bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Heat Shock Protein YbeY Is Required for Optimal Activity of the 30S Ribosomal Subunit
Authors: Rasouly Aviram , Davidovich Chen , Ron Eliora Z. 
Published: July 2010

ABSTRACT

The highly conserved bacterial
ybeY
gene is a heat shock gene whose function is not fully understood. Previously, we showed that the YbeY protein is involved in protein synthesis, as
Escherichia coli
mutants with
ybeY
deleted exhibit severe translational defects
in vivo
. Here we show that the
in vitro
activity of the translation machinery of
ybeY
deletion mutants is significantly lower than that of the wild type. We also show that the lower efficiency of the translation machinery is due to impaired 30S small ribosomal subunits.
The Omptins ofYersinia pestisandSalmonella entericaCleave the Reactive Center Loop of Plasminogen Activator Inhibitor 1
Authors: Haiko Johanna , Laakkonen Liisa , Juuti Katri , Kalkkinen Nisse , Korhonen Timo K. 
Published: July 2010

ABSTRACTPlasminogen activator inhibitor 1 (PAI-1) is a serine protease inhibitor (serpin) and a key molecule that regulates fibrinolysis by inactivating human plasminogen activators. Here we show that two important human pathogens, the plague bacteriumYersinia pestisand the enteropathogenSalmonella entericaserovar Typhimurium, inactivate PAI-1 by cleaving the R346-M347 bait peptide bond in the reactive center loop. No cleavage of PAI-1 was detected withYersinia pseudotuberculosis, an oral/fecal pathogen from whichY. pestishas evolved, or withEscherichia coli. The cleavage and inactivation of PAI-1 were mediated by the outer membrane proteases plasminogen activator Pla ofY. pestisand PgtE protease ofS. enterica, which belong to the omptin family of transmembrane endopeptidases identified in Gram-negative bacteria. Cleavage of PAI-1 was also detected with the omptins Epo ofErwinia pyrifoliaeand Kop ofKlebsiella pneumoniae, which both belong to the same omptin subfamily as Pla and PgtE, whereas no cleavage of PAI-1 was detected with omptins ofShigella flexneriorE. colior theYersiniachromosomal omptins, which belong to other omptin subfamilies. The results reveal a novel serpinolytic mechanism by which enterobacterial species expressing omptins of the Pla subfamily bypass normal control of host proteolysis.
H-NS Silences
gfp
, the Green Fluorescent Protein Gene:
gfp
TCD
Is a Genetically Remastered
gfp
Gene with Reduced Susceptibility to H-NS-Mediated Transcription Silencing and with Enhanced Translation
Authors: Corcoran Colin P. , Cameron Andrew D. S. , Dorman Charles J. 
Published: July 2010

ABSTRACT

The bacterial nucleoid-associated protein H-NS, which preferentially targets and silences A+T-rich genes, binds the ubiquitous reporter gene
gfp
and dramatically reduces local transcription. We have redesigned
gfp
to reduce H-NS-mediated transcription silencing and simultaneously improve translation
in vivo
without altering the amino acid sequence of the GFP protein.
Genome Sequences of
Lactococcus lactis
MG1363 (Revised) and NZ9000 and Comparative Physiological Studies
Authors: Linares Daniel M. , Kok Jan , Poolman Bert 
Published: July 2010

ABSTRACT

Lactococcus lactis
NZ9000 and its parent MG1363 are the most commonly used lactic acid bacteria for expression and physiological studies. We noted unexpected but significant differences in the growth behaviors of both strains. We sequenced the entire genomes of the original NZ9000 and MG1363 strains using an ultradeep sequencing strategy. The analysis of the
L. lactis
NZ9000 genome yielded 79 differences, mostly point mutations, with the annotated genome sequence of
L. lactis
MG1363. Resequencing of the MG1363 strain revealed that 73 out of the 79 differences were due to errors in the published sequence. Comparative transcriptomic studies revealed several differences in the regulation of genes involved in sugar fermentation, which can be explained by two specific mutations in a region of the
ptcC
promoter with a key role in the regulation of cellobiose and glucose uptake.
Regulation of
ciaXRH
Operon Expression and Identification of the CiaR Regulon in
Streptococcus mutans
Authors: Wu Chenggang , Ayala Eduardo A. , Downey Jennifer S. , Merritt Justin , Goodman Steven D. , Qi Fengxia 
Published: July 2010

