bluuebunny/crossref_metadata_2025_split huggingface dataset:
Domain Organization and Evolution of Multifunctional Autoprocessing Repeats-in-Toxin (MARTX) Toxin in
Vibrio vulnificus
Authors: Roig Francisco J. , González-Candelas Fernando , Amaro Carmen 
Published: November 2010

ABSTRACT

The objective of this study was to analyze multifunctional autoprocessing repeats-in-toxin (MARTX) toxin domain organization within the aquatic species
Vibrio vulnificus
as well as to study the evolution of the
rtxA1
gene. The species is subdivided into three biotypes that differ in host range and geographical distribution. We have found three different types (I, II, and III) of
V. vulnificus
MARTX (MARTX
Vv
) toxins with common domains (an autocatalytic cysteine protease domain [CPD], an α
/
β-hydrolase domain, and a domain resembling that of the LifA protein of
Escherichia coli
O127:H6 E2348/69 [Efa/LifA]) and specific domains (a Rho-GTPase inactivation domain [RID], a domain of unknown function [DUF],a domain resembling that of the
rtxA
protein of
Photorhabdus asymbiotica
[
rtxA
PA
], and an actin cross-linking domain [ACD]). Biotype 1 isolates harbor MARTX
Vv
toxin types I and II, biotype 2 isolates carry MARTX
Vv
toxin type III, and biotype 3 isolates have MARTX
Vv
toxin type II. The analyzed biotype 2 isolates harbor two identical copies of
rtxA1
, one chromosomal and the other plasmidic. The evolutionary history of the gene demonstrates that MARTX
Vv
toxins are mosaics, comprising pieces with different evolutionary histories, some of which have been acquired by intra- or interspecific horizontal gene transfer. Finally, we have found evidence that the evolutionary history of the
rtxA1
gene for biotype 2 differs totally from the gene history of biotypes 1 and 3.
Randomized Soil Survey of the Distribution of
Burkholderia pseudomallei
in Rice Fields in Laos
Authors: Rattanavong Sayaphet , Wuthiekanun Vanaporn , Langla Sayan , Amornchai Premjit , Sirisouk Joy , Phetsouvanh Rattanaphone , Moore Catrin E. , Peacock Sharon J. , Buisson Yves , Newton Paul N. 
Published: November 2010

ABSTRACT

Melioidosis is a major cause of morbidity and mortality in Southeast Asia, where the causative organism (
Burkholderia pseudomallei
) is present in the soil. In the Lao People's Democratic Republic (Laos),
B. pseudomallei
is a significant cause of sepsis around the capital, Vientiane, and has been isolated in soil near the city, adjacent to the Mekong River. We explored whether
B. pseudomallei
occurs in Lao soil distant from the Mekong River, drawing three axes across northwest, northeast, and southern Laos to create nine sampling areas in six provinces. Within each sampling area, a random rice field site containing a grid of 100 sampling points each 5 m apart was selected. Soil was obtained from a depth of 30 cm and cultured for
B. pseudomallei
. Four of nine sites (44%) were positive for
B. pseudomallei
, including all three sites in Saravane Province, southern Laos. The highest isolation frequency was in east Saravane, where 94% of soil samples were
B. pseudomallei
positive with a geometric mean concentration of 464 CFU/g soil (95% confidence interval, 372 to 579 CFU/g soil; range, 25 to 10,850 CFU/g soil). At one site in northwest Laos (Luangnamtha), only one sample (1%) was positive for
B. pseudomallei
, at a concentration of 80 CFU/g soil. Therefore,
B. pseudomallei
occurs in Lao soils beyond the immediate vicinity of the Mekong River, alerting physicians to the likelihood of melioidosis in these areas. Further studies are needed to investigate potential climatic, soil, and biological determinants of this heterogeneity.
Phylogeographical Patterns among Mediterranean Sepiolid Squids and TheirVibrioSymbionts: Environment Drives Specificity among Sympatric Species
Authors: Zamborsky D. J. , Nishiguchi M. K. 
Published: November 2010

