bluuebunny/crossref_metadata_2025_split huggingface dataset:
RyhB, an Iron-Responsive Small RNA Molecule, Regulates
Shigella dysenteriae
Virulence
Authors: Murphy Erin R. , Payne Shelley M. 
Published: April 2007

ABSTRACT

Regulation of bacterial gene expression by small RNA (sRNA) molecules is an increasingly recognized phenomenon but one that is not yet fully understood. We show that the sRNA RyhB suppresses several virulence-associated phenotypes of
Shigella dysenteriae
, a causative agent of bacillary dysentery in humans. The virulence genes repressed by
S. dysenteriae
RyhB include those encoding the type III secretion apparatus, its secreted effectors, and specific chaperones. Suppression of
Shigella
virulence occurs via RyhB-dependent repression of the transcriptional activator VirB, leading to reduced expression of genes within the VirB regulon. Efficient repression of
virB
is mediated by a single-stranded region of RyhB that is distinct from the region required for repression of
Shigella sodB
. Regulation of
virB
by RyhB implicates iron as an environmental factor contributing to the complex regulation of
Shigella
virulence determinants.
Heterogeneity in the Activity of MexicanHelicobacter pyloriStrains in Gastric Epithelial Cells and Its Association with Diversity in thecagAGene
Authors: Reyes-Leon Adriana , Atherton John C. , Argent Richard H. , Puente J. L. , Torres J. 
Published: April 2007

ABSTRACTHelicobacter pyloriCagA is translocated into gastric epithelial cells by a type IV secretion system and interacts with the Src homology 2 phosphatase, altering cell morphology. Multiple EPIYA motifs in CagA are associated with increased activity in cells and with gastric cancer. The aim of this work was to study the heterogeneity in activity in cells of multipleH. pylorisingle colonies isolated from a single patient and its association with polymorphism incagA. The presence ofcagA,cagE,cagT, andcag10was studied with 318H. pyloriisolates from the antra and corpora of 18 patients. AGS gastric epithelial cells were infected with 75 isolates, and interleukin-8 (IL-8) secretion, cytoskeletal changes, CagA translocation, and tyrosine phosphorylation were measured. ThecagA3′-variable region was sequenced for 30 isolates to determine the number and types of EPIYA motifs. Isolates from an individual stomach were usually genetically related and had quantitatively similar phenotypic effects on cells (IL-8 induction and cytoskeletal changes). However, strains from different patients with similar CagA EPIYA motif patterns varied widely in these phenotypes. Among isolates with an EPIYA-ABC pattern, the phenotype was variable: IL-8 induction ranged from 200 to 1,200 pg/ml, and morphological changes occurred in 20 to 70% of cells. In several cases,cagAsequence diversity appeared to explain the lack of CagA activity, as isolates with an EPIYA-ACC pattern or a modified B motif had reduced cell activity.cagpathogenicity island-positiveH. pyloriisolates displayed a high level of heterogeneity in the capacity to induce IL-8 secretion and morphological changes; an absent or modified B motif was associated with low activity.
Inhibition of
Enterococcus faecium
Adherence to Collagen by Antibodies against High-Affinity Binding Subdomains of Acm
Authors: Nallapareddy Sreedhar R. , Sillanpää Jouko , Ganesh Vannakambadi K. , Höök Magnus , Murray Barbara E. 
Published: April 2007

ABSTRACT

Strains of
Enterococcus faecium
express a cell wall-anchored protein, Acm, which mediates adherence to collagen. Here, we (i) identify the minimal and high-affinity binding subsegments of Acm and (ii) show that anti-Acm immunoglobulin Gs (IgGs) purified against these subsegments reduced
E. faecium
TX2535 strain collagen adherence up to 73 and 50%, respectively, significantly more than the total IgGs against the full-length Acm A domain (28%) (
P
< 0.0001). Blocking Acm adherence with functional subsegment-specific antibodies raises the possibility of their use as therapeutic or prophylactic agents.
Multiplexed Identification of Blood-Borne Bacterial Pathogens by Use of a Novel 16S rRNA Gene PCR-Ligase Detection Reaction-Capillary Electrophoresis Assay
Authors: Pingle Maneesh R. , Granger Kathleen , Feinberg Philip , Shatsky Rebecca , Sterling Bram , Rundell Mark , Spitzer Eric , Larone Davise , Golightly Linnie , Barany Francis 
Published: April 2007

