bluuebunny/crossref_metadata_2025_split huggingface dataset:
Potential of a tomato MAGIC population to decipher the genetic control of quantitative traits and detect causal variants in the resequencing era
Authors: Pascual Laura , Desplat Nelly , Huang Bevan E. , Desgroux Aurore , Bruguier Laure , Bouchet Jean‐Paul , Le Quang H. , Chauchard Betty , Verschave Philippe , Causse Mathilde 
Published: November 2014

SummaryIdentification of the polymorphisms controlling quantitative traits remains a challenge for plant geneticists. Multiparent advanced generation intercross (MAGIC) populations offer an alternative to traditional linkage or association mapping populations by increasing the precision of quantitative trait loci (QTL) mapping. Here, we present the first tomato MAGIC population and highlight its potential for the valorization of intraspecific variation, QTL mapping and causal polymorphism identification. The population was developed by crossing eight founder lines, selected to include a wide range of genetic diversity, whose genomes have been previously resequenced. We selected 1536 SNPs among the 4 million available to enhance haplotype prediction and recombination detection in the population. The linkage map obtained showed an 87% increase in recombination frequencies compared to biparental populations. The prediction of the haplotype origin was possible for 89% of the MAGIC line genomes, allowing QTL detection at the haplotype level. We grew the population in two greenhouse trials and detected QTLs for fruit weight. We mapped three stable QTLs and six specific of a location. Finally, we showed the potential of the MAGIC population when coupled with whole genome sequencing of founder lines to detect candidate SNPs underlying the QTLs. For a previously cloned QTL on chromosome 3, we used the predicted allelic effect of each founder and their genome sequences to select putative causal polymorphisms in the supporting interval. The number of candidate polymorphisms was reduced from 12 284 (in 800 genes) to 96 (in 54 genes), including the actual causal polymorphism. This population represents a new permanent resource for the tomato genetics community.
Sub‐lethal UV‐C radiation induces callose, hydrogen peroxide and defence‐related gene expression in Arabidopsis thaliana
Authors: Mintoff S. J. L. , Rookes J. E. , Cahill D. M. 
Published: November 2014

AbstractExposure of plants to UV‐C irradiation induces gene expression and cellular responses that are commonly associated with wounding and pathogen defence, and in some cases can lead to increased resistance against pathogen infection. We examined, at a physiological, molecular and biochemical level, the effects of and responses to, sub‐lethal UV‐C exposure on Arabidopsis plants when irradiated with increasing dosages of UV‐C radiation. Following UV‐C exposure plants had reduced leaf areas over time, with the severity of reduction increasing with dosage. Severe morphological changes that included leaf glazing, bronzing and curling were found to occur in plants treated with the 1000 J·m−2 dosage. Extensive damage to the mesophyll was observed, and cell death occurred in both a dosage‐ and time‐dependent manner. Analysis of H2O2 activity and the pathogen defence marker genes PR1 and PDF1.2 demonstrated induction of these defence‐related responses at each UV‐C dosage tested. Interestingly, in response to UV‐C irradiation the production of callose (β‐1,3‐glucan) was identified at all dosages examined. Together, these results show plant responses to UV‐C irradiation at much lower doses than have previously been reported, and that there is potential for the use of UV‐C as an inducer of plant defence.
Negative and positive interactions among plants: effects of competitors and litter on seedling emergence and growth of forest and grassland species
Authors: Loydi A. , Donath T. W. , Otte A. , Eckstein R. L. 
Published: November 2014