ABSTRACTBobtail squid from the generaSepiolaandRondeletiola(Cephalopoda: Sepiolidae) form mutualistic associations with luminous Gram-negative bacteria (Gammaproteobacteria:Vibrionaceae) from the generaVibrioandPhotobacterium. Symbiotic bacteria proliferate inside a bilobed light organ until they are actively expelled by the host into the surrounding environment on a diel basis. This event results in a dynamic symbiont population with the potential to establish the symbiosis with newly hatched sterile (axenic) juvenile sepiolids. In this study, we examined the genetic diversity found in populations of sympatric sepiolid squid species and their symbionts by the use of nested clade analysis with multiple gene analyses. Variation found in the distribution of different species of symbiotic bacteria suggests a strong influence of abiotic factors in the local environment, affecting bacterial distribution among sympatric populations of hosts. These abiotic factors include temperature differences incurred by a shallow thermocline, as well as a lack of strong coastal water movement accompanied by seasonal temperature changes in overlapping niches. Host populations are stable and do not appear to have a significant role in the formation of symbiont populations relative to their distribution across the Mediterranean Sea. Additionally, all squid species examined (Sepiola affinis,S. robusta,S. ligulata,S. intermedia, andRondeletiola minor) are genetically distinct from one another regardless of location and demonstrate very little intraspecific variation within species. These findings suggest that physical boundaries and distance in relation to population size, and not host specificity, are important factors in limiting or defining gene flow within sympatric marine squids and their associated bacterial symbionts in the Mediterranean Sea.
Isolation of Oligotrophic Denitrifiers Carrying Previously Uncharacterized Functional Gene Sequences
Authors: Ishii Satoshi , Ashida Naoaki , Otsuka Shigeto , Senoo Keishi 
Published: November 2010

ABSTRACT

Oligotrophic denitrifying bacteria, including those belonging to the genera
Herbaspirillum
,
Azospirillum
, and
Bradyrhizobium
, were obtained using a single-cell isolation technique. The taxonomic composition of the denitrifier population was similar to those assessed by previous culture-independent studies. The sequencing of nitrite reductase and N
2
O reductase genes of these strains revealed previously unknown links between 16S rRNA and the denitrification-functional gene phylogenies. In particular, we identified
Bradyrhizobium
strains that harbor
nirS
sequences previously detected only in culture-independent studies.
Comparative Genomics and the Evolution of Pathogenicity in Human Pathogenic Fungi
Authors: Moran Gary P. , Coleman David C. , Sullivan Derek J. 
Published: November 2010

ABSTRACT

Because most fungi have evolved to be free-living in the environment and because the infections they cause are usually opportunistic in nature, it is often difficult to identify specific traits that contribute to fungal pathogenesis. In recent years, there has been a surge in the number of sequenced genomes of human fungal pathogens, and comparison of these sequences has proved to be an excellent resource for exploring commonalities and differences in how these species interact with their hosts. In order to survive in the human body, fungi must be able to adapt to new nutrient sources and environmental stresses. Therefore, genes involved in carbohydrate and amino acid metabolism and transport and genes encoding secondary metabolites tend to be overrepresented in pathogenic species (e.g.,
Aspergillus fumigatus
). However, it is clear that human commensal yeast species such as
Candida albicans
have also evolved a range of specific factors that facilitate direct interaction with host tissues. The evolution of virulence across the human pathogenic fungi has occurred largely through very similar mechanisms. One of the most important mechanisms is gene duplication and the expansion of gene families, particularly in subtelomeric regions. Unlike the case for prokaryotic pathogens, horizontal transfer of genes between species and other genera does not seem to have played a significant role in the evolution of fungal virulence. New sequencing technologies promise the prospect of even greater numbers of genome sequences, facilitating the sequencing of multiple genomes and transcriptomes within individual species, and will undoubtedly contribute to a deeper insight into fungal pathogenesis.
Aerobic Degradation of Mercaptosuccinate by the Gram-Negative BacteriumVariovorax paradoxusStrain B4
Authors: Carbajal-Rodríguez Irma , Stöveken Nadine , Satola Barbara , Wübbeler Jan Hendrik , Steinbüchel Alexander 
Published: November 2010

