共查询到20条相似文献,搜索用时 15 毫秒
1.
Zhengqiu Cai Cynthia Penaflor Jennifer V Kuehl James Leebens-Mack John E Carlson Claude W de Pamphilis Jeffrey L Boore Robert K Jansen 《BMC evolutionary biology》2006,6(1):77-20
Background
The magnoliids with four orders, 19 families, and 8,500 species represent one of the largest clades of early diverging angiosperms. Although several recent angiosperm phylogenetic analyses supported the monophyly of magnoliids and suggested relationships among the orders, the limited number of genes examined resulted in only weak support, and these issues remain controversial. Furthermore, considerable incongruence resulted in phylogenetic reconstructions supporting three different sets of relationships among magnoliids and the two large angiosperm clades, monocots and eudicots. We sequenced the plastid genomes of three magnoliids, Drimys (Canellales), Liriodendron (Magnoliales), and Piper (Piperales), and used these data in combination with 32 other angiosperm plastid genomes to assess phylogenetic relationships among magnoliids and to examine patterns of variation of GC content. 相似文献2.
Martin I Sigurdsson Neema Jamshidi Eirikur Steingrimsson Ines Thiele Bernhard Ø Palsson 《BMC systems biology》2010,4(1):140
Background
Well-curated and validated network reconstructions are extremely valuable tools in systems biology. Detailed metabolic reconstructions of mammals have recently emerged, including human reconstructions. They raise the question if the various successful applications of microbial reconstructions can be replicated in complex organisms. 相似文献3.
Paula Jouhten Esa Pitkänen Tiina Pakula Markku Saloheimo Merja Penttilä Hannu Maaheimo 《BMC systems biology》2009,3(1):104-16
Background
The filamentous fungus Trichoderma reesei is an important host organism for industrial enzyme production. It is adapted to nutrient poor environments where it is capable of producing large amounts of hydrolytic enzymes. In its natural environment T. reesei is expected to benefit from high energy yield from utilization of respirative metabolic pathway. However, T. reesei lacks metabolic pathway reconstructions and the utilization of the respirative pathway has not been investigated on the level of in vivo fluxes. 相似文献4.
V.F. Bondici J.R. Lawrence N.H. Khan J.E. Hill E. Yergeau G.M. Wolfaardt J. Warner D.R. Korber 《Journal of applied microbiology》2013,114(6):1671-1686
Aims
To describe the diversity and metabolic potential of microbial communities in uranium mine tailings characterized by high pH, high metal concentration and low permeability.Methods and Results
To assess microbial diversity and their potential to influence the geochemistry of uranium mine tailings using aerobic and anaerobic culture‐based methods, in conjunction with next generation sequencing and clone library sequencing targeting two universal bacterial markers (the 16S rRNA and cpn60 genes). Growth assays revealed that 69% of the 59 distinct culturable isolates evaluated were multiple‐metal resistant, with 15% exhibiting dual‐metal hypertolerance. There was a moderately positive correlation coefficient (R = 0·43, P < 0·05) between multiple‐metal resistance of the isolates and their enzyme expression profile. Of the isolates tested, 17 reduced amorphous iron, 22 reduced molybdate and seven oxidized arsenite. Based on next generation sequencing, tailings depth was shown to influence bacterial community composition, with the difference in the microbial diversity of the upper (0–20 m) and middle (20–40 m) tailings zones being highly significant (P < 0·01) from the lower zone (40–60 m) and the difference in diversity of the upper and middle tailings zone being significant (P < 0·05). Phylotypes closely related to well‐known sulfate‐reducing and iron‐reducing bacteria were identified with low abundance, yet relatively high diversity.Conclusions
The presence of a population of metabolically‐diverse, metal‐resistant micro‐organisms within the tailings environment, along with their demonstrated capacity for transforming metal elements, suggests that these organisms have the potential to influence the long‐term geochemistry of the tailings.Significance and Impact of the study
This study is the first investigation of the diversity and functional potential of micro‐organisms present in low permeability, high pH uranium mine tailings. 相似文献5.
Background
The evolutionary rate at a given homologous position varies across time. When sufficiently pronounced, this phenomenon – called heterotachy – may produce artefactual phylogenetic reconstructions under the commonly used models of sequence evolution. These observations have motivated the development of models that explicitly recognize heterotachy, with research directions proposed along two main axes: 1) the covarion approach, where sites switch from variable to invariable states; and 2) the mixture of branch lengths (MBL) approach, where alignment patterns are assumed to arise from one of several sets of branch lengths, under a given phylogeny. 相似文献6.