AbstractLiving plant neighbours, but also their dead aboveground remains (i.e. litter), may individually exert negative or positive effects on plant recruitment. Although living plants and litter co‐occur in most ecosystems, few studies have addressed their combined effects, and conclusions are ambivalent. Therefore, we examined the response in terms of seedling emergence and growth of herbaceous grassland and forest species to different litter types and amounts and the presence of competitors. We conducted a pot experiment testing the effects of litter type (grass, oak), litter amount (low, medium, high) and interspecific competition (presence or absence of four Festuca arundinacea individuals) on seedling emergence and biomass of four congeneric pairs of hemicryptophytes from two habitat types (woodland, grassland). Interactions between litter and competition were weak. Litter presence increased competitor biomass. It also had positive effects on seedling emergence at low litter amounts and negative effects at high litter amounts, while competition had no effect on seedling emergence. Seedling biomass was negatively affected by the presence of competitors, and this effect was stronger in combination with high amounts of litter. Litter affected seedling emergence while competition determined the biomass of the emerged individuals, both affecting early stages of seedling recruitment. High litter accumulation also reduced seedling biomass, but this effect seemed to be additive to competitor effects. This suggests that live and dead plant mass can affect species recruitment in natural systems, but the mechanisms by which they operate and their timing differ.
Osteopetrosis in obese female rats is site‐specifically inhibited by physical training
Authors: Lacerda Débora Romualdo , Serakides Rogéria , de Melo Ocarino Natalia , Ferreira Adaliene Versiani Matos , Moraes Michele Macedo , Boeloni Jankerle Neves , Silva Juneo Freitas , de Oliveira Marina Chaves , de Barcellos Luiz Alexandre Medrado , Rodrigues Luiz Oswaldo Carneiro , Soares Danusa Dias 
Published: November 2014

New Findings
What is the central question of this study?
Clinical studies suggest that obesity ‘protects’ against osteoporosis. However, these studies used only bone densitometry and assessed only one bone site, which is insufficient to enable conclusions to be drawn about the response of the whole skeleton. Furthermore, the effects of exercise on bone responses in obesity have not been explored previously.

What is the main finding and what is its importance?
We show that obesity causes osteopetrosis. Therefore, the classical perspective of ‘protective effects of obesity’ needs to be reviewed, and exercise is an important tool to avoid these alterations and to maintain the homeostasis of bone.

A sedentary lifestyle and obesity induce systemic inflammatory responses. Although the effects of physical inactivity on osseous tissue have been well established, the effects of obesity on bone tissue remain controversial. Furthermore, the effects of physical training on bone tissue responses in the presence of diet‐induced obesity are unknown. Our aim was to investigate the effects of obesity and physical training at multiple bone sites in rats. Female Wistar rats were divided into the following four groups: (i) control diet, non‐trained (C‐NT); (ii) high‐refined carbohydrate‐containing diet, non‐trained (HC‐NT); (iii) control diet, trained (C‐T); and (iv) high‐refined carbohydrate‐containing diet, trained (HC‐T). At 5 months of age, the rats were submitted to daily exercise for 30 min day−1. After 13 weeks, blood samples, adipose and skeletal tissues were harvested. Two‐way ANOVA was applied to detect differences (significance accepted when P ≤ 0.05). The HC‐NT group exhibited increased body mass, adiposity, serum leptin, serum insulin, insulin resistance index and concentrations of tumour necrosis factor‐α and interleukin‐6. Obese rats (HC‐NT) exhibited thickening of nasal bones, trabecular bones in the lumbar vertebrae and long bones in a site‐dependent manner. The HC‐T group exhibited similar adiposity and inflammatory results. Morphological analysis of the lumbar vertebrae in rats fed the HC diet revealed characteristics of osteopetrosis that were inhibited by exercise. In conclusion, the HC diet induced obesity and inflammatory/hormonal alterations and increased the trabecular bone in a site‐dependent manner. However, obesity caused osteopetrosis in the lumbar vertebrae, which could be inhibited by physical training. Although exercise inhibited the development of bone alterations, physical training did not inhibit the HC diet‐induced obesity responses.
Vagus nerve stimulation reverses ventricular electrophysiological changes induced by hypersympathetic nerve activity
Authors: Huang Jie , Qian Jin , Yao Wei , Wang Neng , Zhang Zhenjian , Cao Chuanbin , Song Bo , Zhang Zhuo 
Published: November 2014

