bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determination of Clonality and Relatedness of
Vibrio cholerae
Isolates by Genomic Fingerprinting, Using Long-Range Repetitive Element Sequence-Based PCR
Authors: Chokesajjawatee Nipa , Zo Young-Gun , Colwell Rita R. 
Published: July 2008

ABSTRACT

A high-throughput method which is applicable for rapid screening, identification, and delineation of isolates of
Vibrio cholerae
, sensitive to genome variation, and capable of providing phylogenetic inferences enhances environmental monitoring of this bacterium. We have developed and optimized a method for genomic fingerprinting of
V. cholerae
based on long-range PCR. The method uses a primer set directed to enterobacterial repetitive intergenic consensus sequences, a high-fidelity DNA polymerase, and analysis via conventional agarose gel electrophoresis. Long (∼10 kb), highly reproducible amplicons were generated from
V. cholerae
isolates, including those from different geographical locations and historical strains isolated during the period 1931-2000. The amplicons yielded reduced variability in their densitometric band patterns to ≤10% and clonal distinction at <90% similarity. Rapid band-matching analysis was accomplished for fingerprints with ≥90% similarity, discriminating O serotypes and biotypes (classical versus El Tor) as well as pathogenic and nonpathogenic strains. Compared to genome similarity measured by DNA-DNA hybridization, the results showed good correlation (
r
= 0.7;
P
< 0.001), with five times less measurement error and without bias. The method permits both phylogenetic inference and clonal differentiation of individual
V. cholerae
strains, enables robust, high-throughput analysis, and does not require specialized equipment to perform. With access to a curated public database furnished with appropriate analytical software applications, the method should prove useful in large-scale multilaboratory surveys, especially those designed to detect specific pathogens in the natural environment.
Secretion and Transcriptional Regulation of the Latex-Clearing Protein, Lcp, by the Rubber-Degrading Bacterium
Streptomyces
sp. Strain K30
Authors: Yikmis Meral , Arenskötter Matthias , Rose Karsten , Lange Nicole , Wernsmann Henrike , Wiefel Lars , Steinbüchel Alexander 
Published: July 2008

ABSTRACT

About 22,000 1-methyl-3-nitro-1-nitrosoguanidine- and UV-induced mutants of the rubber-degrading bacterium
Streptomyces
sp. strain K30 were characterized for the ability to produce clear zones on natural rubber latex overlay agar plates. Thirty-five mutants were defective solely in cleavage of rubber and were phenotypically complemented with the wild-type
lcp
(
l
atex
c
learing
p
rotein) gene. Sixty-nine mutants exhibited a pleiotropic phenotype and were impaired in utilization of rubber and xylan, indicating that the enzymes responsible for the initial cleavage of these polymers are exported by the same secretion pathway (Q. K. Beg, M. Kapoor, L. Mahajan, and G. S. Hoondal, Appl. Microbiol. Biotechnol.
56:
326-3381, 2001; U. K. Laemmli, Nature
227:
680-685, 1970). Analysis of the amino acid sequence encoded by
lcp
revealed a twin-arginine motif, indicating that Lcp is a substrate of the twin-arginine translocation (Tat) pathway (K. Dilks, W. Rose, E. Hartmann, and M. Pohlschröder, J. Bacteriol.
185:
1478-1483, 2003). A
tatC
disruption mutant of
Streptomyces lividans
10-164 harboring
lcp
from
Streptomyces
sp. strain K30 was not capable of forming clear zones on rubber overlay agar plates. Moreover, Lcp and enhanced green fluorescent protein fusion proteins were detected in the supernatant. Using
Escherichia coli
having the twin-arginine motif in the signal peptide upstream of Lcp, clear evidence that Lcp is secreted was obtained. Transcriptional analysis revealed basal expression of Lcp in glucose-grown cells and that transcription of
lcp
is obviously induced in the presence of poly(
cis
-1,4-isoprene). In contrast,
oxiB
and
oxiA
, which are located directly downstream of
lcp
and putatively encode a heteromultimeric aldehyde dehydrogenase oxidizing the primary cleavage products generated by Lcp from poly(
cis
-1,4-isoprene), were expressed only in the presence of poly(
cis
-1,4-isoprene). Expression of
lcp
at a low level is thus required for sensing the polymer in the medium. Rubber degradation products may then induce the transcription of genes coding for enzymes catalyzing the later steps of poly(
cis
-1,4-isoprene) degradation and the transcription of
lcp
itself.
lcp, oxiB
, and
oxiA
seem to constitute an operon, as a polycistronic mRNA comprising these three genes was detected. The transcriptional start site of
lcp
was mapped 400 bp upstream of the
lcp
start codon.
Differential Attachment to and Subsequent Contamination of Agricultural Crops by
Salmonella enterica
Authors: Barak Jeri D. , Liang Anita , Narm Koh-Eun 
Published: July 2008

