bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhanced Alcaligenes faecalis Denitrification Rate with Electrodes as the Electron Donor
Authors: Wang Xin , Yu Ping , Zeng Cuiping , Ding Hongrui , Li Yan , Wang Changqiu , Lu Anhuai 
Published: June 2015

ABSTRACT

The utilization by
Alcaligenes faecalis
of electrodes as the electron donor for denitrification was investigated in this study. The denitrification rate of
A. faecalis
with a poised potential was greatly enhanced compared with that of the controls without poised potentials. For nitrate reduction, although
A. faecalis
could not reduce nitrate, at three poised potentials of +0.06, −0.06, and −0.15 V (versus normal hydrogen electrode [NHE]), the nitrate was partially reduced with −0.15- and −0.06-V potentials at rates of 17.3 and 28.5 mg/liter/day, respectively. The percentages of reduction for −0.15 and −0.06 V were 52.4 and 30.4%, respectively. Meanwhile, for nitrite reduction, the poised potentials greatly enhanced the nitrite reduction. The nitrite reduction rates for three poised potentials (−0.06, −0.15, and −0.30 V) were 1.98, 4.37, and 3.91 mg/liter/h, respectively. When the potentials were cut off, the nitrite reduction rate was maintained for 1.5 h (from 2.3 to 2.25 mg/liter/h) and then greatly decreased, and the reduction rate (0.38 mg/liter/h) was about 1/6 compared with the rate (2.3 mg/liter/h) when potential was on. Then the potentials resumed, but the reduction rate did not resume and was only 2 times higher than the rate when the potential was off.
Treatment of Alkaline Cr(VI)-Contaminated Leachate with an Alkaliphilic Metal-Reducing Bacterium
Authors: Watts Mathew P. , Khijniak Tatiana V. , Boothman Christopher , Lloyd Jonathan R. 
Published: June 2015

ABSTRACT

Chromium in its toxic Cr(VI) valence state is a common contaminant particularly associated with alkaline environments. A well-publicized case of this occurred in Glasgow, United Kingdom, where poorly controlled disposal of a cementitious industrial by-product, chromite ore processing residue (COPR), has resulted in extensive contamination by Cr(VI)-contaminated alkaline leachates. In the search for viable bioremediation treatments for Cr(VI), a variety of bacteria that are capable of reduction of the toxic and highly soluble Cr(VI) to the relatively nontoxic and less mobile Cr(III) oxidation state, predominantly under circumneutral pH conditions, have been isolated. Recently, however, alkaliphilic bacteria that have the potential to reduce Cr(VI) under alkaline conditions have been identified. This study focuses on the application of a metal-reducing bacterium to the remediation of alkaline Cr(VI)-contaminated leachates from COPR. This bacterium, belonging to the
Halomonas
genus, was found to exhibit growth concomitant to Cr(VI) reduction under alkaline conditions (pH 10). Bacterial cells were able to rapidly remove high concentrations of aqueous Cr(VI) (2.5 mM) under anaerobic conditions, up to a starting pH of 11. Cr(VI) reduction rates were controlled by pH, with slower removal observed at pH 11, compared to pH 10, while no removal was observed at pH 12. The reduction of aqueous Cr(VI) resulted in the precipitation of Cr(III) biominerals, which were characterized using transmission electron microscopy and energy-dispersive X-ray analysis (TEM-EDX) and X-ray photoelectron spectroscopy (XPS). The effectiveness of this haloalkaliphilic bacterium for Cr(VI) reduction at high pH suggests potential for its use as an
in situ
treatment of COPR and other alkaline Cr(VI)-contaminated environments.
Three New Cutinases from the Yeast Arxula adeninivorans That Are Suitable for Biotechnological Applications
Authors: Bischoff Felix , Litwińska Katarzyna , Cordes Arno , Baronian Keith , Bode Rüdiger , Schauer Frieder , Kunze Gotthard 
Published: June 2015