New Findings
What is the central question of this study?
Previous studies have shown that hypersympathetic nerve activity results in ventricular electrophysiological changes and facilitates the occurrence of ventricular arrhythmias. Vagus nerve stimulation has shown therapeutic potential for myocardial infarction‐induced ventricular arrhythmias. However, the actions of vagus nerve stimulation on hypersympathetic nerve activity‐induced ventricular electrophysiological changes are still unknown.
What is the main finding and its importance?
We show that vagus nerve stimulation is able to reverse hypersympathetic nerve activity‐induced ventricular electrophysiological changes and suppress the occurrence of ventricular fibrillation. These findings further suggest that vagus nerve stimulation may be an effective treatment option for ventricular arrhythmias, especially in patients with myocardial infarction or heart failure.
Vagus nerve stimulation (VNS) has shown therapeutic potential for myocardial infarction‐induced ventricular arrhythmias. This study aimed to investigate the effects of VNS on ventricular electrophysiological changes induced by hypersympathetic nerve activity. Seventeen open‐chest dogs were subjected to left stellate ganglion stimulation (LSGS) for 4 h to simulate hypersympathetic tone. All animals were randomly assigned to the VNS group (n = 9) or the control group (n = 8). In the VNS group, VNS was performed at the voltage causing a 10% decrease in heart rate for hours 3–4 during 4 h of LSGS. During the first 2 h of LSGS, the ventricular effective refractory period (ERP) and action potential duration (APD) were both progressively and significantly decreased; the spatial dispersion of ERP, maximal slope of the restitution curve and pacing cycle length of APD alternans were all increased. With LSGS + VNS during the next 2 h, there was a significant return of all the altered electrophysiological parameters towards baseline levels. In the eight control dogs that received 4 h of LSGS without VNS, all the parameters changed progressively, but without any reversals. The ventricular fibrillation threshold was higher in the VNS group than in the control group (17.3 ± 3.4 versus 11.3 ± 3.8 V, P < 0.05). The present study demonstrated that VNS was able to reverse LSGS‐induced ventricular electrophysiological changes and suppress the occurrence of ventricular fibrillation.
Microtubule stabilization with paclitaxel does not protect against infarction in isolated rat hearts
Authors: Rodríguez‐Sinovas Antonio , Abad Elena , Sánchez Jose A. , Fernández‐Sanz Celia , Inserte Javier , Ruiz‐Meana Marisol , Alburquerque‐Béjar Juan José , García‐Dorado David 
Published: November 2014

