bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ammonium induces differential expression of methane and nitrogen metabolism‐related genes in Methylocystis sp. strain SC2
Authors: Dam Bomba , Dam Somasri , Kim Yongkyu , Liesack Werner 
Published: December 2013

SummaryNitrogen source and concentration are major determinants of methanotrophic activity, but their effect on global gene expression is poorly studied. Methylocystis sp. strain SC2 produces two isozymes of particulate methane monooxygenase. These are encoded by pmoCAB1 (low‐affinity pMMO1) and pmoCAB2 (high‐affinity pMMO2). We used RNA‐Seq to identify strain SC2 genes that respond to standard (10 mM) and high (30 mM) NH4+ concentrations in the medium, compared with 10 mM NO3–. While the expression of pmoCAB1 was unaffected, pmoCAB2 was significantly downregulated (log2 fold changes of −5.0 to −6.0). Among nitrogen metabolism‐related processes, genes involved in hydroxylamine detoxification (haoAB) were highly upregulated, while those for assimilatory nitrate/nitrite reduction, high‐affinity ammonium uptake and nitrogen regulatory protein PII were downregulated. Differential expression of pmoCAB2 and haoAB was independently validated by end‐point reverse transcription polymerase chain reaction. Methane oxidation by SC2 cells exposed to 30 mM NH4+ was inhibited at ≤ 400 ppmv CH4, where pMMO2 but not pMMO1 is functional. When transferred back to standard nitrogen concentration, methane oxidation capability and pmoCAB2 expression were restored. Given that Methylocystis contributes to atmospheric methane oxidation in upland soils, differential expression of pmoCAB2 explains, at least to some extent, the strong inhibitory effect of ammonium fertilizers on this activity.
Interspecies signalling: Pseudomonas putida efflux pump TtgGHI is activated by indole to increase antibiotic resistance
Authors: Molina‐Santiago Carlos , Daddaoua Abdelali , Fillet Sandy , Duque Estrella , Ramos Juan‐Luis 
Published: December 2013

SummaryIn Gram‐negative bacteria, multidrug efflux pumps are responsible for the extrusion of chemicals that are deleterious for growth. Some of these efflux pumps are induced by endogenously produced effectors, while abiotic or biotic signals induce the expression of other efflux pumps. In Pseudomonas putida, the TtgABC efflux pump is the main antibiotic extrusion system that respond to exogenous antibiotics through the modulation of the expression of this operon mediated by TtgR. The plasmid‐encoded TtgGHI efflux pump in P. putida plays a minor role in antibiotic resistance in the parental strain; however, its role is critical in isogenic backgrounds deficient in TtgABC. Expression of ttgGHI is repressed by the TtgV regulator that recognizes indole as an effector, although P. putida does not produce indole itself. Because indole is not produced by Pseudomonas, the indole‐dependent antibiotic resistance seems to be part of an antibiotic resistance programme at the community level. Pseudomonas putida recognizes indole added to the medium or produced by Escherichia coli in mixed microbial communities. Transcriptomic analyses revealed that the indole‐specific response involves activation of 43 genes and repression of 23 genes. Indole enhances not only the expression of the TtgGHI pump but also a set of genes involved in iron homeostasis, as well as genes for amino acid catabolism. In a ttgABC‐deficient P. putida, background ampicillin and other bactericidal compounds lead to cell death. Co‐culture of E. coli and P. putida ΔttgABC allowed growth of the P. putida mutant in the presence of ampicillin because of induction of the indole‐dependent efflux pump.
Highly polymorphic markers reveal the establishment of an invasive lineage of the citrus bacterial pathogen Xanthomonas citri pv. citri in its area of origin
Authors: Vernière Christian , Bui Thi Ngoc Lan , Jarne Philippe , Ravigné Virginie , Guérin Fabien , Gagnevin Lionel , Le Mai Nhat , Chau Nguyen M. , Pruvost Olivier 
Published: December 2013