ABSTRACTWe have developed a novel high-throughput PCR-ligase detection reaction-capillary electrophoresis (PCR-LDR-CE) assay for the multiplexed identification of 20 blood-borne pathogens (Staphylococcus epidermidis,Staphylococcus aureus,Bacillus cereus,Enterococcus faecalis,Enterococcus faecium,Listeria monocytogenes,Streptococcus pneumoniae,Streptococcus pyogenes,Streptococcus agalactiae,Escherichia coli,Klebsiella pneumoniae,Haemophilus influenzae,Pseudomonas aeruginosa,Acinetobacter baumannii,Neisseria meningitidis,Bacteroides fragilis,Bacillus anthracis,Yersinia pestis,Francisella tularensis, andBrucella abortus), the last four of which are biothreat agents. The method relies on the amplification of two regions within the bacterial 16S rRNA gene, using universal PCR primers and querying the identity of specific single-nucleotide polymorphisms within the amplified regions in a subsequent LDR. The ligation products vary in color and size and are separated by CE. Each organism generates a specific pattern of ligation products, which can be used to distinguish the pathogens using an automated software program we developed for that purpose. The assay has been verified on 315 clinical isolates and demonstrated a detection sensitivity of 98%. Additionally, 484 seeded blood cultures were tested, with a detection sensitivity of 97.7%. The ability to identify geographically variant strains of the organisms was determined by testing 132 isolates obtained from across the United States. In summary, the PCR-LDR-CE assay can successfully identify, in a multiplexed fashion, a panel of 20 blood-borne pathogens with high sensitivity and specificity.
Evaluation of Moxalactam with the BD Phoenix System for Detection of Methicillin Resistance in Coagulase-Negative Staphylococci
Authors: Pupin H. , Renaudin H. , Join-Lambert O. , Bébéar C. , Mégraud F. , Lehours P. 
Published: April 2007

ABSTRACT

The performance of moxalactam with the BD Phoenix system for the detection of methicillin resistance in coagulase-negative staphylococci was evaluated by use of a collection of 186 strains. Moxalactam was a better drug as an indicator of methicillin resistance for
mecA
-positive strains than oxacillin and cefoxitin were. For strains other than
Staphylococcus saprophyticus
, a moxalactam MIC >16 μg/ml was indicative of methicillin resistance.
Nocardial Cerebral Abscess Associated with Mycetoma, Pneumonia, and Membranoproliferative Glomerulonephritis
Authors: Elmaci Ilhan , Senday Durmus , Silav Gökalp , Ekenel Figen , Balak Naci , Ayan Erdogan , Akinci Murat , Işik Nejat , Yazici Saadet 
Published: April 2007

ABSTRACT
Nocardial brain abscesses remain a clinical challenge. We successfully treated a patient with nocardial brain abscess, mycetoma, pneumonia, and glomerulonephritis. Nocardial soft tissue involvement, mycetoma, is well known. However, the fact that actinomycetoma can metastasize may not be as well appreciated. The association between nocardiosis and glomerulonephritis should be better clarified.
Evaluation of Molecular Typing Methods in Characterizing a European Collection of Epidemic Methicillin-Resistant
Staphylococcus aureus
Strains: the HARMONY Collection
Authors: Cookson Barry D. , Robinson D. Ashley , Monk Alastair B. , Murchan Stephen , Deplano Ariane , de Ryck Rafaël , Struelens Marc J. , Scheel Christina , Fussing Vivian , Salmenlinna Saara , Vuopio-Varkila Jaana , Cuny Christina , Witte Wolfgang , Tassios Panayotis T. , Legakis Nikolas J. , van Leeuwen Willem , van Belkum Alex , Vindel Anna , Garaizar Javier , Haeggman Sara , Olsson-Liljequist Barbro , Ransjo Ulrika , Muller-Premru Manica , Hryniewicz Waleria , Rossney Angela , O'Connell Brian , Short Benjamin D. , Thomas Jonathan , O'Hanlon Simon , Enright Mark C. 
Published: April 2007

