bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of RelGsuin Stress Response and Fe(III) Reduction inGeobacter sulfurreducens
Authors: DiDonato Laurie N. , Sullivan Sara A. , Methé Barbara A. , Nevin Kelly P. , England Reg , Lovley Derek R. 
Published: December 2006

ABSTRACTGeobacterspecies are key members of the microbial community in many subsurface environments in which dissimilatory metal reduction is an important process. The genome ofGeobacter sulfurreducenscontains a gene designatedrelGsu, which encodes a RelA homolog predicted to catalyze both the synthesis and the degradation of guanosine 3′,5′-bispyrophosphate (ppGpp), a regulatory molecule that signals slow growth in response to nutrient limitation in bacteria. To evaluate the physiological role of RelGsuinG. sulfurreducens, arelGsumutant was constructed and characterized, and ppGpp levels were monitored under various conditions in both the wild-type andrelGsumutant strains. In the wild-type strain, ppGpp and ppGp were produced in response to acetate and nitrogen deprivation, whereas exposure to oxygen resulted in an accumulation of ppGpp alone. Neither ppGpp nor ppGp could be detected in therelGsumutant. TherelGsumutant consistently grew to a higher cell density than the wild type in acetate-fumarate medium and was less tolerant of oxidative stress than the wild type. The capacity for Fe(III) reduction was substantially diminished in the mutant. Microarray and quantitative reverse transcription-PCR analyses indicated that during stationary-phase growth, protein synthesis genes were up-regulated in therelGsumutant and genes involved in stress responses and electron transport, including several implicated in Fe(III) reduction, were down-regulated in the mutant. The results are consistent with a role for RelGsuin regulating growth, stress responses, and Fe(III) reduction inG. sulfurreducensunder conditions likely to be prevalent in subsurface environments.
Characterization of XynC from
Bacillus subtilis
subsp.
subtilis
Strain 168 and Analysis of Its Role in Depolymerization of Glucuronoxylan
Authors: St. John Franz J. , Rice John D. , Preston James F. 
Published: December 2006

ABSTRACT

Secretion of xylanase activities by
Bacillus subtilis
168 supports the development of this well-defined genetic system for conversion of methylglucuronoxylan (MeGAX
n
[where n represents the number of xylose residues]) in the hemicellulose component of lignocellulosics to biobased products. In addition to the characterized glycosyl hydrolase family 11 (GH 11) endoxylanase designated XynA,
B. subtilis
168 secretes a second endoxylanase as the translated product of the
ynfF
gene. This sequence shows remarkable homology to the GH 5 endoxylanase secreted by strains of
Erwinia chrysanthemi
. To determine its properties and potential role in the depolymerization of MeGAX
n
, the
ynfF
gene was cloned and overexpressed to provide an endoxylanase, designated XynC, which was characterized with respect to substrate preference, kinetic properties, and product formation. With different sources of MeGAX
n
as the substrate, the specific activity increased with increasing methylglucuronosyl substitutions on the β-1,4-xylan chain. With MeGAX
n
from sweetgum as a preferred substrate, XynC exhibited a
V
max
of 59.9 units/mg XynC, a

K
m

of 1.63 mg MeGAX
n
/ml, and a
k
cat
of 2,635/minute at pH 6.0 and 37°C. Matrix-assisted laser desorption ionization—time of flight mass spectrometry and
1
H nuclear magnetic resonance data revealed that each hydrolysis product has a single glucuronosyl substitution penultimate to the reducing terminal xylose. This detailed analysis of XynC from
B. subtilis
168 defines the unique depolymerization process catalyzed by the GH 5 endoxylanases. Based upon product analysis,
B. subtilis
168 secretes both XynA and XynC. Expression of
xynA
was subject to MeGAX
n
induction;
xynC
expression was constitutive with growth on different substrates. Translation and secretion of both GH 11 and GH 5 endoxylanases by the fully sequenced and genetically malleable
B. subtilis
168 recommends this bacterium for the introduction of genes required for the complete utilization of products of the enzyme-catalyzed depolymerization of MeGAX
n
.
B. subtilis
may serve as a model platform for development of gram-positive biocatalysts for conversion of lignocellulosic materials to renewable fuels and chemicals.
BadM Is a Transcriptional Repressor and One of Three Regulators That Control Benzoyl Coenzyme A Reductase Gene Expression in
Rhodopseudomonas palustris
Authors: Peres Caroline M. , Harwood Caroline S. 
Published: December 2006