SummaryInvestigating the population biology of plant pathogens in their native areas is essential to understand the factors that shape their population structure and favour their spread. Monomorphic pathogens dispatch extremely low genetic diversity in invaded areas, and native areas constitute a major reservoir for future emerging strains. One of these, the gammaproteobacterium Xanthomonas citri pv. citri, causes Asiatic canker and is a considerable threat to citrus worldwide. We studied its population genetic structure by genotyping 555 strains from 12 Vietnam provinces at 14 tandem repeat loci and insertion sequences. Discriminant analysis of principal components identified six clusters. Five of them were composed of endemic strains distributed heterogeneously across sampled provinces. A sixth cluster, VN6, displayed a much lower diversity and a clonal expansion structure, suggesting recent epidemic spread. No differences in aggressiveness on citrus or resistance to bactericides were detected between VN6 and other strains. VN6 likely represents a case of bioinvasion following introduction in a native area likely through contaminated plant propagative material. Highly polymorphic markers are useful for revealing migration patterns of recently introduced populations of a monomorphic bacterial plant pathogen.
Toxin GhoT of the GhoT/GhoS toxin/antitoxin system damages the cell membrane to reduce adenosine triphosphate and to reduce growth under stress
Authors: Cheng Hsin‐Yao , Soo Valerie W. C. , Islam Sabina , McAnulty Michael J. , Benedik Michael J. , Wood Thomas K. 
Published: December 2013

SummaryToxin/antitoxin (TA) systems perhaps enable cells to reduce their metabolism to weather environmental challenges although there is little evidence to support this hypothesis. Escherichia coli GhoT/GhoS is a TA system in which toxin GhoT expression is reduced by cleavage of its messenger RNA (mRNA) by antitoxin GhoS, and TA system MqsR/MqsA controls GhoT/GhoS through differential mRNA decay. However, the physiological role of GhoT has not been determined. We show here through transmission electron microscopy, confocal microscopy and fluorescent stains that GhoT reduces metabolism by damaging the membrane and that toxin MqsR (a 5′‐GCU‐specific endoribonuclease) causes membrane damage in a GhoT‐dependent manner. This membrane damage results in reduced cellular levels of ATP and the disruption of proton motive force (PMF). Normally, GhoT is localized to the pole and does not cause cell lysis under physiological conditions. Introduction of an F38R substitution results in loss of GhoT toxicity, ghost cell production and membrane damage while retaining the pole localization. Also, deletion of ghoST or ghoT results in significantly greater initial growth in the presence of antimicrobials. Collectively, these results demonstrate that GhoT reduces metabolism by reducing ATP and PMF and that this reduction in metabolism is important for growth with various antimicrobials.
Transcriptional profiling of Gram‐positive Arthrobacter in the phyllosphere: induction of pollutant degradation genes by natural plant phenolic compounds
Authors: Scheublin Tanja R. , Deusch Simon , Moreno‐Forero Silvia K. , Müller Jochen A. , van der Meer Jan Roelof , Leveau Johan H. J. 
Published: December 2013

SummaryArthrobacter chlorophenolicus A6 is a Gram‐positive, 4‐chlorophenol‐degrading soil bacterium that was recently shown to be an effective colonizer of plant leaf surfaces. The genetic basis for this phyllosphere competency is unknown. In this paper, we describe the genome‐wide expression profile of A. chlorophenolicus on leaves of common bean (Phaseolus vulgaris) compared with growth on agar surfaces. In phyllosphere‐grown cells, we found elevated expression of several genes known to contribute to epiphytic fitness, for example those involved in nutrient acquisition, attachment, stress response and horizontal gene transfer. A surprising result was the leaf‐induced expression of a subset of the so‐called cph genes for the degradation of 4‐chlorophenol. This subset encodes the conversion of the phenolic compound hydroquinone to 3‐oxoadipate, and was shown to be induced not only by 4‐chlorophenol but also hydroquinone, its glycosylated derivative arbutin, and phenol. Small amounts of hydroquinone, but not arbutin or phenol, were detected in leaf surface washes of P. vulgaris by gas chromatography‐mass spectrometry. Our findings illustrate the utility of genomics approaches for exploration and improved understanding of a microbial habitat. Also, they highlight the potential for phyllosphere‐based priming of bacteria to stimulate pollutant degradation, which holds promise for the application of phylloremediation.
Herbivorous rodents (Neotoma spp.) harbour abundant and active foregut microbiota
Authors: Kohl Kevin D. , Miller Aaron W. , Marvin James E. , Mackie Roderick , Dearing M. Denise 
Published: December 2013

