bluuebunny/crossref_metadata_2025 huggingface dataset:
CagA and VacA Polymorphisms Do Not Correlate with Severity of Histopathological Lesions inHelicobacter pylori-Infected Greek Children
Authors: Sgouras Dionyssios N. , Panayotopoulou Effrosini G. , Papadakos Konstantinos , Martinez-Gonzalez Beatriz , Roumbani Aikaterini , Panayiotou Joanna , vanVliet-Constantinidou Cathy , Mentis Andreas F. , Roma-Giannikou Eleftheria
Published: June 2009

The presence of various numbers of EPIYA tyrosine phosphorylation motifs in the CagA protein ofHelicobacter pylorihas been suggested to contribute to pathogenesis in adults. In this prospective study, we characterizedH. pyloriisolates from symptomatic children, with reference to the diversity of functional EPIYA motifs in the CagA protein andvacAisotypes, and assessed the potential correlation with the histopathological manifestations of the infection. We analyzed 105H. pyloriisolates from 98 children and determined the diversity of EPIYA motifs in CagA by amplification and sequencing of the 3′ variable region of thecagAgene as well asvacAisotypes for the signal, middle, and intermediate regions. CagA phosphorylation and levels of secreted IL-8 were determined following in vitro infection of AGS gastric epithelial cells. Histopathological evaluation ofH. pyloricolonization, activity, and severity of the associated gastritis was performed according to the updated Sydney criteria. EPIYA A (GLKN[ST]EPIYAKVNKKK), EPIYA B (Q[V/A]ASPEPIY[A/T]QVAKKVNAKI), and EPIYA C (RS[V/A]SPEPIYATIDDLG) motifs were detected in the ABC (46.6%) and ABCC (17.1%) combinations. No isolates harboring more than two EPIYA C motifs in CagA were found. The presence of isogenic strains with variable numbers of CagA EPIYA C motifs within the same patient was detected in seven cases. Occurrence of increasing numbers of EPIYA C motifs correlated strongly with presence of a high-vacuolation (s1 or s2/i1/m1) phenotype and age. A weak positive correlation was observed between vacuolatingvacAgenotypes and presence of nodular gastritis. However, CagA- and VacA-dependent pathogenicities were not found to contribute to severity of histopathology manifestations inH. pylori-infected children.
Simple, Accurate, Serotype-Specific PCR Assay To Differentiate
Streptococcus pneumoniae
Serotypes 6A, 6B, and 6C
Authors: Jin Ping , Xiao Meng , Kong Fanrong , Oftadeh Shahin , Zhou Fei , Liu Chunyi , Gilbert Gwendolyn L.
Published: June 2009

In this study, we developed a simple, reliable, serotype-specific PCR method to differentiate
Streptococcus pneumoniae
serotypes 6A, 6B, and 6C. It was more efficient and practical than the assays currently being used to identify serotypes 6A, 6B, and 6C. Of 120 selected serogroup 6 isolates from subjects with invasive (
n
= 101) and noninvasive (
n
= 19) pneumococcal disease, most of which were collected after 2003 in New South Wales, 45 had been identified as 6A and 75 had been identified as 6B by the Quellung reaction. PCR analysis confirmed the results for serotype 6B isolates and identified two different subtypes. Fourteen of 45 isolates that had been identified as serotype 6A actually belonged to serotype 6C.
Mycobacterium microti
: More Diverse than Previously Thought
Authors: Smith N. H. , Crawshaw T. , Parry J. , Birtles R. J.
Published: June 2009

Mycobacterium microti
is a member of the
Mycobacterium tuberculosis
complex of bacteria. This species was originally identified as a pathogen of small rodents and shrews and was associated with limited diversity and a much reduced spoligotype pattern. More recently, specific deletions of chromosomal DNA have been shown to define this group of organisms, which can be identified by the absence of chromosomal region RD1
mic
. We describe here the molecular characteristics of 141 strains of the
Mycobacterium tuberculosis
complex isolated in Great Britain over a 14-year period. All strains have characteristic loss of some spoligotype spacers and characteristic alleles at the ETR-E and ETR-F variable-number tandem-repeat (VNTR) loci, and a sample of these strains was deleted for regions RD7, RD9, and RD1
mic
but intact for regions RD4 and RD12. We therefore identified these strains as
M. microti
and show that they have much more diverse spoligotype patterns and VNTR types than previously thought. The most common source of these strains was domestic cats, and we show that the molecular types of
M. microti
are geographically localized in the same way that molecular types of
Mycobacterium bovis
are geographically localized in cattle in the United Kingdom. We describe the pathology of
M. microti
infection in cats and suggest that the feline disease is a spillover from a disease maintained in an unknown wild mammal, probably field voles. The location of the cats with
M. microti
infection suggests that they do not overlap geographically with the strains of
Mycobacterium bovis
in Great Britain.
Evaluation of New Preanalysis Sample Treatment Tools and DNA Isolation Protocols To Improve Bacterial Pathogen Detection in Whole Blood
Authors: Hansen Wendy L. J. , Bruggeman Cathrien A. , Wolffs Petra F. G.
Published: June 2009

Two novel preanalysis sample treatment tools were evaluated in combination with four DNA extraction kits for the selective isolation of bacterial DNA from whole blood. The combination of performing a preanalysis sample treatment and using a larger sample volume increased the detection limit to 50 CFU per ml.
Sputum PCR-Single-Strand Conformational Polymorphism Test for Same-Day Detection of Pyrazinamide Resistance in Tuberculosis Patients
Authors: Sheen Patricia , Méndez Melissa , Gilman Robert H. , Peña Lizeth , Caviedes Luz , Zimic Mirko J. , Zhang Ying , Moore David A. J. , Evans Carlton A.
Published: June 2009

