bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Analysis of the Methanol- and Methylamine-Specific Methyltransferase 2 Genes of
Methanosarcina acetivorans
C2A
Authors: Bose Arpita , Pritchett Matthew A. , Metcalf William W. 
Published: March 2008

ABSTRACT

The entry of methanol into the methylotrophic pathway of methanogenesis is mediated by the concerted effort of two methyltransferases, namely, methyltransferase 1 (MT1) and methyltransferase 2 (MT2). The
mtaA1
,
mtaA2
, and
mtbA
genes of
Methanosarcina acetivorans
C2A encode putative methanol- or methylamine-specific MT2 enzymes. To address the in vivo roles of these genes in growth and methanogenesis from known substrates, we constructed and characterized mutants with deletions of each of these genes. The
mtaA1
gene is required for growth on methanol, whereas
mtaA2
was dispensable. However, the
mtaA2
mutant had a reduced rate of methane production from methanol. Surprisingly, deletion of
mtaA1
in combination with deletions of the genes encoding three methanol-specific MT1 isozymes led to lack of growth on acetate, suggesting that MT1 and MT2 enzymes might play an important role during growth on this substrate. The
mtbA
gene was required for dimethylamine and monomethylamine (MMA) utilization and was important, but not required, for trimethylamine utilization. Analysis of reporter gene fusions revealed that both
mtaA1
and
mtbA
were expressed on all methanogenic substrates tested. However,
mtaA1
expression was induced on methanol, while
mtbA
expression was down-regulated on MMA and acetate.
mtaA2
was expressed at very low levels on all substrates. The
mtaA1
transcript had a large 5′ untranslated region (UTR) (275 bp), while the 5′ UTR of the
mtbA
transcript was only 28 bp long.
Transcriptional Organization of the Region Encoding the Synthesis of the Flagellar Filament in
Pseudomonas fluorescens
Authors: Redondo-Nieto Miguel , Lloret Javier , Larenas Javiera , Barahona Emma , Navazo Ana , Martínez-Granero Francisco , Capdevila Silvia , Rivilla Rafael , Martín Marta 
Published: March 2008

ABSTRACT

Pseudomonas fluorescens
F113 is motile by means of type b flagella. Analysis of the region encoding the synthesis of the flagellar filament has shown a transcriptional organization different from that of type a flagella. Additionally to the promoters driving
fliC
,
fliD
, and
fleQ
expression, we have found promoters upstream of the
flaG
gene and the
fliST
operon. These promoters were functional in vivo. Both promoters have been mapped and appear to be dependent on the vegetative sigma factor and independent of FleQ, the master regulator of flagellum synthesis.
Genome Sequence of the Streptomycin-Producing MicroorganismStreptomyces griseusIFO 13350
Authors: Ohnishi Yasuo , Ishikawa Jun , Hara Hirofumi , Suzuki Hirokazu , Ikenoya Miwa , Ikeda Haruo , Yamashita Atsushi , Hattori Masahira , Horinouchi Sueharu 
Published: March 2008

ABSTRACTWe determined the complete genome sequence ofStreptomyces griseusIFO 13350, a soil bacterium producing an antituberculosis agent, streptomycin, which is the first aminoglycoside antibiotic, discovered more than 60 years ago. The linear chromosome consists of 8,545,929 base pairs (bp), with an average G+C content of 72.2%, predicting 7,138 open reading frames, six rRNA operons (16S-23S-5S), and 66 tRNA genes. It contains extremely long terminal inverted repeats (TIRs) of 132,910 bp each. The telomere's nucleotide sequence and secondary structure, consisting of several palindromes with a loop sequence of 5′-GGA-3′, are different from those of typical telomeres conserved among otherStreptomycesspecies. In accordance with the difference, the chromosome has pseudogenes for a conserved terminal protein (Tpg) and a telomere-associated protein (Tap), and a novel pair of Tpg and Tap proteins is instead encoded by the TIRs. Comparisons with the genomes of two related species,Streptomyces coelicolorA3(2) andStreptomyces avermitilis, clarified not only the characteristics of theS. griseusgenome but also the existence of 24Streptomyces-specific proteins. TheS. griseusgenome contains 34 gene clusters or genes for the biosynthesis of known or unknown secondary metabolites. Transcriptome analysis using a DNA microarray showed that at least four of these clusters, in addition to the streptomycin biosynthesis gene cluster, were activated directly or indirectly by AdpA, which is a central transcriptional activator for secondary metabolism and morphogenesis in the A-factor (a γ-butyrolactone signaling molecule) regulatory cascade inS. griseus.
Sodium Chloride Affects
Helicobacter pylori
Growth and Gene Expression
Authors: Gancz Hanan , Jones Kathleen R. , Merrell D. Scott 
Published: March 2008

