bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of a Mixture of Bacteriophages for Biological Control ofSalmonella entericaStrains in Compost
Authors: Heringa Spencer D. , Kim JinKyung , Jiang Xiuping , Doyle M. P. , Erickson M. C. 
Published: June 2010

ABSTRACTBacteriophages specific toSalmonellastrains were isolated from sewage effluent and characterized. A five-strain bacteriophage mixture was applied to dairy manure compost inoculated withSalmonella entericaserotype Typhimurium. Bacteriophage treatment resulted in a greater than 2-log-unit reduction ofSalmonellawithin 4 h at all moisture levels compared to the controls.
Host Association of
Campylobacter
Genotypes Transcends Geographic Variation
Authors: Sheppard Samuel K. , Colles Frances , Richardson Judith , Cody Alison J. , Elson Richard , Lawson Andrew , Brick Geraldine , Meldrum Richard , Little Christine L. , Owen Robert J. , Maiden Martin C. J. , McCarthy Noel D. 
Published: June 2010

ABSTRACT

Genetic attribution of bacterial genotypes has become a major tool in the investigation of the epidemiology of campylobacteriosis and has implicated retail chicken meat as the major source of human infection in several countries. To investigate the robustness of this approach to the provenance of the reference data sets used, a collection of 742
Campylobacter jejuni
and 261
Campylobacter coli
isolates obtained from United Kingdom-sourced chicken meat was established and typed by multilocus sequence typing. Comparative analyses of the data with those from other isolates sourced from a variety of host animals and countries were undertaken by genetic attribution, genealogical, and population genetic approaches. The genotypes from the United Kingdom data set were highly diverse, yet structured into sequence types, clonal complexes, and genealogical groups very similar to those seen in chicken isolates from the Netherlands, the United States, and Senegal, but more distinct from isolates obtained from ruminant, swine, and wild bird sources. Assignment analyses consistently grouped isolates from different host animal sources regardless of geographical source; these associations were more robust than geographic associations across isolates from three continents. We conclude that, notwithstanding the high diversity of these pathogens, there is a strong signal of association of multilocus genotypes with particular hosts, which is greater than the geographic signal. These findings are consistent with local and international transmission of host-associated lineages among food animal species and provide a foundation for further improvements in genetic attribution.
Isolation and Identification of Persistent Chlorinated Organophosphorus Flame Retardant-Degrading Bacteria
Authors: Takahashi Shouji , Satake Ikuko , Konuma Isao , Kawashima Koji , Kawasaki Manami , Mori Shingo , Morino Jun , Mori Junichi , Xu Hongde , Abe Katsumasa , Yamada Ryo-hei , Kera Yoshio 
Published: June 2010

ABSTRACTTris(2-chloroethyl) and tris(1,3-dichloro-2-propyl) phosphates are chlorinated persistent flame retardants that have recently emerged as environmental pollutants. Two bacterial strains that can degrade the compounds when they are the sole phosphorus sources have been isolated and identified as members of the sphingomonads. The strains can be useful for the bioremediation of environments contaminated with these compounds.
Stereochemistry of Furfural Reduction by a
Saccharomyces cerevisiae
Aldehyde Reductase That Contributes to
In Situ
Furfural Detoxification
Authors: Bowman Michael J. , Jordan Douglas B. , Vermillion Karl E. , Braker Jay D. , Moon Jaewoong , Liu Z. Lewis 
Published: June 2010