ABSTRACT

We analyzed a representative sample of methicillin-resistant
Staphylococcus aureus
(MRSA) from 11 European countries (referred to as the HARMONY collection) using three molecular typing methods used within the HARMONY group to examine their usefulness for large, multicenter MRSA surveillance networks that use these different laboratory methodologies. MRSA isolates were collected based on their prevalence in each center and their genetic diversity, assessed by pulsed-field gel electrophoresis (PFGE). PFGE groupings (≤3 bands difference between patterns) were compared to those made by sequencing of the variable repeats in the protein A gene
spa
and clonal designations based on multilocus sequence typing (MLST), combined with PCR analysis of the staphylococcal chromosome cassette containing the
mec
genes involved in methicillin resistance (SCC
mec
). A high level of discrimination was achieved using each of the three methodologies, with discriminatory indices between 89.5% and 91.9% with overlapping 95% confidence intervals. There was also a high level of concordance of groupings made using each method. MLST/SCC
mec
typing distinguished 10 groups containing at least two isolates, and these correspond to the majority of nosocomial MRSA clones described in the literature. PFGE and
spa
typing resolved 34 and 31 subtypes, respectively, within these 10 MRSA clones, with each subtype differing only slightly from the most common pattern using each method. The HARMONY group has found that the methods used in this study differ in their availability and affordability to European centers involved in MRSA surveillance. Here, we demonstrate that the integration of such technologies is achievable, although common protocols (such as we have developed for PFGE) may also be important, as is the use of centralized Internet sites to facilitate data analysis. PFGE and
spa
-typing data from analysis of MRSA isolates from the many centers that have access to the relevant equipment can be compared to reference patterns/sequences, and clonal designations can be made. In the majority of cases, these will correspond to those made by the (more expensive) method of choice—MLST/SCC
mec
typing—and these alternative methods can therefore be used as frontline typing systems for multicenter surveillance of MRSA.
Rapid and Reliable Method for Quantification of
Mycobacterium paratuberculosis
by Use of the BACTEC MGIT 960 System
Authors: Shin Sung Jae , Han Jun Hee , Manning Elizabeth J. B. , Collins Michael T. 
Published: April 2007

ABSTRACT

A simple method for the enumeration of viable
Mycobacterium paratuberculosis
cells was developed and evaluated using the MGIT 960 culture system. For each of 12
M. paratuberculosis
strains isolated from either cattle or humans, single-cell suspensions of
M. paratuberculosis
cells were adjusted to an optical density at 600 nm of 1.00 (10
7.6
to 10
8.2
cells/ml), and serial dilutions were prepared. Standard curves were established by relating the MGIT time-to-detection data to the log
10
CFU for these suspensions using standard plate counting and BACTEC 460 results as reference methods. Universal and strain-specific standard quantification curves were generated. A one-phase exponential decay equation best fit the universal standard curve and strain-specific curves (
R
2
of 0.96 and >0.99, respectively). Two subgroups within the universal curves were distinguished: one for laboratory-adapted strains and the other for recently isolated low-passage bovine strains. The predictive errors for log
10
estimations using the universal standard curve, each subgroup's standard curve, and strain-specific curves were ±0.87, ±0.45, and ±0.31 log
10
units, respectively. CFU estimations by all three standard curves were highly reproducible, regardless of the
M. paratuberculosis
strain or inoculum volume. In comparison with the previously described BACTEC 460
M. paratuberculosis
counting method, quantification with MGIT 960 was less expensive, more rapid, more accurate, and more sensitive (<10 CFU). This MGIT counting method has broad applications for studies requiring the quantification of viable
M. paratuberculosis
cells, such as drug susceptibility testing or environmental survival studies.
Rotavirus Infection of Infant and Young Adult Nonobese Diabetic Mice Involves Extraintestinal Spread and Delays Diabetes Onset
Authors: Graham Kate L. , O'Donnell Joanne A. , Tan Yan , Sanders Natalie , Carrington Emma M. , Allison Janette , Coulson Barbara S. 
Published: April 2007