ABSTRACT

Epidemiological evidence links high-salt diets and
Helicobacter pylori
infection with increased risk of developing gastric maladies. The mechanism by which elevated sodium chloride content causes these manifestations is unclear. Here we characterize the response of
H. pylori
to temporal changes in sodium chloride concentration and show that growth, cell morphology, survival, and virulence factor expression are all altered by increased salt concentration.
Functional Characterization of a Vitamin B
12
-Dependent Methylmalonyl Pathway in
Mycobacterium tuberculosis
: Implications for Propionate Metabolism during Growth on Fatty Acids
Authors: Savvi Suzana , Warner Digby F. , Kana Bavesh D. , McKinney John D. , Mizrahi Valerie , Dawes Stephanie S. 
Published: March 2008

ABSTRACT

Mycobacterium tuberculosis
is predicted to subsist on alternative carbon sources during persistence within the human host. Catabolism of odd- and branched-chain fatty acids, branched-chain amino acids, and cholesterol generates propionyl-coenzyme A (CoA) as a terminal, three-carbon (C
3
) product. Propionate constitutes a key precursor in lipid biosynthesis but is toxic if accumulated, potentially implicating its metabolism in
M. tuberculosis
pathogenesis. In addition to the well-characterized methylcitrate cycle, the
M. tuberculosis
genome contains a complete methylmalonyl pathway, including a
mutAB
-encoded methylmalonyl-CoA mutase (MCM) that requires a vitamin B
12
-derived cofactor for activity. Here, we demonstrate the ability of
M. tuberculosis
to utilize propionate as the sole carbon source in the absence of a functional methylcitrate cycle, provided that vitamin B
12
is supplied exogenously. We show that this ability is dependent on
mutAB
and, furthermore, that an active methylmalonyl pathway allows the bypass of the glyoxylate cycle during growth on propionate in vitro. Importantly, although the glyoxylate and methylcitrate cycles supported robust growth of
M. tuberculosis
on the C
17
fatty acid heptadecanoate, growth on valerate (C
5
) was significantly enhanced through vitamin B
12
supplementation. Moreover, both wild-type and methylcitrate cycle mutant strains grew on B
12
-supplemented valerate in the presence of 3-nitropropionate, an inhibitor of the glyoxylate cycle enzyme isocitrate lyase, indicating an anaplerotic role for the methylmalonyl pathway. The demonstrated functionality of MCM reinforces the potential relevance of vitamin B
12
to mycobacterial pathogenesis and suggests that vitamin B
12
availability in vivo might resolve the paradoxical dispensability of the methylcitrate cycle for the growth and persistence of
M. tuberculosis
in mice.
The Carriage Population of
Staphylococcus aureus
from Mali Is Composed of a Combination of Pandemic Clones and the Divergent Panton-Valentine Leukocidin-Positive Genotype ST152
Authors: Ruimy Raymond , Maiga Aminata , Armand-Lefevre Laurence , Maiga Ibrahim , Diallo Amadou , Koumaré Abdel Karim , Ouattara Kalilou , Soumaré Sambou , Gaillard Kevin , Lucet Jean-Christophe , Andremont Antoine , Feil Edward J. 
Published: March 2008

ABSTRACT

Staphylococcus aureus
is an important human pathogen, but it appears more commonly in asymptomatic colonization of the nasopharynx than in cases of invasive disease. Evidence concerning the global population structure of
S. aureus
is limited by the overrepresentation in the multilocus sequence testing database of disease isolates recovered from Western Europe, the Americas, Australia, and Japan. We address this by presenting data from the
S. aureus
carriage population in Mali, the first detailed characterization of asymptomatic carriage from an African population. These data confirm the pandemic spread of many of the common
S. aureus
clones in the carriage population. We also note the high frequency (∼24%) of a single divergent genotype, sequence type 152 (ST152), which has not previously been recovered from nasal carriage isolates but corresponds to a sporadic Panton-Valentine leukocidin (PVL)-positive, community-acquired methicillin-resistant
S. aureus
clone noted mostly in Central Europe. We show that 100% of the ST152 isolates recovered from nasal carriage samples in Mali are PVL positive and discuss implications relating to the emergence and spread of this virulent genotype.
CabC, an EF-Hand Calcium-Binding Protein, Is Involved in Ca2+-Mediated Regulation of Spore Germination and Aerial Hypha Formation inStreptomyces coelicolor
Authors: Wang Sheng-Lan , Fan Ke-Qiang , Yang Xu , Lin Zeng-Xi , Xu Xin-Ping , Yang Ke-Qian 
Published: March 2008