New Findings
What is the central question of this study?
The microtubule network is disrupted during myocardial ischaemia–reperfusion injury. It was suggested that prevention of microtubule disruption with paclitaxel might reduce cardiac infarct size; however, the effects on infarction have not been studied.
What is the main finding and its importance?
Paclitaxel caused a reduction in microtubule disruption and cardiomyocyte hypercontracture during ischaemia–reperfusion. However, it induced a greater increase in cytosolic calcium, which may explain the lack of effect against infarction that we have seen in isolated rat hearts. The large increase in perfusion pressure induced by paclitaxel in this model may have clinical implications, because detrimental effects of the drug were reported after its clinical application.
Microtubules play a major role in the transmission of mechanical forces within the myocardium and in maintenance of organelle function. However, this intracellular network is disrupted during myocardial ischaemia–reperfusion. We assessed the effects of prevention of microtubule disruption with paclitaxel on ischaemia–reperfusion injury in isolated rat cardiomyocytes and hearts. Isolated rat cardiomyocytes were submitted to normoxia (1 h) or 45 min of simulated ischaemia (pH 6.4, 0% O2, 37°C) and reoxygenation, without or with treatment with the microtubule stabilizer, paclitaxel (10−5 m), or the inhibitor of microtubule polymerization, colchicine (5 × 10−6 m). Simulated ischaemia leads to microtubule disruption before the onset of ischaemic contracture. Paclitaxel attenuated both microtubule disruption and the incidence of hypercontracture, whereas treatment with colchicine mimicked the effects of simulated ischaemia and reoxygenation. In isolated normoxic rat hearts, treatment with paclitaxel induced concentration‐dependent decreases in heart rate and left ventricular developed pressure and increases in perfusion pressure. Despite protection against hypercontracture, paclitaxel pretreatment did not modify infarct size (60.37 ± 2.27% in control hearts versus 58.75 ± 10.25, 55.44 ± 10.32 and 50.06 ± 10.14% after treatment with 10−6, 3 × 10−6 and 10−5 m of paclitaxel) after 60 min of global ischaemia and reperfusion in isolated rat hearts. Lack of protection was correlated with a higher increase in cytosolic calcium levels during simulated ischaemia in cardiomyocytes treated with paclitaxel (2.32 ± 0.15 versus 1.13 ± 0.16 a.u. in the presence or absence of 10−6 m paclitaxel, respectively, P < 0.05), but not with changes in aortic reactivity. In conclusion, microtubule stabilization with paclitaxel reduces hypercontracture in isolated rat cardiomyocytes but does not protect against infarction in isolated rat hearts.
Recruitment of Gβγ controls the basal activity of G‐protein coupled inwardly rectifying potassium (GIRK) channels: crucial role of distal C terminus of GIRK1
Authors: Kahanovitch Uri , Tsemakhovich Vladimir , Berlin Shai , Rubinstein Moran , Styr Boaz , Castel Ruth , Peleg Sagit , Tabak Galit , Dessauer Carmen W. , Ivanina Tatiana , Dascal Nathan 
Published: November 2014

Key points
The G‐protein coupled inwardly rectifying potassium (GIRK) channel is an important mediator of neurotransmission via Gβγ subunit of the heterotrimeric Gi/o protein released by G‐protein coupled receptor (GPCR) activation.
Channels containing the GIRK1 subunit exhibit high basal currents, whereas channels that are formed by the GIRK2 subunit have very low basal currents.
GIRK1‐containing channels, but not channels consisting of GIRK2 only, recruit Gβγ to the plasma membrane. The Gα subunit of the G protein is not recruited by either GIRK1/2 or GIRK2.
The unique distal C terminus of GIRK1 (G1‐dCT) endows the channel with strong interaction with Gβγ, and deletion of G1‐dCT abolishes the Gβγ recruitment and reduces the basal currents.
These findings suggest that the basal activity of GIRK channels depends on channel‐induced recruitment of Gβγ. The unique C terminus of GIRK1 subunit plays an important role in Gβγ recruitment.
AbstractThe G‐protein coupled inwardly rectifying potassium (GIRK, or Kir3) channels are important mediators of inhibitory neurotransmission via activation of G‐protein coupled receptors (GPCRs). GIRK channels are tetramers comprising combinations of subunits (GIRK1–4), activated by direct binding of the Gβγ subunit of Gi/o proteins. Heterologously expressed GIRK1/2 exhibit high, Gβγ‐dependent basal currents (Ibasal) and a modest activation by GPCR or coexpressed Gβγ. Inversely, the GIRK2 homotetramers exhibit low Ibasal and strong activation by Gβγ. The high Ibasal of GIRK1 seems to be associated with its unique distal C terminus (G1‐dCT), which is not present in the other subunits. We investigated the role of G1‐dCT using electrophysiological and fluorescence assays in Xenopus laevis oocytes and protein interaction assays. We show that expression of GIRK1/2 increases the plasma membrane level of coexpressed Gβγ (a phenomenon we term ‘Gβγ recruitment’) but not of coexpressed Gαi3. All GIRK1‐containing channels, but not GIRK2 homomers, recruited Gβγ to the plasma membrane. In biochemical assays, truncation of G1‐dCT reduces the binding between the cytosolic parts of GIRK1 and Gβγ, but not Gαi3. Nevertheless, the truncation of G1‐dCT does not impair activation by Gβγ. In fluorescently labelled homotetrameric GIRK1 channels and in the heterotetrameric GIRK1/2 channel, the truncation of G1‐dCT abolishes Gβγ recruitment and decreases Ibasal. Thus, we conclude that G1‐dCT carries an essential role in Gβγ recruitment by GIRK1 and, consequently, in determining its high basal activity. Our results indicate that G1‐dCT is a crucial part of a Gβγ anchoring site of GIRK1‐containing channels, spatially and functionally distinct from the site of channel activation by Gβγ.
Plasmid-Mediated Resistance to Cephalosporins and Fluoroquinolones in Various Escherichia coli Sequence Types Isolated from Rooks Wintering in Europe
Authors: Jamborova Ivana , Dolejska Monika , Vojtech Jiri , Guenther Sebastian , Uricariu Raluca , Drozdowska Joanna , Papousek Ivo , Pasekova Katerina , Meissner Wlodzimierz , Hordowski Jozef , Cizek Alois , Literak Ivan 
Published: November 2014

