bluuebunny/crossref_metadata_2025_split huggingface dataset:
Elucidation of the Role of the Methylene-Tetrahydromethanopterin Dehydrogenase MtdA in the Tetrahydromethanopterin-Dependent Oxidation Pathway in Methylobacterium extorquens AM1
Authors: Martinez-Gomez N. Cecilia , Nguyen Sandy , Lidstrom Mary E. 
Published: March 2013

ABSTRACT

The methylotroph
Methylobacterium extorquens
AM1 oxidizes methanol and methylamine to formaldehyde and subsequently to formate, an intermediate that serves as the branch point between assimilation (formation of biomass) and dissimilation (oxidation to CO
2
). The oxidation of formaldehyde to formate is dephosphotetrahydromethanopterin (dH
4
MPT) dependent, while the assimilation of carbon into biomass is tetrahydrofolate (H
4
F) dependent. This bacterium contains two different enzymes, MtdA and MtdB, both of which are dehydrogenases able to use methylene-dH
4
MPT, an intermediate in the oxidation of formaldehyde to formate. Unique to MtdA is a second enzymatic activity with methylene-H
4
F. Since methylene-H
4
F is the entry point into the biomass pathways, MtdA plays a key role in assimilatory metabolism. However, its role in oxidative metabolism via the dH
4
MPT-dependent pathway and its apparent inability to replace MtdB
in vivo
on methanol growth are not understood. Here, we have shown that an
mtdB
mutant is able to grow on methylamine, providing a system to study the role of MtdA. We demonstrate that the absence of MtdB results in the accumulation of methenyl-dH
4
MPT. Methenyl-dH
4
MPT is shown to be a competitive inhibitor of the reduction of methenyl-H
4
F to methylene-H
4
F catalyzed by MtdA, with an estimated

K
i

of 10 μM. Thus, methenyl-dH
4
MPT accumulation inhibits H
4
F-dependent assimilation. Overexpression of
mch
in the
mtdB
mutant strain, predicted to reduce methenyl-dH
4
MPT accumulation, enhances growth on methylamine. Our model proposes that MtdA regulates carbon flux due to differences in its kinetic properties for methylene-dH
4
MPT and for methenyl-H
4
F during growth on single-carbon compounds.
Role of the PAS Sensor Domains in the Bacillus subtilis Sporulation Kinase KinA
Authors: Winnen Brit , Anderson Eric , Cole James L. , King Glenn F. , Rowland Susan L. 
Published: March 2013

ABSTRACT

Histidine kinases are sophisticated molecular sensors that are used by bacteria to detect and respond to a multitude of environmental signals. KinA is the major histidine kinase required for initiation of sporulation upon nutrient deprivation in
Bacillus subtilis
. KinA has a large N-terminal region (residues 1 to 382) that is uniquely composed of three tandem Per-ARNT-Sim (PAS) domains that have been proposed to constitute a sensor module. To further enhance our understanding of this “sensor” region, we defined the boundaries that give rise to the minimal autonomously folded PAS domains and analyzed their homo- and heteroassociation properties using analytical ultracentrifugation, nuclear magnetic resonance (NMR) spectroscopy, and multiangle laser light scattering. We show that PAS
A
self-associates very weakly, while PAS
C
is primarily a monomer. In contrast, PAS
B
forms a stable dimer (

K
d

[dissociation constant] of <10 nM), and it appears to be the main N-terminal determinant of KinA dimerization. Analysis of KinA mutants deficient for one or more PAS domains revealed a critical role for PAS
B
, but not PAS
A
, in autophosphorylation of KinA. Our findings suggest that dimerization of PAS
B
is important for keeping the catalytic domain of KinA in a functional conformation. We use this information to propose a model for the structure of the N-terminal sensor module of KinA.
myo
-Inositol and
d
-Ribose Ligand Discrimination in an ABC Periplasmic Binding Protein
Authors: Herrou Julien , Crosson Sean 
Published: March 2013