ABSTRACT

The rate-limiting enzyme of anaerobic benzoate degradation by
Rhodopseudomonas palustris
, benzoyl coenzyme A (CoA) reductase, is highly sensitive to oxygen, and its synthesis is tightly regulated. We determined that a previously unknown gene in the benzoate gene cluster,
badM
, encodes a transcriptional repressor of benzoyl-CoA reductase gene expression. BadM controls gene expression from the benzoyl-CoA reductase promoter in concert with two previously described transcriptional activators.
Mutational Analysis To Define an Activating Region on the Redox-Sensitive Transcriptional Regulator OxyR
Authors: Wang Xunde , Mukhopadhyay Partha , Wood Matthew J. , Outten F. Wayne , Opdyke Jason A. , Storz Gisela 
Published: December 2006

ABSTRACT

The OxyR transcription factor is a key regulator of the
Escherichia coli
response to oxidative stress. Previous studies showed that OxyR binding to a target promoter enhances RNA polymerase binding and vice versa, suggesting a direct interaction between OxyR and RNA polymerase. To identify the region of OxyR that might contact RNA polymerase, we carried out alanine scanning and random mutagenesis of
oxyR
. The combination of these approaches led to the identification of several mutants defective in the activation of an OxyR target gene. A subset of the mutations map to the DNA-binding domain, other mutations appear to affect dimerization of the regulatory domain, while another group is suggested to affect disulfide bond formation. The two mutations, D142A and R273H, giving the most dramatic phenotype are located in a patch on the surface of the oxidized OxyR protein and possibly define an activating region on OxyR.
Heme Biosynthesis in
Methanosarcina barkeri
via a Pathway Involving Two Methylation Reactions
Authors: Buchenau Bärbel , Kahnt Jörg , Heinemann Ilka U. , Jahn Dieter , Thauer Rudolf K. 
Published: December 2006

ABSTRACT

The methanogenic archaeon
Methanosarcina barkeri
synthesizes protoheme via precorrin-2, which is formed from uroporphyrinogen III in two consecutive methylation reactions utilizing
S
-adenosyl-
l
-methionine. The existence of this pathway, previously exclusively found in the sulfate-reducing δ-proteobacterium
Desulfovibrio vulgaris
, was demonstrated for
M. barkeri
via the incorporation of two methyl groups from methionine into protoheme.
Membrane Topology Mapping of the Na
+
-Pumping NADH: Quinone Oxidoreductase from
Vibrio cholerae
by PhoA- Green Fluorescent Protein Fusion Analysis
Authors: Duffy Ellen B. , Barquera Blanca 
Published: December 2006

ABSTRACT

The membrane topologies of the six subunits of Na
+
-translocating NADH:quinone oxidoreductase (Na
+
-NQR) from
Vibrio cholerae
were determined by a combination of topology prediction algorithms and the construction of C-terminal fusions. Fusion expression vectors contained either bacterial alkaline phosphatase (
phoA
) or green fluorescent protein (
gfp
) genes as reporters of periplasmic and cytoplasmic localization, respectively. A majority of the topology prediction algorithms did not predict any transmembrane helices for NqrA. A lack of PhoA activity when fused to the C terminus of NqrA and the observed fluorescence of the green fluorescent protein C-terminal fusion confirm that this subunit is localized to the cytoplasmic side of the membrane. Analysis of four PhoA fusions for NqrB indicates that this subunit has nine transmembrane helices and that residue T236, the binding site for flavin mononucleotide (FMN), resides in the cytoplasm. Three fusions confirm that the topology of NqrC consists of two transmembrane helices with the FMN binding site at residue T225 on the cytoplasmic side. Fusion analysis of NqrD and NqrE showed almost mirror image topologies, each consisting of six transmembrane helices; the results for NqrD and NqrE are consistent with the topologies of
Escherichia coli
homologs YdgQ and YdgL, respectively. The NADH, flavin adenine dinucleotide, and Fe-S center binding sites of NqrF were localized to the cytoplasm. The determination of the topologies of the subunits of Na
+
-NQR provides valuable insights into the location of cofactors and identifies targets for mutagenesis to characterize this enzyme in more detail. The finding that all the redox cofactors are localized to the cytoplasmic side of the membrane is discussed.
Role ofPseudomonas aeruginosa dinB-Encoded DNA Polymerase IV in Mutagenesis
Authors: Sanders Laurie H. , Rockel Andrea , Lu Haiping , Wozniak Daniel J. , Sutton Mark D. 
Published: December 2006

