiency Virus Type 1 Transcripts
Authors: Mizutani Taketoshi , Ishizaka Aya , Tomizawa Mariko , Okazaki Takuya , Yamamichi Nobutake , Kawana-Tachikawa Ai , Iwamoto Aikichi , Iba Hideo 
Published: September 2009

ABSTRACT

To elucidate the epigenetic regulation of Tat-independent human immunodeficiency virus (HIV) transcription following proviral integration, we constructed an HIV type 1 (HIV-1)-based replication-defective viral vector that expresses a reporter green fluorescent protein (GFP) product from its intact long terminal repeat (LTR). We transduced this construct into human tumor cell lines that were either deficient in or competent for the Brm-type SWI/SNF complex. One day after transduction, single cells that expressed GFP were sorted, and the GFP expression profiles originating from each of these clones were analyzed. Unlike clones of the SWI/SNF-competent cell line, which exhibited clear unimodal expression patterns in all cases, many clones originating from Brm-deficient cell lines either showed a broad-range distribution of GFP expression or were fully silenced. The resorting of GFP-negative populations of these isolated clones showed that GFP silencing is either reversible or irreversible depending upon the proviral integration sites. We further observed that even in these silenced clones, proviral gene transcription initiates to accumulate short transcripts of around 60 bases in length, but no elongation occurs. We found that this termination is caused by tightly closed nucleosome-1 (nuc-1) at the 5′ LTR. Also, nuc-1 is remodeled by exogenous Brm in some integrants. From these results, we propose that Brm is required for the occasional transcriptional elongation of the HIV-1 provirus in the absence of Tat. Since the Brm-type SWI/SNF complex is expressed at marginal levels in resting CD4
+
T cells and is drastically induced upon CD4
+
T-cell activation, we speculate that it plays crucial roles in the early Tat-independent phase of HIV transcription in affected patients.
Receptor Binding and Low pH Coactivate Oncogenic Retrovirus Envelope-Mediated Fusion
Authors: Côté Marceline , Zheng Yi-Min , Liu Shan-Lu 
Published: September 2009

ABSTRACT
Fusion of enveloped viruses with host cells is triggered by either receptor binding or low pH but rarely requires both except for avian sarcoma leukosis virus (ASLV). We recently reported that membrane fusion mediated by an oncogenic Jaagsiekte sheep retrovirus (JSRV) envelope (Env) requires an acidic pH, yet receptor overexpression is required for this process to occur. Here we show that a soluble form of the JSRV receptor, sHyal2, promoted JSRV Env-mediated fusion at a low pH in normally fusion-negative cells and that this effect was blocked by a synthetic peptide analogous to the C-terminal heptad repeat of JSRV Env. In contrast to the receptor of ASLV, sHyal2 induced pronounced shedding of the JSRV surface subunit, as well as unstable conformational rearrangement of its transmembrane (TM) subunit, yet full activation of JSRV Env fusogenicity, associated with strong TM oligomerization, required both sHyal2 and low pH. Consistently, sHyal2 enabled transduction of nonpermissive cells by JSRV Env pseudovirions, with low efficiency, but substantially blocked viral entry into permissive cells at both binding and postbinding steps, indicating that sHyal2 prematurely activates JSRV Env-mediated fusion. Altogether, our study supports a model that receptor priming promotes fusion activation of JSRV Env at a low pH, and that the underlying mechanism is likely to be different from that of ASLV. Thus, JSRV may provide a useful alternate model for the better understanding of virus fusion and cell entry.
A Highly Attenuated Measles Virus Vaccine Strain Encodes a Fully Functional C Protein
Authors: Nakatsu Yuichiro , Takeda Makoto , Iwasaki Masaharu , Yanagi Yusuke 
Published: September 2009

ABSTRACT
The P, V, and C proteins of measles virus are encoded in overlapping reading frames of the P gene, which makes it difficult to analyze the functions of the individual proteins in the context of virus infection. We established a system to analyze the C protein independently from the P and V proteins by placing its gene in an additional transcription unit between the H and L genes. Analyses with this system indicated that a highly attenuated Edmonston lineage vaccine strain encodes a fully functional C protein, and the P and/or V protein is involved in the attenuated phenotype.
Mutations in the C-Terminal Loop of the Nucleocapsid Protein Affect Vesicular Stomatitis Virus RNA Replication and Transcription Differentially
Authors: Harouaka Djamila , Wertz Gail W. 
Published: September 2009

ABSTRACT
The 2.9-Å structure of the vesicular stomatitis virus nucleocapsid (N) protein bound to RNA shows the RNA to be tightly sequestered between the two lobes of the N protein. Domain movement of the lobes of the N protein has been postulated to facilitate polymerase access to the RNA template. We investigated the roles of individual amino acid residues in the C-terminal loop, involved in long-range interactions between N protein monomers, in forming functional ribonucleoprotein (RNP) templates. The effects of specific N protein mutations on its expression, interaction with the phosphoprotein, and formation of RNP templates that supported viral RNA replication and transcription were examined. Mutations introduced into the C-terminal loop, predicted to break contact with other residues in the loop, caused up to 10-fold increases in RNA replication without an equivalent stimulation of transcription. Mutation F348A, predicted to break contact between the C-terminal loop and the N-terminal arm, formed templates that supported wild-type levels of RNA replication but almost no transcription. These data show that mutations in the C-terminal loop of the N protein can disparately affect RNA replication and transcription, indicating that the N protein plays a role in modulating RNP template function beyond its structural role in RNA encapsidation.
Novel Role for Interleukin-2 Receptor-Jak Signaling in Retrovirus Transmission
Authors: Taylor J. M. , Brown M. , Nejmeddine M. , Kim K. J. , Ratner L. , Lairmore M. , Nicot C. 
Published: September 2009

