bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct Interspecies Electron Transfer between Geobacter metallireducens and Methanosarcina barkeri
Authors: Rotaru Amelia-Elena , Shrestha Pravin Malla , Liu Fanghua , Markovaite Beatrice , Chen Shanshan , Nevin Kelly P. , Lovley Derek R. 
Published: May 2014

ABSTRACT

Direct interspecies electron transfer (DIET) is potentially an effective form of syntrophy in methanogenic communities, but little is known about the diversity of methanogens capable of DIET. The ability of
Methanosarcina barkeri
to participate in DIET was evaluated in coculture with
Geobacter metallireducens
. Cocultures formed aggregates that shared electrons via DIET during the stoichiometric conversion of ethanol to methane. Cocultures could not be initiated with a pilin-deficient
G. metallireducens
strain, suggesting that long-range electron transfer along pili was important for DIET. Amendments of granular activated carbon permitted the pilin-deficient
G. metallireducens
isolates to share electrons with
M. barkeri
, demonstrating that this conductive material could substitute for pili in promoting DIET. When
M. barkeri
was grown in coculture with the H
2
-producing
Pelobacter carbinolicus
, incapable of DIET,
M. barkeri
utilized H
2
as an electron donor but metabolized little of the acetate that
P. carbinolicus
produced. This suggested that H
2
, but not electrons derived from DIET, inhibited acetate metabolism.
P. carbinolicus-M. barkeri
cocultures did not aggregate, demonstrating that, unlike DIET, close physical contact was not necessary for interspecies H
2
transfer.
M. barkeri
is the second methanogen found to accept electrons via DIET and the first methanogen known to be capable of using either H
2
or electrons derived from DIET for CO
2
reduction. Furthermore,
M. barkeri
is genetically tractable, making it a model organism for elucidating mechanisms by which methanogens make biological electrical connections with other cells.
Formate Oxidation-Driven Calcium Carbonate Precipitation by Methylocystis parvus OBBP
Authors: Ganendra Giovanni , De Muynck Willem , Ho Adrian , Arvaniti Eleni Charalampous , Hosseinkhani Baharak , Ramos Jose Angel , Rahier Hubert , Boon Nico 
Published: May 2014

ABSTRACT

Microbially induced carbonate precipitation (MICP) applied in the construction industry poses several disadvantages such as ammonia release to the air and nitric acid production. An alternative MICP from calcium formate by
Methylocystis parvus
OBBP is presented here to overcome these disadvantages. To induce calcium carbonate precipitation,
M. parvus
was incubated at different calcium formate concentrations and starting culture densities. Up to 91.4% ± 1.6% of the initial calcium was precipitated in the methane-amended cultures compared to 35.1% ± 11.9% when methane was not added. Because the bacteria could only utilize methane for growth, higher culture densities and subsequently calcium removals were exhibited in the cultures when methane was added. A higher calcium carbonate precipitate yield was obtained when higher culture densities were used but not necessarily when more calcium formate was added. This was mainly due to salt inhibition of the bacterial activity at a high calcium formate concentration. A maximum 0.67 ± 0.03 g of CaCO
3
g of Ca(CHOOH)
2
−1
calcium carbonate precipitate yield was obtained when a culture of 10
9
cells ml
−1
and 5 g of calcium formate liter
−1
were used. Compared to the current strategy employing biogenic urea degradation as the basis for MICP, our approach presents significant improvements in the environmental sustainability of the application in the construction industry.
Handling Temperature Bursts Reaching 464°C: Different Microbial Strategies in the Sisters Peak Hydrothermal Chimney
Authors: Perner Mirjam , Gonnella Giorgio , Kurtz Stefan , LaRoche Julie 
Published: May 2014