ABSTRACTPseudomonas aeruginosais a human opportunistic pathogen that chronically infects the lungs of cystic fibrosis patients and is the leading cause of morbidity and mortality of people afflicted with this disease. A striking correlation between mutagenesis and the persistence ofP. aeruginosahas been reported. In other well-studied organisms, error-prone replication by Y family DNA polymerases contributes significantly to mutagenesis. Based on an analysis of the PAO1 genome sequence,P. aeruginosacontains a single Y family DNA polymerase encoded by thedinBgene. As part of an effort to understand the mechanisms of mutagenesis inP. aeruginosa, we have cloned thedinBgene ofP. aeruginosaand utilized a combination of genetic and biochemical approaches to characterize the activity and regulation of theP. aeruginosaDinB protein (DinBPa). Our results indicate that DinBPais a distributive DNA polymerase that lacks intrinsic proofreading activity in vitro. Modest overexpression of DinBPafrom a plasmid conferred a mutator phenotype in bothEscherichia coliandP. aeruginosa. An examination of this mutator phenotype indicated that DinBPahas a propensity to promote C→A transversions and −1 frameshift mutations within poly(dGMP) and poly(dAMP) runs. The characterization oflexA+and ΔlexA::aacC1 P. aeruginosastrains, together with in vitro DNA binding assays utilizing cell extracts or purifiedP. aeruginosaLexA protein (LexAPa), indicated that the transcription of thedinBgene is regulated as part of an SOS-like response. The deletion of thedinBPagene sensitizedP. aeruginosato nitrofurazone and 4-nitroquinoline-1-oxide, consistent with a role for DinBPain translesion DNA synthesis overN2-dG adducts. Finally,P. aeruginosaexhibited a UV-inducible mutator phenotype that was independent ofdinBPafunction and instead requiredpolAandpolC, which encode DNA polymerase I and the second DNA polymerase III enzyme, respectively. Possible roles of theP. aeruginosa dinB,polA, andpolCgene products in mutagenesis are discussed.
Participation of French general practitioners in end-of-life decisions for their hospitalised patients
Authors: Ferrand E , Jabre P , Fernandez-Curiel S , Morin F , Vincent-Genod C , Duvaldestin P , Lemaire F , Hervé C , Marty J 
Published: December 2006

Background and objective:Assuming the hypothesis that the general practitioner (GP) can and should be a key player in making end-of-life decisions for hospitalised patients, perceptions of GPs’ role assigned to them by hospital doctors in making withdrawal decisions for such patients were surveyed.Design:Questionnaire survey.Setting:Urban (districts located near Paris) and rural (southern France) areas.Participants:GPs.Results:The response rate was 32.2% (161/500), and it was observed that 70.8% of respondents believed that their participation in withdrawal decisions for their hospitalised patients was essential, whereas 42.1% believed that the hospital doctors were sufficiently skilled to make withdrawal decisions without input from the GPs. Most respondents were found to believe that they had the necessary skills (91.9%) and enough time (87.6%) to participate in withdrawal decisions. The last case of treatment withdrawal in hospital for one of their patients was described by 40% (65/161) of respondents, of whom only 40.0% (26/65) believed that they had participated actively in the decision process. The major factors in the multivariate analysis were the GP’s strong belief that his or her participation was essential (p = 0.01), information on admission of the patient given to the GP by the hospital department (p = 0.007), rural practice (p = 0.03), visit to the patient dying in hospital (p = 0.02) and a request by the family to be kept informed about the patient (p = 0.003).Conclusion:Strong interest was evinced among GPs regarding end-of-life issues, as well as considerable experience of patients dying at home. As GPs are more closely corrected to patients’ families, they may be a good choice for third-party intervention in making end-of-life decisions for hospitalised patients.
Non-reporting and inconsistent reporting of race and ethnicity in articles that claim associations among genotype, outcome, and race or ethnicity
Authors: Shanawani H , Dame L , Schwartz D A , Cook-Deegan R 
Published: December 2006