ABSTRACTHuman T-lymphotropic virus type 1 (HTLV-1) is the etiological agent of adult T-cell leukemia/lymphoma, and it encodes a number of nonstructural proteins that are involved in virus replication and immune evasion. The viral protein p12 previously has been characterized to interfere with major histocompatibility complex class, ICAM-1, and ICAM-2 expression, and it activates STAT5. Using a previously established T-cell line immortalized with an HTLV-1 molecular clone deleted for p12, we assessed the role of p12 in regulating cellular growth and virus transmission. These cells were complemented for p12 expression by the transduction of a lentivirus vector expressing p12. We report that p12 conferred a selective growth advantage in vitro and increased the colony formation of human T cells in soft-agar assays. Consistently with previous studies, p12−and p12+cell lines produced similar amounts of virus particles released into the supernatant of cultured cells, although we found that p12 expression greatly enhanced virus transmission. Moreover, we found that interleukin-2 (IL-2) stimulation also increased HTLV-1 transmission whether p12 was expressed or not, and inversely, that the inhibition of Jak signaling significantly reduced HTLV-1 transmission. Intriguingly, IL-2/Jak signaling was not associated with changes in viral gene expression, viral RNA encapsidation, the maturation of the virus particle, cell-cell adherence, or Gag polarization and virological synapse formation. We do demonstrate, however, that IL-2 stimulation and p12 expression significantly increased the rate of syncytium formation, revealing a novel role for IL-2 signaling and Jak activation in HTLV-1 virus transmission.
Defective Human Immunodeficiency Virus-Specific CD8
+
T-Cell Polyfunctionality, Proliferation, and Cytotoxicity Are Not Restored by Antiretroviral Therapy
Authors: Migueles Stephen A. , Weeks Kristin A. , Nou Eric , Berkley Amy M. , Rood Julia E. , Osborne Christine M. , Hallahan Claire W. , Cogliano-Shutta Nancy A. , Metcalf Julia A. , McLaughlin Mary , Kwan Richard , Mican JoAnn M. , Davey Richard T. , Connors Mark 
Published: September 2009

ABSTRACT

Identifying the functions of human immunodeficiency virus (HIV)-specific CD8
+
T cells that are not merely modulated by the level of virus but clearly distinguish patients with immune control from those without such control is of paramount importance. Features of the HIV-specific CD8
+
T-cell response in antiretroviral-treated patients (designated Rx <50) and untreated patients (long-term nonprogressors [LTNP]) matched for very low HIV RNA levels were comprehensively examined. The proliferative capacity of HIV-specific CD8
+
T cells was not restored in Rx <50 to the level observed in LTNP, even though HIV-specific CD4
+
T-cell proliferation in the two patient groups was comparable. This diminished HIV-specific CD8
+
T-cell proliferation in Rx <50 was primarily due to a smaller fraction of antigen-specific cells recruited to divide and not to the numbers of divisions that proliferating cells had undergone. Exogenous interleukin-2 (IL-2) induced proliferating cells to divide further but did not rescue the majority of antigen-specific cells with defective proliferation. In addition, differences in HIV-specific CD8
+
T-cell proliferation could not be attributed to differences in cellular subsets bearing a memory phenotype, IL-2 production, or PD-1 expression. Although polyfunctionality of HIV-specific CD8
+
T cells in Rx <50 was not restored to the levels observed in LTNP despite prolonged suppression of HIV RNA levels, per-cell cytotoxic capacity was the functional feature that most clearly distinguished the cells of LTNP from those of Rx <50. Taken together, these data suggest that there are selective qualitative abnormalities within the HIV-specific CD8
+
T-cell compartment that persist under conditions of low levels of antigen.
Cryo-Electron Microscopy Structure of an Adenovirus-Integrin Complex Indicates Conformational Changes in both Penton Base and Integrin
Authors: Lindert Steffen , Silvestry Mariena , Mullen Tina-Marie , Nemerow Glen R. , Stewart Phoebe L. 
Published: September 2009

ABSTRACT

A structure of adenovirus type 12 (HAdV12) complexed with a soluble form of integrin αvβ5 was determined by cryo-electron microscopy (cryoEM) image reconstruction. Subnanometer resolution (8 Å) was achieved for the icosahedral capsid with moderate resolution (27 Å) for integrin density above each penton base. Modeling with αvβ3 and α
IIb
β3 crystal structures indicates that a maximum of four integrins fit over the pentameric penton base. The close spacing (∼60 Å) of the RGD protrusions on penton base precludes integrin binding in the same orientation to neighboring RGD sites. Flexible penton-base RGD loops and incoherent averaging of bound integrin molecules explain the moderate resolution observed for the integrin density. A model with four integrins bound to a penton base suggests that integrin might extend one RGD-loop in the direction that could induce a conformational change in the penton base involving clockwise untwisting of the pentamer. A global conformational change in penton base could be one step on the way to the release of Ad vertex proteins during cell entry. Comparison of the cryoEM structure with bent and extended models for the integrin ectodomain reveals that integrin adopts an extended conformation when bound to the Ad penton base, a multivalent viral ligand. These findings shed further light on the structural basis of integrin binding to biologically relevant ligands, as well as on the molecular events leading to HAdV cell entry.