Pyrazinamide is a first-line drug for treating tuberculosis, but pyrazinamide resistance testing is usually too slow to guide initial therapy, so some patients receive inappropriate therapy. We therefore aimed to optimize and evaluate a rapid molecular test for tuberculosis drug resistance to pyrazinamide. Tuberculosis PCR-single-strand conformational polymorphism (PCR-SSCP) was optimized to test for mutations causing pyrazinamide resistance directly from sputum samples and
Mycobacterium tuberculosis
isolates. The reliability of PCR-SSCP tests for sputum samples (
n
= 65) and
Mycobacterium tuberculosis
isolates (
n
= 185) from 147 patients was compared with four tests for pyrazinamide resistance: Bactec-460 automated culture, the Wayne biochemical test, DNA sequencing for
pncA
mutations, and traditional microbiological broth culture. PCR-SSCP provided interpretable results for 96% (46/48) of microscopy-positive sputum samples, 76% (13/17) of microscopy-negative sputum samples, and 100% of
Mycobacterium tuberculosis
isolates. There was 100% agreement between PCR-SSCP results from sputum samples and
Mycobacterium tuberculosis
isolates and 100% concordance between 50 blinded PCR-SSCP rereadings by three observers. PCR-SSCP agreement with the four other tests for pyrazinamide resistance varied from 89 to 97%. This was similar to how frequently the four other tests for pyrazinamide resistance agreed with each other: 90 to 94% for Bactec-460, 90 to 95% for Wayne, 92 to 95% for sequencing, and 91 to 95% for broth culture. PCR-SSCP took less than 24 hours and cost approximately $3 to $6, in contrast with the other assays, which took 3 to 14 weeks and cost $7 to $47. In conclusion, PCR-SSCP is a relatively reliable, rapid, and inexpensive test for pyrazinamide resistance that indicates which patients should receive pyrazinamide from the start of therapy, potentially preventing months of inappropriate treatment.
Detection and Quantification of Hepatitis C Virus (HCV) by MultiCode-RTx Real-Time PCR Targeting the HCV 3′ Untranslated Region
Authors: Mulligan Elizabeth K. , Germer J. J. , Arens Max Q. , D'Amore Krista L. , Di Bisceglie Adrian , Ledeboer Nathan A. , Moser Michael J. , Newman Andrew C. , O'Guin Andy K. , Olivo Paul D. , Podzorski Diane S. , Vaughan Kimberly A. , Yao Joseph D. , Elagin Slava A. , Johnson Scott C.
Published: June 2009

A prototype, real-time reverse-transcription PCR assay, based on MultiCode-RTx technology, quantifying hepatitis C virus (HCV) RNA by targeting the HCV 3′ untranslated region demonstrated linearity over 7 logs, with a good correlation between the quantitative results of this assay and the results of two commercially available comparator assays for 466 clinical specimens comprising all six HCV genotypes.
In Vitro Effect of Ultrasound on Bacteria and Suggested Protocol for Sonication and Diagnosis of Prosthetic Infections
Authors: Monsen Tor , Lövgren Elisabeth , Widerström Micael , Wallinder Lars
Published: June 2009

Sonication of implants has been shown to be a promising method for diagnosis of prosthetic infections due to its improved sensitivity, simplicity, and low cost. The aim of the present study was to evaluate the effects of ultrasound performed under different conditions regarding temperature, duration, and composition of sonication tubes on bacterial species often associated with prosthetic infections. We found that ultrasound had an inhibitory effect on bacteria, of which gram-negative bacteria, in particular
Escherichia coli
, were almost eradicated after 5 min of sonication at 35°C. Gram-positive bacteria were found to be resistant to the effect of ultrasound. Four factors were important for the inhibitory effect of sonication: the type of microorganism, the temperature of the sonication buffer, the duration of exposure to ultrasound (minutes), and the material and composition of the sonication tube in which sonication is performed. On the basis of the results from the present study, we propose a protocol for sonication and recovery of bacteria associated with biofilm on infected implants prior to conventional culture. From the present protocol, we recommend sonication for 7 min at 22°C at the maximum effect which permits survival of gram-negative bacteria.
First Report of Human Infection with
Salmonella enterica
Serovar Apapa Resulting from Exposure to a Pet Lizard
Authors: Cooke Fiona J. , De Pinna Elizabeth , Maguire Clare , Guha Simantee , Pickard Derek J. , Farrington Mark , Threlfall E. John
Published: June 2009

We present the first documented human case of
Salmonella enterica
serovar Apapa infection, isolated concurrently from a hospital inpatient and a pet lizard. The isolates were identical by biochemical profiling and pulsed-field gel electrophoresis. This rare serotype is known to be associated with reptiles. The current practice for avoiding reptile-associated infections is reviewed.
Cytoplasmic APOBEC3G Restricts Incoming Vif-Positive Human Immunodeficiency Virus Type 1 and Increases Two-Long Terminal Repeat Circle Formation in Activated T-Helper-Subtype Cells
Authors: Vetter Michael L. , D'Aquila Richard T.
Published: June 2009

