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Background and Aims
Hybridizing species such as oaks may provide a model to study the role of selection in speciation with gene flow. Discrete species'' identities and different adaptations are maintained among closely related oak species despite recurrent gene flow. This is probably due to ecologically mediated selection at a few key genes or genomic regions. Neutrality tests can be applied to identify so-called outlier loci, which demonstrate locus-specific signatures of divergent selection and are candidate genes for further study.Methods
Thirty-six genic microsatellite markers, some with putative functions in flowering time and drought tolerance, and eight non-genic microsatellite markers were screened in two population pairs (n = 160) of the interfertile species Quercus rubra and Q. ellipsoidalis, which are characterized by contrasting adaptations to drought. Putative outliers were then tested in additional population pairs from two different geographic regions (n = 159) to support further their potential role in adaptive divergence.Key Results
A marker located in the coding sequence of a putative CONSTANS-like (COL) gene was repeatedly identified as under strong divergent selection across all three geographically disjunct population pairs. COL genes are involved in the photoperiodic control of growth and development and are implicated in the regulation of flowering time.Conclusions
The location of the polymorphism in the Quercus COL gene and given the potential role of COL genes in adaptive divergence and reproductive isolation makes this a promising candidate speciation gene. Further investigation of the phenological characteristics of both species and flowering time pathway genes is suggested in order to elucidate the importance of phenology genes for the maintenance of species integrity. Next-generation sequencing in multiple population pairs in combination with high-density genetic linkage maps could reveal the genome-wide distribution of outlier genes and their potential role in reproductive isolation between these species. 相似文献5.
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Impact of temperature and atmospheric pressure on the incidence of major acute cardiovascular events
Verberkmoes NJ Soliman Hamad MA Ter Woorst JF Tan ME Peels CH van Straten AH 《Netherlands heart journal》2012,20(5):193-196
Background
The impact of meteorological conditions on the occurrence of various cardiovascular events has been reported internationally. Data about the Dutch situation are limited.Objectives
We sought to find out a correlation between weather conditions and the incidence of major acute cardiovascular events such as type A acute aortic dissection (AAD), acute myocardial infarction (AMI) and acutely presented abdominal aortic aneurysms (AAAA).Methods
Between January 1998 and February 2010, patients who were admitted to our hospital (Catharina Hospital, Eindhoven, the Netherlands) because of AAD (n = 212), AMI (n = 11389) or AAAA (n = 1594) were registered. These data were correlated with the meteorological data provided by the Royal Dutch Meteorological Institute (KNMI) over the same period.Results
During the study period, a total number of 11,412 patients were admitted with AMI, 212 patients with AAD and 1593 patients with AAAA. A significant correlation was found between the daily temperature and the number of hospital admissions for AAD. The lower the daily temperature, the higher the incidence of AAD (p = 0.002). Lower temperature was also a predictor of a higher incidence of AMI (p = 0.02). No significant correlation was found between daily temperature and onset of AAAA.Conclusions
Cold weather is correlated with a higher incidence of AAD and AMI. 相似文献7.
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M. M. Winter S. Romeih B. J. Bouma M. Groenink N. A. Blom A. M. Spijkerboer B. J. M. Mulder 《Netherlands heart journal》2012,20(11):456-462
Objective
20 % of patients with a systemic RV are pacemaker dependent, and unsuitable to undergo cardiac magnetic resonance (CMR). Multidetector row computed tomography (MDCT) could provide a reproducible alternative to CMR in these patients. The aim of this study was to compare variability of MDCT with CMR.Methods
Thirty-five patients with systemic RV underwent either MDCT (n = 15) or CMR (n = 20). Systemic RV volumes and ejection fraction were obtained, and intra- and interobserver variability for both modalities were assessed and compared.Results
We found the intra- and interobserver variability of volumes and function measurements of the systemic RV obtained with MDCT to be higher compared with those obtained with CMR. However, these differences in variability were not significant, the only exception being the interobserver variability of systemic RV stroke volume.Conclusions
MDCT provides a reproducible alternative to CMR for volumes and function assessment in patients with a systemic RV. 相似文献9.
