bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intracellular NADPH Levels Affect the Oligomeric State of the Glucose 6-Phosphate Dehydrogenase
Authors: Saliola Michele , Tramonti Angela , Lanini Claudio , Cialfi Samantha , De Biase Daniela , Falcone Claudio 
Published: October 2012

ABSTRACT

In the yeast
Kluyveromyces lactis
, glucose 6-phosphate dehydrogenase (G6PDH) is detected as two differently migrating forms on native polyacrylamide gels. The pivotal metabolic role of G6PDH in
K. lactis
led us to investigate the mechanism controlling the two activities in respiratory and fermentative mutant strains. An extensive analysis of these mutants showed that the NAD
+
(H)/NADP
+
(H)-dependent cytosolic alcohol (ADH) and aldehyde (ALD) dehydrogenase balance affects the expression of the G6PDH activity pattern. Under fermentative/ethanol growth conditions, the concomitant activation of ADH and ALD activities led to cytosolic accumulation of NADPH, triggering an alteration in the oligomeric state of the G6PDH caused by displacement/release of the structural NADP
+
bound to each subunit of the enzyme. The new oligomeric G6PDH form with faster-migrating properties increases as a consequence of intracellular redox unbalance/NADPH accumulation, which inhibits G6PDH activity
in vivo
. The appearance of a new G6PDH-specific activity band, following incubation of
Saccharomyces cerevisiae
and human cellular extracts with NADP
+
, also suggests that a regulatory mechanism of this activity through NADPH accumulation is highly conserved among eukaryotes.
Metal Resistance and Lithoautotrophy in the Extreme Thermoacidophile Metallosphaera sedula
Authors: Maezato Yukari , Johnson Tyler , McCarthy Samuel , Dana Karl , Blum Paul 
Published: October 2012

ABSTRACTArchaea such asMetallosphaera sedulaare thermophilic lithoautotrophs that occupy unusually acidic and metal-rich environments. These traits are thought to underlie their industrial importance for bioleaching of base and precious metals. In this study, a genetic approach was taken to investigate the specific relationship between metal resistance and lithoautotrophy during biotransformation of the primary copper ore, chalcopyrite (CuFeS2). In this study, a genetic system was developed forM. sedulato investigate parameters that limit bioleaching of chalcopyrite. The functional role of theM. sedula copRTAoperon was demonstrated by cross-species complementation of a copper-sensitiveSulfolobus solfataricus copRmutant. Inactivation of the gene encoding theM. sedulacopper efflux protein,copA, using targeted recombination compromised metal resistance and eliminated chalcopyrite bioleaching. In contrast, a spontaneousM. sedulamutant (CuR1) with elevated metal resistance transformed chalcopyrite at an accelerated rate without affecting chemoheterotrophic growth. Proteomic analysis of CuR1 identified pleiotropic changes, including altered abundance of transport proteins having AAA-ATPase motifs. Addition of the insoluble carbonate mineral witherite (BaCO3) further stimulated chalcopyrite lithotrophy, indicating that carbon was a limiting factor. Since both mineral types were actively colonized, enhanced metal leaching may arise from the cooperative exchange of energy and carbon between surface-adhered populations. Genetic approaches provide a new means of improving the efficiency of metal bioleaching by enhancing the mechanistic understanding of thermophilic lithoautotrophy.
Gateway Role for rRNA Precursors in Ribosome Assembly
Authors: Gutgsell Nancy S. , Jain Chaitanya 
Published: October 2012

ABSTRACT

In
Escherichia coli
, rRNAs are initially transcribed with precursor sequences, which are subsequently removed through processing reactions. To investigate the role of precursor sequences, we analyzed ribosome assembly in strains containing mutations in the processing RNases. We observed that defects in 23S rRNA processing resulted in an accumulation of ribosomal subunits and caused a significant delay in ribosome assembly. These observations suggest that precursor residues in 23S rRNA control ribosome assembly and could be serving a regulatory role to couple ribosome assembly to rRNA processing. The possible mechanisms through which rRNA processing and ribosome assembly could be linked are discussed.
An Archaeal Histone Is Required for Transformation of Thermococcus kodakarensis
Authors: Čuboňová Lubomira , Katano Masahiro , Kanai Tamotsu , Atomi Haruyuki , Reeve John N. , Santangelo Thomas J. 
Published: October 2012