Cytoplasmic APOBEC3G has been reported to block wild-type human immunodeficiency virus type 1 (HIV-1) infection in some primary cells. It is not known whether cytoplasmic APOBEC3G has residual activity in activated T cells, even though virion-packaged APOBEC3G does restrict HIV-1 in activated T cells. Because we found that APOBEC3G expression is greater in activated CD4
+
T-helper type 1 (Th1) lymphocytes than in T-helper type 2 (Th2) lymphocytes, we hypothesized that residual target cell restriction of incoming Vif-positive virions that lack APOBEC3G, if present, would be greater in Th1 than Th2 lymphocytes. Infection of activated Th1 cells with APOBEC3-negative virions did result in decreased amounts of early and late reverse transcription products and integrated virus relative to infection of activated Th2 cells. Two-long terminal repeat (2-LTR) circles, which are formed in the nucleus when reverse transcripts do not integrate, were increased after APOBEC3-negative virus infection of activated Th1 cells relative to infection of activated Th2 cells. In contrast, 2-LTR circle forms were decreased after infection of APOBEC3G-negative cells with APOBEC3G-containing virions relative to APOBEC3G-negative virions and with Th1 cell-produced virions relative to Th2 cell-produced virions. Increasing APOBEC3G in Th2 cells and decreasing APOBEC3G in Th1 cells modulated the target cell phenotypes, indicating causation by APOBEC3G. The comparison between activated Th1 and Th2 cells indicates that cytoplasmic APOBEC3G in activated Th1 cells partially restricts reverse transcription and integration of incoming Vif-positive, APOBEC3G-negative HIV-1. The differing effects of cytoplasmic and virion-packaged APOBEC3G on 2-LTR circle formation indicate a difference in their antiviral mechanisms.
Cell Fusion-Induced Activation of Interferon-Stimulated Genes Is Not Required for Restriction of a Herpes Simplex Virus VP16/ICP0 Mutant in Heterokarya Formed between Permissive and Restrictive Cells
Authors: Hancock Meaghan H. , Mossman Karen L. , Smiley James R.
Published: June 2009

Herpes simplex virus VP16 and ICP0 mutants replicate efficiently in U2OS osteosarcoma cells but are restricted in other cell types. We previously showed that the restrictive phenotype is dominant in a transient cell fusion assay, suggesting that U2OS cells lack an antiviral mechanism present in other cells. Recent data indicate that unscheduled membrane fusion events can activate the expression of interferon-stimulated genes (ISGs) in fibroblasts, raising the possibility that our earlier results were due to a fusion-induced antiviral state. However, we show here that the permissive phenotype is also extinguished following fusion with Vero cells in the absence of ISG induction.
Role of Nitric Oxide in the Pathogenesis of Encephalomyocarditis Virus-Induced Diabetes in Mice
Authors: Lee Young-Sun , Li Na , Shin Seungjin , Jun Hee-Sook
Published: June 2009

The D variant of encephalomyocarditis virus (EMC-D virus) causes diabetes in mice by destroying pancreatic β cells. In mice infected with a low dose of EMC-D virus, macrophages play an important role in β-cell destruction by producing soluble mediators such as interleukin-1β (IL-1β), tumor necrosis factor alpha (TNF-α), and nitric oxide (NO). To investigate the role of NO and inducible NO synthase (iNOS) in the development of diabetes in EMC-D virus-infected mice, we infected iNOS-deficient DBA/2 mice with EMC-D virus (2 × 10
2
PFU/mouse). Mean blood glucose levels in EMC-D virus-infected iNOS-deficient mice and wild-type mice were 205.5 and 466.7 mg/dl, respectively. Insulitis and macrophage infiltration were reduced in islets of iNOS-deficient mice compared with wild-type mice at 3 days after EMC-D virus infection. Apoptosis of β cells was decreased in iNOS-deficient mice, as evidenced by reduced numbers of terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick end labeling-positive cells. There were no differences in mRNA expression of antiapoptotic molecules Bcl-2, Bcl-xL, Bcl-w, Mcl-1, cIAP-1, and cIAP-2 between wild-type and iNOS-deficient mice, whereas expression of proapoptotic Bax and Bak mRNAs was significantly decreased in iNOS-deficient mice. Expression of IL-1β and TNF-α mRNAs was significantly decreased in both islets and macrophages of iNOS-deficient mice compared with wild-type mice after EMC-D virus infection. Nuclear factor κB was less activated in macrophages of iNOS-deficient mice after virus infection. We conclude that NO plays an important role in the activation of macrophages and apoptosis of pancreatic β cells in EMC-D virus-infected mice and that deficient iNOS gene expression inhibits macrophage activation and β-cell apoptosis, contributing to prevention of EMC-D virus-induced diabetes.
Vaccinia Virus CD8
+
T-Cell Dominance Hierarchies Cannot Be Altered by Prior Immunization with Individual Peptides
Authors: Wang Yang , Flesch Inge E. A. , Tscharke David C.
Published: June 2009

Heterologous prime-boost is a common vaccination strategy to elicit CD8
+
T cells (T
CD8+
), and vaccinia virus (VACV) has been widely used as a boosting vector. Studies with other viruses have suggested that priming may reduce responses to native epitopes in boosting vectors as well as improve responses to primed epitopes. We explored this possibility with a VACV model in mice and find that irrespective of an epitope's dominance, prior priming was able to double T
CD8+
responses. More surprisingly, and in contrast to findings for other viruses, responses to remaining epitopes were undisturbed, leaving the overall dominance hierarchy unchanged.
The Infectious Molecular Clone and Pseudotyped Virus Models of Human Immunodeficiency Virus Type 1 Exhibit Significant Differences in Virion Composition with Only Moderate Differences in Infectivity and Inhibition Sensitivity
Authors: Provine Nicholas M. , Puryear Wendy Blay , Wu Xueling , Overbaugh Julie , Haigwood Nancy L.
Published: June 2009

Two frequently employed methods for generating well-characterized, genetically defined infectious human immunodeficiency virus type 1 in vitro include the use of infectious molecular clones (IMCs) and pseudoviruses (PVs) competent for single-round infection. We compared six matched pairs of IMCs and PVs. The relative amounts of Env incorporated and efficiency of cleavage differed substantially between the two systems. Altering the ratio of proviral genome and
env
expression plasmids can produce pseudovirions that are structurally more similar to the matched IMCs. Differences in Env incorporation and cleavage translated into moderate differences in assays infectivity and sensitivity to neutralizing antibodies and entry inhibitors.
Molecular Characterization of Clinical Isolates of Human Immunodeficiency Virus Resistant to the Protease Inhibitor Darunavir
Authors: Šašková Klára Grantz , Kožíšek Milan , Řezáčová Pavlína , Brynda Jiří , Yashina Tatyana , Kagan Ron M. , Konvalinka Jan
Published: June 2009