ABSTRACTThe active venting Sisters Peak (SP) chimney on the Mid-Atlantic Ridge holds the current temperature record for the hottest ever measured hydrothermal fluids (400°C, accompanied by sudden temperature bursts reaching 464°C). Given the unprecedented temperature regime, we investigated the biome of this chimney with a focus on special microbial adaptations for thermal tolerance. The SP metagenome reveals considerable differences in the taxonomic composition from those of other hydrothermal vent and subsurface samples; these could be better explained by temperature than by other available abiotic parameters. The most common species to which SP genes were assigned were thermophilicAciduliprofundumsp. strain MAR08-339 (11.8%),Hippea maritima(3.8%),Caldisericum exile(1.5%), andCaminibacter mediatlanticus(1.4%) as well as to the mesophilicNiastella koreensis(2.8%). A statistical analysis of associations between taxonomic and functional gene assignments revealed specific overrepresented functional categories: forAciduliprofundum, protein biosynthesis, nucleotide metabolism, and energy metabolism genes; forHippeaandCaminibacter, cell motility and/or DNA replication and repair system genes; and forNiastella, cell wall and membrane biogenesis genes. Cultured representatives of these organisms inhabit different thermal niches; i.e.,Aciduliprofundumhas an optimal growth temperature of 70°C,HippeaandCaminibacterhave optimal growth temperatures around 55°C, andNiastellagrows between 10 and 37°C. Therefore, we posit that the different enrichment profiles of functional categories reflect distinct microbial strategies to deal with the different impacts of the local sudden temperature bursts in disparate regions of the chimney.
The
adnAB
Locus, Encoding a Putative Helicase-Nuclease Activity, Is Essential in Streptomyces
Authors: Zhang Lingli , Nguyen Hoang Chuong , Chipot Ludovic , Piotrowski Emilie , Bertrand Claire , Thibessard Annabelle , Leblond Pierre 
Published: May 2014

ABSTRACT

Homologous recombination is a crucial mechanism that repairs a wide range of DNA lesions, including the most deleterious ones, double-strand breaks (DSBs). This multistep process is initiated by the resection of the broken DNA ends by a multisubunit helicase-nuclease complex exemplified by
Escherichia coli
RecBCD,
Bacillus subtilis
AddAB, and newly discovered
Mycobacterium tuberculosis
AdnAB. Here we show that in
Streptomyces
, neither
recBCD
nor
addAB
homologues could be detected. The only putative helicase-nuclease-encoding genes identified were homologous to
M. tuberculosis
adnAB
genes. These genes are conserved as a single copy in all sequenced genomes of
Streptomyces
. The disruption of
adnAB
in
Streptomyces ambofaciens
and
Streptomyces coelicolor
could not be achieved unless an ectopic copy was provided, indicating that
adnAB
is essential for growth. Both
adnA
and
adnB
genes were shown to be inducible in response to DNA damage (mitomycin C) and to be independently transcribed. Introduction of
S. ambofaciens
adnAB
genes in an
E. coli
recB
mutant restored viability and resistance to UV light, suggesting that
Streptomyces
AdnAB could be a functional homologue of RecBCD and be involved in DNA damage resistance.
Control of Gene Expression at a Bacterial Leader RNA, the
agn43
Gene Encoding Outer Membrane Protein Ag43 of Escherichia coli
Authors: Wallecha Anu , Oreh Heather , van der Woude Marjan W. , deHaseth Pieter L. 
Published: May 2014

ABSTRACT

The family of
agn
alleles in
Escherichia coli
pathovars encodes autotransporters that have been implicated in biofilm formation, autoaggregation, and attachment to cells. The alleles all have long leader RNAs preceding the Ag43 translation initiation codon. Here we present an analysis of the
agn43
leader RNA from
E. coli
K-12. We demonstrate the presence of a rho-independent transcription terminator just 28 bp upstream of the main translation start codon and show that it is functional
in vitro
. Our data indicate that an as-yet-unknown mechanism of antitermination of transcription must be operative in earlier phases of growth. However, as bacterial cell cultures mature, progressively fewer transcripts are able to bypass this terminator. In the K-12 leader sequence, two in-frame translation initiation codons have been identified, one upstream and the other downstream of the transcription terminator. For optimal
agn43
expression, both codons need to be present. Translation from the upstream start codon leads to increased downstream
agn43
expression. Our findings have revealed two novel modes of regulation of
agn43
expression in the leader RNA in addition to the previously well-characterized regulation of phase variation at the
agn43
promoter.
Modification of Streptococcus mutans Cnm by PgfS Contributes to Adhesion, Endothelial Cell Invasion, and Virulence
Authors: Avilés-Reyes Alejandro , Miller James H. , Simpson-Haidaris Patricia J. , Hagen Fred K. , Abranches Jacqueline , Lemos José A. 
Published: May 2014