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Georgina Pe?alosa-Ruiz Cristina Aranda Laura Ongay-Larios Maritrini Colon Hector Quezada Alicia Gonzalez 《PloS one》2012,7(9)
Background
Gene duplication and the subsequent divergence of paralogous pairs play a central role in the evolution of novel gene functions. S. cerevisiae possesses two paralogous genes (ALT1/ALT2) which presumably encode alanine aminotransferases. It has been previously shown that Alt1 encodes an alanine aminotransferase, involved in alanine metabolism; however the physiological role of Alt2 is not known. Here we investigate whether ALT2 encodes an active alanine aminotransferase.Principal Findings
Our results show that although ALT1 and ALT2 encode 65% identical proteins, only Alt1 displays alanine aminotransferase activity; in contrast ALT2 encodes a catalytically inert protein. ALT1 and ALT2 expression is modulated by Nrg1 and by the intracellular alanine pool. ALT1 is alanine-induced showing a regulatory profile of a gene encoding an enzyme involved in amino acid catabolism, in agreement with the fact that Alt1 is the sole pathway for alanine catabolism present in S. cerevisiae. Conversely, ALT2 expression is alanine-repressed, indicating a role in alanine biosynthesis, although the encoded-protein has no alanine aminotransferase enzymatic activity. In the ancestral-like yeast L. kluyveri, the alanine aminotransferase activity was higher in the presence of alanine than in the presence of ammonium, suggesting that as for ALT1, LkALT1 expression could be alanine-induced. ALT2 retention poses the questions of whether the encoded protein plays a particular function, and if this function was present in the ancestral gene. It could be hypotesized that ALT2 diverged after duplication, through neo-functionalization or that ALT2 function was present in the ancestral gene, with a yet undiscovered function.Conclusions
ALT1 and ALT2 divergence has resulted in delegation of alanine aminotransferase activity to Alt1. These genes display opposed regulatory profiles: ALT1 is alanine-induced, while ALT2 is alanine repressed. Both genes are negatively regulated by the Nrg1 repressor. Presented results indicate that alanine could act as ALT2 Nrg1-co-repressor. 相似文献11.
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Joyce Wang Justin R Pritchard Louis Kreitmann Alexandre Montpetit Marcel A Behr 《BMC genomics》2014,15(1)
Background
Mycobacterium avium subsp. paratuberculosis (MAP) is an obligate intracellular pathogen that infects many ruminant species. The acquisition of foreign genes via horizontal gene transfer has been postulated to contribute to its pathogenesis, as these genetic elements are absent from its putative ancestor, M. avium subsp. hominissuis (MAH), an environmental organism with lesser pathogenicity. In this study, high-throughput sequencing of MAP transposon libraries were analyzed to qualitatively and quantitatively determine the contribution of individual genes to bacterial survival during infection.Results
Out of 52384 TA dinucleotides present in the MAP K-10 genome, 12607 had a MycoMarT7 transposon in the input pool, interrupting 2443 of the 4350 genes in the MAP genome (56%). Of 96 genes situated in MAP-specific genomic islands, 82 were disrupted in the input pool, indicating that MAP-specific genomic regions are dispensable for in vitro growth (odds ratio = 0.21). Following 5 independent in vivo infections with this pool of mutants, the correlation between output pools was high for 4 of 5 (R = 0.49 to 0.61) enabling us to define genes whose disruption reproducibly reduced bacterial fitness in vivo. At three different thresholds for reduced fitness in vivo, MAP-specific genes were over-represented in the list of predicted essential genes. We also identified additional genes that were severely depleted after infection, and several of them have orthologues that are essential genes in M. tuberculosis.Conclusions
This work indicates that the genetic elements required for the in vivo survival of MAP represent a combination of conserved mycobacterial virulence genes and MAP-specific genes acquired via horizontal gene transfer. In addition, the in vitro and in vivo essential genes identified in this study may be further characterized to offer a better understanding of MAP pathogenesis, and potentially contribute to the discovery of novel therapeutic and vaccine targets.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-415) contains supplementary material, which is available to authorized users. 相似文献13.
Félix Forest Peter Goldblatt John C. Manning David Baker Jonathan F. Colville Dion S. Devey Sarah Jose Maria Kaye Sven Buerki 《Annals of botany》2014,113(2):357-371
Background and Aims
Adaptation to different pollinators has been hypothesized as one of the main factors promoting the formation of new species in the Cape region of South Africa. Other researchers favour alternative causes such as shifts in edaphic preferences. Using a phylogenetic framework and taking into consideration the biogeographical scenario explaining the distribution of the group as well as the distribution of pollinators, this study compares pollination strategies with substrate adaptations to develop hypotheses of the primary factors leading to speciation in Lapeirousia (Iridaceae), a genus of corm-bearing geophytes well represented in the Cape and presenting an important diversity of pollination syndromes and edaphic preferences.Methods
Phylogenetic relationships are reconstructed within Lapeirousia using nuclear and plastid DNA sequence data. State-of-the-art methods in biogeography, divergence time estimation, character optimization and diversification rate assessments are used to examine the evolution of pollination syndromes and substrate shifts in the history of the group. Based on the phylogenetic results, ecological factors are compared for nine sister species pairs in Lapeirousia.Key Results
Seventeen pollinator shifts and ten changes in substrate types were inferred during the evolution of the genus Lapeirousia. Of the nine species pairs examined, all show divergence in pollination syndromes, while only four pairs present different substrate types.Conclusions
The available evidence points to a predominant influence of pollinator shifts over substrate types on the speciation process within Lapeirousia, contrary to previous studies that favoured a more important role for edaphic factors in these processes. This work also highlights the importance of biogeographical patterns in the study of pollination syndromes. 相似文献14.