ABSTRACT

U.S. salmonellosis outbreaks have occurred following consumption of tomato and cantaloupe but not lettuce. We report differential contamination among agricultural seedlings by
Salmonella enterica
via soil. Members of the family Brassicaceae had a higher incidence of outbreak than carrot, lettuce, and tomato. Once they were contaminated, phyllosphere populations were similar, except for tomato. Contamination differences exist among tomato cultivars.
Use of Atomic Force Microscopy and Transmission Electron Microscopy for Correlative Studies of Bacterial Capsules
Authors: Stukalov Oleg , Korenevsky Anton , Beveridge Terry J. , Dutcher John R. 
Published: July 2008

ABSTRACT

Bacteria can possess an outermost assembly of polysaccharide molecules, a capsule, which is attached to their cell wall. We have used two complementary, high-resolution microscopy techniques, atomic force microscopy (AFM) and transmission electron microscopy (TEM), to study bacterial capsules of four different gram-negative bacterial strains:
Escherichia coli
K30,
Pseudomonas aeruginosa
FRD1,
Shewanella oneidensis
MR-4, and
Geobacter sulfurreducens
PCA. TEM analysis of bacterial cells using different preparative techniques (whole-cell mounts, conventional embeddings, and freeze-substitution) revealed capsules for some but not all of the strains. In contrast, the use of AFM allowed the unambiguous identification of the presence of capsules on all strains used in the present study, including those that were shown by TEM to be not encapsulated. In addition, the use of AFM phase imaging allowed the visualization of the bacterial cell within the capsule, with a depth sensitivity that decreased with increasing tapping frequency.
Evidence of Complex Transcriptional, Translational, and Posttranslational Regulation of the Extracytoplasmic Function Sigma Factor σ
E
in
Mycobacterium tuberculosis
Authors: Donà Valentina , Rodrigue Sébastien , Dainese Elisa , Palù Giorgio , Gaudreau Luc , Manganelli Riccardo , Provvedi Roberta 
Published: July 2008

ABSTRACT

The extracytoplasmic factor (ECF) sigma factor σ
E
is one of the most studied sigma factors of
Mycobacterium tuberculosis
. It has been shown to be involved in virulence as well as in survival under conditions of high temperature, alkaline pH, and exposure to detergents and oxidative stress. Unlike many ECF sigma factors, σ
E
does not directly regulate the transcription of its own gene. Two promoters have been identified upstream of the
sigE
gene; one is regulated by the two-component system MprAB, while the other has been shown to be σ
H
dependent. In this paper, we further characterize the regulation of σ
E
by identifying its anti-sigma factor and a previously unknown promoter. Finally, we show that
sigE
can be translated from three different translational start codons, depending on the promoter used. Taken together, our data demonstrate that σ
E
not only is subjected to complex transcriptional regulation but is also controlled at the translational and posttranslational levels.
Antitumor activity of histone deacetylase inhibitors in non-small cell lung cancer cells: development of a molecular predictive model
Authors: Miyanaga Akihiko , Gemma Akihiko , Noro Rintaro , Kataoka Kiyoko , Matsuda Kuniko , Nara Michiya , Okano Tetsuya , Seike Masahiro , Yoshimura Akinobu , Kawakami Akiko , Uesaka Haruka , Nakae Hiroki , Kudoh Shoji 
Published: July 2008