ABSTRACT

Expression of the surface protein Cnm has been directly implicated in the ability of certain strains of
Streptococcus mutans
to bind to collagen and to invade human coronary artery endothelial cells (HCAEC) and in the killing of
Galleria mellonella
. Sequencing analysis of Cnm
+
strains revealed that
cnm
is located between the core genes SMU.2067 and SMU.2069. Reverse transcription-PCR (RT-PCR) analysis showed that
cnm
is cotranscribed with SMU.2067, encoding a putative glycosyltransferase referred to here as PgfS (
p
rotein
g
lycosyltrans
f
erase of
s
treptococci). Notably, Cnm contains a threonine-rich domain predicted to undergo
O
-linked glycosylation. The previously shown abnormal migration pattern of Cnm, the presence of the threonine-rich domain, and the molecular linkage of
cnm
with
pgfS
lead us to hypothesize that PgfS modifies Cnm. A Δ
pgfS
strain showed defects in several traits associated with Cnm expression, including collagen binding, HCAEC invasion, and killing of
G. mellonella
. Western blot analysis revealed that Cnm from the Δ
pgfS
mutant migrated at a lower molecular weight than that from the parent strain. In addition, Cnm produced by Δ
pgfS
was highly susceptible to proteinase K degradation, in contrast to the high-molecular-weight Cnm version found in the parent strain. Lectin-binding analyses confirmed the glycosylated nature of Cnm and strongly suggested the presence of
N
-acetylglucosamine residues attached to Cnm. Based on these findings, the phenotypes observed in Δ
pgfS
are most likely associated with defects in Cnm glycosylation that affects protein function, stability, or both. In conclusion, this study demonstrates that Cnm is a glycoprotein and that posttranslational modification mediated by PgfS contributes to the virulence-associated phenotypes linked to Cnm.
Clinical features of genetic Creutzfeldt-Jakob disease with V180I mutation in the prion protein gene
Authors: Qina Temu , Sanjo Nobuo , Hizume Masaki , Higuma Maya , Tomita Makoto , Atarashi Ryuichiro , Satoh Katsuya , Nozaki Ichiro , Hamaguchi Tsuyoshi , Nakamura Yosikazu , Kobayashi Atsushi , Kitamoto Tetsuyuki , Murayama Shigeo , Murai Hiroyuki , Yamada Masahito , Mizusawa Hidehiro 
Published: May 2014

ObjectivesGenetic Creutzfeldt-Jakob disease (CJD) due to V180I mutation in the prion protein gene (PRNP) is of great interest because of the differences from sporadic CJD and other genetic prion diseases in terms of clinical features, as well as pathological and biochemical findings. However, few systematic observations about the clinical features in patients with this unique mutation have been published. Therefore, the goal of this study was to relate this mutation to other forms of CJD from a clinical perspective.DesignWe analysed clinical symptoms, prion protein genetics, biomarkers in cerebrospinal fluid (CSF) and MRI of patients.Participants186 Japanese patients with the V180I mutation inPRNP.ResultsOur results indicate that the V180I mutation caused CJD at an older age, with a slower progression and a lower possibility of developing myoclonus, cerebellar, pyramidal signs and visual disturbance compared with classical sporadic CJD with methionine homozygosity at codon 129 ofPRNP. Cognitive impairment was the major symptom. Diffuse hyperintensity of the cerebral cortex in diffusion-weighted MRI might be helpful for diagnosis. Owing to the low positivity of PrPScin the CSF, genetic analysis was often required for a differential diagnosis from slowly progressive dementia.ConclusionsWe conclude that the V180I mutation inPRNPproduces a late-developing and slow-developing, less severe form of CJD, whose lesions are uniquely distributed compared with sporadic and other genetic forms of CJD.
Positive correlation between the expression of hEag1 and HIF-1α in breast cancers: an observational study
Authors: Lai Qingxuan , Wang Ting , Guo Qingqing , Zhang Yuxiang , Wang Youxin , Yuan Li , Ling Rui , He Yan , Wang Wei 
Published: May 2014

ObjectivesTo explore the expression patterns of Eag1 (ether á go-go 1) and HIF-1α (hypoxia-inducible factor 1α) in a cohort of patients with breast cancer.SettingDepartment of general surgery in an upper first-class hospital in Xi'an, China.ParticipantsA total of 112 female Han Chinese patients with a diagnosis of invasive ductal carcinoma were included. Patients with main internal diseases, such as cardiovascular, endocrine, gastroenterological, haematological, infectious diseases, etc, were excluded.Primary and secondary outcome measuresExpression profiles of Eag1 and HIF-1α.ResultsEag1 and HIF-1α were overexpressed in the tumour tissues compared with the pair-matched control tissues, p=0.002 and <0.001, respectively. The expression of Eag1 and HIF-1α was negatively correlated with tumour size, p=0.032 and p=0.025, respectively, and lymph node status (p=0.040, p=0.032, respectively). The coexpression of Eag1 and HIF-1α was correlated with tumour size (p=0.012), lymph node status (p=0.027) and tumour stage (p=0.036). HIF-1α has a strong correlation with hEag1 expression (κ=0.731, p<0.001).ConclusionsHIF-1α expression has a strong correlation with hEag1 expression. We are the first to attempt to explore the correlation at the population level.
Improving the efficiency of discharge summary completion by linking to preexisiting patient information databases
Authors: Chan Samuel , P Maurice Andrew , W Pollard Clifford , J Ayre Stephen , L Walters Darren , E Ward Helen 
Published: May 2014

