bluuebunny/crossref_metadata_2025_split huggingface dataset:
No evidence for adaptation to local rhizobial mutualists in the legumeMedicago lupulina
Authors: Harrison Tia L. , Wood Corlett W. , Borges Isabela L. , Stinchcombe John R. 
Published: October 2016

AbstractLocal adaptation is a common but not ubiquitous feature of species interactions, and understanding the circumstances under which it evolves illuminates the factors that influence adaptive population divergence. Antagonistic species interactions dominate the local adaptation literature relative to mutualistic ones, preventing an overall assessment of adaptation within interspecific interactions. Here, we tested whether the legumeMedicago lupulinais adapted to the locally abundant species of mutualistic nitrogen-fixing bacteria (“rhizobia”), which vary in frequency across its eastern North American range. We reciprocally inoculated northern and southernM. lupulinagenotypes with the northern(Ensifer medicae)or southern bacterium(E. meliloti)in a greenhouse experiment. Neither northern nor southern plants produced more seed flowered earlier, or were more likely to flower when inoculated with their local rhizobium species, although plants produced more root nodules (the structures that house the bacteria) wit their local rhizobia. We used a pre-existing dataset to perform a genome scan for loci that showed elevated differentiation between field-collected plants that hosted different bacteria. None of the loci we identified belonged to the well-characterized suite of legume-rhizobia symbiosis genes, suggesting that the rhizobia do not drive genetic divergence betweenM. lupulinapopulations. Our results demonstrate that symbiont local adaptation is weak in this mutualism despite large-scale geographic variation in the identity of the interacting species.
Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis
Authors: Yang Fan , Wang Jiebiao ,   the GTEx consortium, Pierce Brandon L. , Chen Lin S. 
Published: October 2016

ABSTRACTThe impact of inherited genetic variation on gene expression in humans is well-established. The majority of known expression quantitative trait loci (eQTLs) impact expression of local genes (cis-eQTLs). More research is needed to identify effects of genetic variation on distant genes (trans-eQTLs) and understand their biological mechanisms. One common trans-eQTLs mechanism is “mediation” by a local (cis) transcript. Thus, mediation analysis can be applied to genome-wide SNP and expression data in order to identify transcripts that are “cis-mediators” of trans-eQTLs, including those “cis-hubs” involved in regulation of many trans-genes. Identifying such mediators helps us understand regulatory networks and suggests biological mechanisms underlying trans-eQTLs, both of which are relevant for understanding susceptibility to complex diseases. The multi-tissue expression data from the Genotype-Tissue Expression (GTEx) program provides a unique opportunity to study cis-mediation across human tissue types. However, the presence of complex hidden confounding effects in biological systems can make mediation analyses challenging and prone to confounding bias, particularly when conducted among diverse samples. To address this problem, we propose a new method: Genomic Mediation analysis with Adaptive Confounding adjustment (GMAC). It enables the search of a very large pool of variables, and adaptively selects potential confounding variables for each mediation test. Analyses of simulated data and GTEx data demonstrate that the adaptive selection of confounders by GMAC improves the power and precision of mediation analysis. Application of GMAC to GTEx data provides new insights into the observed patterns of cis-hubs and trans-eQTL regulation across tissue types.
Naringin in Ganshuang Granule suppresses activation of hepatic stellate cells for anti‐fibrosis effect by inhibition of mammalian target of rapamycin
Authors: Shi Hongbo , Shi Honglin , Ren Feng , Chen Dexi , Chen Yu , Duan Zhongping 
Published: October 2016