SummarySymbiotic gut microbes have facilitated the success of herbivorous mammals, which are generally grouped into foregut‐ and hindgut‐fermenters. However, rodents are primarily herbivorous and exhibit a variety of gastrointestinal anatomies. Most rodents house microbes in hindgut chambers, such as the caecum and colon. Some rodents also exhibit stomach segmentation with a foregut chamber proximal to the stomach. For over a century, scientists have hypothesized that this foregut chamber houses a microbial community, yet this has never been explicitly examined. We investigated the capacity of each of the gut regions to house microbes by measuring size, pH, bacterial cell density, concentrations of microbial metabolites and digesta transit time in woodrats (Neotoma spp.). We also compared microbial communities across gut chambers, as well as faeces, using 16S rRNA sequencing. This allowed us to test the appropriateness of using faeces as a proxy for microbial communities of other gut chambers. We found that woodrats house foregut microbial communities with similar density and volatile fatty acid concentrations to rumen ecosystems. Resident microbial communities varied between gut chambers, and faecal bacterial communities were significantly different from caecal and colonic communities. The foregut microbiota may provide a number of physiological services to the host.
A pairwise relatedness estimator for polyploids
Authors: Huang Kang , Ritland Kermit , Guo Songtao , Shattuck Milena , Li Baoguo 
Published: December 2013

AbstractStudies in genetics and ecology often require estimates of relatedness coefficients based on genetic marker data. Many diploid estimators have been developed using either method‐of‐moments or maximum‐likelihood estimates. However, there are no relatedness estimators for polyploids. The development of a moment estimator for polyploids with polysomic inheritance, which simultaneously incorporates the two‐gene relatedness coefficient and various ‘higher‐order’ coefficients, is described here. The performance of the estimator is compared to other estimators under a variety of conditions. When using a small number of loci, the estimator is biased because of an increase in ill‐conditioned matrices. However, the estimator becomes asymptotically unbiased with large numbers of loci. The ambiguity of polyploid heterozygotes (when balanced heterozygotes cannot be distinguished from unbalanced heterozygotes) is also considered; as with low numbers of loci, genotype ambiguity leads to bias. A software, PolyRelatedness, implementing this method and supporting a maximum ploidy of 8 is provided.
Microenvironments of reduced salinity harbour biofilms in Dead Sea underwater springs
Authors: Häusler Stefan , Noriega‐Ortega Beatriz E. , Polerecky Lubos , Meyer Volker , de Beer Dirk , Ionescu Danny 
Published: December 2013

SummaryThe Dead Sea is a hypersaline lake where only few types of organisms can grow. Recently, abundant and diverse microbial life was discovered in biofilms covering rocks and permeable sediments around underwater freshwater springs and seeps. We used a newly developed salinity mini‐sensor (spatial resolution 300 μm) to investigate the salinity environment around these biofilms in a flume that simulates an underwater spring. Compared with the hypersaline bulk water, salinity at the sediment surface decreased to zero at seeping velocities of 7 cm s−1. At similar flow velocities, salinity above rocks decreased to 100–200 g L−1 at a distance of 300 μm from the surface. This depended on the position on the rock, and coincided with locations of natural biofilms. The salinity reduction substantially diminished at flow velocities of 3.5 cm s−1. We suggest that locally decreased salinity due to freshwater input is one of the main factors that make areas around underwater freshwater springs and seeps in the Dead Sea more favourable for life. However, due to frequent fluctuations in the freshwater flow, the locally decreased salinity is unstable. Therefore, microorganisms that inhabit these environments must be capable of withstanding large and rapid salinity fluctuations.
Neural mechanisms of high‐risk decisions‐to‐drink in alcohol‐dependent women
Authors: Arcurio Lindsay R. , Finn Peter R. , James Thomas W. 
Published: December 2013