ABSTRACTThe Gram-negative bacteriumVariovorax paradoxusstrain B4 was isolated from soil under mesophilic and aerobic conditions to elucidate the so far unknown catabolism of mercaptosuccinate (MS). During growth with MS this strain released significant amounts of sulfate into the medium. Tn5::mob-induced mutagenesis was successfully employed and yielded nine independent mutants incapable of using MS as a carbon source. In six of these mutants, Tn5::mobinsertions were mapped in a putative gene encoding a molybdenum (Mo) cofactor biosynthesis protein (moeA). In two further mutants the Tn5::mobinsertion was mapped in the gene coding for a putative molybdopterin (MPT) oxidoreductase. In contrast to the wild type, these eight mutants also showed no growth on taurine. In another mutant a gene putatively encoding a 3-hydroxyacyl-coenzyme A dehydrogenase (paaH2) was disrupted by transposon insertion. Upon subcellular fractionation of wild-type cells cultivated with MS as sole carbon and sulfur source, MPT oxidoreductase activity was detected in only the cytoplasmic fraction. Cells grown with succinate, taurine, or gluconate as a sole carbon source exhibited no activity or much lower activity. MPT oxidoreductase activity in the cytoplasmic fraction of the Tn5::mob-induced mutant Icr6 was 3-fold lower in comparison to the wild type. Therefore, a new pathway for MS catabolism inV. paradoxusstrain B4 is proposed: (i) MPT oxidoreductase catalyzes the conversion of MS first into sulfinosuccinate (a putative organo-sulfur compound composed of succinate and a sulfino group) and then into sulfosuccinate by successive transfer of oxygen atoms, (ii) sulfosuccinate is cleaved into oxaloacetate and sulfite, and (iii) sulfite is oxidized to sulfate.
argC
Orthologs from
Rhizobiales
Show Diverse Profiles of Transcriptional Efficiency and Functionality in
Sinorhizobium meliloti
Authors: Díaz Rafael , Vargas-Lagunas Carmen , Villalobos Miguel Angel , Peralta Humberto , Mora Yolanda , Encarnación Sergio , Girard Lourdes , Mora Jaime 
Published: November 2010

ABSTRACT

Several factors can influence ortholog replacement between closely related species. We evaluated the transcriptional expression and metabolic performance of ortholog substitution complementing a
Sinorhizobium meliloti argC
mutant with
argC
from
Rhizobiales
(
Agrobacterium tumefaciens
,
Rhizobium etli
, and
Mesorhizobium loti
). The
argC
gene is necessary for the synthesis of arginine, an amino acid that is central to protein and cellular metabolism. Strains were obtained carrying plasmids with
argC
orthologs expressed under the
speB
and
argC
(
S. meliloti
) and
lac
(
Escherichia coli
) promoters. Complementation analysis was assessed by growth, transcriptional activity, enzymatic activity, mRNA levels, specific detection of ArgC proteomic protein, and translational efficiency. The
argC
orthologs performed differently in each complementation, reflecting the diverse factors influencing gene expression and the ability of the ortholog product to function in a foreign metabolic background. Optimal complementation was directly related to sequence similarity with
S. meliloti
, and was inversely related to species signature, with
M. loti argC
showing the poorest performance, followed by
R. etli
and
A. tumefaciens
. Different copy numbers of genes and amounts of mRNA and protein were produced, even with genes transcribed from the same promoter, indicating that coding sequences play a role in the transcription and translation processes. These results provide relevant information for further genomic analyses and suggest that orthologous gene substitutions between closely related species are not completely functionally equivalent.
Type I Signal Peptidase and Protein Secretion inStaphylococcus epidermidis
Authors: Powers Michael E. , Smith Peter A. , Roberts Tucker C. , Fowler Bruce J. , King Charles C. , Trauger Sunia A. , Siuzdak Gary , Romesberg Floyd E. 
Published: November 2010

ABSTRACTBacterial protein secretion is a highly orchestrated process that is essential for infection and virulence. Despite extensive efforts to predict or experimentally detect proteins that are secreted, the characterization of the bacterial secretome has remained challenging. A central event in protein secretion is the type I signal peptidase (SPase)-mediated cleavage of the N-terminal signal peptide that targets a protein for secretion via the general secretory pathway, and the arylomycins are a class of natural products that inhibit SPase, suggesting that they may be useful chemical biology tools for characterizing the secretome. Here, using an arylomycin derivative, along with two-dimensional gel electrophoresis and liquid chromatography-tandem mass spectrometry (LC-MS/MS), we identify 11 proteins whose secretion from stationary-phaseStaphylococcusepidermidisis dependent on SPase activity, 9 of which are predicted to be translated with canonical N-terminal signal peptides. In addition, we find that the presence of extracellular domains of lipoteichoic acid synthase (LtaS) and the β-lactam response sensor BlaR1 in the medium is dependent on SPase activity, suggesting that they are cleaved at noncanonical sites within the protein. In all, the data define the proteins whose stationary-phase secretion depends on SPase and also suggest that the arylomycins should be valuable chemical biology tools for the study of protein secretion in a wide variety of different bacteria.
Translation Efficiency of Antiterminator Proteins Is a Determinant for the Difference in Glucose Repression of Two β-Glucoside Phosphotransferase System Gene Clusters inCorynebacterium glutamicumR
Authors: Tanaka Yuya , Teramoto Haruhiko , Inui Masayuki , Yukawa Hideaki 
Published: November 2010

