bluuebunny/crossref_metadata_2025_split huggingface dataset:
Paths to selection on life history loci in different natural environments across the native range of Arabidopsis thaliana
Authors: Fournier‐Level Alexandre , Wilczek Amity M. , Cooper Martha D. , Roe Judith L. , Anderson Jillian , Eaton Deren , Moyers Brook T. , Petipas Renee H. , Schaeffer Robert N. , Pieper Bjorn , Reymond Matthieu , Koornneef Maarten , Welch Stephen M. , Remington David L. , Schmitt Johanna 
Published: March 2013

AbstractSelection on quantitative trait loci (QTL) may vary among natural environments due to differences in the genetic architecture of traits, environment‐specific allelic effects or changes in the direction and magnitude of selection on specific traits. To dissect the environmental differences in selection on life history QTL across climatic regions, we grew a panel of interconnected recombinant inbred lines (RILs) of Arabidopsis thaliana in four field sites across its native European range. For each environment, we mapped QTL for growth, reproductive timing and development. Several QTL were pleiotropic across environments, three colocalizing with known functional polymorphisms in flowering time genes (CRY2, FRI and MAF2‐5), but major QTL differed across field sites, showing conditional neutrality. We used structural equation models to trace selection paths from QTL to lifetime fitness in each environment. Only three QTL directly affected fruit number, measuring fitness. Most QTL had an indirect effect on fitness through their effect on bolting time or leaf length. Influence of life history traits on fitness differed dramatically across sites, resulting in different patterns of selection on reproductive timing and underlying QTL. In two oceanic field sites with high prereproductive mortality, QTL alleles contributing to early reproduction resulted in greater fruit production, conferring selective advantage, whereas alleles contributing to later reproduction resulted in larger size and higher fitness in a continental site. This demonstrates how environmental variation leads to change in both QTL effect sizes and direction of selection on traits, justifying the persistence of allelic polymorphism at life history QTL across the species range.
Functional genomic and phenotypic responses to desiccation in natural populations of a desert drosophilid
Authors: Rajpurohit Subhash , Oliveira Cássia C. , Etges William J. , Gibbs Allen G. 
Published: March 2013

AbstractWe used whole‐transcriptome microarrays to assess changes in gene expression and monitored mortality rates and epicuticular hydrocarbons (CHCs) in response to desiccation stress in four natural populations of Drosophila mojavensis from Baja California and mainland Mexico. Desiccation had the greatest effect on gene expression, followed by biogeographical variation at regional and population levels. Genes involved in environmental sensing and cuticular structure were up‐regulated in dry conditions, while genes involved in transcription itself were down‐regulated. Flies from Baja California had higher expression of reproductive and mitochondrial genes, suggesting that these populations have greater fecundity and higher metabolic rates. Host plant differences had a surprisingly minor effect on the transcriptome. In most cases, desiccation‐caused mortality was greater in flies reared on fermenting cactus tissues than that on laboratory media. Water content of adult females and males was significantly different and was lower in Baja California males. Different groups of CHCs simultaneously increased and decreased in amounts due to desiccation exposure of 9 and 18 h and were population‐specific and dependent on larval rearing substrates. Overall, we observed that changes in gene expression involved a coordinated response of behavioural, cuticular and metabolic genes. Together with differential expression of cuticular hydrocarbons, this study revealed some of the mechanisms that have allowed D. mojavensis to exploit its harsh desert conditions. Certainly, for D. mojavensis that uses different host plants, population‐level understanding of responses to stressors associated with future climate change in desert regions must be evaluated across geographical and local ecological scales.
Fleas associated with non‐flying small mammal communities from northern and central Chile: with new host and locality records
Authors: BAZÁN‐LEÓN E. A. , LARESCHI M. , SANCHEZ J. , SOTO‐NILO G. , LAZZONI I. , VENEGAS C. I. , POBLETE Y. , VÁSQUEZ R. A. 
Published: March 2013