Darunavir is the most recently approved human immunodeficiency virus (HIV) protease (PR) inhibitor (PI) and is active against many HIV type 1 PR variants resistant to earlier-generation PIs. Darunavir shows a high genetic barrier to resistance development, and virus strains with lower sensitivity to darunavir have a higher number of PI resistance-associated mutations than viruses resistant to other PIs. In this work, we have enzymologically and structurally characterized a number of highly mutated clinically derived PRs with high levels of phenotypic resistance to darunavir. With 18 to 21 amino acid residue changes, the PR variants studied in this work are the most highly mutated HIV PR species ever studied by means of enzyme kinetics and X-ray crystallography. The recombinant proteins showed major defects in substrate binding, while the substrate turnover was less affected. Remarkably, the overall catalytic efficiency of the recombinant PRs (5% that of the wild-type enzyme) is still sufficient to support polyprotein processing and particle maturation in the corresponding viruses. The X-ray structures of drug-resistant PRs complexed with darunavir suggest that the impaired inhibitor binding could be explained by change in the PR-inhibitor hydrogen bond pattern in the P2′ binding pocket due to a substantial shift of the aminophenyl moiety of the inhibitor. Recombinant virus phenotypic characterization, enzyme kinetics, and X-ray structural analysis thus help to explain darunavir resistance development in HIV-positive patients.
Humanized Mice Show Clinical Signs of Dengue Fever according to Infecting Virus Genotype
Authors: Mota Javier , Rico-Hesse Rebeca
Published: June 2009

We demonstrated that the infection of humanized NOD-
scid IL2r
γ
null
mice with different strains (representing the four genotypes) of dengue virus serotype 2 (DEN-2) can induce the development of human-like disease, including fever, viremia, erythema, and thrombocytopenia. Newborn mice were irradiated and received transplants by intrahepatic inoculation of human cord blood-derived hematopoietic progenitor cells (CD34
+
). After 6 weeks, mouse peripheral blood was tested by flow cytometry to determine levels of human lymphocytes (CD45
+
cells); rates of reconstitution ranged from 16 to 80% (median, 52%). Infection (with approximately 10
6
PFU, the equivalent of a mosquito bite) of these humanized mice with eight low-passage-number strains produced a high viremia extending to days 12 to 18 postinfection. We observed a significant decrease in platelets at day 10 in most of the mice and an increase in body temperature (fever) and erythema (rash) in comparison with humanized mice inoculated with cell culture medium only. Comparison of Southeast (SE) Asian and other genotype viruses (American, Indian, and West African) in this model showed significant differences in magnitude and duration of viremia and rash, with the SE Asian viruses always being highest. Indian genotype viruses produced lower viremias and less thrombocytopenia than the others, and West African (sylvatic) viruses produced the shortest periods of viremia and the lowest rash measurements. These results correlate with virulence and transmission differences described previously for primary human target cells and whole mosquitoes and may correlate with epidemiologic observations around the world. These characteristics make this mouse model ideal for the study of dengue pathogenesis and the evaluation of vaccine attenuation and antivirals.
Transitions to and from the CD4-Bound Conformation Are Modulated by a Single-Residue Change in the Human Immunodeficiency Virus Type 1 gp120 Inner Domain
Authors: Kassa Aemro , Madani Navid , Schön Arne , Haim Hillel , Finzi Andrés , Xiang Shi-Hua , Wang Liping , Princiotto Amy , Pancera Marie , Courter Joel , Smith Amos B. , Freire Ernesto , Kwong Peter D. , Sodroski Joseph
Published: June 2009

Binding to the primary receptor CD4 induces conformational changes in the human immunodeficiency virus type 1 (HIV-1) gp120 envelope glycoprotein that allow binding to the coreceptor (CCR5 or CXCR4) and ultimately trigger viral membrane-cell membrane fusion mediated by the gp41 transmembrane envelope glycoprotein. Here we report the derivation of an HIV-1 gp120 variant, H66N, that confers envelope glycoprotein resistance to temperature extremes. The H66N change decreases the spontaneous sampling of the CD4-bound conformation by the HIV-1 envelope glycoproteins, thus diminishing CD4-independent infection. The H66N change also stabilizes the HIV-1 envelope glycoprotein complex once the CD4-bound state is achieved, decreasing the probability of CD4-induced inactivation and revealing the enhancing effects of soluble CD4 binding on HIV-1 infection. In the CD4-bound conformation, the highly conserved histidine 66 is located between the receptor-binding and gp41-interactive surfaces of gp120. Thus, a single amino acid change in this strategically positioned gp120 inner domain residue influences the propensity of the HIV-1 envelope glycoproteins to negotiate conformational transitions to and from the CD4-bound state.
Identification of a Novel WxSLVK Motif in the N Terminus of Human Immunodeficiency Virus and Simian Immunodeficiency Virus Vif That Is Critical for APOBEC3G and APOBEC3F Neutralization
Authors: Dang Ying , Wang Xiaojun , Zhou Tao , York Ian A. , Zheng Yong-Hui
Published: June 2009