ABSTRACT

The genes
ACUT1
,
ACUT2
, and
ACUT3
, encoding cutinases, were selected from the genomic DNA of
Arxula adeninivorans
LS3. The alignment of the amino acid sequences of these cutinases with those of other cutinases or cutinase-like enzymes from different fungi showed that they all had a catalytic S-D-H triad with a conserved G-Y-S-Q-G domain. All three genes were overexpressed in
A. adeninivorans
using the strong constitutive
TEF1
promoter. Recombinant 6× His (6h)-tagged cutinase 1 protein (p) from
A. adeninivorans
LS3 (Acut1-6hp), Acut2-6hp, and Acut3-6hp were produced and purified by immobilized-metal ion affinity chromatography and biochemically characterized using
p
-nitrophenyl butyrate as the substrate for standard activity tests. All three enzymes from
A. adeninivorans
were active from pH 4.5 to 6.5 and from 20 to 30°C. They were shown to be unstable under optimal reaction conditions but could be stabilized using organic solvents, such as polyethylene glycol 200 (PEG 200), isopropanol, ethanol, or acetone. PEG 200 (50%, vol/vol) was found to be the best stabilizing agent for all of the cutinases, and acetone greatly increased the half-life and enzyme activity (up to 300% for Acut3-6hp). The substrate spectra for Acut1-6hp, Acut2-6hp, and Acut3-6hp were quite similar, with the highest activity being for short-chain fatty acid esters of
p
-nitrophenol and glycerol. Additionally, they were found to have polycaprolactone degradation activity and cutinolytic activity against cutin from apple peel. The activity was compared with that of the 6× His-tagged cutinase from
Fusarium solani
f. sp.
pisi
(FsCut-6hp), also expressed in
A. adeninivorans
, as a positive control. A fed-batch cultivation of the best Acut2-6hp-producing strain,
A. adeninivorans
G1212/YRC102-ACUT2-6H, was performed and showed that very high activities of 1,064 U ml
−1
could be achieved even with a nonoptimized cultivation procedure.
Physiological and Transcriptional Responses of Different Industrial Microbes at Near-Zero Specific Growth Rates
Authors: Ercan Onur , Bisschops Markus M. M. , Overkamp Wout , Jørgensen Thomas R. , Ram Arthur F. , Smid Eddy J. , Pronk Jack T. , Kuipers Oscar P. , Daran-Lapujade Pascale , Kleerebezem Michiel 
Published: June 2015

ABSTRACT

The current knowledge of the physiology and gene expression of industrially relevant microorganisms is largely based on laboratory studies under conditions of rapid growth and high metabolic activity. However, in natural ecosystems and industrial processes, microbes frequently encounter severe calorie restriction. As a consequence, microbial growth rates in such settings can be extremely slow and even approach zero. Furthermore, uncoupling microbial growth from product formation, while cellular integrity and activity are maintained, offers perspectives that are economically highly interesting. Retentostat cultures have been employed to investigate microbial physiology at (near-)zero growth rates. This minireview compares information from recent physiological and gene expression studies on retentostat cultures of the industrially relevant microorganisms
Lactobacillus plantarum
,
Lactococcus lactis
,
Bacillus subtilis
,
Saccharomyces cerevisiae
, and
Aspergillus niger
. Shared responses of these organisms to (near-)zero growth rates include increased stress tolerance and a downregulation of genes involved in protein synthesis. Other adaptations, such as changes in morphology and (secondary) metabolite production, were species specific. This comparison underlines the industrial and scientific significance of further research on microbial (near-)zero growth physiology.
Screening of Chlamydomonas reinhardtii Populations with Single-Cell Resolution by Using a High-Throughput Microscale Sample Preparation for Matrix-Assisted Laser Desorption Ionization Mass Spectrometry
Authors: Krismer Jasmin , Sobek Jens , Steinhoff Robert F. , Fagerer Stephan R. , Pabst Martin , Zenobi Renato 
Published: June 2015