AbstractFleas associated with small mammals from seven localities from northern and central Chile were assessed. We captured 352 small mammals belonging to 12 species from which we obtained 675 fleas belonging to 15 different species. The most frequently captured flea species wereNeotyphloceras crassispina crassispina(n = 198) andN. chilensis(n = 175). High values of flea species richness and diversity were found in Fray Jorge National Park (NP), a north‐central Chilean site, whereas the highest values of mean abundance (MA) and prevalence were found in three diverse sites that include Los Molles River, a high altitude site located in north‐central Chile, Fray JorgeNPand Dichato, in south‐central Chile. On the other hand, high values of flea richness and diversity were found on two rodent species,Abrothrix olivaceaandA. longipilis, whereas the highest values ofMAand prevalence were found onOligoryzomys longicaudatus,A. longipilisandPhyllotis xanthopygus. A total of three new host recordings, nine new localities and nine new host species and locality recordings are reported. Also, this study represents the first known record ofTetrapsyllus(Tetrapsyllus)comisin Chile and the first ecological analysis ofNeotyphloceras chilensis.
Utility of galactomannan antigen detection in bronchoalveolar lavage fluid in immunocompromised patients
Authors: Brownback Kyle R. , Pitts Lucas R. , Simpson Steven Q. 
Published: March 2013

SummaryDiagnosis of invasive pulmonary aspergillosis (IPA) is a challenging process in immunocompromised patients. Galactomannan (GM) antigen detection in bronchoalveolar lavage (BAL) fluid is a method to detect IPA with improved sensitivity over conventional studies. We sought to determine the diagnostic yield of BAL GM assay in a diverse population of immunocompromised patients. A retrospective review of 150 fiberoptic bronchoscopy (FOB) with BAL for newly diagnosed pulmonary infiltrate in immunocompromised patients was performed. Patient information, procedural details and laboratory studies were collected. BAL and serum samples were evaluated for GM using enzyme‐linked immunoassay. Of 150 separate FOB with BAL, BAL GM was obtained in 143 samples. There were 31 positive BAL GM assays. In those 31 positive tests, 13 were confirmed as IPA, giving a positive predictive value of 41.9%. There was one false negative BAL GM. Of the 18 false positive BAL GM, 4 were receiving piperacillin–tazobactam and 11 were receiving an alternative beta‐lactam antibiotic. BAL GM assay shows excellent sensitivity for diagnosing IPA. There was a significant number of false positive BAL GM assays and several of those patients were receiving beta‐lactam antibiotics at the time of bronchoscopy.
SUB1A‐mediated submergence tolerance response in rice involves differential regulation of the brassinosteroid pathway
Authors: Schmitz Aaron J. , Folsom Jing J. , Jikamaru Yusuke , Ronald Pamela , Walia Harkamal 
Published: March 2013

Summary

Submergence 1A (SUB1A), is an ethylene response factor (ERF) that confers submergence tolerance in rice (Oryza sativa) via limiting shoot elongation during the inundation period. SUB1A has been proposed to restrict shoot growth by modulating gibberellic acid (GA) signaling.

Our transcriptome analysis indicated that SUB1A differentially regulates genes associated with brassinosteroid (BR) synthesis during submergence. Consistent with the gene expression data, the SUB1A genotype had higher brassinosteroid levels after submergence compared to the intolerant genotype. Tolerance to submergence can be activated in the intolerant genotype by pretreatment with exogenous brassinolide, which results in restricted shoot elongation during submergence.

BR induced a GA catabolic gene, resulting in lower GA levels in SUB1A plants. BR treatment also induced the DELLA protein SLR1, a known repressor of GA responses such as shoot elongation. We propose that BR limits GA levels during submergence in the SUB1A rice through a GA catabolic enzyme as part of an early response and may repress GA responses by inducing SLR1 after several days of submergence.

Our results suggest that BR biosynthesis is regulated in a SUB1A‐dependent manner during submergence and is involved in modulating the GA signaling and homeostasis.
Photosynthetic performance of submerged macrophytes from lowland stream and lake habitats with contrasting CO2 availability
Authors: Baattrup‐Pedersen Annette , Madsen Tom Vindbæk , Riis Tenna , Cavalli Giulia 
Published: March 2013

Summary

We examine the photosynthetic response of submerged plants from streams and lakes with contrasting free‐CO2 and nitrogen (N) availability. We hypothesized that: the photosynthetic capacity of stream plants is higher because of higher N availability; the photosynthetic N‐use efficiency (PNUE) is also higher because stream plants are acclimated to higher free‐CO2; and PNUE is lower in aquatic compared to terrestrial plants.

We tested these hypotheses by measuring tissue‐N, photosynthetic capacity and inorganic C extraction capacity in plants collected from streams and lakes and by comparing the PNUE of aquatic plants with previously published PNUE of terrestrial plants.

We found that the organic N content was consistently higher in stream (3.8–6.3% w/w) than in lake plants (1.2–4.3% w/w). The photosynthetic capacity correlated positively with tissue‐N. The relationships were similar for stream and lake plants, indicating that N allocation patterns were similar despite variability in free‐CO2 between the two habitats.