ABSTRACT

Archaeal histones wrap DNA into complexes, designated archaeal nucleosomes, that resemble the tetrasome core of a eukaryotic nucleosome. Therefore, all DNA interactions
in vivo
in
Thermococcus kodakarensis
, the most genetically versatile model species for archaeal research, must occur in the context of a histone-bound genome. Here we report the construction and properties of
T. kodakarensis
strains that have TK1413 or TK2289 deleted, the genes that encode HTkA and HTkB, respectively, the two archaeal histones present in this archaeon. All attempts to generate a strain with both TK1413 and TK2289 deleted were unsuccessful, arguing that a histone-mediated event(s) in
T. kodakarensis
is essential. The HTkA and HTkB amino acid sequences are 84% identical (56 of 67 residues) and 94% similar (63 of 67 residues), but despite this homology and their apparent redundancy in terms of supporting viability, the absence of HTkA and HTkB resulted in differences in growth and in quantitative and qualitative differences in genome transcription. A most surprising result was that the deletion of TK1413 (Δ
htkA
) resulted in a
T. kodakarensis
strain that was no longer amenable to transformation, whereas the deletion of TK2289 (Δ
htkB
) had no detrimental effects on transformation. Potential roles for the archaeal histones in regulating gene expression and for HTkA in DNA uptake and recombination are discussed.
Transcriptional Regulation of the CmeABC Multidrug Efflux Pump and the KatA Catalase by CosR in Campylobacter jejuni
Authors: Hwang Sunyoung , Zhang Qijing , Ryu Sangryeol , Jeon Byeonghwa 
Published: October 2012

ABSTRACT

CosR is an essential response regulator in
Campylobacter jejuni
, a major food-borne pathogen causing enteritis worldwide. A transcriptomic analysis performed in this study discovered 93 genes whose transcriptional levels were changed >2-fold due to the repression of CosR expression by antisense peptide nucleic acid. The identified CosR-regulated genes are involved in various cellular functions, such as energy production, protein synthesis and folding, flagellum biogenesis, and lipid metabolism. Interestingly, 17 of the 93 CosR-regulated genes (18.3%) are predicted essential genes, indicating that CosR may participate in the regulation of vital biological processes in
C. jejuni
. In particular, CosR knockdown increased the transcriptional levels of
cmeA
,
cmeB
, and
cmeC
genes, whose protein product (CmeABC) is an important determinant conferring multidrug resistance in
Campylobacter
. Negative regulation of
cmeABC
by CosR was verified by quantitative real-time PCR (qRT-PCR) and P

cmeABC

::
lacZ
assay. The results of electrophoretic mobility shift assays (EMSAs) and DNase I footprinting assays demonstrated that CosR directly binds to the
cmeABC
promoter. Another notable finding is that CosR regulates the transcription of
katA
, the sole catalase gene in
C. jejuni
. Further characterization with qRT-PCR, the catalase enzyme assay, EMSA, and DNase I footprinting assays successfully demonstrated that CosR affects the
katA
transcription and the catalase activity by direct interactions with the
katA
promoter. The findings in this study clearly demonstrated that CosR regulates resistance mechanisms in
C. jejuni
by controlling the expression of genes involved in oxidative stress defense and extrusion of toxic compounds out of the cell.
ArcA and AppY Antagonize IscR Repression of Hydrogenase-1 Expression under Anaerobic Conditions, Revealing a Novel Mode of O
2
Regulation of Gene Expression in Escherichia coli
Authors: Nesbit A. D. , Fleischhacker A. S. , Teter S. J. , Kiley P. J. 
Published: October 2012

ABSTRACT

Transcription of the
Escherichia coli
hydrogenase-1 operon (
hyaABCDEF
) is increased by the transcription factors ArcA and AppY under anaerobic growth conditions. However, IscR, which represses transcription of the
hyaA
promoter (P

hyaA

) under aerobic conditions, was not known to repress transcription of this promoter under anaerobic conditions. Here, we report that ArcA and AppY increase P

hyaA

expression under anaerobic conditions by antagonizing IscR binding at P

hyaA

, since IscR repression is observed when either ArcA or AppY is eliminated. The ability of ArcA and AppY to act as antirepressors of IscR repression of P

hyaA

depended on IscR levels, suggesting that IscR competes with ArcA and/or AppY for binding. In support of this competition model, electrophoretic mobility shift assays and DNase I footprinting showed that the ArcA and IscR binding sites overlap and that binding of ArcA and IscR is mutually exclusive. Unexpectedly, IscR with a C92A mutation (IscR-C92A), which mimics the clusterless form of the protein that is present predominantly under aerobic conditions, was a better repressor under anaerobic conditions of both P