The function of lentiviral Vif proteins is to neutralize the host antiviral cytidine deaminases APOBEC3G (A3G) and APOBEC3F (A3F). Vif bridges a cullin 5-based E3 ubiquitin ligase with A3G and A3F and mediates their degradation by proteasomes. Recent studies have found that Vif uses different domains to bind to A3G and A3F. A
14
DRMR
17
domain binds to A3F,
40
YRHHY
44
binds to A3G, and
69
YxxL
72
binds to both A3G and A3F. Here, we report another functional domain of Vif. Previously, we demonstrated that human immunodeficiency virus type 1 (HIV-1) Vif failed to mediate A3G proteasomal degradation when all 16 lysines were mutated to arginines. Here, we show that K26, and to a lesser extent K22, is critical for A3G neutralization. K22 and K26 are part of a conserved
21
WxSLVK
26
(x represents N, K, or H) motif that is found in most primate lentiviruses and that shows species-specific variation. Both K22 and K26 in this motif regulated Vif specificity only for A3G, whereas the SLV residues regulated Vif specificity for both A3F and A3G. Interestingly, SLV and K26 in HIV-1 Vif did not directly mediate Vif interaction with either A3G or A3F. Previously, other groups have reported an important role for W21 in A3F and A3G neutralization. Thus,
21
WxSLVK
26
is a novel functional domain that regulates Vif activity toward both A3F and A3G and is a potential drug target to inhibit Vif activity and block HIV-1 replication.
A Patch of Positively Charged Amino Acids Surrounding the Human Immunodeficiency Virus Type 1 Vif SLVx4Yx9Y Motif Influences Its Interaction with APOBEC3G
Authors: Chen Gongying , He Zhiwen , Wang Tao , Xu Rongzhen , Yu Xiao-Fang
Published: June 2009

The amino-terminal region of the Vif molecule in human immunodeficiency virus type 1 (HIV-1), HIV-2, and simian immunodeficiency virus (SIV) contains a conserved SLV/Ix4Yx9Y motif that was first described in 1992, but the importance of this motif for Vif function has not yet been examined. Our characterization of the amino acids surrounding this motif in HIV-1 Vif indicated that the region is critical for APOBEC3 suppression. In particular, amino acids K22, K26, Y30, and Y40 were found to be important for the Vif-induced degradation and suppression of cellular APOBEC3G (A3G). However, mutation of these residues had little effect on the Vif-mediated suppression of A3F, A3C, or A3DE, suggesting that these four residues are not important for Vif assembly with the Cul5 E3 ubiquitin ligase or protein folding in general. The LV portion of the Vif SLV/Ix4Yx9Y motif was found to be required for optimal suppression of A3F, A3C, or A3DE. Thus, the SLV/Ix4Yx9Y motif and surrounding amino acids represent an important functional domain in the Vif-mediated defense against APOBEC3. In particular, the positively charged K26 of HIV-1 Vif is invariably conserved within the SLV/Ix4Yx9Y motif of HIV/SIV Vif molecules and was the most critical residue for A3G inactivation. A patch of positively charged and hydrophilic residues (K
22
x
3
K
26
x
3
Y
30
x
9
YRHHY
44
) and a cluster of hydrophobic residues (V
55
xIPLx
4-5
LxΦx2YWxL
72
) were both involved in A3G binding and inactivation. These structural motifs in HIV-1 Vif represent attractive targets for the development of lead inhibitors to combat HIV infection.
Matrix Mediates the Functional Link between Human Immunodeficiency Virus Type 1 RNA Nuclear Export Elements and the Assembly Competency of Gag in Murine Cells
Authors: Sherer Nathan M. , Swanson Chad M. , Papaioannou Stelios , Malim Michael H.
Published: June 2009

Human immunodeficiency virus type 1 (HIV-1) assembles poorly in murine cells, reflecting inefficient targeting of the Gag structural polyprotein to the plasma membrane. Virus particle production can be restored by replacing the
cis
-acting Rev response element (RRE) in Gag-Pol mRNAs with multiple copies of the CTE (4×CTE), suggesting a mechanistic link between HIV-1 RNA trafficking and productive Gag assembly. In this report, we demonstrate that Gag molecules generated from RRE-dependent transcripts are intrinsically defective for assembly in murine 3T3 cells. When controlled for the intracellular Gag level, modulations of the Gag matrix (MA) domain that enhance Gag membrane association (e.g., deletion of the MA globular head) substantially improve assembly for Gag derived from RRE- but not 4×CTE-dependent transcripts. Gag mutants carrying a leucine zipper replacement of the nucleocapsid (NC) domain remain largely assembly defective when derived from RRE-dependent transcripts, indicating that the defect does not reflect aberrant NC/RNA-driven Gag multimerization. We further demonstrate that single changes in uncharged amino acids implicated in Gag/MA myristoyl switch regulation, most notably replacing the leucine at position 21 with serine, improve assembly for Gag derived from RRE-dependent transcripts. In sum, we provide genetic evidence to suggest that HIV-1 RNA metabolism specifically modulates the activation of MA-dependent membrane targeting.
Detection of Clonally Expanded Hepatocytes in Chimpanzees with Chronic Hepatitis B Virus Infection
Authors: Mason William S. , Low Huey-Chi , Xu Chunxiao , Aldrich Carol E. , Scougall Catherine A. , Grosse Arend , Clouston Andrew , Chavez Deborah , Litwin Samuel , Peri Suraj , Jilbert Allison R. , Lanford Robert E.
Published: June 2009

During a hepadnavirus infection, viral DNA integrates at a low rate into random sites in the host DNA, producing unique virus-cell junctions detectable by inverse nested PCR (invPCR). These junctions serve as genetic markers of individual hepatocytes, providing a means to detect their subsequent proliferation into clones of two or more hepatocytes. A previous study suggested that the livers of 2.4-year-old woodchucks (Marmota monax) chronically infected with woodchuck hepatitis virus contained at least 100,000 clones of >1,000 hepatocytes (W. S. Mason, A. R. Jilbert, and J. Summers, Proc. Natl. Acad. Sci. USA102:1139-1144, 2005). However, possible correlations between sites of viral-DNA integration and clonal expansion could not be explored because the woodchuck genome has not yet been sequenced. In order to further investigate this issue, we looked for similar clonal expansion of hepatocytes in the livers of chimpanzees chronically infected with hepatitis B virus (HBV). Liver samples for invPCR were collected from eight chimpanzees chronically infected with HBV for at least 20 years. Fifty clones ranging in size from ∼35 to 10,000 hepatocytes were detected using invPCR in 32 liver biopsy fragments (∼1 mg) containing, in total, ∼3 × 107liver cells. Based on searching the analogous human genome, integration sites were found on all chromosomes except Y, ∼30% in known or predicted genes. However, no obvious association between the extent of clonal expansion and the integration site was apparent. This suggests that the integration site per se is not responsible for the outgrowth of large clones of hepatocytes.
The Adenovirus E4orf4 Protein Induces G
2
/M Arrest and Cell Death by Blocking Protein Phosphatase 2A Activity Regulated by the B55 Subunit
Authors: Li Suiyang , Brignole Claudine , Marcellus Richard , Thirlwell Sara , Binda Olivier , McQuoid Monica J. , Ashby Danita , Chan Helen , Zhang Zhiying , Miron Marie-Joëlle , Pallas David C. , Branton Philip E.
Published: June 2009

