bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dehalogenimonas sp. Strain WBC-2 Genome and Identification of Its
trans
-Dichloroethene Reductive Dehalogenase, TdrA
Authors: Molenda Olivia , Quaile Andrew T. , Edwards Elizabeth A. 
Published: October 2015

ABSTRACT

The
Dehalogenimonas
population in a dechlorinating enrichment culture referred to as WBC-2 was previously shown to be responsible for
trans
-dichloroethene (tDCE) hydrogenolysis to vinyl chloride (VC). In this study, blue native polyacrylamide gel electrophoresis (BN-PAGE) followed by enzymatic assays and protein identification using liquid chromatography coupled with mass spectrometry (LC-MS/MS) led to the functional characterization of a novel dehalogenase, TdrA. This new reductive dehalogenase (RDase) catalyzes the dechlorination of tDCE to VC. A metagenome of the WBC-2 culture was sequenced, and a complete
Dehalogenimonas
genome, only the second
Dehalogenimonas
genome to become publicly available, was closed. The
tdrA
dehalogenase found within the
Dehalogenimonas
genome appears to be on a genomic island similar to genomic islands found in
Dehalococcoides
. TdrA itself is most similar to TceA from
Dehalococcoides
sp. strain FL2 with 76.4% amino acid pairwise identity. It is likely that the horizontal transfer of
rdhA
genes is not only a feature of
Dehalococcoides
but also a feature of other
Dehalococcoidia
, including
Dehalogenimonas.
A set of primers was developed to track
tdrA
in WBC-2 subcultures maintained on different electron acceptors. This newest dehalogenase is an addition to the short list of functionally defined RDases sharing the usual characteristic motifs (including an AB operon, a TAT export sequence, two iron-sulfur clusters, and a corrinoid binding domain), substrate flexibility, and evidence for horizontal gene transfer within the
Dehalococcoidia
.
The Antisense RNA Approach: a New Application for
In Vivo
Investigation of the Stress Response of Oenococcus oeni, a Wine-Associated Lactic Acid Bacterium
Authors: Darsonval Maud , Msadek Tarek , Alexandre Hervé , Grandvalet Cosette 
Published: October 2015

ABSTRACT

Oenococcus oeni
is a wine-associated lactic acid bacterium mostly responsible for malolactic fermentation in wine. In wine,
O. oeni
grows in an environment hostile to bacterial growth (low pH, low temperature, and ethanol) that induces stress response mechanisms. To survive,
O. oeni
is known to set up transitional stress response mechanisms through the synthesis of heat stress proteins (HSPs) encoded by the
hsp
genes, notably a unique small HSP named Lo18. Despite the availability of the genome sequence, characterization of
O. oeni
genes is limited, and little is known about the
in vivo
role of Lo18. Due to the lack of genetic tools for
O. oeni
, an efficient expression vector in
O. oeni
is still lacking, and deletion or inactivation of the
hsp18
gene is not presently practicable. As an alternative approach, with the goal of understanding the biological function of the
O. oeni
hsp18
gene
in vivo
, we have developed an expression vector to produce antisense RNA targeting of
hsp18
mRNA. Recombinant strains were exposed to multiple stresses inducing
hsp18
gene expression: heat shock and acid shock. We showed that antisense attenuation of
hsp18
affects
O. oeni
survival under stress conditions. These results confirm the involvement of Lo18 in heat and acid tolerance of
O. oeni
. Results of anisotropy experiments also confirm a membrane-protective role for Lo18, as previous observations had already suggested. This study describes a new, efficient tool to demonstrate the use of antisense technology for modulating gene expression in
O. oeni
.
Determining Roles of Accessory Genes in Denitrification by Mutant Fitness Analyses
Authors: Vaccaro Brian J. , Thorgersen Michael P. , Lancaster W. Andrew , Price Morgan N. , Wetmore Kelly M. , Poole Farris L. , Deutschbauer Adam , Arkin Adam P. , Adams Michael W. W. 
Published: October 2015