ABSTRACT

The
ciaRH
operon in
Streptococcus mutans
contains 3 contiguous genes,
ciaXRH
. Unlike the CiaRH system in other streptococci, only the
ciaH
-null mutant displays defective phenotypes, while the
ciaR
-null mutant behaves like the wild type. The objective of this study was to determine the mechanism of this unusual property. We demonstrate that the
ciaH
mutation caused a >20-fold increase in
ciaR
transcript synthesis. A
ciaRH
double deletion reversed the
ciaH
phenotype, suggesting that overexpressed
ciaR
might be responsible for the observed
ciaH
phenotypes. When
ciaR
was forced to be overexpressed by a transcriptional fusion to the
ldh
promoter in the wild-type background, the same
ciaH
phenotypes were restored, confirming the involvement of overexpressed
ciaR
in the
ciaH
phenotypes. The
ciaH
mutation and
ciaR
overexpression also caused transcriptional alterations in 100 genes, with 15 genes upregulated >5-fold. Bioinformatics analysis identified a putative CiaR regulon consisting of 8 genes/operons, including the
ciaXRH
operon itself, all of which were upregulated.
In vitro
footprinting on 4 of the 8 promoters revealed a protected region of 26 to 28 bp encompassing two direct repeats, NTTAAG-n5-WTTAAG, 10 bp upstream of the −10 region, indicating direct binding of the CiaR protein to these promoters. Taken together, we conclude that overexpressed CiaR, as a result of either
ciaH
deletion or forced expression from a constitutive promoter, is a mediator in the CiaH-regulated phenotypes.
Pmr, a Histone-Like Protein H1 (H-NS) Family Protein Encoded by the IncP-7 Plasmid pCAR1, Is a Key Global Regulator That Alters Host Function
Authors: Yun Choong-Soo , Suzuki Chiho , Naito Kunihiko , Takeda Toshiharu , Takahashi Yurika , Sai Fumiya , Terabayashi Tsuguno , Miyakoshi Masatoshi , Shintani Masaki , Nishida Hiromi , Yamane Hisakazu , Nojiri Hideaki 
Published: July 2010

ABSTRACTHistone-like protein H1 (H-NS) family proteins are nucleoid-associated proteins (NAPs) conserved among many bacterial species. The IncP-7 plasmid pCAR1 is transmissible among variousPseudomonasstrains and carries a gene encoding the H-NS family protein, Pmr.Pseudomonas putidaKT2440 is a host of pCAR1, which harbors five genes encoding the H-NS family proteins PP_1366 (TurA), PP_3765 (TurB), PP_0017 (TurC), PP_3693 (TurD), and PP_2947 (TurE). Quantitative reverse transcription-PCR (qRT-PCR) demonstrated that the presence of pCAR1 does not affect the transcription of these five genes and that onlypmr,turA, andturBwere primarily transcribed in KT2440(pCAR1).In vitropull-down assays revealed that Pmr strongly interacted with itself and with TurA, TurB, and TurE. Transcriptome comparisons of thepmrdisruptant, KT2440, and KT2440(pCAR1) strains indicated thatpmrdisruption had greater effects on the host transcriptome than did pCAR1 carriage. The transcriptional levels of some genes that increased with pCAR1 carriage, such as themexEF-oprNefflux pump genes andparI, reverted withpmrdisruption to levels in pCAR1-free KT2440. Transcriptional levels of putative horizontally acquired host genes were not altered by pCAR1 carriage but were altered bypmrdisruption. Identification of genome-wide Pmr binding sites by ChAP-chip (chromatin affinity purification coupled with high-density tiling chip) analysis demonstrated that Pmr preferentially binds to horizontally acquired DNA regions. The Pmr binding sites overlapped well with the location of the genes differentially transcribed followingpmrdisruption on both the plasmid and the chromosome. Our findings indicate that Pmr is a key factor in optimizing gene transcription on pCAR1 and the host chromosome.
NtcA Regulates
patA
Expression in
Anabaena
sp. Strain PCC 7120
Authors: Bastet Laurène , Boileau Céline , Bédu Sylvie , Janicki Annick , Latifi Amel , Zhang Cheng-Cai 
Published: July 2010

