bluuebunny/crossref_metadata_2025 huggingface dataset:
Lack of Insertional-Deletional Polymorphism in a Collection of
Mycobacterium ulcerans
Isolates from Ghanaian Buruli Ulcer Patients
Authors: Käser Michael , Gutmann Oliver , Hauser Julia , Stinear Tim , Cole Stewart , Yeboah-Manu Dorothy , Dernick Gregor , Certa Ulrich , Pluschke Gerd
Published: September 2009

Mycobacterium ulcerans
causes the devastating infectious skin disease Buruli ulcer and has a monomorphic population structure. The resolution of conventional genetic fingerprinting methods is therefore not sufficient for microepidemiological studies aiming to characterize transmission pathways. In a previous comparative genomic hybridization analysis with a microarray covering part of the
M. ulcerans
genome, we have found extensive insertional-deletional sequence polymorphisms among
M. ulcerans
isolates of diverse geographic origins that allowed us to distinguish between strains coming from different continents. Since large numbers of insertion sequences are spread over the genome of African
M. ulcerans
strains, we reasoned that these may drive large sequence polymorphisms in otherwise clonal local mycobacterial populations. In this study, we used a printed DNA microarray covering the whole genome of the Ghanaian
M. ulcerans
reference strain Agy99 for comparative genomic hybridization. The assay identified multiple regions of difference when DNA of a Japanese
M. ulcerans
strain was analyzed. In contrast, not a single insertional-deletional genomic variation was found within a panel of disease isolates coming from an area of Ghana where Buruli ulcer is endemic. These results indicate that, despite the expectations deduced from other mycobacterial pathogens, only analyses of single nucleotide polymorphisms will have the potential to differentiate local populations of
M. ulcerans
.
Single Nucleotide Polymorphisms on the Road to Strain Differentiation in
Mycobacterium ulcerans
Authors: Käser Michael , Hauser Julia , Pluschke Gerd
Published: September 2009

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

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

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

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

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

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

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

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

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

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

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

Human 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

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

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.
Viral Adaptation to an Antiviral Protein Enhances the Fitness Level to Above That of the Uninhibited Wild Type
Authors: Cherwa James E. , Sanchez-Soria Pablo ,   Members of the University of Arizona Virology Laboratory Course 2007, Wichman Holly A. , Fane Bentley A.
Published: September 2009

Viruses often evolve resistance to antiviral agents. While resistant strains are able to replicate in the presence of the agent, they generally exhibit lower fitness than the wild-type strain in the absence of the inhibitor. In some cases, resistant strains become dependent on the antiviral agent. However, the agent rarely, if ever, elevates dependent strain fitness above the uninhibited wild-type level. This would require an adaptive mechanism to convert the antiviral agent into a beneficial growth factor. Using an inhibitory scaffolding protein that specifically blocks φX174 capsid assembly, we demonstrate that such mechanisms are possible. To obtain the quintuple-mutant resistant strain, the wild-type virus was propagated for approximately 150 viral life cycles in the presence of increasing concentrations of the inhibitory protein. The expression of the inhibitory protein elevated the strain's fitness significantly above the uninhibited wild-type level. Thus, selecting for resistance coselected for dependency, which was characterized and found to operate on the level of capsid nucleation. To the best of our knowledge, this is the first report of a virus evolving a mechanism to productively utilize an antiviral agent to stimulate its fitness above the uninhibited wild-type level. The results of this study may be predictive of the types of resistant phenotypes that could be selected by antiviral agents that specifically target capsid assembly.
Infection with “Escaped” Virus Variants Impairs Control of Simian Immunodeficiency Virus SIVmac239 Replication inMamu-B*08-Positive Macaques
Authors: Valentine Laura E. , Loffredo John T. , Bean Alex T. , León Enrique J. , MacNair Caitlin E. , Beal Dominic R. , Piaskowski Shari M. , Klimentidis Yann C. , Lank Simon M. , Wiseman Roger W. , Weinfurter Jason T. , May Gemma E. , Rakasz Eva G. , Wilson Nancy A. , Friedrich Thomas C. , O'Connor David H. , Allison David B. , Watkins David I.
Published: September 2009