ABSTRACT

Extended-spectrum-beta-lactamase (ESBL)-producing, AmpC beta-lactamase-producing, and plasmid-mediated quinolone resistance (PMQR) gene-positive strains of
Escherichia coli
were investigated in wintering rooks (
Corvus frugilegus
) from eight European countries. Fecal samples (
n
= 1,073) from rooks wintering in the Czech Republic, France, Germany, Italy, Poland, Serbia, Spain, and Switzerland were examined. Resistant isolates obtained from selective cultivation were screened for ESBL, AmpC, and PMQR genes by PCR and sequencing. Pulsed-field gel electrophoresis and multilocus sequence typing were performed to reveal their clonal relatedness. In total, from the 1,073 samples, 152 (14%) cefotaxime-resistant
E. coli
isolates and 355 (33%)
E. coli
isolates with reduced susceptibility to ciprofloxacin were found. Eighty-two (54%) of these cefotaxime-resistant
E. coli
isolates carried the following ESBL genes:
bla
CTX-M-1
(
n
= 39 isolates),
bla
CTX-M-15
(
n
= 25),
bla
CTX-M-24
(
n
= 4),
bla
TEM-52
(
n
= 4),
bla
CTX-M-14
(
n
= 2),
bla
CTX-M-55
(
n
= 2),
bla
SHV-12
(
n
= 2),
bla
CTX-M-8
(
n
= 1),
bla
CTX-M-25
(
n
= 1),
bla
CTX-M-28
(
n
= 1), and an unspecified gene (
n
= 1). Forty-seven (31%) cefotaxime-resistant
E. coli
isolates carried the
bla
CMY-2
AmpC beta-lactamase gene. Sixty-two (17%) of the
E. coli
isolates with reduced susceptibility to ciprofloxacin were positive for the PMQR genes
qnrS1
(
n
= 54),
qnrB19
(
n
= 4),
qnrS1
and
qnrB19
(
n
= 2),
qnrS2
(
n
= 1), and
aac(6′)-Ib-cr
(
n
= 1). Eleven isolates from the Czech Republic (
n
= 8) and Serbia (
n
= 3) were identified to be CTX-M-15-producing
E. coli
clone B2-O25b-ST131 isolates. Ninety-one different sequence types (STs) among 191 ESBL-producing, AmpC-producing, and PMQR gene-positive
E. coli
isolates were determined, with ST58 (
n
= 15), ST10 (
n
= 14), and ST131 (
n
= 12) predominating. The widespread occurrence of highly diverse ESBL- and AmpC-producing and PMQR gene-positive
E. coli
isolates, including the clinically important multiresistant ST69, ST95, ST117, ST131, and ST405 clones, was demonstrated in rooks wintering in various European countries.
Modeling the Recovery of Heat-Treated Bacillus licheniformis Ad978 and Bacillus weihenstephanensis KBAB4 Spores at Suboptimal Temperature and pH Using Growth Limits
Authors: Trunet C. , Mtimet N. , Mathot A.-G. , Postollec F. , Leguerinel I. , Sohier D. , Couvert O. , Carlin F. , Coroller L. 
Published: November 2014