ABSTRACTCorynebacterium glutamicumR has two β-glucoside phosphoenolpyruvate, carbohydrate phosphotransferase systems (PTS) encoded bybglFandbglF2located in the respective clusters,bglF-bglA-bglGandbglF2-bglA2-bglG2. Previously, we reported that whereas β-glucoside-dependent induction ofbglFis strongly repressed by glucose, glucose repression ofbglF2is very weak. Here, we reveal the mechanism behind the different effects of glucose on the twobglgenes. Deletion of the ribonucleic antiterminator sequence and transcriptional terminator located upstream of the translation initiation codon ofbglFmarkedly relieved the glucose repression of abglF-lacZfusion, indicating that glucose affects the antitermination mechanism that is responsible for the β-glucoside-dependent induction of thebglFcluster. The glucose repression ofbglFmRNA was also relieved by introducing a multicopy plasmid carrying thebglGgene encoding an antiterminator of thebglFcluster. Moreover, replacement of the GUG translation initiation codon ofbglGwith AUG was effective in relieving the glucose repression ofbglFandbglG. Inversely, expression ofbglF2andbglG2was subject to strict glucose repression in a mutant strain in which the AUG translation initiation codon ofbglG2encoding antiterminator of thebglF2cluster was replaced with GUG. These results suggest that the translation initiation efficiency of the antiterminator proteins, at least in part, determines whether the target genes are subject to glucose repression. We also found thatbglFexpression was induced by glucose in the BglG-overexpressing strains, which may be explained by the ability of BglF to transport glucose.
Complete Genome Sequence of Japanese
Erwinia
Strain Ejp617, a Bacterial Shoot Blight Pathogen of Pear
Authors: Park Duck Hwan , Thapa Shree Prasad , Choi Beom-Soon , Kim Won-Sik , Hur Jang Hyun , Cho Jun Mo , Lim Jong-Sung , Choi Ik-Young , Lim Chun Keun 
Published: November 2010

ABSTRACT

The Japanese
Erwinia
strain Ejp617 is a plant pathogen that causes bacterial shoot blight of pear in Japan. Here, we report the complete genome sequence of strain Ejp617 isolated from Nashi pears in Japan to provide further valuable insight among related
Erwinia
species.
Complete Genome Sequence of Adherent Invasive
Escherichia
coli
UM146 Isolated from Ileal Crohn's Disease Biopsy Tissue
Authors: Krause Denis O. , Little Ainsley C. , Dowd Scot E. , Bernstein Charles N. 
Published: November 2010

ABSTRACT

Escherichia
coli
UM146 was isolated from the ileum of a Crohn's disease patient. It adheres to and invades enterocytes and can replicate inside macrophages. Its complete genome sequence reveals that it is most closely related to the human urinary tract pathogen
E
.
coli
CFT073, but it has a host of genes that are novel and to which no function has been ascribed.
Genome Sequence of
Leuconostoc fallax
KCTC 3537
Authors: Nam Seong-Hyeuk , Choi Sang-Haeng , Kang Aram , Kim Dong-Wook , Kim Dae-Soo , Kim Ryong Nam , Kim Aeri , Park Hong-Seog 
Published: November 2010

ABSTRACT

Leuconostoc fallax
is known to be present during the manufacturing process of kimchi, the best-known traditional Korean dish. Here, we present the draft genome sequence of the type strain
Leuconostoc fallax
KCTC 3537 (1,638,971 bp, with a G+C content of 37.5%), which consists of 30 large contigs (>100 bp in size).
Translation of mechanical exposure in the workplace into common metrics for meta-analysis: a reliability and validity study
Authors: Griffith Lauren E , Wells Richard P , Shannon Harry S , Walter Stephen D , Cole Donald C , Côté Pierre , Frank John , Hogg-Johnson Sheilah , Langlois Lacey E 
Published: November 2010

ObjectivesWe previously assessed inter-rater reliability of expert raters using six scales to estimate the intensity of literature-based mechanical exposures. The objectives of this study were to estimate the impact on the inter-rater reliability of using non-expert (NE) raters and to assess the validity of our scales.MethodsWe used 7-point scales to represent three dimensions of mechanical exposures at work: 1) trunk posture, 2) weight lifted or force exerted and 3) spinal loading. We estimated both peak and cumulative loads and called this an “interpretive translation” of exposure. A second method, “algorithmic translation”, used the original units in which the exposure data was collected. These data were used to assess the inter-rater reliability and validity of the NE interpretive translation of exposure.ResultsThe NE inter-rater reliability for the scales ranged from 0.24 to 0.46. The correlation between the means of the NE and expert ratings were >0.7. Although there was a strong relationship between the NE interpretive and the algorithmic translation, there was some evidence that the interpretive translation plateaus at higher level of exposure.ConclusionsThis study supports using NE raters to estimate the intensity of literature-based mechanical exposure metrics using a common set of scales which can be applied across epidemiologic studies. We would need to average the ratings of at least five NE raters to have an acceptable level of reliability (>0.7). These metrics may be useful to quantify the relationship between workplace mechanical exposure and low back pain in a systematic review and meta-analysis.
Loss of PTEN Permits CXCR4-Mediated Tumorigenesis through ERK1/2 in Prostate Cancer Cells
Authors: Chetram Mahandranauth A. , Odero-Marah Valerie , Hinton Cimona V. 
Published: November 2010