ABSTRACT

Ari1p from
Saccharomyces cerevisiae
, recently identified as an intermediate-subclass short-chain dehydrogenase/reductase, contributes
in situ
to the detoxification of furfural. Furfural inhibits efficient ethanol production by yeast, particularly when the carbon source is acid-treated lignocellulose, which contains furfural at a relatively high concentration. NADPH is Ari1p's best known hydride donor. Here we report the stereochemistry of the hydride transfer step, determined by using (4
R
)-[4-
2
H]NADPD and (4
S
)-[4-
2
H]NADPD and unlabeled furfural in Ari1p-catalyzed reactions and following the deuterium atom into products 2-furanmethanol or NADP
+
. Analysis of the products demonstrates unambiguously that Ari1p directs hydride transfer from the
si
face of NADPH to the
re
face of furfural. The singular orientation of substrates enables construction of a model of the Michaelis complex in the Ari1p active site. The model reveals hydrophobic residues near the furfural binding site that, upon mutation, may increase specificity for furfural and enhance enzyme performance. Using (4
S
)-[4-
2
H]NADPD and NADPH as substrates, primary deuterium kinetic isotope effects of 2.2 and 2.5 were determined for the steady-state parameters
k
cat
NADPH
and
k
cat
/

K
m

NADPH
, respectively, indicating that hydride transfer is partially rate limiting to catalysis.
Simple, Fast, and Sensitive Method for Quantification of Tellurite in Culture Media
Authors: Molina Roberto C. , Burra Radhika , Pérez-Donoso José M. , Elías Alex O. , Muñoz Claudia , Montes Rebecca A. , Chasteen Thomas G. , Vásquez Claudio C. 
Published: June 2010

ABSTRACT

A fast, simple, and reliable chemical method for tellurite quantification is described. The procedure is based on the NaBH
4
-mediated reduction of TeO
3
2−
followed by the spectrophotometric determination of elemental tellurium in solution. The method is highly reproducible, is stable at different pH values, and exhibits linearity over a broad range of tellurite concentrations.
Antibiotic Resistance Patterns and Detection ofblaDHA-1inSalmonellaSpecies Isolates from Chicken Farms in South Korea
Authors: Rayamajhi Nabin , Jung Byeong Yeal , Cha Seung Bin , Shin Min Kyung , Kim Aeran , Kang Min Su , Lee Kang Mu , Yoo Han Sang 
Published: June 2010

ABSTRACTFifteen nonrepetitive ampicillin-resistantSalmonellaspp. were identified among 91Salmonellasp. isolates during nationwide surveillance ofSalmonellain waste from 131 chicken farms during 2006 and 2007. Additional phenotyping and genetic characterization of these 15 isolates by using indicator cephalosporins demonstrated that resistance to ampicillin and reduced susceptibility to cefoxitin in three isolates was caused by TEM-1 and DHA-1 β-lactamases. Plasmid profiling and Southern blot analysis of these three DHA-1-positiveSalmonellaserovar Indiana isolates and previously reported unrelated clinical isolates of DHA-1-positiveSalmonellaserovar Montevideo,Klebsiella pneumoniae, andEscherichia colifrom humans and swine indicated the involvement of the large-size plasmid. Restriction enzyme digestion of the plasmids from the transconjugants showed variable restriction patterns except for the twoSalmonellaserovar Indiana isolates identified in this study. To the best of our knowledge, this is the first report of the presence of the DHA-1 gene amongSalmonellaspp. of animal origin.
Contribution of SMC (Structural Maintenance of Chromosomes) and SpoIIIE to Chromosome Segregation in Staphylococci
Authors: Yu Wenqi , Herbert Silvia , Graumann Peter L. , Götz Friedrich 
Published: June 2010

ABSTRACT

In contrast to rod-shaped bacteria, little is known about chromosomal maintenance and segregation in the spherical
Staphylococcus aureus
. The analysis of chromosomal segregation in
smc
(structural maintenance of chromosomes) and
spoIIIE
single and double mutants unravels differences in the chromosome dynamics in the spherical staphylococcal cells compared to the model in rods.
Carbonic Anhydrase Is Essential forStreptococcus pneumoniaeGrowth in Environmental Ambient Air
Authors: Burghout Peter , Cron Lorelei E. , Gradstedt Henrik , Quintero Beatriz , Simonetti Elles , Bijlsma Jetta J. E. , Bootsma Hester J. , Hermans Peter W. M. 
Published: June 2010