ABSTRACT

patA
expression is induced 3 to 6 h after nitrogen step-down. We establish that the transcription of
patA
is under the positive control of NtcA. The
patA
promoter region shows two conserved NtcA-binding boxes. These NtcA-binding sites and their interaction with NtcA are key elements for
patA
expression in heterocysts.
Complete Genome Sequence of the Diesel-Degrading
Acinetobacter
sp. Strain DR1
Authors: Jung Jaejoon , Baek Jeong-Hun , Park Woojun 
Published: July 2010

ABSTRACT

The genus
Acinetobacter
is ubiquitous in soil, aquatic, and sediment environments and includes pathogenic strains, such as
A. baumannii
. Many
Acinetobacter
species isolated from various environments have biotechnological potential since they are capable of degrading a variety of pollutants.
Acinetobacter
sp. strain DR1 has been identified as a diesel degrader. Here we report the complete genome sequence of
Acinetobacter
sp. DR1 isolated from the soil of a rice paddy.
Genome Sequence of
Fulvimarina pelagi
HTCC2506
T
, a Mn(II)-Oxidizing Alphaproteobacterium Possessing an Aerobic Anoxygenic Photosynthetic Gene Cluster and Xanthorhodopsin
Authors: Kang Ilnam , Oh Hyun-Myung , Lim Seung-Il , Ferriera Steve , Giovannoni Stephen J. , Cho Jang-Cheon 
Published: July 2010

ABSTRACT

Fulvimarina pelagi
is a Mn(II)-oxidizing marine heterotrophic bacterium in the order
Rhizobiales
. Here we announce the draft genome sequence of
F. pelagi
HTCC2506
T
, which was isolated from the Sargasso Sea by using dilution-to-extinction culturing. The genome sequence contained a xanthorhodopsin gene as well as a photosynthetic gene cluster, which suggests the coexistence of two different phototrophic mechanisms in a single microorganism.
Urinary neopterin and nitric oxide metabolites as markers of interferon β-1a activity in primary progressive multiple sclerosis
Authors: Rejdak K. , Leary SM , Petzold A. , Thompson AJ , Miller DH , Giovannoni G. 
Published: July 2010

Background: Interferon beta has not been demonstrated to be effective in exploratory phase 2 clinical trials in primary progressive multiple sclerosis. However, using more sensitive indicators of a treatment response, such as biomarkers, might help to identify sub-groups of patients who may benefit from therapy. Objective: To assess the utility of measuring urinary neopterin and nitric oxide metabolite excretion for monitoring interferon β-1a (IFNβ-1a) treatment in patients with primary progressive multiple sclerosis. Methods: Fifty patients from a phase II trial of IFNβ-1a (Placebo n = 20; Avonex® 1 × 30 μg/week (IFN-30), n = 15; Avonex® 1 × 60 μg/week (IFN-60), n = 15), were enrolled. Patients were assessed using the Expanded Disability Status Scale. Urine samples were collected on each visit, 3 months apart, for a period of 24 months. Nitric oxide metabolites, nitrite/nitrate (NOx), were measured by colorimetric assay and neopterin and creatinine (Cr) were assayed using a high-performance liquid chromatography technique. NOx/creatinine ratio (NOxCR) and urinary neopterin/creatinine ratio (UNCR) quotients were calculated. Results: There was no significant difference between pre-dose, baseline levels of UNCR or NOxCR between the study groups. On the intention-to-treat analysis, there was a significant difference in UNCR levels between the placebo compared with IFN-30 ( p = 0.03) or IFN-60 ( p = 0.002) groups. The IFN-30 and IFN-60 groups did not differ. Within IFNβ-1a-treated patients with primary progressive multiple sclerosis, median UNCR values were significantly higher in clinically stable (no Expanded Disability Status Scale change) compared with progressive patients ( p = 0.002). IFNβ-1a treatment did not significantly influence NOx excretion in patients with primary progressive multiple sclerosis. Conclusions: Urinary neopterin is a potential biomarker to monitor the in vivo effects of IFNβ-1a in primary progressive multiple sclerosis and other multiple sclerosis sub-types.
Review: Association between angiotensin converting enzyme G2350A polymorphism and hypertension risk: a meta-analysis
Authors: Wenquan Niu  , Yue Qi  , Pingjin Gao  , Dingliang Zhu  
Published: July 2010