Abstract
Loss of PTEN is frequently observed in androgen-independent prostate cancer, resulting in the deregulation of metastatic events. SDF1α activation of CXCR4 induces signaling pathways that have been implicated in prostate metastasis and progression to an advanced disease. The pathways of CXCR4 and PTEN converge, leading to the promotion and regulation of tumorigenesis, respectively. However, loss of PTEN may permit CXCR4 to progress prostate cancer to an advanced disease. In the present study, we investigated the involvement of PTEN in CXCR4-mediated tumorigenesis. When screening advanced metastatic prostate cancer cell lines for PTEN, we observed a loss of expression in PC3 and LNCaP cells whereas Du145 expressed wild-type PTEN. All three cell lines were positive for surface expression of CXCR4. Reconsitution of PTEN induced a mesenchymal to epithelial like morphologic change and inhibited CXCR4-mediated migration and proliferation in PC3 cells. Downregulation of PTEN by siRNA enhanced the CXCR4-mediated migratory behavior of Du145 cells. By Western blot analysis, we observed that PTEN inhibited basal AKT phosphorylation but not ERK1/2 phosphorylation in PTEN-expressing cells. Upon CXCR4 stimulation, PTEN inhibited ERK1/2 phosphorylation but not phosphorylation of AKT. The CXCR4-mediated migration of PC3 cells was through the ERK1/2 pathway, as confirmed by chemical inhibitors. On the basis of these studies, we suggest that loss of PTEN permits CXCR4-mediated functions in prostate cancer cells through the ERK1/2 pathway. Antagonizing CXCR4 and downstream signaling cascades may provide an efficient approach for treating patients with advanced prostate cancer when hormone therapy fails to the stop the growth and containment of tumors. Mol Cancer Res; 9(1); 90–102 ©2010 AACR.
Proanthocyanidins Inhibit UV-Induced Immunosuppression Through IL-12–Dependent Stimulation of CD8+ Effector T Cells and Inactivation of CD4+ T Cells
Authors: Vaid Mudit , Singh Tripti , Li Anna , Katiyar Nandan , Sharma Samriti , Elmets Craig A. , Xu Hui , Katiyar Santosh K. 
Published: November 2010

AbstractThe inhibition of UVB-induced immunosuppression by dietary grape seed proanthocyanidins (GSP) has been associated with the induction of interleukin (IL)-12 in mice, and we now confirm that GSPs do not inhibit UVB-induced immunosuppression in IL-12p40 knockout (IL-12 KO) mice and that treatment of these mice with recombinant IL-12 restores the inhibitory effect. To characterize the cell population responsible for the GSP-mediated inhibition of UVB-induced immunosuppression and the role of IL-12 in this process, we used an adoptive transfer approach. Splenocytes and draining lymph nodes were harvested from mice that had been administered dietary GSPs (0.5%–1.0%, w/w), exposed to UVB, and sensitized by the application of 2,4-dinitrofluorobenzene (DNFB) onto the UVB-exposed skin. CD8+ and CD4+ T cells were positively selected and transferred into naive mice that were subsequently challenged by application of DNFB on the ear skin. Naive recipients that received CD8+ T cells from GSP-treated, UVB-irradiated donors exhibited full contact hypersensitivity (CHS) response. Naive mice that received CD4+ suppressor T cells from GSP-treated, UVB-exposed mice could mount a CHS response after sensitization and subsequent challenge with DNFB. On culture, the CD8+ T cells from GSP-treated, UVB-exposed mice secreted higher levels (5- to 8-fold) of Th1 cytokines than CD8+ T cells from UVB-irradiated mice not treated with GSPs. CD4+ T cells from GSP-treated, UVB-exposed mice secreted significantly lower levels (80%–100%) of Th2 cytokines than CD4+ T cells from UVB-exposed mice not treated with GSPs. These data suggest that GSPs inhibit UVB-induced immunosuppression by stimulating CD8+ effector T cells and diminishing regulatory CD4+ T cells. Cancer Prev Res; 4(2); 238–47. ©2010 AACR.