ABSTRACT

Enzymes of the denitrification pathway play an important role in the global nitrogen cycle, including release of nitrous oxide, an ozone-depleting greenhouse gas. In addition, nitric oxide reductase, maturation factors, and proteins associated with nitric oxide detoxification are used by pathogens to combat nitric oxide release by host immune systems. While the core reductases that catalyze the conversion of nitrate to dinitrogen are well understood at a mechanistic level, there are many peripheral proteins required for denitrification whose basic function is unclear. A bar-coded transposon DNA library from
Pseudomonas stutzeri
strain RCH2 was grown under denitrifying conditions, using nitrate or nitrite as an electron acceptor, and also under molybdenum limitation conditions, with nitrate as the electron acceptor. Analysis of sequencing results from these growths yielded gene fitness data for 3,307 of the 4,265 protein-encoding genes present in strain RCH2. The insights presented here contribute to our understanding of how peripheral proteins contribute to a fully functioning denitrification pathway. We propose a new low-affinity molybdate transporter, OatABC, and show that differential regulation is observed for two MoaA homologs involved in molybdenum cofactor biosynthesis. We also propose that NnrS may function as a membrane-bound NO sensor. The dominant HemN paralog involved in heme biosynthesis is identified, and a CheR homolog is proposed to function in nitrate chemotaxis. In addition, new insights are provided into nitrite reductase redundancy, nitric oxide reductase maturation, nitrous oxide reductase maturation, and regulation.
The Siderophore Metabolome of Azotobacter vinelandii
Authors: Baars Oliver , Zhang Xinning , Morel François M. M. , Seyedsayamdost Mohammad R. 
Published: October 2015

ABSTRACT

In this study, we performed a detailed characterization of the siderophore metabolome, or “chelome,” of the agriculturally important and widely studied model organism
Azotobacter vinelandii
. Using a new high-resolution liquid chromatography-mass spectrometry (LC-MS) approach, we found over 35 metal-binding secondary metabolites, indicative of a vast chelome in
A. vinelandii
. These include vibrioferrin, a siderophore previously observed only in marine bacteria. Quantitative analyses of siderophore production during diazotrophic growth with different sources and availabilities of Fe showed that, under all tested conditions, vibrioferrin was present at the highest concentration of all siderophores and suggested new roles for vibrioferrin in the soil environment. Bioinformatic searches confirmed the capacity for vibrioferrin production in
Azotobacter
spp. and other bacteria spanning multiple phyla, habitats, and lifestyles. Moreover, our studies revealed a large number of previously unreported derivatives of all known
A. vinelandii
siderophores and rationalized their origins based on genomic analyses, with implications for siderophore diversity and evolution. Together, these insights provide clues as to why
A. vinelandii
harbors multiple siderophore biosynthesis gene clusters. Coupled with the growing evidence for alternative functions of siderophores, the vast chelome in
A. vinelandii
may be explained by multiple, disparate evolutionary pressures that act on siderophore production.
Depletion of
UBC9
Causes Nuclear Defects during the Vegetative and Sexual Life Cycles in Tetrahymena thermophila
Authors: Yang Qianyi , Nasir Amjad M. , Coyne Robert S. , Forney James D. 
Published: October 2015

ABSTRACT

Ubc9p is the sole E2-conjugating enzyme for SUMOylation, and its proper function is required for regulating key nuclear events such as transcription, DNA repair, and mitosis. In
Tetrahymena thermophila
, the genome is separated into a diploid germ line micronucleus (MIC) that divides by mitosis and a polyploid somatic macronucleus (MAC) that divides amitotically. This unusual nuclear organization provides novel opportunities for the study of SUMOylation and Ubc9p function. We identified the
UBC9
gene and demonstrated that its complete deletion from both MIC and MAC genomes is lethal. Rescue of the lethal phenotype with a
GFP-UBC9
fusion gene driven by a metallothionein promoter generated a cell line with CdCl
2
-dependent expression of green fluorescent protein (GFP)-Ubc9p. Depletion of Ubc9p in vegetative cells resulted in the loss of MICs, but MACs continued to divide. In contrast, expression of catalytically inactive Ubc9p resulted in the accumulation of multiple MICs. Critical roles for Ubc9p were also identified during the sexual life cycle of
Tetrahymena
. Cell lines that were depleted for Ubc9p did not form mating pairs and therefore could not complete any of the subsequent stages of conjugation, including meiosis and macronuclear development. Mating between cells expressing catalytically inactive Ubc9p resulted in arrest during macronuclear development, consistent with our observation that Ubc9p accumulates in the developing macronucleus.
Characterization of a Novel Prevacuolar Compartment in Neurospora crassa
Authors: Bowman Barry J. , Draskovic Marija , Schnittker Robert R. , El-Mellouki Tarik , Plamann Michael D. , Sánchez-León Eddy , Riquelme Meritxell , Bowman Emma Jean 
Published: October 2015