hyaA

and a constitutive promoter containing the IscR binding site from P

hyaA

than wild-type IscR, which is predominantly in the [2Fe-2S] form under anaerobic conditions. This observation could not be explained by differences in DNA binding affinities or IscR levels, so we conclude that [2Fe-2S]-IscR is a weaker repressor of P

hyaA

than clusterless IscR. In sum, a combination of ArcA and AppY antirepression of IscR function, lower levels of IscR, and weak repression by [2Fe-2S]-IscR leads to increased P

hyaA

expression under anaerobic conditions.
Level of phosphohistone H3 among various types of human cancers
Authors: Sun Amy , Zhou Wei , Lunceford Jared , Strack Peter , Dauffenbach Lisa M , Kerfoot Christopher A 
Published: October 2012

ObjectivesAnti-phosphorylated histone H3 (pHH3) antibodies specifically detect the core protein histone H3 only when phosphorylated at serine 10 (Ser10) or serine 28 (Ser28). Measurement of pHH3 levels can be used for quantifying mitosis and the effectiveness of mitotic inhibitors in early drug development. However, data on the expression level of pHH3 (Ser10) and pHH3 (Ser28) among different cancers are limited. This study was designed to investigate the expression levels of pHH3 across different types of cancers, using uniform techniques and assay platforms in a single laboratory.DesignRetrospective study.SettingSingle laboratory.SpecimensFormalin-fixed, paraffin-embedded various human cancer specimens were provided by Mosaic Laboratories Tissue Bank.Primary and secondary outcome measuresUsing immunohistochemistry, pHH3 levels were measured using both pHH3 (Ser10) and (Ser28) antibodies among 10 human melanoma and 10 ovarian tumour samples. The samples were reviewed blindly by two reviewers. pHH3 (Ser10) was then selected to measure the pHH3 levels in cancers of breast, colorectal, oesophageal, gastric, head and neck and lung (n=5 for each cancer).ResultsThe pHH3 (Ser10) expression was higher than pHH3 (Ser28) in both melanoma and ovarian cancers (p<0.01), with the mean (SD) levels of 1.28% (0.47%) for Ser10 and 0.53% (0.44%) for Ser28 among melanoma and 3.47% (3.51%) for Ser10 and 0.62% (0.68%) for Ser28 among ovarian cancers, respectively. No statistically significant differences were observed among different cancer types tested for pHH3 using Ser10 (p=0.197). No reviewer effect was identified.ConclusionsThe pHH3 Ser10 was significantly higher than Ser28 and may serve as the more robust of two pHH3 assays for measuring mitotic index.
Effects of myocardial fibrosis assessed by MRI on dynamic left ventricular outflow tract obstruction in patients with hypertrophic cardiomyopathy: a retrospective database analysis
Authors: Biagini Elena , Lorenzini Massimiliano , Olivotto Iacopo , Rocchi Guido , Lovato Luigi , Lai Francesco , Rosmini Stefania , Pazzi Chiara , Pasquale Ferdinando , Reggiani Maria Letizia Bacchi , Fattori Rossella , Rapezzi Claudio 
Published: October 2012

BackgroundWhile implications of myocardial fibrosis on left ventricular (LV) function at rest have been studied in hypertrophic cardiomyopathy (HCM), the pathophysiological consequences on dynamic LV outflow tract (LVOT) gradient have so far not been investigated in detail.ObjectiveTo evaluate the influence of myocardial fibrosis, detected by MRI as late-gadolinium enhancement (LGE), on LVOT gradient in HCM.DesignRetrospective database analysis.SettingA single Italian cardiomyopathies referral centre.PatientsSeventy-six HCM patients with normal ejection fraction at rest.InterventionsPatients underwent cardiac MR and performed bicycle exercise echocardiogram within a month.ResultsLGE was present in 54 patients (71%), ranging from 0.2% to 32.4% of LV mass. There was a weak correlation between the amount of fibrosis and LVOT gradient variation during exercise in the overall population (r=−0.243, p=0.034) and a stronger correlation in patients with obstructive HCM at rest (r=−0.524, p=0.021). Patients with an LVOT gradient increase ≥50 mm Hg during exercise had a significantly lesser extent of fibrosis than those with an increase <50 mm Hg (0.7% (IQR 0–2.4) vs 3.2% (IQR 0.2–7.4), p=0.006). The extent of fibrosis was significantly lower among the highest quartiles of LVOT gradient increase (p=0.009).ConclusionsIn patients with HCM and normal ejection fraction at rest, myocardial fibrosis was associated with a lower increase in LVOT gradient during exercise, probably due to a lesser degree of myocardial contractility recruitment. This negative association was more evident in patients with an obstructive form at rest.
Expression of prostaglandin E receptor subtype EP4 in conjunctival epithelium of patients with ocular surface disorders: case-control study
Authors: Ueta Mayumi , Sotozono Chie , Yamada Keiko , Yokoi Norihiko , Inatomi Tsutomu , Kinoshita Shigeru 
Published: October 2012