Background:The use of race as a category in medical research is the focus of an intense debate, complicated by the inconsistency of presumed independent variables, race and ethnicity, on which analysis depends. Interpretation is made difficult by inconsistent methods for determining the race or ethnicity of a participant. The failure to specify how race or ethnicity was determined is common in the published literature.Hypothesis:Criteria by which they assign a research participant to racial or ethnic categories are not reported by published articles.Methods:Methods were reviewed for assigning race and ethnicity of research participants in 268 published reports reporting associations among race (or ethnicity), health outcome and genotype.Results:Of the 268 published reports reviewed, it was found that 192 (72%) did not explain their methods for assigning race or ethnicity as an independent variable. This was despite the fact that 180 (67%) of those reports reached conclusions about associations among genetics, health outcome and race or ethnicity.Conclusions:More attention needs to be given to the definition of race and ethnicity in genetic studies, especially in those diseases where health disparities are known to exist.
Doctor–patient sexual relationships in medical oaths: Table 1
Authors: Pérez S G , Gelpi R J , Rancich A M 
Published: December 2006

Background:Doctor–patient sexual relationship is considered to be unfair because the first party would be abusing the second party’s vulnerability. The prohibition of this relationship is noted in the Hippocratic oath. Currently, a reprise of the use of oaths in medical schools can be observed.Aim:To determine whether the prohibition has been maintained and how its expression has varied in the oaths during different periods.Methods:50 oaths were studied: 13 ancient–medieval and 37 modern–contemporary. Of the 50 texts, 19 were versions of the original oaths. The oaths that pointed out the prohibited doctor–patient relationship referred to any sexual aspect or included paragraphs that began as the Hippocratic oath does were noted.Results:Of the 24 (48%) texts that expressed the prohibition, 8 (62%) were ancient–medieval and 16 (43%) were modern–contemporary. Some expressly call it Hippocratic oath, many use general terminology (corruption or vice) and others describe it in association with other commitments (abortion and euthanasia).Conclusions:The clause on the prohibition of the doctor–patient sexual relationship in Hippocratic oath was included to be for legal, economic and social reasons at the time. That the clause is found mostly in the ancient–medieval oaths can be attributed to the influence of the original. This commitment is generalised and associated with others by contemporary formulas. Currently, sexual relationships are the subject of legal and ethical analysis and their inclusion in the oaths is being debated.
Reporting ethics committee approval and patient consent by study design in five general medical journals
Authors: Schroter S , Plowman R , Hutchings A , Gonzalez A 
Published: December 2006

Background:Authors are required to describe in their manuscripts ethical approval from an appropriate committee and how consent was obtained from participants when research involves human participants.Objective:To assess the reporting of these protections for several study designs in general medical journals.Design:A consecutive series of research papers published in theAnnals of Internal Medicine,BMJ,JAMA,LancetandThe New England Journal of Medicinebetween February and May 2003 were reviewed for the reporting of ethical approval and patient consent. Ethical approval, name of approving committee, type of consent, data source and whether the study used data collected as part of a study reported elsewhere were recorded. Differences in failure to report approval and consent by study design, journal and vulnerable study population were evaluated using multivariable logistic regression.Results:Ethical approval and consent were not mentioned in 31% and 47% of manuscripts, respectively. 88 (27%) papers failed to report both approval and consent. Failure to mention ethical approval or consent was significantly more likely in all study designs (except case–control and qualitative studies) than in randomised controlled trials (RCTs). Failure to mention approval was most common in theBMJand was significantly more likely than inThe New England Journal of Medicine. Failure to mention consent was most common in theBMJand was significantly more likely than in all other journals. No significant differences in approval or consent were found when comparing studies of vulnerable and non-vulnerable participants.Conclusion:The reporting of ethical approval and consent in RCTs has improved, but journals are less good at reporting this information for other study designs. Journals should publish this information for all research on human participants.
The Objective Structured Clinical Examination and student collusion: marks do not tell the whole truth
Authors: Parks R , Warren P M , Boyd K M , Cameron H , Cumming A , Lloyd-Jones G 
Published: December 2006