ABSTRACT

Using confocal microscopy, we observed ring-like organelles, similar in size to nuclei, in the hyphal tip of the filamentous fungus
Neurospora crassa
. These organelles contained a subset of vacuolar proteins. We hypothesize that they are novel prevacuolar compartments (PVCs). We examined the locations of several vacuolar enzymes and of fluorescent compounds that target the vacuole. Vacuolar membrane proteins, such as the vacuolar ATPase (VMA-1) and the polyphosphate polymerase (VTC-4), were observed in the PVCs. A pigment produced by adenine auxotrophs, used to visualize vacuoles, also accumulated in PVCs. Soluble enzymes of the vacuolar lumen, alkaline phosphatase and carboxypeptidase Y, were not observed in PVCs. The fluorescent molecule Oregon Green 488 carboxylic acid diacetate, succinimidyl ester (carboxy-DFFDA) accumulated in vacuoles and in a subset of PVCs, suggesting maturation of PVCs from the tip to distal regions. Three of the nine Rab GTPases in
N. crassa
, RAB-2, RAB-4, and RAB-7, localized to the PVCs. RAB-2 and RAB-4, which have similar amino acid sequences, are present in filamentous fungi but not in yeasts, and no function has previously been reported for these Rab GTPases in fungi. PVCs are highly pleomorphic, producing tubular projections that subsequently become detached. Dynein and dynactin formed globular clusters enclosed inside the lumen of PVCs. The size, structure, dynamic behavior, and protein composition of the PVCs appear to be significantly different from those of the well-studied prevacuolar compartment of yeasts.
Adaptations of the Secretome of Candida albicans in Response to Host-Related Environmental Conditions
Authors: Klis Frans M. , Brul Stanley 
Published: October 2015

ABSTRACTThe wall proteome and the secretome of the fungal pathogenCandida albicanshelp it to thrive in multiple niches of the human body. Mass spectrometry has allowed researchers to study the dynamics of both subproteomes. Here, we discuss some major responses of the secretome to host-related environmental conditions. Three β-1,3-glucan-modifying enzymes, Mp65, Sun41, and Tos1, are consistently found in large amounts in culture supernatants, suggesting that they are needed for construction and expansion of the cell wall β-1,3-glucan layer and thus correlate with growth and might serve as diagnostic biomarkers. The genesENG1,CHT3, andSCW11, which encode an endoglucanase, the major chitinase, and a β-1,3-glucan-modifying enzyme, respectively, are periodically expressed and peak in M/G1. The corresponding protein abundances in the medium correlate with the degree of cell separation during single-yeast-cell, pseudohyphal, and hyphal growth. We also discuss the observation that cells treated with fluconazole, or other agents causing cell surface stress, form pseudohyphal aggregates. Fluconazole-treated cells secrete abundant amounts of the transglucosylase Phr1, which is involved in the accumulation of β-1,3-glucan in biofilms, raising the question whether this is a general response to cell surface stress. Other abundant secretome proteins also contribute to biofilm formation, emphasizing the important role of secretome proteins in this mode of growth. Finally, we discuss the relevance of these observations to therapeutic intervention. Together, these data illustrate thatC. albicansactively adapts its secretome to environmental conditions, thus promoting its survival in widely divergent niches of the human body.
What matters to children with CFS/ME? A conceptual model as the first stage in developing a PROM
Authors: Parslow Roxanne , Patel Aarti , Beasant Lucy , Haywood Kirstie , Johnson Debbie , Crawley Esther 
Published: October 2015