AbstractA previous study has demonstrated that Ganshuang granule (GSG) plays an anti‐fibrotic role partially by deactivation of hepatic stellate cells (HSCs). In HSCs activation, mammalian target of rapamycin (mTOR)‐autophagy plays an important role. We attempted to investigate the role of mTOR‐autophagy in anti‐fibrotic effect of GSG. The cirrhotic mouse model was prepared to demonstrate the anti‐fibrosis effect of GSG. High performance liquid chromatography (HPLC) analyses were used to identify the active component of GSG. The primary mouse HSCs were isolated and naringin was added into activated HSCs to observe its anti‐fibrotic effect. 3‐methyladenine (3‐MA) and Insulin‐like growth factor‐1 (IGF‐1) was added, respectively, into fully activated HSCs to explore the role of autophagy and mTOR. GSG played an anti‐fibrotic role through deactivation of HSCs in cirrhotic mouse model. The concentration of naringin was highest in GSG by HPLC analyses and naringin markedly suppressed HSCs activation in vitro, which suggested that naringin was the main active component of GSG. The deactivation of HSCs caused by naringin was not because of the autophagic activation but mTOR inhibition, which was supported by the following evidence: first, naringin induced autophagic activation, but when autophagy was blocked by 3‐MA, deactivation of HSCs was not attenuated or reversed. Second, naringin inhibited mTOR pathway, meanwhile when mTOR was activated by IGF‐1, deactivation of HSCs was reversed. In conclusion, we have demonstrated naringin in GSG suppressed activation of HSCs for anti‐fibrosis effect by inhibition of mTOR, indicating a potential therapeutic application for liver cirrhosis.
Listeria monocytogenes in Stone Fruits Linked to a Multistate Outbreak: Enumeration of Cells and Whole-Genome Sequencing
Authors: Chen Yi , Burall Laurel S. , Luo Yan , Timme Ruth , Melka David , Muruvanda Tim , Payne Justin , Wang Charles , Kastanis George , Maounounen-Laasri Anna , De Jesus Antonio J. , Curry Phillip E. , Stones Robert , K'Aluoch Okumu , Liu Eileen , Salter Monique , Hammack Thomas S. , Evans Peter S. , Parish Mickey , Allard Marc W. , Datta Atin , Strain Errol A. , Brown Eric W. 
Published: October 2016

ABSTRACT

In 2014, the identification of stone fruits contaminated with
Listeria monocytogenes
led to the subsequent identification of a multistate outbreak. Simultaneous detection and enumeration of
L. monocytogenes
were performed on 105 fruits, each weighing 127 to 145 g, collected from 7 contaminated lots. The results showed that 53.3% of the fruits yielded
L. monocytogenes
(lower limit of detection, 5 CFU/fruit), and the levels ranged from 5 to 2,850 CFU/fruit, with a geometric mean of 11.3 CFU/fruit (0.1 CFU/g of fruit). Two serotypes, IVb-v1 and 1/2b, were identified by a combination of PCR- and antiserum-based serotyping among isolates from fruits and their packing environment; certain fruits contained a mixture of both serotypes. Single nucleotide polymorphism (SNP)-based whole-genome sequencing (WGS) analysis clustered isolates from two case-patients with the serotype IVb-v1 isolates and distinguished outbreak-associated isolates from pulsed-field gel electrophoresis (PFGE)-matched, but epidemiologically unrelated, clinical isolates. The outbreak-associated isolates differed by up to 42 SNPs. All but one serotype 1/2b isolate formed another WGS cluster and differed by up to 17 SNPs. Fully closed genomes of isolates from the stone fruits were used as references to maximize the resolution and to increase our confidence in prophage analysis. Putative prophages were conserved among isolates of each WGS cluster. All serotype IVb-v1 isolates belonged to singleton sequence type 382 (ST382); all but one serotype 1/2b isolate belonged to clonal complex 5.

IMPORTANCE
WGS proved to be an excellent tool to assist in the epidemiologic investigation of listeriosis outbreaks. The comparison at the genome level contributed to our understanding of the genetic diversity and variations among isolates involved in an outbreak or isolates associated with food and environmental samples from one facility. Fully closed genomes increased our confidence in the identification and comparison of accessory genomes. The diversity among the outbreak-associated isolates and the inclusion of PFGE-matched, but epidemiologically unrelated, isolates demonstrate the high resolution of WGS. The prevalence and enumeration data could contribute to our further understanding of the risk associated with
Listeria monocytogenes
contamination, especially among high-risk populations.
Interkingdom Cross-Feeding of Ammonium from Marine Methylamine-Degrading Bacteria to the Diatom Phaeodactylum tricornutum
Authors: Suleiman Marcel , Zecher Karsten , Yücel Onur , Jagmann Nina , Philipp Bodo 
Published: October 2016