ABSTRACTThe respiratory tract pathogenStreptococcus pneumoniaeneeds to adapt to the different levels of carbon dioxide (CO2) it encounters during transmission, colonization, and infection. Since CO2is important for various cellular processes, factors that allow optimal CO2sequestering are likely to be important for pneumococcal growth and survival. In this study, we showed that the putative pneumococcal carbonic anhydrase (PCA) is essential forin vitrogrowth ofS. pneumoniaeunder the CO2-poor conditions found in environmental ambient air. Enzymatic analysis showed that PCA catalyzes the reversible hydration of CO2to bicarbonate (HCO3−), an essential step to prevent the cellular release of CO2. The addition of unsaturated fatty acids (UFAs) reversed the CO2-dependentin vitrogrowth inhibition ofS. pneumoniaestrains lacking thepcagene (Δpca), indicating that PCA-mediated CO2fixation is at least associated with HCO3−-dependentde novobiosynthesis of UFAs. Besides being necessary for growth in environmental ambient conditions, PCA-mediated CO2fixation pathways appear to be required for intracellular survival in host cells. This effect was especially pronounced during invasion of human brain microvascular endothelial cells (HBMEC) and uptake by murine J774 macrophage cells but not during interaction ofS. pneumoniaewith Detroit 562 pharyngeal epithelial cells. Finally, the highly conservedpcagene was found to be invariably present in both CO2-independent and naturally circulating CO2-dependent strains, suggesting a conserved essential role for PCA and PCA-mediated CO2fixation pathways for pneumococcal growth and survival.
The MerR/NmlR Family Transcription Factor of
Streptococcus pneumoniae
Responds to Carbonyl Stress and Modulates Hydrogen Peroxide Production
Authors: Potter Adam J. , Kidd Stephen P. , McEwan Alastair G. , Paton James C. 
Published: June 2010

ABSTRACT

The NmlR
sp
transcription factor of
Streptococcus pneumoniae
is shown to induce
adhC
(alcohol dehydrogenase) expression in the presence of both formaldehyde and methylglyoxal.

nmlR
sp

and
adhC
mutant strains display altered and opposite aerobic growth phenotypes. The

nmlR
sp

strain exhibits increased resistance to high oxygen tension, attributable to decreased H
2
O
2
production, which correlated with downregulation of carbamoyl phosphate synthase (
carB
). This indicates a possible role for AdhC in aldehyde metabolism and a broader role for NmlR
sp
in the regulation of carbon metabolism.
Polar Remodeling and Histidine Kinase Activation, Which Is Essential for
Caulobacter
Cell Cycle Progression, Are Dependent on DNA Replication Initiation
Authors: Iniesta Antonio A. , Hillson Nathan J. , Shapiro Lucy 
Published: June 2010

ABSTRACT

Caulobacter crescentus
initiates a single round of DNA replication during each cell cycle. Following the initiation of DNA replication, the essential CckA histidine kinase is activated by phosphorylation, which (via the ChpT phosphotransferase) enables the phosphorylation and activation of the CtrA global regulator. CtrA∼P then blocks the reinitiation of replication while regulating the transcription of a large number of cell cycle-controlled genes. It has been shown that DNA replication serves as a checkpoint for flagellar biosynthesis and cell division and that this checkpoint is mediated by the availability of active CtrA. Because CckA∼P promotes the activation of CtrA, we addressed the question of what controls the temporal activation of CckA. We found that the initiation of DNA replication is a prerequisite for remodeling the new cell pole, which includes the localization of the DivL protein kinase to that pole and, consequently, the localization, autophosphorylation, and activation of CckA at that pole. Thus, CckA activation is dependent on polar remodeling and a DNA replication initiation checkpoint that is tightly integrated with the polar phospho-signaling cascade governing cell cycle progression.
Complete Genome Sequence of
Bacillus thuringiensis
Mutant Strain BMB171
Authors: He Jin , Shao Xiaohu , Zheng Huajun , Li Mingshun , Wang Jieping , Zhang Qingye , Li Lin , Liu Ziduo , Sun Ming , Wang Shengyue , Yu Ziniu 
Published: June 2010