Human adenovirus E4orf4 protein is toxic in human tumor cells. Its interaction with the Bα subunit of protein phosphatase 2A (PP2A) is critical for cell killing; however, the effect of E4orf4 binding is not known. Bα is one of several mammalian B-type regulatory subunits that form PP2A holoenzymes with A and C subunits. Here we show that E4orf4 protein interacts uniquely with B55 family subunits and that cell killing increases with the level of E4orf4 expression. Evidence suggesting that Bα-specific PP2A activity, measured in vitro against phosphoprotein substrates, is reduced by E4orf4 binding was obtained, and two potential B55-specific PP2A substrates, 4E-BP1 and p70
S6K
, were seen to be hypophosphorylated in vivo following expression of E4orf4. Furthermore, treatment of cells with low levels of the phosphatase inhibitor okadaic acid or coexpression of the PP2A inhibitor I
1
PP2A
enhanced E4orf4-induced cell killing and G
2
/M arrest significantly. These results suggested that E4orf4 toxicity results from the inhibition of B55-specific PP2A holoenzymes, an idea that was strengthened by an observed growth arrest resulting from treatment of H1299 cells with Bα-specific RNA interference. We believe that E4orf4 induces growth arrest resulting in cell death by reducing the global level of B55-specific PP2A activity, thus preventing the dephosphorylation of B55-specific PP2A substrates, including those involved in cell cycle progression.
Epigenetic Modulation of Gene Expression from Quiescent Herpes Simplex Virus Genomes
Authors: Ferenczy Michael W. , DeLuca Neal A.
Published: June 2009

The ability of herpes simplex virus to persist in cells depends on the extent of viral-gene expression, which may be controlled by epigenetic mechanisms. We used quiescent infection with the viral mutants d109 and d106 to explore the effects of cell type and the presence of the viral protein ICP0 on the expression and chromatin structure of the human cytomegalovirus (HCMV) tk and gC promoters on the viral genome. Expression from the HCMV promoter on the d109 genome decreased with time and was considerably less in HEL cells than in Vero cells. Expression from the HCMV promoter in d106 was considerably more abundant than in d109, and this increased with time in both cell types. The same pattern of expression was seen on the tk and gC genes on the viral genomes, although the levels of tk and gC RNA were approximately 10
2
- and 10
5
-fold lower than those of wild-type virus in d106 and d109, respectively. In micrococcal-nuclease digestion experiments, nucleosomes were evident on the d109 genome, and the amount of total H3 as determined by chromatin immunoprecipitation was considerably greater on d109 than d106 genomes. The acetylation of histone H3 on the d106 genomes was evident at early and late times postinfection in Vero cells, but only at late times in HEL cells. The same pattern was observed for H3 acetylated on lysine 9. Trimethylation of H3K9 on d109 genomes was evident only at late times postinfection in Vero cells, while it was observed both early and late in HEL cells. Heterochromatin protein 1γ (HP1γ) was generally present only on d109 genomes at late times postinfection of HEL cells. The observations of chromatin structure correlate with the expression patterns of the three analyzed genes on the quiescent genomes. Therefore, several mechanisms generally affect the expression and contribute to the silencing of persisting genomes. These are the abundance of nucleosomes, the acetylation state of the histones, and heterochromatin. The extents to which these different mechanisms contribute to repression vary in different cell types and are counteracted by the presence of ICP0.
Transient Expression of Herpes Simplex Virus Type 1 ICP22 Represses Viral Promoter Activity and Complements the Replication of an ICP22 Null Virus
Authors: Bowman J. Jason , Orlando Joseph S. , Davido David J. , Kushnir Anna S. , Schaffer Priscilla A.
Published: June 2009

Of the five herpes simplex virus type 1 immediate early (IE) proteins, the least is known about the function of ICP22 during productive infection and latency. Research characterizing the physical and functional properties of the protein has been limited because ICP22 has proven to be difficult to express in transient assays. In addition, genetic analysis of ICP22 has been complicated by the fact that the C terminus of ICP22 is expressed as a discrete protein product. In order to characterize properties of mutant and wild-type ICP22, we developed a transient expression system. We found that ICP22 can be expressed at detectable levels when placed under the control of the cytomegalovirus IE promoter, confirming recent observations by K. A. Fraser and S. A. Rice (J. Virol. 81:5091-5101, 2007). We extended this analysis to show that ICP22 can also be expressed from its own promoter in the presence of other viral factors, either by coexpression with ICP0 or by infection with an ICP22 null virus. Notably, infection of cells transfected with an ICP22 expression vector yielded ICP22 protein that was modified in a manner similar to that of ICP22 protein detected in wild-type-infected cells. We go on to demonstrate that the failure of ICP22 protein to be expressed in transiently transfected cells was not due to inactivity of the ICP22 promoter, but rather to the ability of ICP22 to inhibit expression of reporter gene activity, including its own, in transient assays. Of special note was the observation that expression of ICP22 was sufficient to prevent transactivation of reporter genes by ICP0. Finally, transient expression of ICP22 was sufficient to complement replication of an ICP22 null virus, demonstrating that this system can be used to study functional properties of ICP22. Collectively, this transient expression system facilitates tests of the physical and functional properties of ICP22 and ICP22 mutants prior to introduction of mutant genes into the viral genome.
Protective Anti-Hepatitis B Virus Responses in Rhesus Monkeys Primed with a Vectored Measles Virus and Boosted with a Single Dose of Hepatitis B Surface Antigen
Authors: Reyes-del Valle Jorge , Hodge Gregory , McChesney Michael B. , Cattaneo Roberto
Published: June 2009