ABSTRACT

Methylamines occur ubiquitously in the oceans and can serve as carbon, nitrogen, and energy sources for heterotrophic bacteria from different phylogenetic groups within the marine bacterioplankton. Diatoms, which constitute a large part of the marine phytoplankton, are believed to be incapable of using methylamines as a nitrogen source. As diatoms are typically associated with heterotrophic bacteria, the hypothesis came up that methylotrophic bacteria may provide ammonium to diatoms by degradation of methylamines. This hypothesis was investigated with the diatom
Phaeodactylum tricornutum
and monomethylamine (MMA) as the substrate. Bacteria supporting photoautotrophic growth of
P. tricornutum
with MMA as the sole nitrogen source could readily be isolated from seawater. Two strains,
Donghicola
sp. strain KarMa, which harbored genes for both monomethylamine dehydrogenase and the
N
methylglutamate pathway, and
Methylophaga
sp. strain M1, which catalyzed MMA oxidation by MMA dehydrogenase, were selected for further characterization. While strain M1 grew with MMA as the sole substrate, strain KarMa could utilize MMA as a nitrogen source only when, e.g., glucose was provided as a carbon source. With both strains, release of ammonium was detected during MMA utilization. In coculture with
P. tricornutum
, strain KarMa supported photoautotrophic growth with 2 mM MMA to the same extent as with the equimolar amount of NH
4
Cl. In coculture with strain M1, photoautotrophic growth of
P. tricornutum
was also supported, but to a much lower degree than by strain KarMa. This proof-of-principle study with a synthetic microbial community suggests that interkingdom cross-feeding of ammonium from methylamine-degrading bacteria is a contribution to phytoplankton growth which has been overlooked so far.

IMPORTANCE
Interactions between diatoms and heterotrophic bacteria are important for marine carbon cycling. In this study, a novel interaction is described. Bacteria able to degrade monomethylamine, which is a ubiquitous organic nitrogen compound in marine environments, can provide ammonium to diatoms. This interkingdom metabolite transfer enables growth under photoautotrophic conditions in coculture, which would not be possible in the respective monocultures. This proof-of-principle study calls attention to a so far overlooked contribution to phytoplankton growth.
Pendimethalin Nitroreductase Is Responsible for the Initial Pendimethalin Degradation Step in Bacillus subtilis Y3
Authors: Ni Hai-yan , Wang Fei , Li Na , Yao Li , Dai Chen , He Qin , He Jian , Hong Qing 
Published: October 2016

ABSTRACT

Pendimethalin [
N
-(1-ethylpropyl)-2,6-dinitro-3,4-xylidine] is a selective preemergence dinitroaniline herbicide. Several fungi and bacteria have been reported to degrade pendimethalin, but the enzymes or genes involved in this process have not been characterized. Nitroreduction is the initial degradation and detoxification step for pendimethalin. In this study, a pendimethalin nitroreductase (PNR), responsible for the nitroreduction of pendimethalin, was purified from the pendimethalin-degrading strain
Bacillus subtilis
Y3. Based on a comparison of its mass fingerprints with all of the deduced proteins from the draft genome of strain Y3, a protein annotated as a nitroreductase was identified, and its corresponding encoding gene was termed
pnr
. PNR was a functional homodimer with a subunit molecular mass of approximately 23 kDa. PNR reduced the C-6 nitro group of the aromatic ring of pendimethalin, yielding 2-nitro-6-amino-
N
-(1-ethylpropyl)-3,4-xylidine. PNR could also catalyze the nitroreduction of three other major varieties of dinitroaniline herbicides, including butralin, oryzalin, and trifluralin. However, the number of reduced nitro groups was two instead of one, which differed from the nitroreduction of pendimethalin by PNR and which may be due to the symmetry in the chemical structures of the two nitro groups. A detoxification assay revealed that 2-nitro-6-amino-
N
-(1-ethylpropyl)-3,4-xylidine (PNR-reduced pendimethalin) showed no inhibitory effect on the growth of
Saccharomyces cerevisiae
BY4741, whereas pendimethalin showed an obvious inhibitory effect on its growth, indicating the detoxification effect of pendimethalin by PNR. Therefore, PNR has potential in pendimethalin detoxification applications. This report describes an enzyme (and corresponding gene) involved in the biodegradation of pendimethalin and dinitroaniline herbicides.