AbstractA hallmark of alcohol dependence (AD) is continually drinking despite the risk of negative consequences. Currently, it is not known if the pattern of disordered activation in AD is more compatible with an over‐sensitive reward system, a deficit in control systems or a combination of both to produce the high risk‐taking behavior observed in alcohol dependents (ADs). Here, alcohol cues were used in an ecological decisions‐to‐drink task that involved high‐ and low‐risk scenarios where the chance of serious negative imagined consequences was varied. Non‐alcohol cues were included as control stimuli. Functional magnetic resonance imaging (fMRI) was used to measure blood oxygen level‐dependent (BOLD) signal change in 15 alcohol‐dependent and 16 control women. This design allowed us to address two major questions concerning AD: first, is there a specific pattern of disordered activation that drives the heightened endorsement of high‐risk decisions‐to‐drink in ADs? And, second, is that pattern specific to decisions‐to‐drink or does it generalize to other appetitive and/or neutral cues? The results showed that, during high‐risk decisions‐to‐drink, alcohol‐dependent women activated reward circuits, cognitive control circuits and regions of the default‐mode network (DMN), while control women deactivated approach circuits and showed enhanced activation in regions of the DMN. Group differences were found only for decisions‐to‐drink, suggesting that they are specific to alcohol cues. Simultaneous activation of reward networks, cognitive control networks and the DMN in alcohol‐dependent women suggests that over‐endorsement of high‐risk drinking decisions by alcohol‐dependent women may be due to a problem with switching between different neural networks.
Uric acid has a J‐shaped association with cardiovascular and all‐cause mortality in kidney transplant recipients
Authors: Dahle Dag Olav , Jenssen Trond , Holdaas Hallvard , Leivestad Torbjørn , Vårdal Mari , Mjøen Geir , Reisæter Anna V. , Toft Ingrid , Hartmann Anders 
Published: December 2013

AbstractThe association between serum uric acid and kidney graft and recipient survival is uncertain. During 2000–2011, we measured serum uric acid at week 10 after transplantation. Of 2748 transplanted patients, 2200 (80.1%) attended this visit. After a median follow‐up of 7.4 yr, 378 patients had died, 143 from a cardiovascular cause, and 185 patients lost their graft. The third quintile of uric acid levels (357–405 μM) had the lowest mortality risk and was used as reference group. In Cox proportional hazard models adjusting for graft and patient characteristics, the fifth quintile of uric acid levels (>474 μM) was independently associated with cardiovascular mortality (hazard ratio [HR] = 2.87 [1.55–5.32], p = 0.001) and all‐cause mortality (HR = 1.57 [1.09–2.25], p = 0.02). Also, the lowest quintile of uric acid levels (<309 μM) showed a trend toward increased risk of cardiovascular mortality (HR = 1.79 [0.90–3.58], p = 0.10) and all‐cause mortality (HR = 1.31 [0.89–1.93], p = 0.18). The increased risk at low uric acid levels was confined to diabetic recipients. Uric acid was not associated with death‐censored graft loss. In conclusion, uric acid has a J‐shaped association with cardiovascular and all‐cause mortality in kidney transplant recipients.
Association of pre‐transplant blood pressure with post‐transplant outcomes
Authors: Molnar Miklos Z. , Foster Clarence E. , Sim John J. , Remport Adam , Krishnan Mahesh , Kovesdy Csaba P. , Kalantar‐Zadeh Kamyar 
Published: December 2013