ABSTRACT

The periplasmic binding protein (PBP) IbpA mediates the uptake of
myo
-inositol by the IatP-IatA ATP-binding cassette transmembrane transporter. We report a crystal structure of
Caulobacter crescentus
IbpA bound to
myo
-inositol at 1.45 Å resolution. This constitutes the first structure of a PBP bound to inositol. IbpA adopts a type I PBP fold consisting of two α-β lobes that surround a central hinge. A pocket positioned between the lobes contains the
myo
-inositol ligand, which binds with submicromolar affinity (0.76 ± 0.08 μM). IbpA is homologous to ribose-binding proteins and binds
d
-ribose with low affinity (50.8 ± 3.4 μM). On the basis of IbpA and ribose-binding protein structures, we have designed variants of IbpA with inverted binding specificity for
myo
-inositol and
d
-ribose. Five mutations in the ligand-binding pocket are sufficient to increase the affinity of IbpA for
d
-ribose by 10-fold while completely abolishing binding to
myo
-inositol. Replacement of
ibpA
with these mutant alleles unable to bind
myo
-inositol abolishes
C. crescentus
growth in medium containing
myo
-inositol as the sole carbon source. Neither deletion of
ibpA
nor replacement of
ibpA
with the high-affinity ribose binding allele affected
C. crescentus
growth on
d
-ribose as a carbon source, providing evidence that the IatP-IatA transporter is specific for
myo
-inositol. This study outlines the evolutionary relationship between ribose- and inositol-binding proteins and provides insight into the molecular basis upon which these two related, but functionally distinct, classes of periplasmic proteins specifically bind carbohydrate ligands.
Bacillus subtilis Mutants with Knockouts of the Genes Encoding Ribonucleases RNase Y and RNase J1 Are Viable, with Major Defects in Cell Morphology, Sporulation, and Competence
Authors: Figaro Sabine , Durand Sylvain , Gilet Laetitia , Cayet Nadège , Sachse Martin , Condon Ciarán 
Published: March 2013

ABSTRACT

The genes encoding the ribonucleases RNase J1 and RNase Y have long been considered essential for
Bacillus subtilis
cell viability, even before there was concrete knowledge of their function as two of the most important enzymes for RNA turnover in this organism. Here we show that this characterization is incorrect and that Δ
rnjA
and Δ
rny
mutants are both viable. As expected, both strains grow relatively slowly, with doubling times in the hour range in rich medium. Knockout mutants have major defects in their sporulation and competence development programs. Both mutants are hypersensitive to a wide range of antibiotics and have dramatic alterations to their cell morphologies, suggestive of cell envelope defects. Indeed, RNase Y mutants are significantly smaller in diameter than wild-type strains and have a very disordered peptidoglycan layer. Strains lacking RNase J1 form long filaments in tight spirals, reminiscent of mutants of the actin-like proteins (Mre) involved in cell shape determination. Finally, we combined the
rnjA
and
rny
mutations with mutations in other components of the degradation machinery and show that many of these strains are also viable. The implications for the two known RNA degradation pathways of
B. subtilis
are discussed.
RfaH Promotes the Ability of the Avian Pathogenic Escherichia coli O2 Strain E058 To Cause Avian Colibacillosis
Authors: Gao Qingqing , Xu Huiqing , Wang Xiaobo , Zhang Debao , Ye Zhengqin , Gao Song , Liu Xiufan 
Published: March 2013

ABSTRACT

Avian pathogenic
Escherichia coli
(APEC) infection causes avian colibacillosis, which refers to any localized or systemic infection, such as acute fatal septicemia or subacute pericarditis and airsacculitis. The RfaH transcriptional regulator in
E. coli
is known to regulate a number of phenotypic traits. The direct effect of RfaH on the virulence of APEC has not been investigated yet. Our results showed that the inactivation of
rfaH
significantly decreased the virulence of APEC E058. The attenuation was assessed by
in vivo
and
in vitro
assays, including chicken infection assays, an ingestion and intracellular survival assay, and a bactericidal assay with serum complement. The virulence phenotype was restored to resemble that of the wild type by complementation of the
rfaH
gene in
trans
. The results of the quantitative real-time reverse transcription-PCR (qRT-PCR) analysis and animal system infection experiments indicated that the deletion of
rfaH
correlated with decreased virulence of the APEC E058 strain.
Small-Angle X-Ray Scattering for Imaging of Surface Layers on Intact Bacteria in the Native Environment
Authors: Sekot Gerhard , Schuster David , Messner Paul , Pum Dietmar , Peterlik Herwig , Schäffer Christina 
Published: March 2013