AbstractThe discharge summary (DS) is a document that contains the diagnosis, comorbidities, procedures, complications, and future treatment plan for a particular patient after an inpatient hospital stay. The DS is completed by junior medical staff and is delivered to the general practitioner (GP). DS completion is time consuming and tedious, and DSs are usually not completed within the recommended time frame after a patient is discharged. Time spent completing DSs correlate to junior doctor overtime, which costs the hospital money in overtime pay.Information that is required in the DS is generally already entered into numerous electronic information systems in the hospital, including the “electronic patient journey board” which lists all the patients in a given ward with their clinical information. This information is constantly updated by all staff in the hospital. A program was developed that transferred this information directly into the patient DS. Ten junior doctors in two departments kept daily records for one week of the time spent compiling DSs, the time at work and the actual overtime claimed, before and after the introduction of the intervention.The mean (± SD) time for DS compilation per week reduced by 2.8 (± 2.4) hours from 10.0 (±3.5) hours (p<0.01) and the mean overtime worked per week reduced by 2.8 (± 3.1) hours from 8.5 (± 4.4) hours (p<0.05). The mean overtime claimed reduced by 1.8 (± 2.8) hours from 5.3 (± 5.4) hours per week (p<0.05), resulting in reduction in mean overtime payment of $114.95 from $290.57 per doctor, per week. Extrapolating to the 60 ward based junior doctors, the potential annual savings for the hospital budget are over $350,000. Additionally, the number of DSs completed within 48 hours increased from 45% to 58%.In summary, the transfer of electronic data from the electronic patient journey board to the discharge summary program has yielded improvements in DS completion rates and overtime worked by medical staff, resulting in significant reduction in overtime costs.
Improving the education and experience of foundation doctors in general surgery
Authors: Martel Gareth , Magee Cathy 
Published: May 2014

AbstractReduced working hours and fragmentation of the surgical firm has resulted in a gradual change in FY1 duties. Locally, FY1 doctors were no longer routinely seeing surgical emergency admissions, while FY1s informally reported reduced confidence in dealing with surgical emergencies. The goal of this project was to assess the current training of FY1 doctors within the unit, and to attempt to improve this by increasing exposure to surgical emergencies.Two months into their four month surgical rotation, FY1s completed an anonymous online survey that focused on their confidence in dealing with emergency surgical admissions. Working practice was then changed by the creation of a formal emergency foundation year one (FY1) rota, and the introduction of a baton bleep. The expectation was that all emergency admissions would be clerked by an FY1 doctor. The cohort were asked to repeat the survey after implementation of change.Across all areas assessed, the confidence and experience of the junior doctors was improved. Initially 70% of FY1s felt exposure to emergency surgical cases was inadequate, falling to 0% after the intervention. This was associated with a rise in the average number of acute cases clerked by each FY1 per week from 1.2 to 4.0. At baseline, only 30% of those surveyed felt that they were gaining the skills and experience necessary to prepare them for an FY2 job in general surgery, and after the intervention this increased to 100%.The increased pressures of service provision within reduced working hours does not necessitate the exclusion FY1 doctors from the assessment and management of surgical emergencies. We have demonstrated that preserving this exposure is a priority in the training of junior doctors, resulting in more experienced and confident medical staff.
CSF xanthochromia: correlation with brain imaging and its usefulness as an out-of-hours test
Authors: Ahmed Farhan , Gibbons Stephen , El-Kadiki Alia 
Published: May 2014

BackgroundSubarachnoid haemorrhage (SAH) is a spontaneous bleed into the subarachnoid space which is investigated by CT head and cerebrospinal fluid (CSF) xanthochromia. The aim of this study was to compare CSF xanthochromia with brain imaging and evaluate the need for out of hours (OOH) testing for CSF xanthochromia.MethodDischarge summaries and brain imaging of patients with positive xanthochromia screen were reviewed over 12 months retrospectively. Timings of CSF xanthochromia and hospital discharge of 30 consecutive patients with negative xanthochromia screen were also examined.ResultsFrom 289 xanthochromia requests, 23 were positive but only 2 patients had an actual bleed. In 30 consecutive negative xanthochromia results, all brain imaging results suggested no bleed. Eight of these requests were performed OOH, and as a result, 1 patient was discharged early.ConclusionsCSF xanthochromia has a poor positive predictive value (8.7%) but has a good negative predictive value (100%) for SAH. Analysis of CSF xanthochromia OOH, in patients with negative CT head, did not speed up the discharge process from the hospital.
International Variation in Lung Cancer Mortality Rates and Trends among Women
Authors: Torre Lindsey A. , Siegel Rebecca L. , Ward Elizabeth M. , Jemal Ahmedin 
Published: May 2014