ABSTRACT

The consequences of cellular heterogeneity, such as biocide persistence, can only be tackled by studying each individual in a cell population. Fluorescent tags provide tools for the high-throughput analysis of genomes, RNA transcripts, or proteins on the single-cell level. However, the analysis of lower-molecular-weight compounds that elude tagging is still a great challenge. Here, we describe a novel high-throughput microscale sample preparation technique for single cells that allows a mass spectrum to be obtained for each individual cell within a microbial population. The approach presented includes spotting
Chlamydomonas reinhardtii
cells, using a noncontact microarrayer, onto a specialized slide and controlled lysis of cells separated on the slide. Throughout the sample preparation, analytes were traced and individual steps optimized using autofluorescence detection of chlorophyll. The lysates of isolated cells are subjected to a direct, label-free analysis using matrix-assisted laser desorption ionization mass spectrometry. Thus, we were able to differentiate individual cells of two
Chlamydomonas reinhardtii
strains based on single-cell mass spectra. Furthermore, we showed that only population profiles with real single-cell resolution render a nondistorted picture of the phenotypes contained in a population.
Adaptive Evolution of Thermotoga maritima Reveals Plasticity of the ABC Transporter Network
Authors: Latif Haythem , Sahin Merve , Tarasova Janna , Tarasova Yekaterina , Portnoy Vasiliy A. , Nogales Juan , Zengler Karsten 
Published: June 2015

ABSTRACT

Thermotoga maritima
is a hyperthermophilic anaerobe that utilizes a vast network of ABC transporters to efficiently metabolize a variety of carbon sources to produce hydrogen. For unknown reasons, this organism does not metabolize glucose as readily as it does glucose di- and polysaccharides. The leading hypothesis implicates the thermolability of glucose at the physiological temperatures at which
T. maritima
lives. After a 25-day laboratory evolution, phenotypes were observed with growth rates up to 1.4 times higher than and glucose utilization rates exceeding 50% those of the wild type. Genome resequencing revealed mutations in evolved cultures related to glucose-responsive ABC transporters. The native glucose ABC transporter, GluEFK, has more abundant transcripts either as a result of gene duplication-amplification or through mutations to the operator sequence regulating this operon. Conversely, BglEFGKL, a transporter of beta-glucosides, is substantially downregulated due to a nonsense mutation to the solute binding protein or due to a deletion of the upstream promoter. Analysis of the ABC2 uptake porter families for carbohydrate and peptide transport revealed that the solute binding protein, often among the transcripts detected at the highest levels, is predominantly downregulated in the evolved cultures, while the membrane-spanning domain and nucleotide binding components are less varied. Similar trends were observed in evolved strains grown on glycerol, a substrate that is not dependent on ABC transporters. Therefore, improved growth on glucose is achieved through mutations favoring GluEFK expression over BglEFGKL, and in lieu of carbon catabolite repression, the ABC transporter network is modulated to achieve improved growth fitness.
The N-Linked Outer Chain Mannans and the Dfg5p and Dcw1p Endo-α-1,6-Mannanases Are Needed for Incorporation of Candida albicans Glycoproteins into the Cell Wall
Authors: Ao Jie , Chinnici Jennifer L. , Maddi Abhiram , Free Stephen J. 
Published: June 2015

ABSTRACT

A biochemical pathway for the incorporation of cell wall protein into the cell wall of
Neurospora crassa
was recently proposed. In this pathway, the DFG-5 and DCW-1 endo-α-1,6-mannanases function to covalently cross-link cell wall protein-associated N-linked galactomannans, which are structurally related to the yeast outer chain mannans, into the cell wall glucan-chitin matrix. In this report, we demonstrate that the mannosyltransferase enzyme Och1p, which is needed for the synthesis of the N-linked outer chain mannan, is essential for the incorporation of cell wall glycoproteins into the
Candida albicans
cell wall. Using endoglycosidases, we show that
C. albicans
cell wall proteins are cross-linked into the cell wall via their N-linked outer chain mannans. We further demonstrate that the Dfg5p and Dcw1p α-1,6-mannanases are needed for the incorporation of cell wall glycoproteins into the
C. albicans
cell wall. Our results support the hypothesis that the Dfg5p and Dcw1p α-1,6-mannanases incorporate cell wall glycoproteins into the
C. albicans
cell wall by cross-linking outer chain mannans into the cell wall glucan-chitin matrix.
Young people's perceptions of tobacco packaging: a comparison of EU Tobacco Products Directive & Ireland's Standardisation of Tobacco Act
Authors: Babineau Kate , Clancy Luke 
Published: June 2015