ObjectivesTo confirm the downregulation of PTGER4 mRNA in the conjunctiva of Stevens-Johnson syndrome/toxic epidermal necrolysis (SJS/TEN) and ocular cicatricial pemphigoid (OCP) patients and to examine the expression of its EP4 protein in the conjunctival epithelium of patients with various ocular surface disorders.DesignCase-control study.Setting and participantsWe performed quantitative reverse transcription-PCR (RT-PCR) analysis ofPTGER4mRNA in conjunctival tissue sections from patients with SJS/TEN and OCP to confirm the downregulation ofPTGER4mRNA expression. We also analysed EP4 immunohistologically in other ocular surface disorders. Conjunctival tissues were obtained from patients undergoing surgical reconstruction of the ocular surface due to chemical eye burns, subacute SJS/TEN or chronic SJS/TEN, chronic OCP, severe graft versus host disease (GVHD) and from patients with Mooren's ulcers treated by resection of the inflammatory conjunctiva.Primary and secondary outcome measuresThe expression ofPTGER4mRNA and EP4 protein assessed by quantitative RT-PCR assay and immunohistological methods.ResultsPTGER4mRNA was significantly lower in conjunctival tissues from SJS and OCP patients than in the control conjunctivochalasis samples. EP4 protein was detected in conjunctival epithelium from patients with chemical eye burn and in control conjunctival epithelium from patients with conjunctivochalasis. Its expression varied in conjunctival epithelium from patients with Mooren's ulcer. We did not detect EP4 immunoreactivity in conjunctival epithelium from patients with subacute SJS/TEN, severe GVHD, chronic SJS/TEN or OCP.ConclusionsThe strong downregulation of EP4 expression in conjunctival epithelium from patients with OCP or SJS/TEN may be attributable to ocular surface inflammation.
Prevalence of respiratory symptoms at two time points in a population of children in Manchester—a cohort study
Authors: Linehan Mary F , Niven Robert M , Baxter David N , Morris Julie A , Frank Timothy L 
Published: October 2012

ObjectiveAlthough the prevalence of asthma and atopy has been noted to have increased in recent decades, patterns of asthma prevalence have, traditionally, been difficult to track. Most reports on trends in childhood asthma have been cross-sectional measuring the prevalence in cohorts of similar aged children at different time points. The aim of this paper is to report on the prevalence of symptoms in the same cohort at two separate time points.DesignRetrospective cohort study.SettingCommunity-based study, Central Manchester.ParticipantsMANCAS1, study n=5086, participation n=2414. MANCAS2, study n=6338, participation n=1608. Children born in a hospital in Manchester within specified dates and still living or attending a school in Central Manchester were eligible for inclusion. Children on an ‘at-risk’ register or living with short-term carers were excluded.Outcome measuresData on respiratory symptoms were collected at two separate time points using parent completed questionnaires.ResultsResponse rate for MANCAS1 was 47.5% and 25.4% for MANCAS2. There were 801 individuals for whom a response to both studies was received. There was a significant reduction in the prevalence of night cough (29.5% vs 18.3%, McNemar <0.01) and antibiotic use for respiratory infections (9.1% vs 4.3%, McNemar <0.01) between the two study time points. The prevalence of hay fever/eczema increased (41.6% vs 46.9%, McNemar <0.01) between the two studies. There was no significant difference in the prevalence of wheeze, exercise-induced wheeze or asthma medication.ConclusionsAlthough this report of respiratory symptom prevalence in the same population at two time points over a 7-year period shows a constant burden of asthma symptoms, there is some suggestion of variability in asthma symptom prevalence within the cohort as the children matured while the burden of allergy symptoms increased.
The effect of smoking on health-related quality of life in lung cancer patients: a systematic review
Authors: Rowland Christine , Eiser Christine , Rowe Richard , Danson Sarah 
Published: October 2012