ABSTRACTCa2+was reported to regulate spore germination and aerial hypha formation in streptomycetes; the underlying mechanism of this regulation is not known.cabC, a gene encoding an EF-hand calcium-binding protein, was disrupted or overexpressed inStreptomyces coelicolorM145. On R5− agar, the disruption ofcabCresulted in denser aerial hyphae with more short branches, swollen hyphal tips, and early-germinating spores on the spore chain, whilecabCoverexpression significantly delayed development. Manipulation of the Ca2+concentration in R5− agar could reverse the phenotypes ofcabCdisruption or overexpression mutants and mimic mutant phenotypes with M145, suggesting that the mutant phenotypes were due to changes in the intracellular Ca2+concentration. CabC expression was strongly activated in aerial hyphae, as determined by Western blotting against CabC and confocal laser scanning microscopy detection of CabC::enhanced green fluorescent protein (EGFP). CabC::EGFP fusion proteins were evenly distributed in substrate mycelia, aerial mycelia, and spores. Taken together, these results demonstrate that CabC is involved in Ca2+-mediated regulation of spore germination and aerial hypha formation inS. coelicolor. CabC most likely acts as a Ca2+buffer and exerts its regulatory effects by controlling the intracellular Ca2+concentration.
A new predictive indicator for development of pressure ulcers in bedridden patients based on common laboratory tests results
Authors: Hatanaka N , Yamamoto Y , Ichihara K , Mastuo S , Nakamura Y , Watanabe M , Iwatani Y 
Published: March 2008

Background:Various scales have been devised to predict development of pressure ulcers on the basis of clinical and laboratory data, such as the Braden Scale (Braden score), which is used to monitor activity and skin conditions of bedridden patients. However, none of these scales facilitates clinically reliable prediction.Aims:To develop a clinical laboratory data-based predictive equation for the development of pressure ulcers.Methods:Subjects were 149 hospitalised patients with respiratory disorders who were monitored for the development of pressure ulcers over a 3-month period. The proportional hazards model (Cox regression) was used to analyse the results of 12 basic laboratory tests on the day of hospitalisation in comparison with Braden score.Results:Pressure ulcers developed in 38 patients within the study period. A Cox regression model consisting solely of Braden scale items showed that none of these items contributed to significantly predicting pressure ulcers. Rather, a combination of haemoglobin (Hb), C-reactive protein (CRP), albumin (Alb), age, and gender produced the best model for prediction. Using the set of explanatory variables, we created a new indicator based on a multiple logistic regression equation. The new indicator showed high sensitivity (0.73) and specificity (0.70), and its diagnostic power was higher than that of Alb, Hb, CRP, or the Braden score alone.Conclusions:The new indicator may become a more useful clinical tool for predicting presser ulcers than Braden score. The new indicator warrants verification studies to facilitate its clinical implementation in the future.
The role of nurses in euthanasia and physician-assisted suicide in The Netherlands
Authors: van Bruchem-van de Scheur G G , Arend A J G van der , Abu-Saad H Huijer , Spreeuwenberg C , van Wijmen F C B , ter Meulen R H J 
Published: March 2008

Background:Issues concerning legislation and regulation with respect to the role of nurses in euthanasia and physician-assisted suicide gave the Minister for Health reason to commission a study of the role of nurses in medical end-of-life decisions in hospitals, home care and nursing homes.Aim:This paper reports the findings of a study of the role of nurses in euthanasia and physician-assisted suicide, conducted as part of a study of the role of nurses in medical end-of-life decisions. The findings for hospitals, home care and nursing homes are described and compared.Method:A questionnaire was sent to 1509 nurses, employed in 73 hospitals, 55 home care organisations and 63 nursing homes. 1179 responses (78.1%) were suitable for analysis. The questionnaire was pilot-tested among 106 nurses, with a response rate of 85%.Results:In 37.0% of cases, the nurse was the first person with whom patients discussed their request for euthanasia or physician-assisted suicide. Consultation between physicians and nurses during the decision-making process took place quite often in hospitals (78.8%) and nursing homes (81.3%) and less frequently in home care situations (41.2%). In some cases (12.2%), nurses administered the euthanatics.Conclusions:The results show substantial differences between the intramural sector (hospitals and nursing homes) and the extramural sector (home care), which are probably linked to the organisational structure of the institutions. Consultation between physicians and nurses during the decision-making process needs improvement, particularly in home care. Some nurses had administered euthanatics, although this task is by law exclusively reserved to physicians.
Malawians permit research bronchoscopy due to perceived need for healthcare
Authors: Mtunthama N , Malamba R , French N , Molyneux M E , Zijlstra E E , Gordon S B 
Published: March 2008