ABSTRACT

The apparent heat resistance of spores of
Bacillus weihenstephanensis
and
Bacillus licheniformis
was measured and expressed as the time to first decimal reduction (δ value) at a given recovery temperature and pH. Spores of
B. weihenstephanensis
were produced at 30°C and 12°C, and spores of
B. licheniformis
were produced at 45°C and 20°C.
B. weihenstephanensis
spores were then heat treated at 85°C, 90°C, and 95°C, and
B. licheniformis
spores were heat treated at 95°C, 100°C, and 105°C. Heat-treated spores were grown on nutrient agar at a range of temperatures (4°C to 40°C for
B. weihenstephanensis
and 15°C to 60°C for
B. licheniformis
) or a range of pHs (between pH 4.5 and pH 9.5 for both strains). The recovery temperature had a slight effect on the apparent heat resistance, except very near recovery boundaries. In contrast, a decrease in the recovery pH had a progressive impact on apparent heat resistance. A model describing the heat resistance and the ability to recover according to the sporulation temperature, temperature of treatment, and recovery temperature and pH was proposed. This model derived from secondary mathematical models for growth prediction. Previously published cardinal temperature and pH values were used as input parameters. The fitting of the model with apparent heat resistance data obtained for a wide range of spore treatment and recovery conditions was highly satisfactory.
Pyrosequencing of
mcrA
and Archaeal 16S rRNA Genes Reveals Diversity and Substrate Preferences of Methanogen Communities in Anaerobic Digesters
Authors: Wilkins David , Lu Xiao-Ying , Shen Zhiyong , Chen Jiapeng , Lee Patrick K. H. 
Published: November 2014

ABSTRACT

Methanogenic archaea play a key role in biogas-producing anaerobic digestion and yet remain poorly taxonomically characterized. This is in part due to the limitations of low-throughput Sanger sequencing of a single (16S rRNA) gene, which in the past may have undersampled methanogen diversity. In this study, archaeal communities from three sludge digesters in Hong Kong and one wastewater digester in China were examined using high-throughput pyrosequencing of the methyl coenzyme M reductase (
mcrA
) and 16S rRNA genes.
Methanobacteriales
,
Methanomicrobiales
, and
Methanosarcinales
were detected in each digester, indicating that both hydrogenotrophic and acetoclastic methanogenesis was occurring. Two sludge digesters had similar community structures, likely due to their similar design and feedstock. Taxonomic classification of the
mcrA
genes suggested that these digesters were dominated by acetoclastic methanogens, particularly
Methanosarcinales
, while the other digesters were dominated by hydrogenotrophic
Methanomicrobiales
. The proposed euryarchaeotal order
Methanomassiliicoccales
and the uncultured WSA2 group were detected with the 16S rRNA gene, and potential
mcrA
genes for these groups were identified. 16S rRNA gene sequencing also recovered several crenarchaeotal groups potentially involved in the initial anaerobic digestion processes. Overall, the two genes produced different taxonomic profiles for the digesters, while greater methanogen richness was detected using the
mcrA
gene, supporting the use of this functional gene as a complement to the 16S rRNA gene to better assess methanogen diversity. A significant positive correlation was detected between methane production and the abundance of
mcrA
transcripts in digesters treating sludge and wastewater samples, supporting the
mcrA
gene as a biomarker for methane yield.