Claire C Morgan Noeleen B Loughran Thomas A Walsh Alan J Harrison Mary J O'Connell 《BMC evolutionary biology》2010,10(1):39
Background
Reproductive proteins are central to the continuation of all mammalian species. The evolution of these proteins has been greatly influenced by environmental pressures induced by pathogens, rival sperm, sexual selection and sexual conflict. Positive selection has been demonstrated in many of these proteins with particular focus on primate lineages. However, the mammalia are a diverse group in terms of mating habits, population sizes and germ line generation times. We have examined the selective pressures at work on a number of novel reproductive proteins across a wide variety of mammalia. 相似文献7.
Jan Schellenberger Junyoung O Park Tom M Conrad Bernhard Ø Palsson 《BMC bioinformatics》2010,11(1):213
Background
Genome-scale metabolic reconstructions under the Constraint Based Reconstruction and Analysis (COBRA) framework are valuable tools for analyzing the metabolic capabilities of organisms and interpreting experimental data. As the number of such reconstructions and analysis methods increases, there is a greater need for data uniformity and ease of distribution and use. 相似文献8.
9.
Nicole Borel Claudia Dumrese Urs Ziegler Andrea Schifferli Carmen Kaiser Andreas Pospischil 《BMC microbiology》2010,10(1):201
Background
Chlamydiae induce persistent infections, which have been associated with a wide range of chronic diseases in humans and animals. Mixed infections with Chlamydia and porcine epidemic diarrhea virus (PEDV) may result in generation of persistent chlamydial infections. To test this hypothesis, an in vitro model of dual infection with cell culture-adapted PEDV and Chlamydia abortus or Chlamydia pecorum in Vero cells was established. 相似文献10.
11.
Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploid wheat 总被引:5,自引:0,他引:5
Martin Trick Nikolai Maria Adamski Sarah G Mugford Cong-Cong Jiang Melanie Febrer Cristobal Uauy 《BMC plant biology》2012,12(1):14
Background
Next generation sequencing (NGS) technologies are providing new ways to accelerate fine-mapping and gene isolation in many species. To date, the majority of these efforts have focused on diploid organisms with readily available whole genome sequence information. In this study, as a proof of concept, we tested the use of NGS for SNP discovery in tetraploid wheat lines differing for the previously cloned grain protein content (GPC) gene GPC-B1. Bulked segregant analysis (BSA) was used to define a subset of putative SNPs within the candidate gene region, which were then used to fine-map GPC-B1. 相似文献12.
Alexander Keller Frank Förster Tobias Müller Thomas Dandekar Jörg Schultz Matthias Wolf 《Biology direct》2010,5(1):4
Background
In several studies, secondary structures of ribosomal genes have been used to improve the quality of phylogenetic reconstructions. An extensive evaluation of the benefits of secondary structure, however, is lacking. 相似文献13.
Background
Owl monkeys, belonging to the genus Aotus, have been extensively used as animal models in biomedical research but few reports have focused on the taxonomy and phylogeography of this genus. Moreover, the morphological similarity of several Aotus species has led to frequent misidentifications, mainly at the boundaries of their distribution. In this study, sequence data from five mitochondrial regions and the nuclear, Y-linked, SRY gene were used for species identification and phylogenetic reconstructions using well characterized specimens of Aotus nancymaae, A. vociferans, A. lemurinus, A. griseimembra, A. trivirgatus, A. nigriceps, A. azarae boliviensis and A. infulatus. 相似文献14.