ObjectivesTo measure young people's perceptions of tobacco packaging according to two current pieces of legislation: The EU Tobacco Products Directive (TPD) and Ireland's Public Health (Standardisation of Tobacco Products) Act.DesignWithin-subject experimental cross-sectional survey of a representative sample of secondary school students. School-based pen and paper survey.Setting27 secondary schools across Ireland, randomly stratified for size, geographic location, gender, religious affiliation and school-level socioeconomic status. Data were collected between March and May 2014.Participants1378 fifth year secondary school students aged 16–17 in Ireland.Main outcome measuresYoung people's perceptions of attractiveness, health risk and smoker characteristics of packs according to EU and Irish branding and packaging guidelines.ResultsPacks with more branding elements were thought to be healthier than standardised packs for Silk Cut (χ2=158.58, p<0.001), Marlboro (χ2=113.65, p<0.001), and Benson and Hedges (χ2=137.95, p<0.001) brands. Generalized estimating equation binary regressions found that gender was a significant predictor of pack attractiveness for Silk Cut, with females being more likely to find the EU packs attractive (β=−0.45, p=0.007). Gender was a significant predictor for females with regards to the perceived popularity of the Silk Cut brand (β=−0.37, p=0.03).ConclusionsThe removal of brand identifiers, including colour, font and embossing, reduces the perceived appeal of cigarette packs for young people across all three tested brands. Packs standardised according to Irish legislation are perceived as less attractive, less healthy and smoked by less popular people than packs which conform to the EU TPD 2014 guidelines.
Acupuncture for psoriasis: protocol for a systematic review
Authors: Wang Lei , Yang Haoyu , Li Nuo , Wang Weiming , Bai Yanping 
Published: June 2015

IntroductionThe described systematic review aims to assess the effectiveness and safety of acupuncture for psoriasis.Methods and analysisWe will electronically search for randomised controlled trials in the following databases from inception to 31 March 2015: OVID MEDLINE, EMBASE, Cochrane Central Register of Controlled Trials, Chinese Biomedical Literature Database, Chinese Medical Current Content, Chinese Scientific Journal Database (VIP database), Wan-Fang Database and China National Knowledge Infrastructure. We will also try to obtain literature by manually searching reference lists, conference proceedings and registers of clinical trials (eg, the Meta Register of Controlled Trials and the Chinese Clinical Trial Registry). Changes in disease status as evaluated by clinical signs or any available tool will be measured as the primary outcome. Global changes as well as changes in participant status (as evaluated by quality of life), safety (as measured by the prevalence and severity of adverse effects or adverse events) and costs (if available) will be measured as secondary outcomes. Two researchers will independently undertake selection of studies, data extraction and assessment of the quality of included studies. Data synthesis and subgroup analyses will be performed using special software (Review Manager). Data will be combined with a random effect model. Results will be presented as risk ratios for dichotomous data and the standardised mean difference for continuous data.Ethics and disseminationEthical approval will not be required as this is a protocol for a systematic review. The systematic review will evaluate the current evidence regarding acupuncture therapy for psoriasis. Findings will be disseminated through peer-reviewed publications and conference presentations.Trial registration numberPROSPERO CRD 42014013695.
Impact of ethnicity on progress of glycaemic control in 131 935 newly diagnosed patients with type 2 diabetes: a nationwide observational study from the Swedish National Diabetes Register
Authors: Rawshani Araz , Svensson Ann-Marie , Rosengren Annika , Zethelius Björn , Eliasson Björn , Gudbjörnsdottir Soffia 
Published: June 2015