Abstract
To ascertain the potential for histone deacetylase (HDAC) inhibitor-based treatment in non-small cell lung cancer (NSCLC), we analyzed the antitumor effects of trichostatin A (TSA) and suberoylanilide hydroxamic acid (vorinostat) in a panel of 16 NSCLC cell lines via 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. TSA and vorinostat both displayed strong antitumor activities in 50% of NSCLC cell lines, suggesting the need for the use of predictive markers to select patients receiving this treatment. There was a strong correlation between the responsiveness to TSA and vorinostat (P &lt; 0.0001). To identify a molecular model of sensitivity to HDAC inhibitor treatment in NSCLC, we conducted a gene expression profiling study using cDNA arrays on the same set of cell lines and related the cytotoxic activity of TSA to corresponding gene expression pattern using a modified National Cancer Institute program. In addition, pathway analysis was done with Pathway Architect software. We used nine genes, which were identified by gene-drug sensitivity correlation and pathway analysis, to build a support vector machine algorithm model by which sensitive cell lines were distinguished from resistant cell lines. The prediction performance of the support vector machine model was validated by an additional nine cell lines, resulting in a prediction value of 100% with respect to determining response to TSA and vorinostat. Our results suggested that (a) HDAC inhibitors may be promising anticancer drugs to NSCLC and (b) the nine-gene classifier is useful in predicting drug sensitivity to HDAC inhibitors and may contribute to achieving individualized therapy for NSCLC patients. [Mol Cancer Ther 2008;7(7):1923–30]
Antitumor activity and pharmacokinetic properties of PF-00299804, a second-generation irreversible pan-erbB receptor tyrosine kinase inhibitor
Authors: Gonzales Andrea J. , Hook Kenneth E. , Althaus Irene W. , Ellis Paul A. , Trachet Erin , Delaney Amy M. , Harvey Patricia J. , Ellis Teresa A. , Amato Danielle M. , Nelson James M. , Fry David W. , Zhu Tong , Loi Cho-Ming , Fakhoury Stephen A. , Schlosser Kevin M. , Sexton Karen E. , Winters R. Thomas , Reed Jessica E. , Bridges Alex J. , Lettiere Daniel J. , Baker Deborah A. , Yang Jianxin , Lee Helen T. , Tecle Haile , Vincent Patrick W. 
Published: July 2008

Abstract
Signaling through the erbB receptor family of tyrosine kinases contributes to the proliferation, differentiation, migration, and survival of a variety of cell types. Abnormalities in members of this receptor family have been shown to play a role in oncogenesis, thus making them attractive targets for anticancer treatments. PF-00299804 is a second-generation irreversible pan-erbB receptor tyrosine kinase inhibitor currently in phase I clinical trials. PF-00299804 is believed to irreversibly inhibit erbB tyrosine kinase activity through binding at the ATP site and covalent modification of nucleophilic cysteine residues in the catalytic domains of erbB family members. Oral administration of PF-00299804 causes significant antitumor activity, including marked tumor regressions in a variety of human tumor xenograft models that express and/or overexpress erbB family members or contain the double mutation (L858R/T790M) in erbB1 (EGFR) associated with resistance to gefitinib and erlotinib. Furthermore, PF-00299804 shows exceptional distribution to human tumor xenografts and excellent pharmacokinetic properties across species. [Mol Cancer Ther 2008;7(7):1880–9]
Identification and characterization of NVP-BEZ235, a new orally available dual phosphatidylinositol 3-kinase/mammalian target of rapamycin inhibitor with potent in vivo antitumor activity
Authors: Maira Sauveur-Michel , Stauffer Frédéric , Brueggen Josef , Furet Pascal , Schnell Christian , Fritsch Christine , Brachmann Saskia , Chène Patrick , De Pover Alain , Schoemaker Kevin , Fabbro Doriano , Gabriel Daniela , Simonen Marjo , Murphy Leon , Finan Peter , Sellers William , García-Echeverría Carlos 
Published: July 2008

Abstract
The phosphatidylinositol 3-kinase (PI3K)/Akt/mammalian target of rapamycin inhibitor (mTOR) pathway is often constitutively activated in human tumor cells, providing unique opportunities for anticancer therapeutic intervention. NVP-BEZ235 is an imidazo[4,5-c]quinoline derivative that inhibits PI3K and mTOR kinase activity by binding to the ATP-binding cleft of these enzymes. In cellular settings using human tumor cell lines, this molecule is able to effectively and specifically block the dysfunctional activation of the PI3K pathway, inducing G1 arrest. The cellular activity of NVP-BEZ235 translates well in in vivo models of human cancer. Thus, the compound was well tolerated, displayed disease stasis when administered orally, and enhanced the efficacy of other anticancer agents when used in in vivo combination studies. Ex vivo pharmacokinetic/pharmacodynamic analyses of tumor tissues showed a time-dependent correlation between compound concentration and PI3K/Akt pathway inhibition. Collectively, the preclinical data show that NVP-BEZ235 is a potent dual PI3K/mTOR modulator with favorable pharmaceutical properties. NVP-BEZ235 is currently in phase I clinical trials. [Mol Cancer Ther 2008;7(7):1–13 [Mol Cancer Ther 2008;7(7):1851–13]
RANK ligand inhibition plus docetaxel improves survival and reduces tumor burden in a murine model of prostate cancer bone metastasis
Authors: Miller Robert E. , Roudier Martine , Jones Jon , Armstrong Allison , Canon Jude , Dougall William C. 
Published: July 2008