High climate velocity and population fragmentation may constrain climate‐driven range shift of the key habitat former Fucus vesiculosus 下载免费PDF全文
Per R. Jonsson Jonne Kotta Helén C. Andersson Kristjan Herkül Elina Virtanen Antonia Nyström Sandman Kerstin Johannesson 《Diversity & distributions》2018,24(7):892-905
Aim
The Baltic Sea forms a unique regional sea with its salinity gradient ranging from marine to nearly freshwater conditions. It is one of the most environmentally impacted brackish seas worldwide, and the low biodiversity makes it particularly sensitive to anthropogenic pressures including climate change. We applied a novel combination of models to predict the fate of one of the dominant foundation species in the Baltic Sea, the bladder wrack Fucus vesiculosus.Location
The Baltic Sea.Methods
We used a species distribution model to predict climate change‐induced displacement of F. vesiculosus and combined these projections with a biophysical model of dispersal and connectivity to explore whether the dispersal rate of locally adapted genotypes may match estimated climate velocities to recolonize the receding salinity gradient. In addition, we used a population dynamic model to assess possible effects of habitat fragmentation.Results
The species distribution model showed that the habitat of F. vesiculosus is expected to dramatically shrink, mainly caused by the predicted reduction of salinity. In addition, the dispersal rate of locally adapted genotypes may not keep pace with estimated climate velocities rendering the recolonization of the receding salinity gradient more difficult. A simplistic model of population dynamics also indicated that the risk of local extinction may increase due to future habitat fragmentation.Main conclusions
Results point to a significant risk of locally adapted genotypes being unable to shift their ranges sufficiently fast considering the restricted dispersal and long generation time. The worst scenario is that F. vesiculosus may disappear from large parts of the Baltic Sea before the end of this century with large effects on the biodiversity and ecosystem functioning. We finally discuss how to reduce this risk through conservation actions, including assisted colonization and assisted evolution. 相似文献15.
Background
Recent theoretical and empirical work points toward a significant role for sex-chromosome linked genes in the evolution of traits that induce reproductive isolation and for traits that evolve under influence of sexual selection. Empirical studies including recently diverged (Pleistocene), short-lived avian species pairs with short generation times have found that introgression occurs on the autosomes but not on the Z-chromosome. Here we study genetic differentiation and gene flow in the long-lived greater spotted eagle (Aquila clanga) and lesser spotted eagle (A. pomarina), two species with comparatively long generation times. 相似文献16.
Background
Escherichia coli can respire anaerobically using dimethyl sulfoxide (DMSO) or trimethylamine-N-oxide (TMAO) as the terminal electron acceptor for anaerobic energy generation. Expression of the dmsABC genes that encode the membrane-associated DMSO/TMAO reductase is positively regulated during anaerobic conditions by the Fnr protein and negatively regulated by the NarL protein when nitrate is present. 相似文献17.
Astrid Lewin Daniela Baus Elisabeth Kamal Fabienne Bon Ralph Kunisch Sven Maurischat Michaela Adonopoulou Katharina Eich 《BMC microbiology》2008,8(1):91
Background
Pathogenic mycobacteria such as M. tuberculosis, M. bovis or M. leprae are characterised by their extremely slow growth rate which plays an important role in mycobacterial virulence and eradication of the bacteria. Various limiting factors influence the generation time of mycobacteria, and the mycobacterial DNA-binding protein 1 (MDP1) has also been implicated in growth regulation. Our strategy to investigate the role of MDP1 in mycobacterial growth consisted in the generation and characterisation of a M. bovis BCG derivative expressing a MDP1-antisense gene. 相似文献18.
Samantha C Lewis Leslie A Dyal Caroline F Hilburn Stephanie Weitz Wei-Siang Liau Craig W LaMunyon Dee R Denver 《BMC evolutionary biology》2009,9(1):15
Background
As exemplified by the famously successful model organism Caenorhabditis elegans, nematodes offer outstanding animal systems for investigating diverse biological phenomena due to their small genome sizes, short generation times and ease of laboratory maintenance. Nematodes in the genus Panagrolaimus have served in comparative development and anhydrobiosis studies, and the Antarctic species P. davidi offers a powerful paradigm for understanding the biological mechanisms of extreme cold tolerance. Panagrolaimus nematodes are also unique in that examples of gonochoristic, hermaphroditic and parthenogenetic reproductive modes have been reported for members of this genus. The evolutionary origins of these varying reproductive modes and the Antarctic species P. davidi, however, remain enigmatic. 相似文献19.
Background
Saccharomyces cerevisiae is the first eukaryotic organism for which a multi-compartment genome-scale metabolic model was constructed. Since then a sequence of improved metabolic reconstructions for yeast has been introduced. These metabolic models have been extensively used to elucidate the organizational principles of yeast metabolism and drive yeast strain engineering strategies for targeted overproductions. They have also served as a starting point and a benchmark for the reconstruction of genome-scale metabolic models for other eukaryotic organisms. In spite of the successive improvements in the details of the described metabolic processes, even the recent yeast model (i.e., i MM904) remains significantly less predictive than the latest E. coli model (i.e., i AF1260). This is manifested by its significantly lower specificity in predicting the outcome of grow/no grow experiments in comparison to the E. coli model. 相似文献20.