Shubhra Rastogi Alok Kalra Vikrant Gupta Feroz Khan Raj Kishori Lal Anil Kumar Tripathi Sriram Parameswaran Chellappa Gopalakrishnan Gopalakrishna Ramaswamy Ajit Kumar Shasany 《BMC genomics》2015,16(1)
Background
Ocimum sanctum L. (O. tenuiflorum) family-Lamiaceae is an important component of Indian tradition of medicine as well as culture around the world, and hence is known as “Holy basil” in India. This plant is mentioned in the ancient texts of Ayurveda as an “elixir of life” (life saving) herb and worshipped for over 3000 years due to its healing properties. Although used in various ailments, validation of molecules for differential activities is yet to be fully analyzed, as about 80 % of the patents on this plant are on extracts or the plant parts, and mainly focussed on essential oil components. With a view to understand the full metabolic potential of this plant whole nuclear and chloroplast genomes were sequenced for the first time combining the sequence data from 4 libraries and three NGS platforms.Results
The saturated draft assembly of the genome was about 386 Mb, along with the plastid genome of 142,245 bp, turning out to be the smallest in Lamiaceae. In addition to SSR markers, 136 proteins were identified as homologous to five important plant genomes. Pathway analysis indicated an abundance of phenylpropanoids in O. sanctum. Phylogenetic analysis for chloroplast proteome placed Salvia miltiorrhiza as the nearest neighbor. Comparison of the chemical compounds and genes availability in O. sanctum and S. miltiorrhiza indicated the potential for the discovery of new active molecules.Conclusion
The genome sequence and annotation of O. sanctum provides new insights into the function of genes and the medicinal nature of the metabolites synthesized in this plant. This information is highly beneficial for mining biosynthetic pathways for important metabolites in related species.Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1640-z) contains supplementary material, which is available to authorized users. 相似文献15.
L. Ringoir S. S. Pedersen J. W. M. G. Widdershoven V. J. M. Pop 《Netherlands heart journal》2014,22(2):71-76
Background
Recent guidelines on cardiovascular disease prevention advocate the importance of psychological risk factors, as they contribute to the risk of developing cardiovascular disease. However, most previous research on psychological distress and cardiovascular factors has focused on selected populations with cardiovascular disease.Aim
The primary aim was to determine the prevalence of depression, anxiety, and Type D personality in elderly primary care patients with hypertension. Secondary aim was to examine the relation between elevated systolic blood pressure and depression, anxiety, and Type D personality.Design and Setting
A cross-sectional study in primary care practices located in the south of the Netherlands.Method
Primary care hypertension patients (N = 605), between 60 and 85 years (45 % men, mean age = 70 ± 6.6), were recruited for this study. All patients underwent a structured interview including validated self-report questionnaires to assess depression (PHQ-9), anxiety (GAD-7), and Type D personality (DS14) as well as blood pressure assessment.Results and Conclusion
Depression was prevalent in 5 %, anxiety in 5 %, and Type D personality in 8 %. None of the distress measures were associated with elevated systolic blood pressure of >160 mmHg (all p-values >0.05). This study showed no relation between psychological distress and elevated systolic blood pressure in elderly primary care patients with hypertension. 相似文献16.
Hortensia Moreno-Macías Douglas W Dockery Joel Schwartz Diane R Gold Nan M Laird Juan J Sienra-Monge Blanca E Del Río-Navarro Matiana Ramírez-Aguilar Albino Barraza-Villarreal Huiling Li Stephanie J London Isabelle Romieu 《Respiratory research》2013,14(1):14
Background
We previously reported that asthmatic children with GSTM1 null genotype may be more susceptible to the acute effect of ozone on the small airways and might benefit from antioxidant supplementation. This study aims to assess the acute effect of ozone on lung function (FEF25-75) in asthmatic children according to dietary intake of vitamin C and the number of putative risk alleles in three antioxidant genes: GSTM1, GSTP1 (rs1695), and NQO1 (rs1800566).Methods
257 asthmatic children from two cohort studies conducted in Mexico City were included. Stratified linear mixed models with random intercepts and random slopes on ozone were used. Potential confounding by ethnicity was assessed. Analyses were conducted under single gene and genotype score approaches.Results
The change in FEF25-75 per interquartile range (60 ppb) of ozone in persistent asthmatic children with low vitamin C intake and GSTM1 null was −91.2 ml/s (p = 0.06). Persistent asthmatic children with 4 to 6 risk alleles and low vitamin C intake showed an average decrement in FEF25-75 of 97.2 ml/s per 60 ppb of ozone (p = 0.03). In contrast in children with 1 to 3 risk alleles, acute effects of ozone on FEF25-75 did not differ by vitamin C intake.Conclusions
Our results provide further evidence that asthmatic children predicted to have compromised antioxidant defense by virtue of genetic susceptibility combined with deficient antioxidant intake may be at increased risk of adverse effects of ozone on pulmonary function. 相似文献17.