ObjectivesStudies on ethnic disparities in glycaemic control have been contradictory, and compromised by excessively broad categories of ethnicity and inadequate adjustment for socioeconomic differences. We aimed to study the effect of ethnicity on glycaemic control in a large cohort of patients with type 2 diabetes.SettingWe used nationwide data (mainly from primary care) from the Swedish National Diabetes Register (2002–2011) to identify patients with newly diagnosed (within 12 months) type 2 diabetes.ParticipantsWe included 131 935 patients (with 713 495 appointments), representing 10 ethnic groups, who were followed up to 10 years.Primary and secondary outcome measuresProgress of glycated haemoglobin (HbA1c) for up to 10 years was examined. Mixed models were used to correlate ethnicity with HbA1c (mmol/mol). The effect of glycaemic disparities was examined by assessing the risk of developing albuminuria. The impact of ethnicity was compared to that of income, education and physical activity.ResultsImmigrants, particularly those of non-Western origin, received glucose-lowering therapy earlier, had 30% more appointments but displayed poorer glycaemic control (2–5 mmol/mol higher HbA1c than native Swedes). Probability of therapy failure was 28–111% higher for non-Western groups than for native Swedes. High-income Western groups remained below the target-level of HbA1c for 4–5 years, whereas non-Western populations never reached the target level. These disparities translated into 51–92% higher risk of developing albuminuria. The impact of ethnicity was greater than the effect of income and education, and equal to the effect of physical activity.ConclusionsDespite earlier pharmacological treatment and more frequent appointments, immigrants of non-Western origin display poorer glycaemic control and this is mirrored in a higher risk of developing albuminuria.
A comparison of the recording of comorbidity in primary and secondary care by using the Charlson Index to predict short-term and long-term survival in a routine linked data cohort
Authors: Crooks C J , West J , Card T R 
Published: June 2015

ObjectiveHospital admission records provide snapshots of clinical histories for a subset of the population admitted to hospital. In contrast, primary care records provide continuous clinical histories for complete populations, but might lack detail about inpatient stays. Therefore, combining primary and secondary care records should improve the ability of comorbidity scores to predict survival in population-based studies, and provide better adjustment for case-mix differences when assessing mortality outcomes.DesignCohort study.SettingEnglish primary and secondary care 1 January 2005 to 1 January 2010.ParticipantsAll patients 20 years and older registered to a primary care practice contributing to the linked Clinical Practice Research Datalink from England.OutcomeThe performance of the Charlson index with mortality was compared when derived from either primary or secondary care data or both. This was assessed in relation to short-term and long-term survival, age, consultation rate, and specific acute and chronic diseases.Results657 264 people were followed up from 1 January 2005. Although primary care recorded more comorbidity than secondary care, the resulting C statistics for the Charlson index remained similar: 0.86 and 0.87, respectively. Higher consultation rates and restricted age bands reduced the performance of the Charlson index, but the index's excellent performance persisted over longer follow-up; the C statistic was 0.87 over 1 year, and 0.85 over all 5 years of follow-up. The Charlson index derived from secondary care comorbidity had a greater effect than primary care comorbidity in reducing the association of upper gastrointestinal bleeding with mortality. However, they had a similar effect in reducing the association of diabetes with mortality.ConclusionsThese findings support the use of the Charlson index from linked data and show that secondary care comorbidity coding performed at least as well as that derived from primary care in predicting survival.
Accuracy of flat panel detector CT with integrated navigational software with and without MR fusion for single-pass needle placement
Authors: Mabray Marc C , Datta Sanjit , Lillaney Prasheel V , Moore Teri , Gehrisch Sonja , Talbott Jason F , Levitt Michael R , Ghodke Basavaraj V , Larson Paul S , Cooke Daniel L 
Published: June 2015

PurposeFluoroscopic systems in modern interventional suites have the ability to perform flat panel detector CT (FDCT) with navigational guidance. Fusion with MR allows navigational guidance towards FDCT occult targets. We aim to evaluate the accuracy of this system using single-pass needle placement in a deep brain stimulation (DBS) phantom.Materials and methodsMR was performed on a head phantom with DBS lead targets. The head phantom was placed into fixation and FDCT was performed. FDCT and MR datasets were automatically fused using the integrated guidance system (iGuide, Siemens). A DBS target was selected on the MR dataset. A 10 cm, 19 G needle was advanced by hand in a single pass using laser crosshair guidance. Radial error was visually assessed against measurement markers on the target and by a second FDCT. Ten needles were placed using CT-MR fusion and 10 needles were placed without MR fusion, with targeting based solely on FDCT and fusion steps repeated for every pass.ResultsMean radial error was 2.75±1.39 mm as defined by visual assessment to the centre of the DBS target and 2.80±1.43 mm as defined by FDCT to the centre of the selected target point. There were no statistically significant differences in error between MR fusion and non-MR guided series.ConclusionsSingle pass needle placement in a DBS phantom using FDCT guidance is associated with a radial error of approximately 2.5–3.0 mm at a depth of approximately 80 mm. This system could accurately target sub-centimetre intracranial lesions defined on MR.