An understanding of the mechanism(s) by which some individuals spontaneously control human immunodeficiency virus (HIV)/simian immunodeficiency virus replication may aid vaccine design. Approximately 50% of Indian rhesus macaques that express the major histocompatibility complex (MHC) class I alleleMamu-B*08become elite controllers after infection with simian immunodeficiency virus SIVmac239. Mamu-B*08 has a binding motif that is very similar to that of HLA-B27, a human MHC class I allele associated with the elite control of HIV, suggesting that SIVmac239-infectedMamu-B*08-positive (Mamu-B*08+) animals may be a good model for the elite control of HIV. The association with MHC class I alleles implicates CD8+T cells and/or natural killer cells in the control of viral replication. We therefore introduced point mutations into eight Mamu-B*08-restricted CD8+T-cell epitopes to investigate the contribution of epitope-specific CD8+T-cell responses to the development of the control of viral replication. TenMamu-B*08+macaques were infected with this mutant virus, 8X-SIVmac239. We compared immune responses and viral loads of these animals to those of wild-type SIVmac239-infectedMamu-B*08+macaques. The five most immunodominant Mamu-B*08-restricted CD8+T-cell responses were barely detectable in 8X-SIVmac239-infected animals. By 48 weeks postinfection, 2 of 10 8X-SIVmac239-infectedMamu-B*08+animals controlled viral replication to <20,000 viral RNA (vRNA) copy equivalents (eq)/ml plasma, while 10 of 15 wild-type-infectedMamu-B*08+animals had viral loads of <20,000 vRNA copy eq/ml (P= 0.04). Our results suggest that these epitope-specific CD8+T-cell responses may play a role in establishing the control of viral replication inMamu-B*08+macaques.
Epitope Specificity and Relative Clonal Abundance Do Not Affect CD8 Differentiation Patterns during Lymphocytic Choriomeningitis Virus Infection
Authors: Munitic Ivana , Decaluwe Hélène , Evaristo César , Lemos Sara , Wlodarczyk Myriam , Worth Andrew , Le Bon Agnès , Selin Liisa K. , Rivière Yves , Di Santo James P. , Borrow Persephone , Rocha Benedita
Published: September 2009

To evaluate the impact of immunodominance on CD8 T-cell properties, we compared the functional properties of dominant and subdominant populations in the response to lymphocytic choriomeningitis virus (LCMV). To improve functional discrimination, in addition to the usual tests of phenotype and function, we used a sensitive technique that allows the screening of all CD8 effector genes simultaneously in single cells. Surprisingly, these methods failed to reveal a major impact of clonal dominance in CD8 properties throughout the response. Aiming to increase clonal dominance, we examined high-frequency transferred P14 T-cell receptor transgenic (TCR Tg) cells. Under these conditions LCMV is cleared faster, and accordingly we found an accelerated response. However, when Tg and endogenous cells were studied in the same mice, where they should be subjected to the same antigen load, they showed overlapping properties, and the presence of P14 cells did not modify endogenous responses to other LCMV epitopes or a perturbed immunodominance hierarchy in the memory phase. Using allotype-labeled Tg cells, we found that during acute infection up to 80% downregulated their TCR and were undetectable by tetramer binding, and that tetramer-negative and tetramer-positive cells had very different features. Since Tg cells are not available to evaluate immune responses in humans and, in many cases, are not available from the mouse, the tetramer-based evaluation of early immune responses in most situations of high viremia may be incomplete and biased.
The AKV Murine Leukemia Virus Is Restricted and Hypermutated by Mouse APOBEC3
Authors: Langlois Marc-André , Kemmerich Kristin , Rada Cristina , Neuberger Michael S.
Published: September 2009

APOBEC3 proteins are potent restriction factors against retroviral infection in primates. This restriction is accompanied by hypermutations in the retroviral genome that are attributable to the cytidine deaminase activity of the APOBEC3 proteins. Studies of nucleotide sequence diversity among endogenous gammaretroviruses suggest that the evolution of endogenous retroelements could have been shaped by the mutagenic cytidine deaminase activity of APOBEC3. In mice, however, APOBEC3 appears to restrict exogenous murine retroviruses in the absence of detectable levels of deamination. AKV is an endogenous retrovirus that is involved in causing a high incidence of thymic lymphoma in AKR mice. A comparative analysis of several mouse strains revealed a relatively low level of APOBEC3 expression in AKR mice. Here we show that endogenous mouse APOBEC3 restricts AKV infection and that this restriction likely reflects polymorphisms affecting APOBEC3 abundance rather than differences in the APOBEC3 isoforms expressed. We also observe that restriction of AKV by APOBEC3 is accompanied by G→A hypermutations in the viral genome. Our findings demonstrate that APOBEC3 acts as a restriction factor in rodents affecting the strain tropism of AKV, and they provide good support for the proposal that APOBEC3-mediated hypermutation contributed to the evolution of endogenous rodent retroviral genomes.
General and Target-Specific RNA Binding Properties of Epstein-Barr Virus SM Posttranscriptional Regulatory Protein
Authors: Han Zhao , Verma Dinesh , Hilscher Chelsey , Dittmer Dirk P. , Swaminathan Sankar
Published: September 2009