ABSTRACT

Bacillus thuringiensis
has been widely used as a biopesticide for a long time. Here we report the finished and annotated genome sequence of
B. thuringiensis
mutant strain BMB171, an acrystalliferous mutant strain with a high transformation frequency obtained and stocked in our laboratory.
Identification of Potential Serum Biomarkers of Glioblastoma: Serum Osteopontin Levels Correlate with Poor Prognosis
Authors: Sreekanthreddy Peddagangannagari , Srinivasan Harish , Kumar Durairaj Mohan , Nijaguna Mamatha Bangalore , Sridevi Sambandam , Vrinda Marigowda , Arivazhagan Arimappamagan , Balasubramaniam Anandh , Hegde Alangar Sathyaranjandas , Chandramouli Bangalore A. , Santosh Vani , Rao Manchanahalli R.S. , Kondaiah Paturu , Somasundaram Kumaravel 
Published: June 2010

Abstract
Background: The aim of this study is to identify serum biomarkers with classification and prognosis utility for astrocytoma, in particular glioblastoma (GBM).
Methods: Our previous glioma microarray database was mined to identify genes that encode secreted or membrane-localized proteins. Subsequent analysis was done using significant analysis of microarrays, followed by reverse transcription-quantitative PCR (RT-qPCR) and immunohistochemical validation in tumor tissues, ELISA and Western blot validation in sera, and correlation with survival of GBM patients.
Results: Significant analysis of microarrays identified 31 upregulated and 3 downregulated genes specifically in GBMs. RT-qPCR validation on an independent set of samples confirmed the GBM-specific differential expression of several genes, including three upregulated (CALU, CXCL9, and TIMP1) and two downregulated (GPX3 and TIMP3) novel genes. With respect to osteopontin (OPN), we show the GBM-specific upregulation by RT-qPCR and immunohistochemical staining of tumor tissues. Elevated serum OPN levels in GBM patients were also shown by ELISA and Western blot. GBM patients with high serum OPN levels had poorer survival than those with low serum OPN levels (median survival 9 versus 22 months respectively; P = 0.0001). Further, we also show high serum TIMP1 levels in GBM patients compared with grade II/III patients by ELISA and downregulation of serum GPX3 and TIMP3 proteins in GBMs compared with normal control by Western blot analysis.
Conclusions: Several novel potential serum biomarkers of GBM are identified and validated. High serum OPN level is found as a poor prognostic indicator in GBMs.
Impact: Identified serum biomarkers may have potential utility in astrocytoma classification and GBM prognosis. Cancer Epidemiol Biomarkers Prev; 19(6); 1409–22. ©2010 AACR.
Serum Adiponectin, Leptin, C-Peptide, Homocysteine, and Colorectal Adenoma Recurrence in the Polyp Prevention Trial
Authors: Bobe Gerd , Murphy Gwen , Rogers Connie J. , Hance Kenneth W. , Albert Paul S. , Laiyemo Adeyinka O. , Sansbury Leah B. , Lanza Elaine , Schatzkin Arthur , Cross Amanda J. 
Published: June 2010