AbstractBackgroundPrevious studies have indicated U‐shaped associations between blood pressure (BP) and mortality in dialysis patients. We hypothesized that a similar association exists between pre‐transplant BP and post‐transplant outcomes in dialysis patients who undergo successful kidney transplantation.MethodsData from the Scientific Registry of Transplant Recipients were linked to the five‐yr cohort of a large dialysis organization in the United States. We identified all dialysis patients who received a kidney transplant during this period. Unadjusted and multivariate adjusted predictors of transplant outcomes were examined.ResultsA total of 13 881 patients included in our study were 47 ± 14 yr old and included 42% women. There was no association between pre‐transplant systolic BP and post‐transplant mortality, although a decreased risk trend was observed in those with low post‐dialysis systolic BP. Compared to patients with pre‐dialysis diastolic BP 70 to <80 mmHg, patients with pre‐dialysis diastolic BP <50 mmHg experienced lower risk of post‐transplant death (hazard ratios [HR]: 0.74, 95% CI: 0.55–0.99). However, compared to patients with post‐dialysis diastolic BP 70 to <80 mmHg, patients with post‐dialysis diastolic BP ≥100 mmHg experienced higher risk of death (HR: 3.50, 95% CI: 1.57–7.84). In addition, very low (<50 mmHg for diastolic BP and <110 mmHg for systolic BP) pre‐transplant BP was associated with lower risk of graft loss.ConclusionsLow post‐dialysis systolic BP and low pre‐dialysis diastolic BP are associated with lower post‐transplant risk of death, whereas very high post‐dialysis diastolic BP is associated with higher mortality in kidney transplant recipients. BP variations in dialysis patients prior to kidney transplantation may have a bearing on post‐transplant outcome, which warrants additional studies.
Improving the potential for organ donation in an inner city Muslim American community: the impact of a religious educational intervention
Authors: Hafzalah Mina , Azzam Ruba , Testa Giuliano , Hoehn K. Sarah 
Published: December 2013

AbstractObjectiveWe aimed to assess the willingness of Muslim Americans to be potential organ donors, to describe potential religious barriers to organ donation, and to evaluate the efficacy of a brief religious educational intervention.MethodsFace‐to‐face survey with English‐, Arabic‐, and Urdu‐speaking Muslim American adults in places of worship and gatherings. The two‐part survey included questions about demographics and organ donation. A brief educational intervention followed, which included an explanation of organ donation, along with the evidence for Islam's support for organ donation. After this intervention, the questions about organ donation and brain death were repeated.ResultsThe response rate was 81% (231 of 285). Fifty percent of the respondents would donate their organs. Twenty‐five percent changed their opinion and accepted the idea of being donors after the educational intervention. Lack of awareness of the support of Islam to organ donation and fear of disfigurement were the most common barriers cited.ConclusionMuslim Americans are less likely than Caucasian Americans to be organ donors, and the perceived lack of support from Islam for organ donation is a factor. The effectiveness of our brief religious education intervention suggests that further education may improve organ donation rates among the Muslim community.
Associations between alcohol, smoking, socioeconomic status and comorbidities: Evidence from the 45 and Up Study
Authors: Bonevski Billie , Regan Tim , Paul Chris , Baker Amanda L. , Bisquera Alessandra 
Published: December 2013

AbstractIntroduction and Aims.Understanding how tobacco, alcohol and mental health are related is important for developing population‐level policies and individual‐level treatments that target comorbidities. The current study aimed to examine sociodemographic characteristics and mental health comorbidities associated with the odds of using tobacco and harmful levels of alcohol concurrently.Design and Methods.Data were drawn from the 45 and Up Study, a large cohort study with 267 153 adults aged 45 years and over in New South Wales, Australia. Participants completed a survey assessing alcohol, smoking, psychological distress, treatment for depression and anxiety, and a range of socioeconomic status indicators. Univariate analyses and three multiple‐logistic regression models were used to determine associations with (i) tobacco but not alcohol use; (ii) alcohol but not tobacco use; and (iii) concurrent tobacco and risky levels of alcohol use.Results.Being female, younger, lower individual and area‐level socioeconomic status (SES) and depression and psychological distress were associated with tobacco use alone. Factors associated with alcohol use alone were older age, male gender, higher SES, and lower psychological distress and no recent depression treatment. Factors associated with concurrent risky alcohol consumption and tobacco use included being 45–64, being male, less education, earning <$30 000, being employed, and living in lower‐SES areas, treatment for depression, and high distress on the Kessler‐10.Discussion and Conclusions.Results suggest strong links between SES, treatment for depression, psychological distress, and concurrent tobacco and alcohol use. This has implications for public health policies and clinical treatment for tobacco and alcohol use, suggesting greater emphasis on addressing multiple health and social concerns. [Bonevski B, Regan T, Paul C, Baker AL, Bisquera A. Associations between alcohol, smoking, socioeconomic status and comorbidities: Evidence from the 45 and Up Study. Drug Alcohol Rev 2014;33:169–176]