Epstein-Barr virus (EBV) SM protein is an essential nuclear shuttling protein expressed by EBV early during the lytic phase of replication. SM acts to increase EBV lytic gene expression by binding EBV mRNAs and enhancing accumulation of the majority of EBV lytic cycle mRNAs. SM increases target mRNA stability and nuclear export, in addition to modulating RNA splicing. SM and its homologs in other herpesvirus have been hypothesized to function in part by binding viral RNAs and recruiting cellular export factors. Although activation of gene expression by SM is gene specific, it is unknown whether SM binds to mRNA in a specific manner or whether its RNA binding is target independent. SM-mRNA complexes were isolated from EBV-infected B-lymphocyte cell lines induced to permit lytic EBV replication, and a quantitative measurement of mRNAs corresponding to all known EBV open reading frames was performed by real-time quantitative reverse transcription-PCR. The results showed that although SM has broad RNA binding properties, there is a clear hierarchy of affinities among EBV mRNAs with respect to SM complex formation. In vitro binding assays with two of the most highly SM-associated transcripts suggested that SM binds preferentially to specific sequences or structures present in noncoding regions of some EBV mRNAs. Furthermore, the presence of these sequences conferred responsiveness to SM. These data are consistent with a mechanism of action similar to that of hnRNPs, which exert sequence-specific effects on gene expression despite having multiple degenerate consensus binding sites common to a large number of RNAs.
Peripheral Immunization Blocks Lethal Actions of Vesicular Stomatitis Virus within the Brain
Authors: Ozduman Koray , Wollmann Guido , Ahmadi Sebastian A. , van den Pol Anthony N.
Published: September 2009

Vesicular stomatitis virus (VSV) is the prototype virus for 75 or more negative-strand RNA viruses in the rhabdovirus family. Some of these viruses, including VSV, can cause neurological impairment or death upon brain infection. VSV has shown promise in the prevention and treatment of disease as a vaccine vector and an oncolytic virus, but infection of the brain remains a concern. Three VSV variants, the wild-type-related VSV-G/GFP and two attenuated viruses, VSV-CT1 and VSV-CT9-M51, were compared for neuroinvasiveness and neuromorbidity. In nonimmunized mice, direct VSV-G/GFP injection into the brain invariably resulted in lethal encephalitis; in contrast, partial survival was seen after direct injection of the attenuated VSV strains. In addition, both attenuated VSV strains showed significantly reduced neuroinvasiveness after intranasal inoculation of young postnatal day 16 mice. Of the three tested variants, VSV-CT9-M51 generated the lowest degree of neuropathology. Despite its attenuated state, peripheral inoculations of VSV-CT9-M51 targeted and killed human glioblastoma implanted into the mouse brain. Importantly, we show here that intranasal or intramuscular immunization prevents the lethal effects of subsequent VSV-G/GFP, VSV-CT1, and VSV-CT9-M51 injections into the brain. These results indicate that attenuated recombinant viruses show reduced neurovirulence and that peripheral immunization blocks the lethal actions of all VSVs tested.
Adsorption of tetramethylthiourea in concentrated NaClO4 solutions
Authors: Sieńko Dorota , Gugała-Fekner Dorota , Nieszporek Jolanta , Fekner Zygmunt , Saba Jadwiga
Published: September 2009

Tetramethylthiourea electrosorption behaviour on the mercury electrode in 2, 3 and 4 mol l–1 NaClO4 was determined by means of double-layer differential capacity measurements. The relative surface excess Γ′ of the adsorbate calculated from the surface pressures depended on the NaClO4 concentration. A clear influence of NaClO4 concentration appeared in the changes of interaction parameter A obtained from the Flory–Huggins isotherm and in the permittivity parameter of the inner layer.
MEASUREMENT ACCURACY OF MODE-LOCKED LASER
Authors: WEN QIAO , SUN LIQUN , ZHANG ENYAO , TIAN QIAN
Published: September 2009