ABSTRACTRotaviruses have been implicated as a possible viral trigger for exacerbations in islet autoimmunity, suggesting they might modulate type 1 diabetes development. In this study, the ability of rotavirus strain RRV to infect the pancreas and affect insulitis and diabetes was examined in nonobese diabetic (NOD) mice, an experimental model of type 1 diabetes. Mice were inoculated either orally or intraperitoneally as infants or young adults. In infant mice inoculated orally, rotavirus antigen was detected in pancreatic macrophages outside islets and infectious virus was found in blood cells, pancreas, spleen, and liver. Extraintestinal RRV spread and pancreatic presence of infectious virus also occurred in intraperitoneally inoculated infant and adult mice. The initiation of insulitis was unaltered by infection. The onset of diabetes was delayed in infant mice inoculated orally and infant and adult mice inoculated intraperitoneally. In contrast, adult mice inoculated orally showed no evidence of pancreatic RRV, the lowest rate of detectable RRV replication, and no diabetes modulation. Thus, the ability of RRV infection to modulate diabetes development in infant and young adult NOD mice was related to the overall extent of detectable virus replication and the presence of infectious virus extraintestinally, including in the pancreas. These studies show that RRV infection of infant and young adult NOD mice provides significant protection against diabetes. As these findings do not support the hypothesis that rotavirus triggers autoimmunity related to type 1 diabetes, further research is needed to resolve this issue.
Potent Rescue of Human Immunodeficiency Virus Type 1 Late Domain Mutants by ALIX/AIP1 Depends on Its CHMP4 Binding Site
Authors: Usami Yoshiko , Popov Sergei , Göttlinger Heinrich G. 
Published: April 2007

ABSTRACT
The release of human immunodeficiency virus type 1 (HIV-1) and of other retroviruses from certain cells requires the presence of distinct regions in Gag that have been termed late assembly (L) domains. HIV-1 harbors a PTAP-type L domain in the p6 region of Gag that engages an endosomal budding machinery through Tsg101. In addition, an auxiliary L domain near the C terminus of p6 binds to ALIX/AIP1, which functions in the same endosomal sorting pathway as Tsg101. In the present study, we show that the profound release defect of HIV-1 L domain mutants can be completely rescued by increasing the cellular expression levels of ALIX and that this rescue depends on an intact ALIX binding site in p6. Furthermore, the ability of ALIX to rescue viral budding in this system depended on two putative surface-exposed hydrophobic patches on its N-terminal Bro1 domain. One of these patches mediates the interaction between ALIX and the ESCRT-III component CHMP4B, and mutations which disrupt the interaction also abolish the activity of ALIX in viral budding. The ability of ALIX to rescue a PTAP mutant also depends on its C-terminal proline-rich domain (PRD), but not on the binding sites for Tsg101, endophilin, CIN85, or for the newly identified binding partner, CMS, within the PRD. Our data establish that ALIX can have a dramatic effect on HIV-1 release and suggest that the ability to use ALIX may allow HIV-1 to replicate in cells that express only low levels of Tsg101.
Emergence of Mammalian Cell-Adapted Vesicular Stomatitis Virus from Persistent Infections of Insect Vector Cells
Authors: Novella Isabel S. , Ebendick-Corpus Bonnie E. , Zárate Selene , Miller Eric L. 
Published: April 2007

ABSTRACT
Arboviruses (arthropod-borne viruses) represent quintessential generalists, with the ability to infect and perform well in multiple hosts. However, antagonistic pleiotropy imposed a cost during the adaptation to persistent replication of vesicular stomatitis virus in sand fly cells and resulted in strains that initially replicated poorly in hamster cells, even when the virus was allowed to replicate periodically in the latter. Once a debilitated strain started replicating continuously in mammalian cells, fitness increased significantly. Fitness recovery did not entail back mutations or compensatory mutations, but instead, we observed the replacement of persistence-adapted genomes by mammalian cell-adapted strains with a full set of new, unrelated sequence changes. These mammalian cell-adapted genomes were present at low frequencies in the populations with a history of persistence for up to a year and quickly became dominant during mammalian infection, but coexistence was not stable in the long term. Periodic acute replication in mammalian cells likely contributed to extending the survival of minority genomes, but these genomes were also found in strictly persistent populations.
Effect of Preexisting Immunity to Adenovirus Human Serotype 5 Antigens on the Immune Responses of Nonhuman Primates to Vaccine Regimens Based on Human- or Chimpanzee-Derived Adenovirus Vectors
Authors: McCoy Kimberly , Tatsis Nia , Korioth-Schmitz Birgit , Lasaro Marcio O. , Hensley Scott E. , Lin Shih-Wen , Li Yan , Giles-Davis Wynetta , Cun Ann , Zhou Dongming , Xiang Zhiquan , Letvin Norman L. , Ertl Hildegund C. J. 
Published: April 2007