ABSTRACT

Crystalline cell surface layers (S-layers) represent a natural two-dimensional (2D) protein self-assembly system with nanometer-scale periodicity that decorate many prokaryotic cells. Here, we analyze the S-layer on intact bacterial cells of the Gram-positive organism
Geobacillus stearothermophilus
ATCC 12980 and the Gram-negative organism
Aquaspirillum serpens
MW5 by small-angle X-ray scattering (SAXS) and relate it to the structure obtained by transmission electron microscopy (TEM) after platinum/carbon shadowing. By measuring the scattering pattern of X rays obtained from a suspension of bacterial cells, integral information on structural elements such as the thickness and lattice parameters of the S-layers on intact, hydrated cells can be obtained nondestructively. In contrast, TEM of whole mounts is used to analyze the S-layer lattice type and parameters as well as the physical structure in a nonaqueous environment and local information on the structure is delivered. Application of SAXS to S-layer research on intact bacteria is a challenging task, as the scattering volume of the generally thin (3- to 30-nm) bacterial S-layers is low in comparison to the scattering volume of the bacterium itself. For enhancement of the scattering contrast of the S-layer in SAXS measurement, either silicification (treatment with tetraethyl orthosilicate) is used, or the difference between SAXS signals from an S-layer-deficient mutant and the corresponding S-layer-carrying bacterium is used for determination of the scattering signal. The good agreement of the SAXS and TEM data shows that S-layers on the bacterial cell surface are remarkably stable.
Regulation of Iron Metabolism by Pyrococcus furiosus
Authors: Zhu Yixuan , Kumar Sunil , Menon Angeli L. , Scott Robert A. , Adams Michael W. W. 
Published: March 2013

ABSTRACT

Iron is an essential element for the hyperthermophilic archaeon
Pyrococcus furiosus
, and many of its iron-containing enzymes have been characterized. How iron assimilation is regulated, however, is unknown. The genome sequence contains genes encoding two putative iron-responsive transcription factors, DtxR and Fur. Global transcriptional profiles of the
dtxR
deletion mutant (ΔDTXR) and the parent strain under iron-sufficient and iron-limited conditions indicated that DtxR represses the expression of the genes encoding two putative iron transporters, Ftr1 and FeoAB, under iron-sufficient conditions. Under iron limitation, DtxR represses expression of the gene encoding the iron-containing enzyme aldehyde ferredoxin oxidoreductase and a putative ABC-type transporter. Analysis of the
dtxR
gene sequence indicated an incorrectly predicted translation start site, and the corrected full-length DtxR protein, in contrast to the truncated version, specifically bound to the promoters of
ftr1
and
feoAB
, confirming its role as a transcription regulator. Expression of the gene encoding Ftr1 was dramatically upregulated by iron limitation, but no phenotype was observed for the ΔFTR1 deletion mutant under iron-limited conditions. The intracellular iron concentrations of ΔFTR1 and the parent strain were similar, suggesting that under the conditions tested, Ftr1 is not an essential iron transporter despite its response to iron. In contrast to DtxR, the Fur protein appears not to be a functional regulator in
P. furiosus
, since it did not bind to the promoters of any of the iron-regulated genes and the deletion mutant (ΔFUR) revealed no transcriptional responses to iron availability. DtxR is therefore the key iron-responsive transcriptional regulator in
P. furiosus
.
Social inequality in breast, lung and colorectal cancers: a sibling approach
Authors: Søndergaard Grethe , Mortensen, Laust Hvas , Andersen Anne-Marie Nybo , Andersen P K , Dalton Susanne Oksbjerg , Osler Merete 
Published: March 2013

ObjectiveTo examine whether family factors shared by siblings explained the association between education and risk of lung, colorectal and breast cancer.DesignWe used conventional cohort and intersibling Cox regression analyses to analyse the association between education and risk of cancer.SettingDenmark.ParticipantsWe retrieved register data from Statistics Denmark on individuals born in Denmark 1950–1979 with at least one full sibling. The cohorts included between 391 931 and 1 381 369 individuals followed from age 28 for incident lung, colorectal and breast cancer until the end of 2009.ResultsIn the cohort analysis, low education was associated with an increased risk of colorectal cancer before age 45 and lung cancer, and with a decreased risk of colorectal cancer after age 45 and breast cancer. When compared with the cohort analyses, the intersibling associations were stronger for colorectal cancer after age 45 and weaker for lung cancer. Serious health conditions in childhood/young adulthood did not explain the associations.ConclusionsFamily factors shared by siblings confounded some of the association between education and colorectal cancer after age 45 and lung cancer, but not the associations found for colorectal cancer before age 45 or breast cancer.
The clustering of cardiovascular disease risk factors and their impacts on annual medical expenditure in Japan: community-based cost analysis using Gamma regression models
Authors: Murakami Yoshitaka , Okamura Tomonori , Nakamura Koshi , Miura Katsuyuki , Ueshima Hirotsugu 
Published: March 2013