Using a simple signal processing approach and taking into account the finite linewidth of each longitudinal mode in a mode-locked laser, we investigate the measurement accuracy of the mode-locked laser and analyze the mode-locked pulse train coherence characteristic. Results show that the measurement accuracy in the interference between two mode-locked pulses with the same repetition rate depends on mode-locking stability rather than pulse duration. Mode-locking stability can be achieved by reducing the longitudinal mode linewidth. The mode-locked pulse amplitude is modulated by a modulation envelope function, rather than illimitably continuous pulses because of the finite linewidth of the longitudinal modes. A mode-locked laser emits numerous pulse modulation envelopes one by one and each pulse modulation envelope is described by the same function. Powerful ways are proposed to decrease the linewidth and improve mode-locking stability and measurement accuracy.
GENERALIZED SYNCHRONIZATION OF DIFFERENT DIMENSIONAL CHAOTIC SYSTEMS BASED ON PARAMETER IDENTIFICATION
Authors: YU YONGGUANG , LI HAN-XIONG , YU JUNZHI
Published: September 2009

This paper investigates the generalized synchronization issue for two different dimensional chaotic systems with unknown parameters. Based on Lyapunov stability theory and adaptive control theory, an adaptive controller is derived to achieve the generalized synchronization whether the dimension of drive system is greater than the one of the response system or not. Meanwhile, corresponding parameter updating laws can be obtained so as to exactly identify uncertain parameters. This technique has been successfully applied to two examples, the generalized synchronization of hyperchaotic Rössler system and chaotic Lorenz system, chaotic Chen system and generalized Lorenz system. Numerical simulations are finally shown to illustrate the effectiveness of the proposed approach.
NONLINEAR VIBRATION CHARACTERISTICS OF FLUID-FILLED DOUBLE-WALLED CARBON NANOTUBES
Authors: YAN Y. , WANG W. Q. , ZHANG L. X.
Published: September 2009

Nonlinear vibration behaviors of double-walled carbon nanotubes (DWCNTs) with fluid inside the inner tube are investigated based on Donnell's cylindrical shell model and the more refined van der Waals (vdW) interaction formula. The Galerkin method and harmonic balance method are used to study the issue. The results obtained show that the radial vibrational modes of simply supported DWCNTs have twice the dynamical mode transitions as the frequency increases. The transitions correspond to twice the noncoaxial vibrations which play a critical role in electronic and transport properties of CNTs. Moreover, comparisons of the dynamical behaviors of fluid-filled DWCNTs with different wave numbers, radii and aspect ratios demonstrate that the amplitude–frequency curve topological forms are identical. Meanwhile, it is also concluded that the existence of fluid is significant for the value of amplitude ratio corresponding to noncoaxial vibration whereas it does not change the nonlinear vibrating topological pattern of amplitude–frequency curves.
IMPEDANCE SPECTROSCOPIC STUDIES OF BiFeO3-Pb(ZrTi)O3 NANOCOMPOSITES
Authors: CHOUDHARY R. N. P. , BARIK SUBRAT K. , KATIYAR R. S.
Published: September 2009

BiFeO 3- Pb ( ZrTi ) O 3 [i.e., ( Bi 1-x Pb x)( Fe 1-x Zr 0.6x Ti 0.4x) O 3 (x = 0.15, 0.25, 0.40, 0.50)] nanocomposites were synthesized using mechanical activation followed by a solid-state reaction technique. The dielectric parameters (capacitance, dissipation factor D, impedance Z and phase angle Φ) of all the samples were measured in a wide range of frequencies (1 kHz–1 MHz) and temperatures (300–630 K) in air atmosphere using an impedance analyzer with low signal amplitude of 500 mV. Electrical properties of the compounds were studied using a complex impedance spectroscopy (CIS) technique. The frequency dependence of electrical data was analyzed in the framework of conductivity and modulus formalisms. AC conductivity spectrum obeys Jonscher's universal power law.
RECOGNITION OF SOME FINITE SIMPLE GROUPS OF TYPE Dn(q) BY SPECTRUM
Authors: HE HUAIYU , SHI WUJIE
Published: September 2009

The spectrum ω(G) of a finite group G is the set of element orders of G. Let L be finite simple group Dn(q) with disconnected Gruenberg–Kegel graph. First, we establish that L is quasi-recognizable by spectrum except D4(2) and D4(3), i.e., every finite group G with ω(G) = ω(L) has a unique nonabelian composition factor that is isomorphic to L. Second, for some special series of integers n, we prove that L is recognizable by spectrum, i.e., every finite group G with ω(G) = ω(L) is isomorphic to L.
VARIETIES OF DIFFERENTIAL MODES EMBEDDABLE INTO SEMIMODULES
Authors: PILITOWSKA A. , ROMANOWSKA A. B. , STANOVSKÝ D.
Published: September 2009