Zhike Liang Qingling Zhang Catherine MR Thomas Kirandeep K Chana David Gibeon Peter J Barnes Kian Fan Chung Pankaj K Bhavsar Louise E Donnelly 《Respiratory research》2014,15(1):72
Background
Bacteria are frequently cultured from sputum samples of severe asthma patients suggesting a defect in bacterial clearance from the airway. We measured the capacity of macrophages from patients with asthma to phagocytose bacteria.Methods
Phagocytosis of fluorescently-labelled polystyrene beads, Haemophilus influenzae or Staphylococcus aureus by broncholaveolar lavage alveolar macrophages (AM) and by monocyte-derived macrophages (MDM) from non-asthmatics, mild-moderate and severe asthmatic patients was assessed using fluorimetry.Results
There were no differences in phagocytosis of polystyrene beads by AMs or MDMs from any of the subject groups. There was reduced phagocytosis of Haemophilus influenzae and Staphylococcus aureus in MDMs from patients with severe asthma compared to non-severe asthma (p < 0.05 and p < 0.01, respectively) and healthy subjects (p < 0.01and p < 0.001, respectively). Phagocytosis of Haemophilus influenzae and Staphylococcus aureus by AM was also reduced in severe asthma compared to normal subjects (p < 0.05). Dexamethasone and formoterol did not suppress phagocytosis of bacteria by MDMs from any of the groups.Conclusions
Persistence of bacteria in the lower airways may result partly from a reduced phagocytic capacity of macrophages for bacteria. This may contribute to increased exacerbations, airway colonization and persistence of inflammation. 相似文献18.
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Huihui Li Prashant Vikram Ravi Prakash Singh Andrzej Kilian Jason Carling Jie Song Juan Andres Burgueno-Ferreira Sridhar Bhavani Julio Huerta-Espino Thomas Payne Deepmala Sehgal Peter Wenzl Sukhwinder Singh 《BMC genomics》2015,16(1)
Background
Genotyping-by-sequencing (GBS) is a high-throughput genotyping approach that is starting to be used in several crop species, including bread wheat. Anchoring GBS tags on chromosomes is an important step towards utilizing them for wheat genetic improvement. Here we use genetic linkage mapping to construct a consensus map containing 28644 GBS markers.Results
Three RIL populations, PBW343 × Kingbird, PBW343 × Kenya Swara and PBW343 × Muu, which share a common parent, were used to minimize the impact of potential structural genomic variation on consensus-map quality. The consensus map comprised 3757 unique positions, and the average marker distance was 0.88 cM, obtained by calculating the average distance between two adjacent unique positions. Significant variation of segregation distortion was observed across the three populations. The consensus map was validated by comparing positions of known rust resistance genes, and comparing them to wheat reference genome sequences recently published by the International Wheat Genome Sequencing Consortium, Rye and Ae. tauschii genomes. Three well-characterized rust resistance genes (Sr58/Lr46/Yr29, Sr2/Yr30/Lr27, and Sr57/Lr34/Yr18) and 15 published QTLs for wheat rusts were validated with high resolution. Fifty-two per cent of GBS tags on the consensus map were successfully aligned through BLAST to the right chromosomes on the wheat reference genome sequence.Conclusion
The consensus map should provide a useful basis for analyzing genome-wide variation of complex traits. The identified genes can then be explored as genetic markers to be used in genomic applications in wheat breeding.Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1424-5) contains supplementary material, which is available to authorized users. 相似文献20.
I. A. W. van Rijsingen S. C. A. M. Bekkers S. Schalla J. F. Hermans-van Ast G. Snoep B. S. N. Alzand Y. H. J. M. Arens A. van den Wijngaard H. J. G. M. Crijns Y. M. Pinto 《Netherlands heart journal》2011,19(4):168-174