Abstract
Tumor cells induce excessive osteoclastogenesis, mediating pathologic bone resorption and subsequent release of growth factors and calcium from bone matrix, resulting in a “vicious cycle” of bone breakdown and tumor proliferation. RANK ligand (RANKL) is an essential mediator of osteoclast formation, function, and survival. In metastatic prostate cancer models, RANKL inhibition directly prevents osteolysis via blockade of osteoclastogenesis and indirectly reduces progression of skeletal tumor burden by reducing local growth factor and calcium concentrations. Docetaxel, a well-established chemotherapy for metastatic hormone-refractory prostate cancer, arrests the cell cycle and induces apoptosis of tumor cells. Suppression of osteoclastogenesis through RANKL inhibition may enhance the effects of docetaxel on skeletal tumors. We evaluated the combination of the RANKL inhibitor osteoprotegerin-Fc (OPG-Fc) with docetaxel in a murine model of prostate cancer bone metastasis. Tumor progression, tumor area, and tumor proliferation and apoptosis were assessed. OPG-Fc alone reduced bone resorption (P &lt; 0.001 versus PBS), inhibited progression of established osteolytic lesions, and reduced tumor area (P &lt; 0.0001 versus PBS). Docetaxel alone reduced tumor burden (P &lt; 0.0001 versus PBS) and delayed the development of osteolytic lesions. OPG-Fc in combination with docetaxel suppressed skeletal tumor burden (P = 0.0005) and increased median survival time by 16.7% (P = 0.0385) compared with docetaxel alone. RANKL inhibition may enhance docetaxel effects by increasing tumor cell apoptosis as evident by increased active caspase-3. These studies show that inhibition of RANKL provides an additive benefit to docetaxel treatment in a murine model of prostate cancer bone metastasis and supports clinical evaluation of this treatment option in patients. [Mol Cancer Ther 2008;7(7):2160–9]
Differing management of people with advanced cancer and delirium by four sub-specialties
Authors: Agar M , Currow DC , Plummer J , Chye R , Draper B 
Published: July 2008

Introduction: Delirium in advanced cancer is prevalent, with limited prospective data to guide management. The aim was to survey current practice of specialists using two contrasting cases of delirium in cancer. Methods: A questionnaire was designed to identify investigations and treatment used, in relation to two cases. Results: Overall response rate ( n = 270) was 30%. Place of care: Only 35% of medical oncologists would consider care at home for a patient with reversible delirium compared with 66% of other specialists. Investigations: 85% specialists would order basic bloods, however, medical oncologists were more likely to use oxygen saturation and head computed tomography, psychogeriatricians more likely to order thyroid function and palliative medicine specialists less likely to order chest X-ray and urine culture. Greater than 40% of specialists would do no investigations for terminal delirium. Treatment: Medical oncologists use more pre-emptive therapies and more likely to use a benzodiazepine as agent of choice, and Palliative medicine specialists used significantly more neuroleptics to treat hypoactive symptoms of delirium. Discussion: The survey emphasise significant areas of variability in the management of delirium in advanced cancer. Furthermore, evidence to guide management in ways that draw on the strengths and knowledge of each specialty is urgently needed.
Complications of Distraction Lengthening in the Hand
Authors: HEO C. Y. , KWON S. , BACK G. H. , CHUNG M. S. 
Published: July 2008