AbstractBackground: There is no recent comprehensive global analysis of lung cancer mortality in women. We describe contemporary mortality rates and trends among women globally.Methods: We used the World Health Organization's Cancer Mortality Database covering 65 populations on six continents to calculate age-standardized (1960 Segi world standard) lung cancer death rates during 2006 to 2010 and annual percent change in rates for available years from 1985 to 2011 and for the most recent five data years by population and age group (30–49 and 50–74 years).Results: Lung cancer mortality rates (per 100,000) among young women (30–49 years) during 2006 to 2010 ranged from 0.7 in Costa Rica to 14.8 in Hungary. Rates among young women were stable or declining in 47 of 52 populations examined. Rates among women 50 to 74 years ranged from 8.8 in Georgia and Egypt to 120.0 in Scotland. In both age groups, rates were highest in parts of Europe (Scotland, Hungary, Denmark) and North America and lowest in Africa, Asia, and Latin America. Rates in older women were increasing for more than half (36/64) of populations examined, including most countries in Southern, Eastern, and Western Europe and South America.Conclusions: Although widespread reductions in lung cancer in young women provide evidence of tobacco control success, rates continue to increase among older women in many countries.Impact: More concentrated efforts to initiate or expand tobacco control programs in these countries globally will be required to attenuate the future lung cancer burden. Cancer Epidemiol Biomarkers Prev; 23(6); 1025–36. ©2014 AACR.
Discordant In Vitro and In Vivo Chemopotentiating Effects of the PARP Inhibitor Veliparib in Temozolomide-Sensitive versus -Resistant Glioblastoma Multiforme Xenografts
Authors: Gupta Shiv K. , Mladek Ann C. , Carlson Brett L. , Boakye-Agyeman Felix , Bakken Katrina K. , Kizilbash Sani H. , Schroeder Mark A. , Reid Joel , Sarkaria Jann N. 
Published: May 2014

Abstract
Purpose: Effective sensitizing strategies potentially can extend the benefit of temozolomide (TMZ) therapy in patients with glioblastoma (GBM). We previously demonstrated that robust TMZ-sensitizing effects of the [poly (ADP-ribose) polymerase] (PARP) inhibitor veliparib (ABT-888) are restricted to TMZ-sensitive GBM xenografts. The focus of this study is to provide an understanding for the differential sensitization in paired TMZ-sensitive and -resistant GBM models.
Experimental Design: The impact of veliparib on TMZ-induced cytotoxicity and DNA damage was evaluated in vitro and in vivo in models of acquired TMZ resistance (GBM12TMZ-mgmtHigh, GBM12TMZ-mgmtLow, and U251TMZ), inherent TMZ resistance (T98G), and TMZ-sensitive (U251 and GBM12). In vivo drug efficacy, pharmacokinetics, and pharmacodynamics were analyzed using clinically relevant dosing regimens.
Results: Veliparib enhanced TMZ cytotoxicity and DNA-damage signaling in all GBM models in vitro with more pronounced effects in TMZ-resistant lines at 3 to 10 μmol/L veliparib. In vivo, combined TMZ/veliparib, compared with TMZ alone, significantly delayed tumor growth and enhanced DNA-damage signaling and γH2AX levels in the sensitive GBM12 xenograft line but not in the resistant GBM12TMZ lines. The pharmacokinetic profile of veliparib was similar for GBM12 and GBM12TMZ tumors with Cmax (∼1.5 μmol/L) in tissue significantly lower than concentrations associated with optimal in vitro sensitizing effects for resistant tumors. In contrast, robust suppression of PARP-1 expression by shRNA significantly increased TMZ sensitivity of U251TMZ in vitro and in vivo.
Conclusions: In vitro cytotoxicity assays do not adequately model the therapeutic index of PARP inhibitors, as concentrations of veliparib and TMZ required to sensitize TMZ-resistant cancer cells in vivo cannot be achieved using a tolerable dosing regimen. Clin Cancer Res; 20(14); 3730–41. ©2014 AACR.