The widely used hepatitis B virus (HBV) vaccine is based on three doses of hepatitis B surface antigen (HBsAg) protein. We previously showed that vectored measles viruses (MV) expressing HBsAg retain measles vaccine function in monkeys but do not induce a protective anti-HBs response in all animals. We show here that a single dose of HBsAg protein following a three-dose vaccination regimen with an optimized HBsAg-expressing MV elicits protective anti-HBs responses in all four vaccinated Rhesus monkeys. Vaccination strategies coupling the effective, long-term immunity elicited by the high-coverage MV vaccine to prophylactic HBV immunity are discussed.
Analysis of Human Immunodeficiency Virus Type 1 Viremia and Provirus in Resting CD4+T Cells Reveals a Novel Source of Residual Viremia in Patients on Antiretroviral Therapy
Authors: Brennan Timothy P. , Woods John O. , Sedaghat Ahmad R. , Siliciano Janet D. , Siliciano Robert F. , Wilke Claus O.
Published: June 2009

Highly active antiretroviral therapy (HAART) can reduce human immunodeficiency virus type 1 (HIV-1) viremia to clinically undetectable levels. Despite this dramatic reduction, some virus is present in the blood. In addition, a long-lived latent reservoir for HIV-1 exists in resting memory CD4+T cells. This reservoir is believed to be a source of the residual viremia and is the focus of eradication efforts. Here, we use two measures of population structure—analysis of molecular variance and the Slatkin-Maddison test—to demonstrate that the residual viremia is genetically distinct from proviruses in resting CD4+T cells but that proviruses in resting and activated CD4+T cells belong to a single population. Residual viremia is genetically distinct from proviruses in activated CD4+T cells, monocytes, and unfractionated peripheral blood mononuclear cells. The finding that some of the residual viremia in patients on HAART stems from an unidentified cellular source other than CD4+T cells has implications for eradication efforts.
Facile and efficient synthesis of indazole derivatives by 1,3-cycloaddition of arynes with diazo compounds and azomethine imides
Authors: Jin Tienan , Yang Fan , Yamamoto Yoshinori
Published: June 2009

N-Unsubstituted indazoles 3 and 1-arylindazoles 4 are readily available in good to high yields through [3+2] cycloaddition of 2-(trimethylsilyl)aryl triflates 1 and diazo compounds in the presence of KF or CsF under mild reaction conditions. Furthermore, we found that azomethine imides also underwent cycloaddition reaction with 2-(trimethylsilyl)phenyl triflates (1a) in the presence of KF to afford indazolone derivatives 6 in moderate yields.
Suicide among male regular UK Armed Forces personnel, 1984–2007
Authors: Fear N T , Ward V R , Harrison K , Davison L , Williamson S , Blatchley N F
Published: June 2009

Objective:

To examine the number of suicide and open verdict deaths in the regular UK Armed Forces and to make comparisons with the UK general population.

Methods:

Age and calendar year-adjusted standardised mortality ratios (SMRs) and 95% CI were calculated to compare the number of suicides among the UK Armed Forces with the general population of the UK.

Results:

Between 1984 and 2007, there were 694 suicide and open verdict deaths among male UK Armed Forces personnel. The UK Armed Forces had statistically significantly fewer suicides than expected compared with the UK general population (SMR = 58, 95% CI 54 to 63, based on 694 deaths). This was evident for each of the three Services (Naval Service, Army and Royal Air Force). For each age group, the number of suicides in each Service was lower than the number expected based on UK general population rates, except for Army males under 20 years of age, where there were 1.5 times more deaths than expected (SMR = 150, 95% CI 118 to 190, based on 68 deaths).

Conclusion:

The UK Armed Forces are subject to a number of unique occupational stressors, so it is reassuring that they experience lower than expected numbers of suicides in comparison with the UK general population. This is true for each Service and all age groups except young Army males.
DEVELOPMENT AND EVALUATION OF VISION MULTIPLEXING DEVICES FOR VISION IMPAIRMENTS
Authors: PELI ELI , LUO GANG , BOWERS ALEX , RENSING NOA
Published: June 2009

We have proposed a novel concept of vision multiplexing for the visually impaired – superimposing contour images over their natural view of a scene or over original images presented on a TV screen. We have implemented the concept using an optical see-through head mounted display to provide either visual field expansion to patients with peripheral field loss or vision enhancement to patients with central vision loss. We have also implemented the concept in a video player with dynamic magnification for patients with central vision loss. Results of initial testing in the lab and on the street are promising.
INTEGRATION OF EMG AND EGT MODALITIES FOR THE DEVELOPMENT OF AN ENHANCED CURSOR CONTROL SYSTEM
Authors: CHIN CRAIG A. , BARRETO ARMANDO , ADJOUADI MALEK
Published: June 2009

While Eye Gaze Tracking (EGT) systems have demonstrated their potential as computer cursor control devices, their application outside the laboratory environment has been less prominent than originally expected. This may be due to limitations in the stability of the cursor controlled by EGT devices and in the potential for unintended selections ("clicks"). To address these EGT limitations, we have developed a cursor control system that integrates electromyogram-based control with EGT-based control. This integrated system allows a user to perform small cursor displacements and selection operations ("left click") by detecting distinct changes in electromyogram (EMG) signals generated during specific facial movements. Specifically, the system monitors and processes, in real time, EMG signals from four electrodes attached to the head of the subject. We compared the performance of this EMG/EGT integrated system, with the performance of a stand-alone EGT system and a hand-held mouse, in point-and-click trials. Statistical analysis of the results indicates that the EMG/EGT system is slower than the EGT system and the mouse, but it also revealed that it is significantly less error-prone than the EGT-only system. The analysis also revealed that the performance of the EMG/EGT system does not seem to be well matched to Fitts' model.
IMAGE ENHANCEMENT FOR IMPAIRED VISION: THE CHALLENGE OF EVALUATION
Authors: PELI ELI , WOODS RUSSELL L.
Published: June 2009