Objectives:Bronchoalveolar lavage obtained at bronchoscopy is useful for research on pulmonary defence mechanisms. Bronchoscopy involves some discomfort and risk to subjects. We audited the process of consent, experienced adverse effects and reasons for participation among research bronchoscopy volunteers.Design:100 consecutive volunteer research subjects attending for bronchoscopy, repeat bronchoscopy or routine recruitment clinic were interviewed. Information was gathered about volunteer motivation, perception of the consent process and adverse effects of bronchoscopy. Suggestions for improvement were requested. Responses were themed by a second investigator prior to data analysis.Results:81 bronchoscopy-experienced subjects (total of 263 procedures) and 19 new volunteers were interviewed. 19 subjects (21%) reported adverse symptoms during or after bronchoscopy, but no symptoms were of sufficient severity that they would not repeat the procedure. The frequency of symptoms was not related to gender, the quality of the lavage or the HIV status of the subject. 76 subjects (94%) reported that the information given pre-procedure was useful and adequate but 43 (56%) had further questions mostly relating to their own results. The reasons given for research participation were access to health assessment (75 subjects), access to treatment when ill (61 subjects), desire to participate in research (15 subjects) and remuneration (6 subjects). 7 subjects complained that the remuneration was inadequate.Conclusions:The main incentive to participation in research bronchoscopy was access to healthcare. Informed consent and procedure technique were adequate but subjects would value more feedback about individual and project results.
Exposure to nicotine and a tobacco-specific carcinogen increase with duration of use of smokeless tobacco
Authors: Hecht S S , Carmella S G , Edmonds A , Murphy S E , Stepanov I , Luo X , Hatsukami D K 
Published: March 2008

Background:Smokeless tobacco is an efficient delivery vehicle for nicotine and can contain significant amounts of carcinogens. However, few studies have examined factors that might moderate levels of nicotine or carcinogen exposure.Aims:To determine the effect of duration of smokeless tobacco use on the uptake of nicotine and a tobacco-specific carcinogen, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK).Methods:Questionnaires on use of smokeless tobacco were administered, and urine samples from 212 smokeless tobacco users were analysed for biomarkers of uptake of nicotine and NNK. The biomarkers were cotinine and total 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL). Male smokeless tobacco users were recruited for studies designed to investigate methods of reducing smokeless tobacco use. The questionnaire and biomarker data were obtained at baseline, prior to reduction.Results:Levels of cotinine (p<0.001) and total NNAL (p<0.001) were significantly correlated with duration (in years) of use of smokeless tobacco products. Median cotinine and total NNAL were 2.4 and 2.1 times higher, respectively, in the ⩾21 years of use than in the 0–5 years of use category.Conclusions:Smokeless tobacco users adjust their intensity of use with experience in order to increase their nicotine dose, resulting in a corresponding increase in exposure to NNK, a powerful carcinogen. These results indicate the importance of educating smokeless tobacco users about the effects of prolonged use of these products.
The Signatures of Autozygosity among Patients with Colorectal Cancer
Authors: Bacolod Manny D. , Schemmann Gunter S. , Wang Shuang , Shattock Richard , Giardina Sarah F. , Zeng Zhaoshi , Shia Jinru , Stengel Robert F. , Gerry Norman , Hoh Josephine , Kirchhoff Tomas , Gold Bert , Christman Michael F. , Offit Kenneth , Gerald William L. , Notterman Daniel A. , Ott Jurg , Paty Philip B. , Barany Francis 
Published: March 2008