The slope of the relationship between photosynthetic capacity and tissue‐N was lower than found for terrestrial plants, whereas the compensatory N content for photosynthesis was similar. This suggests that PNUE is lower in aquatic plants, perhaps reflecting that the selection pressure for a high C fixation rate per unit N is reduced as a result of low inorganic C availability in the aquatic environment.
Zinc Finger Protein 6 (ZFP6) regulates trichome initiation by integrating gibberellin and cytokinin signaling in Arabidopsis thaliana
Authors: Zhou Zhongjing , Sun Lili , Zhao Yongqin , An Lijun , Yan An , Meng Xiaofang , Gan Yinbo 
Published: March 2013

Summary

The Arabidopsis trichome is a model system for studying cell development, cell differentiation and the cell cycle in plants. Our previous studies have shown that the ZINC FINGER PROTEIN5 (ZFP5) controls shoot maturation and epidermal cell fate through GA signaling in Arabidopsis.

We have identified a novel C2H2 zinc finger protein ZINC FINGER PROTEIN 6 (ZFP6) which plays a key role in regulating trichome development in Arabidopsis.

Overexpression of ZFP6 results in ectopic trichomes on carpels and other inflorescence organs. Gain‐ and loss‐of‐function analyses have shown that the zfp6 mutant exhibits a reduced number of trichomes in sepals of flowers, cauline leaves, lateral branch and main inflorescence stems in comparison to wild‐type plants.

Molecular and genetic analyses suggest that ZFP6 functions upstream of GIS, GIS2, ZFP8, ZFP5 and key trichome initiation regulators GL1 and GL3.We reveal that ZFP6 and ZFP5 mediate the regulation of trichome initiation by integrating GA and cytokinin signaling in Arabidopsis. These findings provide new insights into the molecular mechanism of plant hormone control of epidermal trichome patterning through C2H2 transcriptional factors.
Silicon alleviates iron deficiency in cucumber by promoting mobilization of iron in the root apoplast
Authors: Pavlovic Jelena , Samardzic Jelena , Maksimović Vuk , Timotijevic Gordana , Stevic Nenad , Laursen Kristian H. , Hansen Thomas H. , Husted Søren , Schjoerring Jan K. , Liang Yongchao , Nikolic Miroslav 
Published: March 2013

Summary

Root responses to lack of iron (Fe) have mainly been studied in nutrient solution experiments devoid of silicon (Si). Here we investigated how Si ameliorates Fe deficiency in cucumber (Cucumis sativus) with focus on the storage and utilization of Fe in the root apoplast.

A combined approach was performed including analyses of apoplastic Fe, reduction‐based Fe acquisition and Fe‐mobilizing compounds in roots along with the expression of related genes.

Si‐treated plants accumulated higher concentrations of root apoplastic Fe, which rapidly decreased when Fe was withheld from the nutrient solution. Under Fe‐deficient conditions, Si also increased the accumulation of Fe‐mobilizing compounds in roots. Si supply stimulated root activity of Fe acquisition at the early stage of Fe deficiency stress through regulation of gene expression levels of proteins involved in Fe acquisition. However, when the period of Fe deprivation was extended, these reactions further decreased as a consequence of Si‐induced enhancement of the Fe status of the plants.

This work provides new evidence for the beneficial role of Si in plant nutrition and clearly indicates that Si‐mediated alleviation of Fe deficiency includes an increase of the apoplastic Fe pool in roots and an enhancement of Fe acquisition.
Functional dissection of the PROPEP2 and PROPEP3 promoters reveals the importance of WRKY factors in mediating microbe‐associated molecular pattern‐induced expression
Authors: Logemann Elke , Birkenbihl Rainer P. , Rawat Vimal , Schneeberger Korbinian , Schmelzer Elmon , Somssich Imre E. 
Published: March 2013

Summary

In Arabidopsis thaliana, small peptides (AtPeps) encoded by PROPEP genes act as damage‐associated molecular patterns (DAMPs) that are perceived by two leucine‐rich repeat receptor kinases, PEPR1 and PEPR2, to amplify defense responses. In particular, expression of PROPEP2 and PROPEP3 is strongly and rapidly induced by AtPeps, in response to bacterial, oomycete, and fungal pathogens, and microbe‐associated molecular patterns (MAMPs).

The cis‐regulatory modules (CRMs) within the PROPEP2 and PROPEP3 promoters that mediate MAMP responsiveness were delineated, employing parsley (Petroselinum crispum) protoplasts and transgenic A. thaliana plants harboring promoter‐reporter constructs. By chromatin immunoprecipitation in vivo, DNA interactions with a specific transcription factor were detected. Furthermore, the phastCons program was used to identify conserved regions of the PROPEP3 locus in different Brassicaceae species.