Background and objective: An exonic polymorphism G2350A (rs4343) in angiotensin converting enzyme (protein: ACE; gene: ACE) was shown to exert the most significant influence on plasma ACE levels. We therefore performed a meta-analysis to investigate association of ACE G2350A polymorphism with hypertension. Methods: Published case-control studies in English were identified. A total of four studies with 1699 cases and 1274 controls were identified. A random-effects model was performed irrespective of the between-study heterogeneity. Study quality was assessed in duplicate. Results: Compared with 2350G, the ACE 2350A allele conferred a protective effect on hypertension (odds ratio (OR) = 0.81; 95% confidence interval (CI), 0.56—1.18; p = .28). Similarly, comparisons of 2350AA and 2350GA with 2350GG generated a nonsignificant reduced risk, respectively. Under the dominant model, the ACE 2350A allele conferred a reduced hypertension risk and such associations were divergent between Han Chinese and Muslims from the Arab Gulf and Pakistan. Under the recessive model, this protective effect was totally reversed (OR = 1.01; 95% CI, 0.77—1.33; p = .94). Subgroup analyses indicated a significant protective effect of ACE 2350A compared with 2350G among Muslims from the Arab Gulf and Pakistan (OR = 0.55; 95% CI, 0.42—0.71; p < .00001). No publication biases were observed. Conclusions: Our results demonstrate that the ACE 2350A allele is associated with a significantly reduced hypertension risk among Muslims from the Arab Gulf and Pakistan, yet an elevated risk among Han Chinese.
Methylprednisolone infusion for life-threatening H1N1-virus infection
Authors: Confalonieri Marco , Cifaldi Rossella , Dreas Lorella , Viviani Marino , Biolo Marco , Gabrielli Marco 
Published: July 2010

Background: During winter 2009 we treated with prolonged corticosteroid infusion eight consecutive patients affected by H1N1-virus infection and severe pneumonia. The most severe patient was a previously healthy 30-year-old man admitted to hospital because of bilateral pneumonia and severe acute respiratory failure. Method: H1N1-virus infection was detected by broncho-alveolar lavage performed on day 1. After some days following admission the patient was still in a life-threatening state, not responding to oseltamivir, protective mechanical ventilation and veno-arterial extracorporeal membrane oxygenation (ECMO). Results: The addition of methylprednisolone infusion at a stress dose (1 mg/kg/24 h) as rescue therapy significantly and rapidly improved the clinical condition. Weaning from ECMO and invasive mechanical ventilation was possible within a relatively few days. Conclusion: According to the literature reports more than 34% of H1N1-virus severe infections were treated with corticosteroids. This report and our experience may suggest a possible life-saving use of corticosteroids at a stress dose in severely ill patients with an H1N1-virus infection that is not responding to the most advanced treatments.
Integration of physical and genetic maps of common bean through BAC-derived microsatellite markers
Authors: Córdoba Juana M , Chavarro Carolina , Schlueter Jessica A , Jackson Scott A , Blair Matthew W 
Published: July 2010