Objective:To determine whether the marks in the third year Objective Structured Clinical Examination (OSCE) were affected by the collusion reported by the students themselves on an electronic discussion board.Design:A review of the student discussion, examiners’ feedback and a comparison of the marks obtained on the 2 days of the OSCE.Participants:255 third year medical students.Setting:An OSCE consisting of 15 stations, administered on three sites over 2 days at a UK medical school.Results:40 students contributed to the discussion on the electronic discussion board. The main points raised were perceived inequity between students who did, or did not, have prior knowledge of the station content, and the lack of honesty and professionalism of their peers. Most contributors claimed to have received, or knew of others receiving, prior knowledge, but none confessed to passing on information. No significant difference (p = 0.16) was observed in the overall mark for the OSCE on day 1 (mean 390 (SD 37)) and day 2 (mean 397 (38)). On day 2, marks were considerably greater for four stations and markedly lower for three stations. It was not obvious why collusion should affect these station marks. A clear indication of the effects of collusion could only be obtained from a single subsection of an individual station (pathology) where 82 students on day 2 incorrectly gave the diagnosis from day 1.Conclusion:Marks do not provide a sound inference of student collusion in an OSCE and may mask the aspects of professional development of students.
The truth-telling issue and changes in lifestyle in patients with cancer
Authors: Kostopoulou V , Katsouyanni K 
Published: December 2006

Objective:To compare the attitudes of patients with cancer toward making changes in lifestyle, according to their awareness of the diagnosis.Method:Personal interviews with 50 patients with breast cancer, 24 patients with prostate cancer and 50 patients with colorectal cancer were conducted in a cancer hospital in Athens, Greece.Analysis:Multiple logistic regression models were used to estimate the odds ratio as a measure of the association of the characteristics of participants with changes in lifestyle.Results:Overall, 22.6% of the patients were not aware of the diagnosis. Among the changes in lifestyle, 41.1% reported changing their diet to a healthier one, 22.6% of the smokers reduced or stopped smoking and 13.7% added new physical activity. Compared with uninformed patients, those who were aware of the diagnosis, after adjusting for the confounding effect of educational status (an index of socioeconomic status), were 2.5 times as likely to make dietary changes (p<0.1). Among the other characteristics under study, older patients were less likely to add new physical activity than younger ones (p<0.01), and newly diagnosed patients were more likely to stop or reduce smoking (p<0.1) than patients with a diagnosis made more than 12 months previously.Conclusion:Patients with cancer are motivated to attempt changes in lifestyle and can benefit from more factual information about the diagnosis.
What people close to death say about euthanasia and assisted suicide: a qualitative study: Table 1
Authors: Chapple A , Ziebland S , McPherson A , Herxheimer A 
Published: December 2006

Objective:To explore the experiences of people with a “terminal illness”, focusing on the patients’ perspective of euthanasia and assisted suicide.Method:A qualitative study using narrative interviews was conducted throughout the UK. The views of the 18 people who discussed euthanasia and assisted suicide were explored. These were drawn from a maximum variation sample, who said that they had a “terminal” illness, malignant or non-malignant.Results:That UK law should be changed to allow assisted suicide or voluntary euthanasia was felt strongly by most people. Those who had seen others die were particularly convinced that this should be a right. Some had multiple reasons, including pain and anticipated pain, fear of indignity, loss of control and cognitive impairment. Those who did not want to be a burden also had other reasons for wanting euthanasia. Suicide was contemplated by a few, who would have preferred a change in the law to allow them to end their lives with medical help and in the company of family or friends. The few who opposed a change in UK law, or who felt ambivalent, focused on involuntary euthanasia, cited religious reasons or worried that new legislation might be open to abuse.Conclusion:Qualitative research conducted on people who know they are nearing death is an important addition to the international debate on euthanasia and assisted suicide. Those who had seen others die were particularly convinced that the law should be changed to allow assisted death.
Towards viscosity approximations of hierarchical fixed-point problems
Authors: Moudafi A , Maingé P-E 
Published: December 2006

AbstractWe introduce methods which seem to be a new and promising tool in hierarchical fixed-point problems. The goal of this note is to analyze the convergence properties of these new types of approximating methods for fixed-point problems. The limit attained by these curves is the solution of the general variational inequality, "Equation missing", where "Equation missing" denotes the normal cone to the set of fixed point of the original nonexpansive mapping "Equation missing" and "Equation missing" a suitable nonexpansive mapping criterion. The link with other approximation schemes in this field is also made.