Abstract
Previous studies have shown that among populations with a high rate of consanguinity, there is a significant increase in the prevalence of cancer. Single nucleotide polymorphism (SNP) array data (Affymetrix, 50K XbaI) analysis revealed long regions of homozygosity in genomic DNAs taken from tumor and matched normal tissues of colorectal cancer (CRC) patients. The presence of these regions in the genome may indicate levels of consanguinity in the individual's family lineage. We refer to these autozygous regions as identity-by-descent (IBD) segments. In this study, we compared IBD segments in 74 mostly Caucasian CRC patients (mean age of 66 years) to two control data sets: (a) 146 Caucasian individuals (mean age of 80 years) who participated in an age-related macular degeneration (AMD) study and (b) 118 cancer-free Caucasian individuals from the Framingham Heart Study (mean age of 67 years). Our results show that the percentage of CRC patients with IBD segments (≥4 Mb length and 50 SNPs probed) in the genome is at least twice as high as the AMD or Framingham control groups. Also, the average length of these IBD regions in the CRC patients is more than twice the length of the two control data sets. Compared with control groups, IBD segments are found to be more common among individuals of Jewish background. We believe that these IBD segments within CRC patients are likely to harbor important CRC-related genes with low-penetrance SNPs and/or mutations, and, indeed, two recently identified CRC predisposition SNPs in the 8q24 region were confirmed to be homozygous in one particular patient carrying an IBD segment covering the region. [Cancer Res 2008;68(8):2610–21]
Silencing Bcl-2 in models of mantle cell lymphoma is associated with decreases in cyclin D1, nuclear factor-κB, p53, bax, and p27 levels
Authors: Tucker Catherine A. , Kapanen Anita I. , Chikh Ghania , Hoffman Brad G. , Kyle Alastair H. , Wilson Ian M. , Masin Dana , Gascoyne Randy D. , Bally Marcel , Klasa Richard J. 
Published: March 2008

Abstract
Molecular mechanisms responsible for lymphoma resistance to apoptosis often involve the bcl-2 pathway. In this study, we investigated the cell signaling pathways activated in bcl-2-overexpressing human mantle cell lymphoma cell lines (JVM-2 and Z-138) that have been treated with oblimersen, a molecular gene silencing strategy that effectively suppresses bcl-2 in vitro and in vivo. Z-138 cells expressed higher levels of bcl-2 and were more sensitive to the effects of bcl-2 silencing, mediated by oblimersen or bcl-2 small interfering RNA, in vitro. Tumors derived following injection of Z-138 cells were sensitive to oblimersen as judged by decreases in tumor growth rate and decreases in cell proliferation (as measured by Ki-67). Immunohistochemistry and Western blot analysis of oblimersen-treated Z-138 tumors revealed a dose-dependent decrease in bcl-2 levels and an associated increase in the proapoptotic proteins caspase-3 and caspase-9. Silencing bcl-2 in Z-138 xenografts revealed an associated dose-dependent suppression of bax, a decrease in nuclear factor-κB and phospho-nuclear factor-κB, and transient loss of p53 levels. Coimmunoprecipitation studies suggest that the latter observation is mediated by an association between bcl-2 and phospho-mdm2. Bcl-2 silencing also led to p27 down-regulation and coimmunoprecipitation studies point to a role for bcl-2 in regulation of p27 localization/degradation. Bcl-2 silencing was also correlated with loss of cyclin D1a protein levels but not cyclin D1b levels. Coimmunoprecipitation studies indicate that bcl-2 may mediate its effects on cyclin D1a via interaction with p38 mitogen-activated protein kinase as well as a previously unreported interaction between bcl-2 and cyclin D1a. [Mol Cancer Ther 2008;7(4):749–58]
BRAF and NRAS mutations in melanoma: potential relationships to clinical response to HSP90 inhibitors
Authors: Banerji Udai , Affolter Annette , Judson Ian , Marais Richard , Workman Paul 
Published: March 2008

Abstract
Oncogenic BRAF and NRAS mutations are frequent in malignant melanoma. BRAF that is activated by the common V600E and other mutations, as well as by upstream NRAS mutations, has been shown to require the molecular chaperone heat shock protein 90 (HSP90) for stabilization and is depleted by the HSP90 inhibitor 17-allylamino-17-demethoxygeldanamycin (17-AAG)]. Here, we explore the possible relationship between tumor BRAF and NRAS mutations and clinical response to 17-AAG in six patients with metastatic malignant melanoma who received pharmacologically active doses of 17-AAG as part of a phase I clinical trial. One patient with disease stabilization for 49 months had a G13DNRAS mutation and WTBRAF. A second patient who had stable disease for 15 months had a V600EBRAF mutation and WTNRAS. These preliminary results suggest that BRAF and NRAS mutation status should be determined in prospective phase II studies of HSP90 inhibitors in melanoma. [Mol Cancer Ther 2008;7(4):737–9]