AbstractBackgroundCommon bean (Phaseolus vulgarisL.) is the most important legume for direct human consumption and the goal of this study was to integrate a recently constructed physical map for the species with a microsatellite based genetic map using a BAC library from the genotype G19833 and the recombinant inbred line population DOR364 × G19833.ResultsWe searched for simple sequence repeats (SSRs) in the 89,017 BAC-end sequences (BES) from the physical map and genetically mapped any polymorphic BES-SSRs onto the genetic map. Among the BES it was possible to identify 623 contig-linked SSRs, most of which were highly AT-rich. A subgroup of 230 di-nucleotide and tri-nucleotide based SSR primer pairs from these BACs was tested on the mapping parents with 176 single copy loci and 114 found to be polymorphic markers. Of these, 99 were successfully integrated into the genetic map. The 99 linkages between the genetic and physical maps corresponded to an equal number of contigs containing a total of 5,055 BAC clones.ConclusionsClass II microsatellites were more common in the BES than longer class I microsatellites. Both types of markers proved to be valuable for linking BAC clones to the genetic map and were successfully placed across all 11 linkage groups. The integration of common bean physical and genetic maps is an important part of comparative genome analysis and a prelude to positional cloning of agronomically important genes for this crop.
The role of prostaglandin E2 (PGE 2) in toll-like receptor 4 (TLR4)-mediated colitis-associated neoplasia
Authors: Hernandez Yasmin , Sotolongo John , Breglio Keith , Conduah Daisy , Chen Anli , Xu Ruliang , Hsu David , Ungaro Ryan , Hayes Lory A , Pastorini Cristhine , Abreu Maria T , Fukata Masayuki 
Published: July 2010

AbstractBackgroundWe have previously found that TLR4-deficient (TLR4-/-) mice demonstrate decreased expression of mucosal PGE2and are protected against colitis-associated neoplasia. However, it is still unclear whether PGE2is the central factor downstream of TLR4 signaling that promotes intestinal tumorigenesis. To further elucidate critical downstream pathways involving TLR4-mediated intestinal tumorigenesis, we examined the effects of exogenously administered PGE2in TLR4-/- mice to see if PGE2bypasses the protection from colitis-associated tumorigenesis.MethodMouse colitis-associated neoplasia was induced by azoxymethane (AOM) injection followed by two cycles of dextran sodium sulfate (DSS) treatment. Two different doses of PGE2(high dose group, 200 μg, n = 8; and low dose group, 100 μg, n = 6) were administered daily during recovery period of colitis by gavage feeding. Another group was given PGE2during DSS treatment (200 μg, n = 5). Inflammation and dysplasia were assessed histologically. Mucosal Cox-2 and amphiregulin (AR) expression, prostanoid synthesis, and EGFR activation were analyzed.ResultsIn control mice treated with PBS, the average number of tumors was greater in WT mice (n = 13) than in TLR4-/- mice (n = 7). High dose but not low dose PGE2treatment caused an increase in epithelial proliferation. 28.6% of PBS-treated TLR4-/- mice developed dysplasia (tumors/animal: 0.4 ± 0.2). By contrast, 75.0% (tumors/animal: 1.5 ± 1.2, P < 0.05) of the high dose group and 33.3% (tumors/animal: 0.3 ± 0.5) of the low dose group developed dysplasia in TLR4-/- mice. Tumor size was also increased by high dose PGE2treatment. Endogenous prostanoid synthesis was differentially affected by PGE2treatment during acute and recovery phases of colitis. Exogenous administration of PGE2increased colitis-associated tumorigenesis but this only occurred during the recovery phase. Lastly, PGE2treatment increased mucosal expression of AR and Cox-2, thus inducing EGFR activation and forming a positive feedback mechanism to amplify mucosal Cox-2.ConclusionsThese results highlight the importance of PGE2as a central downstream molecule involving TLR4-mediated intestinal tumorigenesis.
Relationship between H.Pylori infection and clinicopathological features and prognosis of gastric cancer
Authors: Qiu Hai-Bo , Zhang Li-Yi , Keshari Rajiv-Prasad , Wang Guo-Qiang , Zhou Zhi-Wei , Xu Da-Zhi , Wang Wei , Zhan You-Qin , Li Wei 
Published: July 2010

Abstract

Background
Aimed to assess the relationship between H.Pylori and the clinicopathological features and prognosis of gastric cancer by quantitative detection of H.Pylori.