IMPORTANCE
Pendimethalin [
N
-(1-ethylpropyl)-2,6-dinitro-3,4-xylidine] is a widely used selective preemergence dinitroaniline herbicide, and its residue has been frequently detected in the environment. The U.S. Environmental Protection Agency (EPA) has classified pendimethalin as a persistent bioaccumulative toxin. To date, no enzymes or genes involved in pendimethalin biodegradation have been reported. In the present study, the gene
pnr
, which encodes the nitroreductase PNR, responsible for the nitroreduction of pendimethalin, was cloned from the pendimethalin-degrading strain
Bacillus subtilis
Y3. PNR could also catalyze the nitroreduction of three other major varieties of dinitroaniline herbicides, including butralin, oryzalin, and trifluralin. The reduction of pendimethalin by PNR might eliminate its toxicity against
Saccharomyces cerevisiae
BY4741, indicating the application potential of PNR in the detoxification of pendimethalin.
Soil Nutrient Depletion Is Associated with the Presence of Burkholderia pseudomallei
Authors: Hantrakun Viriya , Rongkard Patpong , Oyuchua Malinee , Amornchai Premjit , Lim Cherry , Wuthiekanun Vanaporn , Day Nicholas P. J. , Peacock Sharon J. , Limmathurotsakul Direk 
Published: October 2016

ABSTRACT

Burkholderia pseudomallei
is a soil-dwelling bacterium and the cause of melioidosis, which kills an estimated 89,000 people per year worldwide. Agricultural workers are at high risk of infection due to repeated exposure to the bacterium. Little is known about the soil physicochemical properties associated with the presence or absence of the organism. Here, we evaluated the soil physicochemical properties and presence of
B. pseudomallei
in 6,100 soil samples collected from 61 rice fields in Thailand. The presence of
B. pseudomallei
was negatively associated with the proportion of clay, proportion of moisture, level of salinity, percentage of organic matter, presence of cadmium, and nutrient levels (phosphorus, potassium, calcium, magnesium, and iron). The presence of
B. pseudomallei
was not associated with the level of soil acidity (
P
= 0.54). In a multivariable logistic regression model, the presence of
B. pseudomallei
was negatively associated with the percentage of organic matter (odds ratio [OR], 0.06; 95% confidence interval [CI], 0.01 to 0.47;
P
= 0.007), level of salinity (OR, 0.06; 95% CI, 0.01 to 0.74;
P
= 0.03), and percentage of soil moisture (OR, 0.81; 95% CI, 0.66 to 1.00;
P
= 0.05). Our study suggests that
B. pseudomallei
thrives in rice fields that are nutrient depleted. Some agricultural practices result in a decline in soil nutrients, which may impact the presence and amount of
B. pseudomallei
bacteria in affected areas.

IMPORTANCE
Burkholderia pseudomallei
is an environmental Gram-negative bacillus and the cause of melioidosis. Humans acquire the disease following skin inoculation, inhalation, or ingestion of the bacterium in the environment. The presence of
B. pseudomallei
in soil defines geographic regions where humans and livestock are at risk of melioidosis, yet little is known about the soil properties associated with the presence of the organism. We evaluated the soil properties and presence of
B. pseudomallei
in 61 rice fields in East, Central, and Northeast Thailand. We demonstrated that the organism was more commonly found in soils with lower levels of organic matter and nutrients, including phosphorus, potassium, calcium, magnesium, and iron. We also demonstrated that crop residue burning after harvest, which can reduce soil nutrients, was not uncommon. Some agricultural practices result in a decline in soil nutrients, which may impact the presence and amount of
B. pseudomallei
bacteria in affected areas.
Interactions of Plutonium with Pseudomonas sp. Strain EPS-1W and Its Extracellular Polymeric Substances
Authors: Boggs Mark A. , Jiao Yongqin , Dai Zurong , Zavarin Mavrik , Kersting Annie B. 
Published: October 2016

ABSTRACT

Safe and effective nuclear waste disposal, as well as accidental radionuclide releases, necessitates our understanding of the fate of radionuclides in the environment, including their interaction with microorganisms. We examined the sorption of Pu(IV) and Pu(V) to
Pseudomonas
sp. strain EPS-1W, an aerobic bacterium isolated from plutonium (Pu)-contaminated groundwater collected in the United States at the Nevada National Security Site (NNSS) in Nevada. We compared Pu sorption to cells with and without bound extracellular polymeric substances (EPS). Wild-type cells with intact EPS sorbed Pu(V) more effectively than cells with EPS removed. In contrast, cells with and without EPS showed the same sorption affinity for Pu(IV).
In vitro
experiments with extracted EPS revealed rapid reduction of Pu(V) to Pu(IV). Transmission electron microscopy indicated that 2- to 3-nm nanocrystalline Pu(IV)O
2
formed on cells equilibrated with high concentrations of Pu(IV) but not Pu(V). Thus, EPS, while facilitating Pu(V) reduction, inhibit the formation of nanocrystalline Pu(IV) precipitates.