Abstract
Background: Serum adiponectin, leptin, C-peptide, and homocysteine are indicators for obesity, hyperinsulinemia, and chronic inflammation, which have all been associated with colorectal cancer.
Aims: To determine whether serum adiponectin, leptin, C-peptide, and homocysteine are associated with fat, fiber, fruit and vegetable, flavonol, or dry bean intake and colorectal adenoma recurrence.
Methods: Using logistic regression, we estimated odds ratios (OR) and 95% confidence intervals (95% CI) for adenoma recurrence in 627 participants from the control arm of the Polyp Prevention Trial, a 4-year trial that examined the effectiveness of a low-fat, high-fiber, high-fruit and vegetable diet on adenoma recurrence.
Results: Serum concentrations of C-peptide and homocysteine were inversely related to fiber, fruit and vegetable, and flavonol intake and positively related to percentage of calories from fat (all Ptrend ≤0.01). High homocysteine concentrations were associated with any (4th versus 1st quartile: OR, 2.26; 95% CI, 1.30-3.94) and more than one adenoma recurrence (OR, 2.11; 95% CI, 1.01-4.40). Individuals in the highest, versus lowest, tertile of serum leptin concentration had a decreased risk of advanced adenoma recurrence (OR, 0.22; 95% CI, 0.06-0.79).
Conclusion: Our results suggest that serum homocysteine may serve as an indicator of dietary exposure, including a low-fat and high-fiber, high-fruit and vegetable, and high-flavonol diet, as well as colorectal adenoma recurrence.
Impact: Discovering biomarkers that are both modifiable and can predict cancer risk is critical. We identified serum homocysteine as a novel indicator that is modified by diet and predicts risk of adenoma recurrence. Cancer Epidemiol Biomarkers Prev; 19(6); 1441–52. ©2010 AACR.
Esophageal Adenocarcinoma Incidence: Are We Reaching the Peak?
Authors: Pohl Heiko , Sirovich Brenda , Welch H. Gilbert 
Published: June 2010

Abstract
Background: A steep increase in the incidence of esophageal adenocarcinoma has been observed between 1973 and 2001, but recent trends have not been reported. Our aim was to examine recent trends in esophageal adenocarcinoma incidence.
Methods: We used the Surveillance Epidemiology and End Results database of the National Cancer Institute to identify all patients who were diagnosed with esophageal adenocarcinoma between 1973 and 2006. Incidence trends were analyzed for esophageal adenocarcinoma overall and by stage using joinpoint regression.
Results: Overall esophageal adenocarcinoma incidence increased from 3.6 per million in 1973 to 25.6 per million in 2006. Incidence trend analysis, however, suggests that the increase has slowed, from an 8.2% annual increase prior to 1996 to 1.3% increase in subsequent years (P = 0.03). Stage-specific trend analyses suggest that the change in overall esophageal adenocarcinoma incidence largely reflects a plateau in the incidence of early stage disease. Its slope has changed direction, from a 10% annual increase prior to 1999 to a 1.6% decline in subsequent years (P = 0.01).
Conclusions: The incidence of early stage esophageal adenocarcinoma seems to have plateaued.
Impact: Although definitive conclusions will require additional years of data, the plateau in early stage disease might portend stabilization in the overall incidence of esophageal adenocarcinoma. Cancer Epidemiol Biomarkers Prev; 19(6); 1468–70. ©2010 AACR.
Safety, Efficacy, Pharmacokinetics, and Pharmacodynamics of the Combination of Sorafenib and Tanespimycin
Authors: Vaishampayan Ulka N. , Burger Angelika M. , Sausville Edward A. , Heilbrun Lance K. , Li Jing , Horiba M. Naomi , Egorin Merrill J. , Ivy Percy , Pacey Simon , LoRusso Patricia M. 
Published: June 2010

Abstract
Purpose: Heat shock protein (Hsp) 90 inhibition affects the Raf kinase signaling pathway and could enhance antitumor effects of sorafenib, a Raf kinase inhibitor. The combination of sorafenib and tanespimycin [17-allyl-amino-geldanamycin (17-AAG); NSC 330507/KOS-953] was evaluated in a phase I trial with the primary objective of defining a phase II dose.
Patients and Methods: The dose cohorts consisted of fixed continuous oral dosing of 400 mg sorafenib twice daily, starting at 14 days before tanespimycin, which was administered intravenously at escalating doses (starting at 300 mg/m,2 with 50 mg/m2 increments), on days 1, 8, and 15 in a 28-day cycle. Toxicity was assessed weekly, and response was evaluated every two cycles.
Results: Twenty-seven toxicity-evaluable patients were enrolled and treated at four dose levels. Predominant primary malignancies were renal cancer (12), melanoma (6), and colorectal cancer (4). Dose-limiting toxicities of grade 4 transaminitis and grade 3 hand-foot syndrome in one patient each were observed at 450 mg/m2 of tanespimycin. One hundred fourteen cycles were administered with a median of four cycles (range 1–17 cycles). Plasma concentrations of sorafenib and metabolites reached steady state after 7 days. Tanespimycin did not alter sorafenib concentrations. Pharmacodynamics showed a decrease in Hsp90 levels and induction of Hsp70. Clinical efficacy was observed in 9 of 12 renal cancer patients and 4 of 6 melanoma patients
Conclusions: Recommended phase II doses of this combination are 400 mg sorafenib twice daily and 400 mg/m2 tanespimycin on days 1, 8, and 15, every 28 days. Clinical and pharmacodynamic activity was observed in kidney cancer and melanoma. Clin Cancer Res; 16(14); 3795–804. ©2010 AACR.
Patients with Advanced Head and Neck Cancers Have Similar Progression-Free Survival on Phase I Trials and Their Last Food and Drug Administration–Approved Treatment
Authors: Garrido-Laguna Ignacio , Janku Filip , Falchook Gerald S. , Fu Siqing , Hong David S. , Naing Aung , Aaron Joanne , Wang Xuemei , Kies Merrill , Kurzrock Razelle 
Published: June 2010