The major MAMP‐responsive CRM within the PROPEP2 promoter is composed of several W boxes and an as1/OCS (activation sequence‐1/octopine synthase) enhancer element, while in the PROPEP3 promoter the CRM is comprised of six W boxes. The WRKY33 transcription factor binds in vivo to these promoter regions in a MAMP‐dependent manner. Both the position and orientation of the six W boxes are conserved within the PROPEP3 promoters of four other Brassicaceae family members.

WRKY factors are the major regulators of MAMP‐induced PROPEP2 and PROPEP3 expression.
Combined phosphate and nitrogen limitation generates a nutrient stress transcriptome favorable for arbuscular mycorrhizal symbiosis in Medicago truncatula
Authors: Bonneau Laurent , Huguet Stéphanie , Wipf Daniel , Pauly Nicolas , Truong Hoai‐Nam 
Published: March 2013

Summary

Arbuscular mycorrhizal (AM) symbiosis is stimulated by phosphorus (P) limitation and contributes to P and nitrogen (N) acquisition. However, the effects of combined P and N limitation on AM formation are largely unknown.

Medicago truncatula plants were cultivated in the presence or absence of Rhizophagus irregularis (formerly Glomus intraradices) in P‐limited (LP), N‐limited (LN) or combined P‐ and N‐limited (LPN) conditions, and compared with plants grown in sufficient P and N.

The highest AM formation was observed in LPN, linked to systemic signaling by the plant nutrient status. Plant free phosphate concentrations were higher in LPN than in LP, as a result of cross‐talk between P and N. Transcriptome analyses suggest that LPN induces the activation of NADPH oxidases in roots, concomitant with an altered profile of plant defense genes and a coordinate increase in the expression of genes involved in the methylerythritol phosphate and isoprenoid‐derived pathways, including strigolactone synthesis genes.

Taken together, these results suggest that low P and N fertilization systemically induces a physiological state of plants favorable for AM symbiosis despite their higher P status. Our findings highlight the importance of the plant nutrient status in controlling plant–fungus interaction.
Chromium supplementation in overweight and obesity: a systematic review and meta‐analysis of randomized clinical trials
Authors: Onakpoya I. , Posadzki P. , Ernst E. 
Published: March 2013

SummaryThe increased prevalence of obesity has made the use of dietary supplements as weight reducing agents highly popular, but their efficacy has not been proven. One such supplement is chromium. The purpose of this review was to evaluate the evidence for or against the efficacy of chromium supplementation in overweight and obese individuals. Electronic searches were conducted in Medline, Embase, Amed and The Cochrane Library. The bibliographies of located articles were also searched. No age, gender or language restrictions were imposed. The reporting quality of identified randomized clinical trials (RCTs) was assessed using a methodological checklist adapted from the Consolidated Standard of Reporting Trials Statement and Preferred Reporting Items for Systematic Reviews and Meta‐Analyses guidelines. Thirty‐nine trials were identified and 20 were included. There were variations in reporting quality of included studies. A meta‐analysis of 11 studies showed a statistically significant difference in weight loss favouring chromium over placebo (mean difference (MD): −0.50 kg; 95% confidence interval (CI): −0.97, −0.03). There was a high statistical heterogeneity. Adverse events included watery stools, vertigo, headaches and urticaria. The evidence from available RCTs shows that chromium supplementation generates statistically significant reductions in body weight. The magnitude of the effect is small, and the clinical relevance is uncertain. Future trials should last at least 16 weeks and greater uniformity in the measuring and assessment tools for body composition is recommended.
Adiponectin and incident coronary heart disease and stroke. A systematic review and meta‐analysis of prospective studies
Authors: Kanhai D. A. , Kranendonk M. E. , Uiterwaal C. S. P. M. , van der Graaf Y. , Kappelle L. J. , Visseren F. L. J. 
Published: March 2013