BackgroundPaediatric chronic fatigue syndrome (CFS)/myalgic encephalomyelitis (ME) is relatively common and disabling. Research is hampered because current patient-reported outcome measures (PROMs) do not capture outcomes that are important to children with CFS/ME.AimThe aim of this study was to explore the aspects of life and health outcomes that matter to children with CFS/ME.MethodsTwenty-five children with CFS/ME were interviewed (11 males, 14 females; mean age 12.9 years (SD 2.2), range 8–17). Twelve were trial participants interviewed during the trial and 13 were recruited as part of a follow-up qualitative study. Parents were present in 19 interviews with their children. Three mothers participated in a focus group. All the interviews and the focus group were audio-recorded and transcribed. Data were analysed thematically using techniques of constant comparison. NVivo was used to structure and categorise data in a systematic way.ResultsChildren identified four key themes (health outcome domains): ‘symptoms’ that fluctuated, which caused an unpredictable reduction in both ‘physical activity’ and ‘social participation’ all of which impacted on ‘emotional well-being’. These domains were influenced by both ‘management’ and ‘contextual factors’, which could be positive and negative. The relationship between healthcare and school was considered pivotal.ConclusionsChildren's descriptions helped to inform a conceptual model that is necessary to develop a new paediatric CFS/ME PROM. Doctors need to be aware of how children conceptualise CFS/ME; the relationship between healthcare and school is fundamental to ameliorate the impact of CFS/ME.Trial registration numberISRCTN81456207.
Diabetes and glucose disturbances in patients with psychosis in Sweden
Authors: Olsson Eric , Westman Jeanette , Sudic Hukic Dzana , Eriksson Sven V , Edman Gunnar , Bodén Robert , Jedenius Erik , Reutfors Johan , Berntsson Anders , Hilding Agneta , Schalling Martin , Östenson Claes-Göran , Ösby Urban 
Published: October 2015

ObjectiveThe objectives of this study were to (1) analyze the prevalence of diabetes, prediabetes, and antidiabetic medication in patients with psychosis compared with control subjects and (2) determine what factors in patients with psychosis were associated with antidiabetic medication.MethodWe studied 977 patients with psychosis recruited from outpatient clinics in Stockholm County, Sweden, and they were compared with 3908 non-psychotic control subjects for fasting plasma glucose levels; prevalence of diabetes, prediabetes, antidiabetic treatment, and tobacco use; and blood pressure, weight, height, and waist circumference. Group differences were evaluated with analysis of variance and χ2test, and factors associated with antidiabetic treatment were evaluated with logistic regression.ResultsDiabetes was observed in 94 (10%) patients with psychosis, 2.7 times the prevalence observed in control subjects. Among patients with psychosis, 87 (10%) had prediabetes (fasting glucose, 6.1–6.9 mmol/L) compared with 149 (3.8%) control subjects. Most patients with psychosis (77%) who had prediabetes fulfilled criteria for metabolic syndrome. In patients with psychosis, both lipid-lowering medication and fasting glucose were significantly associated with antidiabetic treatment. There was no significant relation between antidiabetic treatment and lifestyle factors such as smoking or degree of psychiatric illness.ConclusionsThe high prevalence of impaired fasting glucose and metabolic syndrome in patients with psychosis warrants further clinical research in preventing or delaying the onset of diabetes in these patients by pharmacotherapy and/or lifestyle intervention.
Evaluating the validity of self-reported smoking in Mexican adolescents
Authors: Valladolid-López María del Carmen , Barrientos-Gutiérrez Tonatiuh , Reynales-Shigematsu Luz Myriam , Thrasher James F , Peláez-Ballestas Ingris , Lazcano-Ponce Eduardo , Hernández-Ávila Mauricio 
Published: October 2015

ObjectivesWe aimed to evaluate the validity of the self-reported smoking indicator used in the Global Youth Tobacco Survey (GYTS).Setting43 middle and high-school classrooms from 26 schools were selected from Mexico City and Cuernavaca, Morelos.ParticipantsA total of 1257 students provided both a questionnaire and a urine sample.Primary and secondary outcomeSensitivity and specificity of self-reported smoking compared to urinary cotinine. Validity indices were evaluated by subgroups of gender, social acceptability of smoking (ie, smoking parents or friends) and smoking frequency.ResultsSensitivity and specificity for current smoking were 93.2% and 81.7%, respectively. Validity indices remained stable across gender. Parental smoking status moderated the validity of self-report, which had lower sensitivity in adolescents with non-smoking parents (86.7%) than in adolescents with smoking parents (96.6%). Sensitivity and specificity increased with smoking frequency.ConclusionsThis first validation study of self-reported current smoking used in the GYTS among Mexican adolescents suggests that self-reported smoking in the past 30 days is a valid and stable indicator of current smoking behaviour. This measure appears suitable for public health research and surveillance.
Women's weight and disordered eating in a large Norwegian community sample: the Nord-Trøndelag Health Study (HUNT)
Authors: Eik-Nes Trine , Romild Ulla , Guzey Ismail , Holmen Turid , Micali Nadia , Bjørnelv Sigrid 
Published: October 2015