Methods
157 patients were enrolled, all patients had a record of clinicopathological parameters. Specimens including the tumor and non-neoplastic were detected for H.Pylori by Real-Time PCR and analyzed clinical data retrospectively. Variables independently affecting prognosis were investigated by means of multivariate analysis using the Cox proportional hazards model.

Results
H.Pylori infection was greater in non-neoplastic tissue than the tumor tissue (p < 0.05), H.Pylori infection and its copies were related to the tumor site and N staging (p < 0.05). Overall survival (OS) in all 157 patients has no correlation with the H.Pylori infection status (p = 0.715). As to the patients who underwent a curative surgery, relapse-free survival (RFS) has no correlation with the H.Pylori infection status (p = 0.639). Among the H.Pylori positive patients, OS and RFS of those with higher copies were longer than in patients with low copies, but there was no significant statistical difference.

Conclusions
H.Pylori infection status and its copies were related to N staging. The OS and RFS in patients with positive H.Pylori status has no significant difference from the patients with negative H.Pylori status.
A diagnostic PCR assay for the detection of an Australian epidemic strain of Pseudomonas aeruginosa
Authors: Williams Heidi L , Turnbull Lynne , Thomas Susan J , Murphy Anna , Stinear Tim , Armstrong David S , Whitchurch Cynthia B 
Published: July 2010

Abstract

Background
Chronic lung infection with the bacterium Pseudomonas aeruginosa is one of the hallmarks of cystic fibrosis (CF) and is associated with worsening lung function, increased hospitalisation and reduced life expectancy. A virulent clonal strain of P. aeruginosa (Australian epidemic strain I; AES-I) has been found to be widespread in CF patients in eastern Australia.

Methods
Suppression subtractive hybridization (SSH) was employed to identify genetic sequences that are present in the AES-I strain but absent from the sequenced reference strain PAO1. We used PCR to evaluate the distribution of several of the AES-I loci amongst a collection of 188 P. aeruginosa isolates which was comprised of 35 AES-I isolates (as determined by PFGE), 78 non-AES-I CF isolates including other epidemic CF strains as well as 69 P. aeruginosa isolates from other clinical and environmental sources.

Results
We have identified a unique AES-I genetic locus that is present in all 35 AES-I isolates tested and not present in any of the other 153 P. aeruginosa strains examined. We have used this unique AES-I locus to develop a diagnostic PCR and a real-time PCR assay to detect the presence of P. aeruginosa and AES-I in patient sputum samples.

Conclusions
We have developed diagnostic PCR assays that are 100% sensitive and 100% specific for the P. aeruginosa strain AES-I. We have also shown that Whatman FTA® Elute cards may be used with PCR-based assays to rapidly detect the presence of P. aeruginosa strains in CF sputum.
Expression and intracellular localization of duck enteritis virus pUL38 protein
Authors: Xiang Jun , Ma Guangpeng , Zhang Shunchuan , Cheng Anchun , Wang Mingshu , Zhu Dekang , Jia Renyong , Luo Qihui , Chen Zhengli , Chen Xiaoyue 
Published: July 2010

Abstract
Knowledge of the intracellular location of a protein can provide useful insights into its function. Bioinformatic studies have predicted that the DEV pUL38 mainly targets the cytoplasm and nucleus. In this study, we obtained anti-pUL38 polyclonal sera. These antibodies were functional in western blotting and immunofluorescence in DEV-infected duck embryo fibroblasts (DEFs). pUL38 was expressed as a 51-kDa protein from 8 h post-infection onward, initially showing a diffuse distribution throughout the cytoplasm, and later in the nucleus. Furthermore, pUL38 was found in purified virus. These results provide the first evidence of the kinetics of expression and intracellular localization of DEV pUL38.