AbstractPurpose: To compare clinical outcomes of metastatic head and neck cancer patients treated in phase I clinical trials with clinical outcomes of those patients who had their last Food and Drug Administration (FDA)–approved therapy in the setting of metastatic disease.Experimental Design: We retrospectively reviewed the outcomes of 61 consecutive patients with head and neck tumors treated in 36 phase I trials at The University of Texas M.D. Anderson Cancer Center between July 2004 and September 2009.Results: The most common histology was head and neck squamous cell carcinoma (62%). Median age was 55 years (range, 26-80). Eastern Cooperative Oncology Group performance status was 0 to 1 for 95% of patients. Fifty-nine patients had received FDA-approved drugs as the backbone of their last systemic therapy before inclusion in phase I trials (median, 2 systemic therapies). Progression-free survival (PFS) on phase I trials was not inferior to PFS on their last FDA-approved therapies (12 versus 10.7 weeks, log-rank P = 0.87). Fifty-three patients were evaluable for response by Response Evaluation Criteria in Solid Tumors criteria. Four (7%) had partial responses and 16 (26%) had stable disease for ≥4 months. In univariate analysis, number of metastatic sites, lactate dehydrogenase (LDH) levels at baseline, and Royal Marsden Hospital prognosis scores were significant predictors of survival. Only LDH was significant in multivariate analysis (hazard ratio, 6.35; P ≤ 0.0001).Conclusions: For patients with heavily pretreated advanced head and neck tumors, PFS on phase I trials is not inferior to PFS with their last FDA-approved therapy. The only significant predictor of survival in the multivariate analysis was baseline LDH. Clin Cancer Res; 16(15); 4031–7. ©2010 AACR.
Securing the circuit of intrathecally administered cancer drugs: example of a collective approach
Authors: Marliot Guillaume , Le Rhun Emilie , Sakji Ilyes , Bonneterre Jacques , Cazin Jean-Louis 
Published: June 2010

The treatment of leptomeningeal metastasis is based on protocols linking systemic chemotherapies and intrathecal injections of antineoplastic agents. Since the late 1960s, cases of accidental intrathecal injections of vinca-alkaloids, which have almost always proved fatal, have been documented. The most concerned countries, supported by the WHO, have published numerous recommendations aimed at reducing this type of risk. The aim of our work was to improve safety procedures for the intrathecal administration of antineoplastic drugs in an oncology hospital: the Centre Oscar Lambret, Lille, France. To this end, we compiled and analyzed a total of eight international recommendations. Our method was to meet the requirements of the AFSSAPS (French agency for the safety of health products), then to adopt recommended procedures in other countries, where appropriate. We considered the whole drugs circuit from prescription to administration. Improvements basically focused on the computerization of prescription, the dilution in mini-bags of vinca-alkaloids, and the additional labeling of intrathecally administered preparations as well as those with some vinca-alkaloids. This multidisciplinary approach to improve our practices complements the precautions taken by healthcare teams.