SummaryThe plasma concentration of adiponectin, an adipokine that has anti‐inflammatory, anti‐atherogenic and insulin sensitizing properties, is lower in obese subjects and could therefore be a target for therapy. In order to review and meta‐analyse prospective cohort studies investigating adiponectin concentration and the risk for incident coronary heart disease (CHD) or stroke, a systematic search of MEDLINE, EMBASE and Cochrane databases was performed. Two independent reviewers selected prospective cohort studies investigating the relationship between adiponectin level and incident CHD or stroke using ‘adiponectin’ and ‘cardiovascular disease’ or ‘stroke’ and their synonyms, excluding patients with clinically manifest vascular disease. Random‐effects models were used to calculate pooled relative risks (RRs) and 95% confidence intervals (95% CI). Generalized least squares regression was used to assess dose–response relationships for adiponectin concentrations from studies that provided RRs solely based upon categorical data regression. In total, 16 prospective cohort studies, comprising 23,919 patients and 6,870 CHD or stroke outcome events, were included in the meta‐analyses. An increase of 1 standard deviation in log‐transformed adiponectin did not lower the risk for CHD (RR 0.97; 95% CI 0.86–1.09). A 10 μg mL–1 increase in adiponectin conferred a RR of 0.91 (95% CI 0.80–1.03) for CHD and a RR 1.01 (95% CI 0.97–1.06) for stroke. In conclusion, plasma adiponectin is not related to the risk for incident CHD or stroke.
Fasciola hepatica tegumental coat antigen suppresses MAPK signalling in dendritic cells and up‐regulates the expression of SOCS3
Authors: Vukman K. V. , Adams P. N. , O'Neill S. M. 
Published: March 2013

SummaryFasciola hepatica tegumental coat antigen (FhTeg) suppresses dendritic cell maturation and function by inhibiting IL‐6, tumour necrosis factor (TNF)‐α, IL‐10 and IL‐12 production and CD80, CD86 and CD40 cell surface marker expression in TLR4‐stimulated dendritic cells. Fasciola hepatica also impairs dendritic cell function by inhibiting its phagocytic capacity and its ability to prime T cells. We have shown previously that activation of mast cells with bacterial ligands is also inhibited by FhTeg. Fasciola hepatica suppresses LPS‐induced NF‐κB and MAPK pathway (ERK) activation in these cells. Previously, we demonstrated that FhTeg induces expression of suppressor of cytokine signalling (SOCS)3, a negative regulator of the TLR pathway in mast cells. In this study, we show the same inhibitory effect of FhTeg on the activation of the other members of the MAPKs pathway (ERK, p38, JNK) in dendritic cells and demonstrate an enhanced expression of SOCS3, but not SOCS1, SOCS5 or PIAS3 in this process. These studies enhance our understanding of the immunomodulatory effect of helminth molecules on the TLR pathway.
Organic matter fractions and N mineralization in vegetable‐cropped sandy soils
Authors: Jegajeevagan K. , Sleutel S. , Ameloot N. , Kader M. A. , De Neve S. 
Published: March 2013

AbstractSoil organic nitrogen mineralization rates and possible predictors thereof were investigated for vegetable‐growing soils in Belgium. Soil organic matter (SOM) was fractionated into sand (> 53 μm) and silt+clay (< 53 μm) fractions. The latter fraction was further separated into 6%NaOCl‐oxidation labile (6%NaOCl‐ox) and resistant N and C and subsequently into 10%HF‐extractable (mineral bound) and resistant (recalcitrant) N and C. The N mineralization turnover rate (% of soil N/year) correlated with several of the investigated N or C fractions and stepwise linear regression confirmed that the 6%NaOCl‐ox N was the best predictor. However, the small R² (0.42) of the regression model suggests that soil parameters other than the soil fractions isolated here would be required to explain the significant residual variation in N mineralization rate. A next step could be to look for alternative SOM fractionations capable of isolating bioavailable N. However, it would appear that the observed relationships between N fractions and N mineralization may not be causal but indirect. The number of vegetable crops per rotation did not influence N mineralization, but it did influence 6%NaOCl‐ox N, probably as an effect of differences in crop residues returned and organic manure supply. However, the nature of this relation between management, SOM quality and N mineralization is not clear. Explanation of correlations between N mineralization and presumed bioavailable N fractions, like the 6%NaOCl‐ox N, requires further mechanistic elucidation of the N mineralization process.
Filtering free resolutions
Authors: Eisenbud David , Erman Daniel , Schreyer Frank-Olaf 
Published: March 2013

AbstractA recent result of Eisenbud–Schreyer and Boij–Söderberg proves that the Betti diagram of any graded module decomposes as a positive rational linear combination of pure diagrams. When does this numerical decomposition correspond to an actual filtration of the minimal free resolution? Our main result gives a sufficient condition for this to happen. We apply it to show the non-existence of free resolutions with some plausible-looking Betti diagrams and to study the semigroup of quiver representations of the simplest ‘wild’ quiver.