ABSTRACT
In this study we compared a prime-boost regimen with two serologically distinct replication-defective adenovirus (Ad) vectors derived from chimpanzee serotypes C68 and C1 expressing Gag, Pol, gp140, and Nef of human immunodeficiency virus type 1 with a regimen in which replication-defective Ad vectors of the human serotype 5 (AdHu5) were given twice. Experiments were conducted in rhesus macaques that had or had not been preexposed to antigens of AdHu5. There was no significant difference in T-cell responses tested from peripheral blood of the different groups, although responses were overall highest in nonpreexposed animals immunized with the chimpanzee Ad vectors. Preexisting immunity to AdHu5 completely inhibited induction of transgene product-specific antibodies by the AdHu5 vectors without affecting antibody responses to the chimpanzee vectors. Upon euthanasia, T-cell responses were tested from a number of tissues. Preexisting immunity to AdHu5, commonly found in humans, changed the homing pattern of vaccine-induced T cells. In AdHu5-preexposed animals vaccinated with the chimpanzee Ad vectors, frequencies of transgene-specific T cells were higher in spleens than in blood, and in most preexposed animals vaccinated either with AdHu5 vectors or chimpanzee adenovirus vectors, frequencies of such T cells were exceptionally high in livers. The latter results indicate that analysis of T-cell responses solely from blood mononuclear cells of vaccine recipients may not suffice to compare the potencies of different vaccine regimens.
Mutagenesis of the Herpesvirus Saimiri Terminal Repeat Region Reveals Important Elements for Virus Production
Authors: White Robert E. , Carline Lindsay , Allday Martin J. 
Published: April 2007

ABSTRACT
Deletion of the terminal repeats (TR) from herpesvirus saimiri (HVS) renders it unable to produce infectious virus or generate plaques. However, a TR-deleted HVS bacterial artificial chromosome can form replication compartments. Complementation of this mutant shows that one copy of the TR, plus the right junction of the genome with the TR, is sufficient for efficient plaque formation and generation of infectious virus. Within the TR unit, the region around the cleavage site of the genome appears both necessary and sufficient for virus production. Analysis of episomes from productive cells indicates a propensity to amplify TR numbers during the lytic cycle.
Soil and biogeochemical signatures of the Aripuanã base metal deposit, Mato Grosso, Brazil
Authors: Cornelius M. , Porto C. G. , Dunn C. E. , Butt C. R. M. , Oates C. , Coelho R. 
Published: April 2007

A geochemical survey was undertaken along two traverses at the Aripuanã base metal deposit in the Mato Grosso province of Brazil. Traverse 1 has residual and colluvial soils and intersects a 130-m-long gossan body near the top of a ridge. Traverse 2 intersects 10–20-m-wide base metal mineralization concealed by
c.
5–10 m of transported cover. Humic (A-horizon) and clay-rich and reddish (B-horizon) samples were collected on both traverses; saprolite was sampled on Traverse 1. The compositions of these regolith samples were compared with those of litter and bark samples from Traverse 1, and litter samples from Traverse 2. The soil samples were split into <75-μm and 75-250-μm fractions and, with saprolite samples, analysed for 68 elements following multi-acid, aqua regia or fusion digests. Samples of litter and bark from the imbauba tree (Moraceae family,
Cecropia
genus) were prepared by digesting dry tissue and ash in mixed acids.

Humic A-horizon soil samples exhibit the greatest anomaly contrast of all sample media. Fine-grained samples (<75 μm) are preferable for regional exploration, whereas coarser material (75–250 μm) is more suitable for prospect-scale surveys seeking gossan outcrops. Litter samples have similar contrasts to those in B-horizon samples, and delineate the gossan zones along both traverses. Bark samples from trees over the gossan are all anomalous and may indicate mineralization beneath barren regolith. The element suite that best identifies mineralization in soil at Aripuanã comprises the target elements Cu, Pb, Zn and Au, and associated pathfinder elements In, Mo and Hg. In dry litter, the best anomaly contrast is exhibited by Cu, Pb, Zn, As, Mo, Sb and In. In dry bark, the best indicators are Pb, Mo and Sb.
In depositional terrain, such as Traverse 2, both soil and litter appear to identify the location of mineralization but the number of samples is insufficient to exclude the possibility (at a probability >95%) of obtaining the same results by chance.