ObjectiveThe clustering of cardiovascular disease (CVD) risk factors is a serious threat for increasing medical expenses. The age-specific proportion and distribution of medical expenditure attributable to CVD risk factors, especially focused on the elderly, is thus indispensable for formulating public health policy given the extent of the ageing population in developed countries.DesignCost analysis using individuals’ medical expenses and their corresponding health examination measures.SettingShiga prefecture, Japan, from April 2000 to March 2006.Participants33 213 participants aged 40 years and over.Main outcome measuresMean medical expenditure per year.MethodsGamma regression models were applied to examine how the number of CVD risk factors affects mean medical expenditure. The four CVD risk factors analysed in this study were defined as follows: hypertension (systolic blood pressure ≥140 mm Hg or diastolic blood pressure ≥90 mm Hg), hypercholesterolaemia (serum total cholesterol ≥240 mg/dl), high blood glucose (casual blood glucose ≥200 mg/dl) and smoking (current smoker). Sex-specific and age-specific investigations were carried out on the elderly (aged 65 and over) and non-elderly (aged 40–64) populations.ResultsThe mean medical expenditure (per year) for the no CVD risk-factor group was only 110 000 yen at age 50 (men, 110 708 yen; women, 107 109 yen), but this expenditure was 6–7 times higher for 80-year-olds who have three or four CVD risk factors (men, 603 351 yen; women, 765 673 yen). The total overspend (excess fraction) was larger for the non-elderly (men, 15.4%; women, 11.1%) than that for the elderly (men, 0.1%; women, 5.2%) and largely driven by people with one or two CVD risk factors, except for elderly men.ConclusionsThe age-specific proportion and distribution of medical expenditure attributable to CVD risk factors showed that a high-risk approach for the elderly and a population approach for the majority are both necessary to reduce total medical expenditure in Japan.
Long-acting versus short-acting methylphenidate for paediatric ADHD: a systematic review and meta-analysis of comparative efficacy
Authors: Punja Salima , Zorzela Liliane , Hartling Lisa , Urichuk Liana , Vohra Sunita 
Published: March 2013

ObjectiveTo synthesise existing knowledge of the efficacy and safety of long-acting versus short-acting methylphenidate for paediatric attention deficit hyperactivity disorder (ADHD).DesignSystematic review and meta-analysis.Data sourcesElectronic literature search of CENTRAL, MEDLINE, PreMEDLINE, CINAHL, EMBASE, PsychINFO, Scopus and Web of Science for articles published in the English language between 1950 and 2012. Reference lists of included studies were checked for additional studies.Study selectionRandomised controlled trials of paediatric ADHD patients (<18 years), comparing a long-acting methylphenidate form to a short-acting methylphenidate form.Data extractionTwo authors independently selected trials, extracted data and assessed risk of bias. Continuous outcomes were compared using standardised mean differences (SMDs) between treatment groups. Adverse events were compared using risk differences between treatment groups. Heterogeneity was explored by subgroup analysis based on the type of long-acting formulation used.ResultsThirteen RCTs were included; data from 882 participants contributed to the analysis. Meta-analysis of three studies which used parent ratings to report on hyperactivity/impulsivity had an SMD of −0.30 (95% CI −0.51 to −0.08) favouring the long-acting forms. In contrast, three studies used teacher ratings to report on hyperactivity and had an SMD of 0.29 (95% CI 0.05 to 0.52) favouring the short-acting methylphenidate. In addition, subgroup analysis of three studies which used parent ratings to report on inattention/overactivity indicate that the osmotic release oral system generation long-acting formulation was favoured with an SMD of −0.35 (95% CI −0.52 to −0.17), while the second generation showed less efficacy than the short-acting formulation with an SMD of 0.42 (95% CI 0.17 to 0.68). The long-acting formulations presented with slightly more total reported adverse events (n=578) as compared with the short-acting formulation (n=566).ConclusionsThe findings from this systematic review indicate that the long-acting forms have a modest effect on the severity of inattention/overactivity and hyperactivity/impulsivity according to parent reports, whereas the short-acting methylphenidate was preferred according to teacher reports for hyperactivity.
The impact of advance care planning of place of death, a hospice retrospective cohort study
Authors: Abel Julian , Pring Andy , Rich Alison , Malik Tariq , Verne Julia 
Published: March 2013