ObjectivesAn increasing part of the population is affected by disordered eating (DE) even though they do not meet the full eating disorder (ED) criteria. To improve treatment in the range of weight-related disorders, there is a need to improve our knowledge about DE and relevant correlates of weight problems such as underweight, overweight and obesity. However, studies investigating DE and weight problems in a wide range of ages in the general population have been lacking. This paper explores DE, weight problems, dieting and weight dissatisfaction among women in a general population sample.DesignCross-sectional study.SettingThe third survey of the Nord-Trøndelag Health Study (HUNT3).ParticipantsThe population included 27 252 women, aged 19–99 years, with information on DE outcomes and covariates.OutcomesDE was assessed with an 8-item version of the Eating Attitude Test and the Eating Disorder Scale-5. Body mass index (BMI) was objectively measured. Data on dieting and weight dissatisfaction were collected from self-reported questionnaires and analysed across weight categories. Crude and adjusted logistic and multinomial logistic regression models were used.ResultsHigh rates of overweight (38%) and obesity (23%) were found. DE was associated with weight problems. In women aged <30 years, 11.8% (95% CI 10.3 to 13.1) reported DE, and 12% (95% CI 11.5 to 12.6) reported DE in women aged >30 years. In those of younger ages (19–29 years), lower weight predicted DE, while increasing weight predicted DE in older aged women (30–99 years). The majority of women were dissatisfied with their weight (58.8%), and 54.1% of the women reported dieting. Neither BMI status nor age was associated with dieting or weight dissatisfaction.ConclusionsA high prevalence of DE was observed, and findings suggest that weight problems and DE are not distinct from one another. Dieting was associated with women's weight dissatisfaction, rather than with actual weight. This requires further investigations about directionality of effects.
Symptom appraisal and healthcare-seeking for symptoms suggestive of colorectal cancer: a qualitative study
Authors: Hall N , Birt L , Banks J , Emery J , Mills K , Johnson M , Rubin G P , Hamilton W , Walter F M 
Published: October 2015

ObjectivesTimely diagnosis of colorectal cancer is important to improve survival. This study explored symptom appraisal and help-seeking among patients referred to specialist services with symptoms of colorectal cancer.DesignQualitative in-depth interview study.Setting and participantsParticipants were recruited on referral to gastroenterology clinics (North East and East of England); interviews were conducted soon after referral. We purposively sampled participants to ensure a range of accounts in terms of age, sex, diagnosis and geographical location.MethodsData collection and analysis were underpinned by the Model of Pathways to Treatment. Framework analysis was used to explore the data within and across cases, focusing on patient beliefs and experiences, disease factors and healthcare influences.Results40 participants were interviewed (aged 43–87 years, 17 women, 18 diagnosed with colorectal cancer). Patients diagnosed with and without colorectal cancer had similar symptom pathways. We found a range of interacting and often competing biopsychosocial, contextual and cultural influences on the way in which people recognised, interpreted and acted on their symptoms. People attempted to ‘maintain normality’ through finding benign explanations for their symptoms. Bodily changes were appraised within the context of usual bowel patterns, comorbidities and life events, and decisions to seek help were made in relation to expectations about the course of symptoms. The ‘private nature’ of colorectal cancer symptoms could affect both their identification and discussions with others including healthcare professionals. Within the context of the National Health Service, people needed to legitimise appropriate use of healthcare services and avoid being thought of as wasting doctors’ time.ConclusionsFindings provide guidance for awareness campaigns on reducing stigma around appraising and discussing bowel movements, and the importance of intermittent and non-specific symptoms. Altering perceptions about the appropriate use of health services could have a beneficial effect on time to presentation.