IMPORTANCE
Our results indicate that EPS are an effective reductant for Pu(V) and sorbent for Pu(IV) and may impact Pu redox cycling and mobility in the environment. Additionally, the resulting Pu morphology associated with EPS will depend on the concentration and initial Pu oxidation state. While our results are not directly applicable to the Pu transport situation at the NNSS, the results suggest that, in general, stationary microorganisms and biofilms will tend to limit the migration of Pu and provide an important Pu retardation mechanism in the environment. In a broader sense, our results, along with a growing body of literature, highlight the important role of microorganisms as producers of redox-active organic ligands and therefore as modulators of radionuclide redox transformations and complexation in the subsurface.
Patient-reported outcome measure for neuromyelitis optica: pretesting of preliminary instrument and protocol for further development in accordance with international guidelines
Authors: Moore P , Jackson C , Mutch K , Methley A , Pollard C , Hamid S , Jacob A 
Published: October 2016

ObjectiveThis study outlines the development of a patient-reported outcome measure (PROM), an instrument to obtain self-reported health status for neuromyeltis optica (NMO), a disabling neurological condition.DesignDevelopment was conducted in accordance with international guidance for PROMs including systematic review of existing literature, item generation guided by qualitative interviews, health-related quality of life conceptual framework and clinical expert panel and cognitive interviews with NMO patients.SettingParticipants were identified through a national NMO clinic in a tertiary NHS neurosciences service.Participants15 individuals with NMO participated in cognitive interviews requiring review and ranking of proposed PROM items and qualitative feedback on content, layout and response options.ResultsParticipants endorsed the draft instrument as reflecting their experience of the condition and as being easy to understand. Rating and ranking of item relevance and importance reduced the draft instrument from 106 to 48 items. Participant feedback on overlapping items eliminated a further 2 items and resulted in a preliminary instrument of 46 items. As a direct result of participant feedback ordering of the 10 domains was revised, a 4 option Likert scale was employed and a 4-week recall period for impact of symptoms was selected.ConclusionsA 46-item instrument developed in accordance with international PROM development guidelines through literature review, developed by subject matter experts and refined through pretesting examining content validity provides a preliminary measure for assessing patient-report of health status in NMO. Further evaluation is proposed including sensitivity to clinical change, and international contributions to evaluating the measure are encouraged.
Effectiveness of the ‘Back-to-Sleep’ campaigns among healthcare professionals in the past 20 years: a systematic review
Authors: de Luca Federico , Hinde Andrew 
Published: October 2016

ObjectivesFrom the late 1980s ‘Back-to-Sleep’ (BTS) campaigns were run in most developed countries to increase awareness of the supine position's protective effect against sleep-related infant deaths. Once the media awareness-raising action associated with these campaigns ended, healthcare professionals' role became crucial. The goal of this paper is to determine if healthcare professionals' knowledge and parent advice consistent with evidence-based infant sleep recommendations have changed over the past 20 years.SettingAll studies investigating healthcare professionals' knowledge and/or advice to parents were included in a systematic review. The search was performed in PubMed and in MEDLINE, and 21 studies were identified.ResultsThe correctness of healthcare professionals' knowledge and parent advice about the supine sleeping position increased over the past 20 years. However, the percentage of those aware that parents should avoid putting their babies to sleep in a prone position is decreasing over time: from about 97% in the 1990s to about 90% at the end of the 2000s.ConclusionsThe effectiveness of the BTS campaigns in publicising the benefits of the supine position is confirmed by this paper. More and more healthcare professionals know that it is the best position to reduce the risk of sleep-related deaths and they recommend it exclusively. However, the decrease in the knowledge about non-prone positions suggests that the campaigns may not have focused enough on the dangers of the prone position.