ObjectivesThere is limited evidence of the impact of advance care planning (ACP) on outcomes. We conducted a retrospective cohort study on deaths of all patients known to a hospice in a 2.5-year period to see if use of ACP affected actual place of death, hospital use and cost of hospital care in the last year.Results969 patients were included. 550 (57%) people completed ACP. 414 (75%) achieved their choice of place of death. For those who chose home, 34 (11.3%) died in hospital; a care home 2 (1.7%) died in hospital; a hospice 14 (11.2%) died in hospital and 6 (86%) who chose to die in hospital did so. 112 (26.5%) of people without ACP died in hospital. Mean number of days in hospital in the last year of life was 18.1 in the ACP group and 26.5 in the non-ACP group(p<0.001). Mean cost of hospital treatment during the last year of life for those who died in hospital was £11,299, those dying outside of hospital £7,730 (p<0.001). Mean number of emergency admissions for those who died in hospital was 2.2 and who died elsewhere was 1.7 (p<0.001).ConclusionsACP can be used routinely in a hospice setting. Those who used ACP spent less time in hospital in their last year. ACP is associated with a reduction in the number of days in hospital in the last year of life with less hospital costs, supporting the assumptions made in the End of Life Care Strategy 2008.
Initial experience using the Penumbra coil 400: comparison of aneurysm packing, cost effectiveness, and coil efficiency
Authors: Milburn James , Pansara Ankit Limba , Vidal Gabriel , Martinez Raisa Coral 
Published: March 2013

Background/objectiveThis was a retrospective single operator experience of aneurysm coiling at the Ochsner Clinic, comparing the Penumbra coil 400 with the other most commonly used coil types, Orbit and Galaxy.Methods40 aneurysms treated exclusively with Orbit or Galaxy coils and 18 aneurysms treated only with Penumbra coils from 2010 to February 2012 were compared. Measurements included packing density, number of coils per unit aneurysm volume, and total coil length per unit aneurysm volume.ResultsMean packing density of 33.7% using Penumbra coils was significantly greater than 24.4% for Orbit/Galaxy coils. The number of coils per aneurysm volume of 0.026 coils/mm3for the Penumbra coil was significantly lower than 0.114 coils/mm3for the Orbit/Galaxy coils. Aneurysm occlusion rates were similar in both groups.ConclusionsCompared with the Orbit/Galaxy coils, our analysis suggests that the Penumbra coil is more efficient and cost effective in the treatment of intracranial aneurysms.
LCK Is an Important Mediator of B-Cell Receptor Signaling in Chronic Lymphocytic Leukemia Cells
Authors: Talab Fatima , Allen John C. , Thompson Victoria , Lin Ke , Slupsky Joseph R. 
Published: March 2013

Abstract
B-cell receptor (BCR) signals promote survival of chronic lymphocytic leukemia (CLL) cells, and it is believed that overexpressed and constitutively active Lyn mediates this signaling. Here, we show that CLL cells express lymphocyte-specific protein tyrosine kinase (LCK) and that inhibition of this Src family tyrosine kinase with the specific inhibitor [4-amino-5-(4-phenoxyphenyl)-7H-pyrrolo[3,2-d]pyrimidin-7-yl-cyclopentane (Lck-i)], or reduction of its expression with siRNA, blocks the induction of CD79a, Syk, inhibitor of IκB kinase (IKK), Akt, and extracellular signal–regulated kinase (ERK) phosphorylation by BCR cross-linking in these cells. Furthermore, we show that CLL cells with high levels of LCK expression have higher levels of BCR-mediated IKK, Akt, and ERK phosphorylation as well as cell survival than CLL cells with low levels of LCK expression. We also show that treatment of CLL cells with Lck-i inhibits BCR cross-linking–induced cell survival. Taken together, these data show a major role for LCK in proximal and distal BCR-mediated signaling in CLL cells and suggest that LCK expression is important in the pathogenesis of this disease. On a clinical level, these studies advocate the use of specific LCK inhibitors in the treatment of progressive CLL. Mol Cancer Res; 11(5); 541–54. ©2013 AACR.