With the aging of the population, the prevalence of eye diseases and thus of vision impairment is increasing. The TV watching habits of people with vision impairments are comparable to normally sighted people,1however their vision loss prevents them from fully benefiting from this medium. For over 20 years we have been developing video image-enhancement techniques designed to assist people with visual impairments, particularly those due to central retinal vision loss. A major difficulty in this endeavor is the lack of evaluation techniques to assess and compare the effectiveness of various enhancement methods. This paper reviews our approaches to image enhancement and the results we have obtained, with special emphasis on the difficulties encountered in the evaluation of the benefits of enhancement and the solutions we have developed to date.
ALTERNATIVE WHEELCHAIR CONTROL INVOLVING INTENTIONAL MUSCLE CONTRACTIONS
Authors: FELZER TORSTEN , STRAH BRUNO , NORDMANN RAINER , MIGLIETTA SEBASTIAN
Published: June 2009

This paper deals with various ways of controlling an electrically powered wheelchair beyond the usual method involving a manual joystick. The main focus is on the newest version of HaWCoS – the "HAnds-free Wheelchair COntrol System" – allowing persons with severe disabilities to reliably navigate a power wheelchair without the need to use the hands. All the user has to do is to produce a sequence of tiny contractions of an arbitrary muscle, e.g., by raising the eyebrow. The working prototype of the system, which has been realized as a stand-alone device, is introduced in detail, together with a closer look at the muscle-based control principle and a brief description of a PC-based simulator. The advantages and the drawbacks of the system are discussed on the basis of a rather simple real-life experiment. The paper also elaborates on possible approaches to improve HaWCoS (by reducing or eliminating its problems) in the future. In addition to a quick software solution and a controller implementation involving supplemental sensory information, planned "improvements" include the development of an "intelligent wheelchair" with HaWCoS being some sort of a prototype for the User Interface component.
QUINTIC POLYNOMIALS OF HASHIMOTO–TSUNOGAI, BRUMER AND KUMMER
Authors: KIDA MASANARI , RENAULT GUÉNAËL , YOKOYAMA KAZUHIRO
Published: June 2009

We establish an isomorphism between the quintic cyclic polynomials discovered by Hashimoto–Tsunogai and those arising from Kummer theory for certain algebraic tori. This enables us to solve the isomorphism problem for Hashimoto–Tsunogai polynomials and also Brumer's quintic polynomials.
CONGRUENCES FOR DYSON'S RANKS
Authors: BRINGMANN KATHRIN
Published: June 2009

In this paper, we prove infinite families of congruences for coefficients of harmonic Maass forms whose coefficients encode Dyson's rank. This generalizes the earlier joint work of the author with Ken Ono.
CHARACTERIZING ALGEBRAIC CURVES WITH INFINITELY MANY INTEGRAL POINTS
Authors: ALVANOS PARASKEVAS , BILU YURI , POULAKIS DIMITRIOS
Published: June 2009

A classical theorem of Siegel asserts that the set of S-integral points of an algebraic curveC over a number field is finite unless C has genus 0 and at most two points at infinity. In this paper, we give necessary and sufficient conditions for C to have infinitely many S-integral points.
SUMS OF PRODUCTS OF CONGRUENCE CLASSES AND OF ARITHMETIC PROGRESSIONS
Authors: KONYAGIN SERGEI V. , NATHANSON MELVYN B.
Published: June 2009

Consider the congruence class Rm(a) = {a + im : i ∈ Z} and the infinite arithmetic progression Pm(a) = {a + im : i ∈ N0}. For positive integers a,b,c,d,m the sum of products set Rm(a)Rm(b) + Rm(c)Rm(d) consists of all integers of the form (a+im) · (b+jm)+(c+km)(d+ℓm) for some i,j,k,ℓ ∈ Z. It is proved that if gcd (a,b,c,d,m) = 1, then Rm(a)Rm(b) + Rm(c)Rm(d) is equal to the congruence class Rm(ab+cd), and that the sum of products set Pm(a)Pm(b)+Pm(c)Pm eventually coincides with the infinite arithmetic progression Pm(ab+cd).
PRIMES IN A PRESCRIBED ARITHMETIC PROGRESSION DIVIDING THE SEQUENCE $\{a^k+b^k\}_{k=1}^{\infty}$
Authors: MOREE P. , SURY B.
Published: June 2009

Given positive integers a,b,c and d such that c and d are coprime, we show that the primes p ≡ c ( mod d) dividing ak+bkfor some k ≥ 1 have a natural density and explicitly compute this density. We demonstrate our results by considering some claims of Fermat that he made in a 1641 letter to Mersenne.
DISTRIBUTION PROPERTIES OF GENERALIZED VAN DER CORPUT–HALTON SEQUENCES AND THEIR SUBSEQUENCES
Authors: HOFER ROSWITHA , KRITZER PETER , LARCHER GERHARD , PILLICHSHAMMER FRIEDRICH
Published: June 2009

We study the distribution properties of sequences which are a generalization of the well-known van der Corput–Halton sequences on one hand, and digital (T,s)-sequences on the other. In this paper, we give precise results concerning the distribution properties of such sequences in the s-dimensional unit cube. Moreover, we consider subsequences of the above-mentioned sequences and study their distribution properties. Additionally, we give discrepancy estimates for some special cases, including subsequences of van der Corput and van der Corput–Halton sequences.