IntroductionGiven poor survival rates for lung cancer, health-related quality of life (HRQoL) is very important. Smoking is prevalent among those diagnosed with lung cancer, and continued smoking is associated with compromised HRQoL in other patient groups.AimsA systematic review was conducted to determine: (i) differences in HRQoL between lung cancer patients who smoke compared with those who quit or never smoked and (ii) changes in HRQoL in patients who continue to smoke after diagnosis compared with those who quit or never smoked.MethodScopus, Medline, PubMed, PsychINFO and Web of Knowledge from January 1995 to June 2010 were searched. The included studies were assessed and given a score for quality.ResultsEight studies met the inclusion criteria. Four studies showed that lung cancer patients who smoked report impaired HRQoL compared with those who never smoked or had quit. Smokers reported significantly lower HRQoL than former smokers, who in turn reported lower HRQoL than never smokers. This finding remained consistent over time.ConclusionsWhen taking account of methodological quality, smoking is associated with poorer HRQoL in lung cancer patients. These results suggest that programmes are needed to address the specific support needs of this group and promote HRQoL during their final months. Longitudinal research is necessary to further understand the association between smoking and HRQoL.
HYPERVENTILATION PROVOKES SYMPTOMS OF CARPAL TUNNEL SYNDROME
Authors: Aslam U. , Afzal S. , Syed Shakir 
Published: October 2012

Hyperventilation causes respiratory alkalosis. The nervous system is more excitable in alkalosis. This phenomenon can be observed as paraesthesia in fingers and toes as well as around the lips in anxious patients breathing rapidly. We wanted to test this phenomenon on already irritable nerves like the median nerve in carpal tunnel syndrome (CTS). We deployed 50 patients who came in to the day case unit for carpal tunnel decompression with electro-physiologically proven diagnosis. We devised a test whereby patients were made to hyperventilate under prescribed conditions and repeated Phalen's test and Tinel's sign for comparison. These were compared with a control group chosen randomly among hospital staff. 86% patients had a positive result which was just behind Phalen's test in sensitivity. It was also 100% specific as there were no false positives. Hyperventilation is a phenomenon which provokes carpal tunnel syndrome. Its clinical value remains to be seen due to cumbersome method and probable patient non-compliance but it is a new discovery. It may be useful in other irritable-nerve-syndromes as a test to add to our available armament. It may be an additional factor or a primary reason for nocturnal paraesthesias in CTS patients.
USE OF CONTINUOUS HORIZONTAL MATTRESS SUTURE TECHNIQUE IN END-TO-SIDE MICROSURGICAL ANASTOMOSIS
Authors: Başar Hakan , Erol Bülent , Tetik Cihangir 
Published: October 2012

Purpose: The aim of our study was to improve the new suturing method which increases the success rate of end to side microsurgical anastomosis. Methods: Thirty-six Sprague-Dawrey rats were randomly divided into three groups that consist of 12 rats in closed envelope method. The end-to-side microsurgical anastomosis procedures were applied by the same surgeon between left main carotid artey and left external jugular vein. The surgical evaluations were performed with anastomosis duration, leakage evaluation, vessels patency, aneurysm improvement and histological assesment. Results: End-to-side anastomosis, which was applied with Continuous Horizontal Mattress suture, gave significantly better results in terms of leakage, anastomosis openness, aneurysm and histologic assesment. Also anastomosis duration of Continuous Horizontal suture was significantly faster than Simple Intermittent suture. Discussion: Our study revealed that the Continuous Horizontal Mattress suture technique had the advantages of providing uninterrupted vessel flow in a shorter time, and minimal intraluminal suture material, which increase thrombosis risk. Also 'sac-mouth' effect of Continuous suture technique was prevented by Horizontal Mattress technique.
Global software development and collaboration
Authors: Noll John , Beecham Sarah , Richardson Ita 
Published: October 2012

While organisations recognise the advantages offered by global software development, many socio-technical barriers affect successful collaboration in this inter-cultural environment. In this paper, we present a review of the global software development literature where we highlight collaboration problems experienced by a cross-section of organisations in twenty-six studies. We also look at the literature to answer how organisations are overcoming these barriers in practice. We build on our previous study on global software development where we define collaboration as four practices related to agreeing, allocating, and planning goals, objectives, and tasks among distributed teams.
We found that the key barriers to collaboration are geographic, temporal, cultural, and linguistic distance; the primary solutions to overcoming these barriers include site visits, synchronous communication technology, and knowledge sharing infrastructure to capture implicit knowledge and make it explicit.