Differential modes provide examples of modes that do not embed as subreducts into semimodules over commutative semirings. The current paper studies differential modes, so-called Szendrei differential modes, which actually do embed into semimodules. These algebras form a variety. The main result states that the lattice of nontrivial subvarieties is dually isomorphic to the (nonmodular) lattice of congruences of the free commutative monoid on two generators. Consequently, all varieties of Szendrei differential modes are finitely based.
Invasion Biology, Ecology, and Management of the Light Brown Apple Moth (Tortricidae)
Authors: Suckling D.M. , Brockerhoff E.G.
Published: September 2009

Epiphyas postvittana (Walker) (Lepidoptera: Tortricidae), the light brown apple moth (LBAM), is an important leafroller pest with an exceptionally wide host range that includes many horticultural crops and other woody and herbaceous plants. LBAM is native to southeastern Australia but has invaded Western Australia, New Zealand, Hawaii, much of England, and in 2007, it was confirmed as established in California. The discovery of this pest in California has led to a major detection and regulatory effort because of concerns about economic and environmental impacts. Its recent discovery in Sweden is also of note. LBAM has often been intercepted on imports of fruit and other plant parts, and it has the potential to become a successful invader in temperate and subtropical regions worldwide. The importance of the insect has prompted development of classical biological control programs together with a wide variety of other management interventions that can be used in integrated pest management or integrated pest eradication.
Retinoic acid-induced nNOS expression depends on a novel PI3K/Akt/DAX1 pathway in human TGW-nu-I neuroblastoma cells
Authors: Nagl Florian , Schönhofer Katrin , Seidler Barbara , Mages Jörg , Allescher Hans-Dieter , Schmid Roland M. , Schneider Günter , Saur Dieter
Published: September 2009

Neuronal nitric oxide synthase (nNOS)-derived nitric oxide (NO) acts as a neurotransmitter and intracellular signaling molecule in the central and peripheral nervous system. NO regulates multiple processes like neuronal development, plasticity, and differentiation and is a mediator of neurotoxicity. The nNOS gene is highly complex with 12 alternative first exons, exon 1a–1l, transcribed from distinct promoters, leading to nNOS variants with different 5′-untranslated regions. Transcriptional control of the nNOS gene is not understood in detail. To investigate regulation of nNOS gene expression by retinoic acid (RA), we used the human neuroblastoma cell line TGW-nu-I as a model system. We show that RA induces nNOS transcription in a protein synthesis-dependent fashion. We identify the phosphatidylinositol 3-kinase (PI3K)/Akt signaling pathway and the atypical orphan nuclear receptor DAX1 (NR0B1) as critical mediators involved in RA-induced nNOS gene transcription. RA treatment increases DAX1 expression via PI3K/Akt signaling. Upregulation of DAX1 expression in turn induces nNOS transcription in response to RA. These results identify nNOS as a target gene of a novel RA/PI3K/Akt/DAX1-dependent pathway in human neuroblastoma cells and stress the functional importance of the transcriptional regulator DAX1 for nNOS gene expression in response to RA treatment.
Impact of Roux-en-Y gastric bypass surgery on rat intestinal glucose transport
Authors: Stearns Adam T. , Balakrishnan Anita , Tavakkolizadeh Ali
Published: September 2009

Roux-en-Y gastric bypass (RYGB) has become the gold-standard bariatric procedure, partly because of the rapid resolution of accompanying diabetes. There is increasing evidence this is mediated by duodenal exclusion. We hypothesize that duodenal exclusion suppresses intestinal Na+/glucose cotransporter SGLT1-mediated glucose transport, improving glucose handling, and aimed to test this in a rodent RYGB model. Sprague-Dawley rats underwent sham procedure or duodenal exclusion by RYGB (10 cm Roux, 16 cm biliopancreatic limbs). Animals were maintained for 3 wk on a Western diet, before harvest at 10 AM, 4 PM, and 10 PM. Sections were taken from each limb for hematoxylin and eosin staining, and morphological assessment was performed. Functional glucose uptake studies, along with Western blotting and quantitative PCR, were performed on Roux limb. Histology showed morphometric changes in Roux and common limbs, with increase in villus height and crypt depth compared with BP and sham jejunum. Despite this, glucose transport was reduced by up to 68% ( P < 0.001) in the Roux limb compared with sham jejunum. Normal diurnal rhythms in glucose uptake were ablated. This occurred at a posttranscriptional level, with little change in message but appearance of different weight species of Sglt1 on Western blotting. We have shown duodenal exclusion significantly influences both intestinal structure and glucose transport function, with glucose absorptive capacity reduced after RYGB. This provides a novel mechanistic explanation for some of the antidiabetic effects of RYGB.