This study examined the features of 16 complications from 51 distraction lengthenings in the hands of 43 patients. From 1996 to 2006, 24 metacarpals and 27 phalanges were lengthened at a rate of 0.5 and 0.25 mm/day, respectively, using a callus distraction technique. The indications were congenital (33 cases in 27 patients) and traumatic (18 cases in 16 patients) deformities. The average percentage lengthening in the phalanges and metacarpals was 62% (16 mm) and 63% (34 mm), respectively. The distraction rates in the phalanges and metacarpals were 69 and 52 days/cm, respectively. The overall complication rate was 31%. Major complications requiring secondary procedures were non-union (one case), fracture (one case), premature union (one case), angulations (two cases) and dislodgment of pins (two cases). The minor complications encountered were delayed callus formation (four cases), joint stiffness (four cases) and soft tissue thinning (one case). Traumatic deformities had more complications than the congenital ones (nine of 18 cases and seven of 33 cases, respectively). The phalanges had a higher rate of complication than the metacarpals (11 of 27 cases and four of 24 cases, respectively). Most patients with complications except for two children with dislodgment were as satisfied with the final results as those without complications. Although callus distraction in the hand requires a long treatment period and has a relatively high rate of complication, it appears to be effective in achieving adequate bone length. A high level of patient compliance and prompt management of complications by an experienced surgeon are essential for achieving good results.
High density linkage disequilibrium maps of chromosome 14 in Holstein and Angus cattle
Authors: Marques Elisa , Schnabel Robert D , Stothard Paul , Kolbehdari Davood , Wang Zhiquan , Taylor Jeremy F , Moore Stephen S 
Published: July 2008

Abstract

Background
Linkage disequilibrium (LD) maps can provide a wealth of information on specific marker-phenotype relationships, especially in areas of the genome where positional candidate genes with similar functions are located. A recently published high resolution radiation hybrid map of bovine chromosome 14 (BTA14) together with the bovine physical map have enabled the creation of more accurate LD maps for BTA14 in both dairy and beef cattle.

Results
Over 500 Single Nucleotide Polymorphism (SNP) markers from both Angus and Holstein animals had their phased haplotypes estimated using GENOPROB and their pairwise r2 values compared. For both breeds, results showed that average LD extends at moderate levels up to 100 kilo base pairs (kbp) and falls to background levels after 500 kbp. Haplotype block structure analysis using HAPLOVIEW under the four gamete rule identified 122 haplotype blocks for both Angus and Holstein. In addition, SNP tagging analysis identified 410 SNPs and 420 SNPs in Holstein and Angus, respectively, for future whole genome association studies on BTA14. Correlation analysis for marker pairs common to these two breeds confirmed that there are no substantial correlations between r-values at distances over 10 kbp. Comparison of extended haplotype homozygosity (EHH), which calculates the LD decay away from a core haplotype, shows that in Holstein there is long range LD decay away from the DGAT1 region consistent with the selection for milk fat % in this population. Comparison of EHH values for Angus in the same region shows very little long range LD.

Conclusion
Overall, the results presented here can be applied in future single or haplotype association analysis for both populations, aiding in confirming or excluding potential polymorphisms as causative mutations, especially around Quantitative Trait Loci regions. In addition, knowledge of specific LD information among markers will aid the research community in selecting appropriate markers for whole genome association studies.
Cost per case or total cost? The potential of prevention of hand injuries in young children – Retrospective and prospective studies
Authors: Ljungberg Elinor M , Carlsson Katarina Steen , Dahlin Lars B 
Published: July 2008

Abstract

Background
Health-care costs for hand and forearm injuries in young children are poorly documented. We examined costs in 533 children injured years 1996–2003.

Methods
Health-care costs and costs for lost productivity were retrospectively calculated in children from three catchment areas in Sweden. Seven case categories corresponding to alternative prevention strategies were constructed.

Results
Over time, diminishing number of ward days reduced the health-care cost per case. Among children, the cost of lost productivity due to parental leave was 14 percent of total cost. Fingertip injuries had low median costs but high total costs due to their frequency. Complex injuries by machine or rifle had high costs per case, and despite a low number of cases, total cost was high. Type of injury, surgery and physiotherapy sessions were associated with variations in health-care cost. Low age and ethnic background had a significant effect on number of ward days.

Conclusion
The costs per hand injury for children were lower compared to adults due to both lower health-care costs and to the fact that parents had comparatively short periods of absence from work. Frequent simple fingertip injuries and rare complex injuries induce high costs for society. Such costs should be related to costs for prevention of these injuries.