共查询到20条相似文献,搜索用时 31 毫秒
1.
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2.
Background
Currently, there exists tens of different microbial and eukaryotic metabolic reconstructions (e.g., Escherichia coli, Saccharomyces cerevisiae, Bacillus subtilis) with many more under development. All of these reconstructions are inherently incomplete with some functionalities missing due to the lack of experimental and/or homology information. A key challenge in the automated generation of genome-scale reconstructions is the elucidation of these gaps and the subsequent generation of hypotheses to bridge them. 相似文献3.
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4.
Karin Radrich Yoshimasa Tsuruoka Paul Dobson Albert Gevorgyan Neil Swainston Gino Baart Jean-Marc Schwartz 《BMC systems biology》2010,4(1):114
Background
Genome-scale metabolic reconstructions have been recognised as a valuable tool for a variety of applications ranging from metabolic engineering to evolutionary studies. However, the reconstruction of such networks remains an arduous process requiring a high level of human intervention. This process is further complicated by occurrences of missing or conflicting information and the absence of common annotation standards between different data sources. 相似文献5.
Paul D Thomas 《BMC bioinformatics》2010,11(1):312
Background
Phylogenetic relationships between genes are not only of theoretical interest: they enable us to learn about human genes through the experimental work on their relatives in numerous model organisms from bacteria to fruit flies and mice. Yet the most commonly used computational algorithms for reconstructing gene trees can be inaccurate for numerous reasons, both algorithmic and biological. Additional information beyond gene sequence data has been shown to improve the accuracy of reconstructions, though at great computational cost. 相似文献6.
Background
Recent analysis of the yeast gene network shows that most genes have few inputs, indicating that enumerative gene reconstruction methods are both useful and computationally feasible. A simple enumerative reconstruction method based on a discrete dynamical system model is used to study how microarray experiments involving modulated global perturbations can be designed to obtain reasonably accurate reconstructions. The method is tested on artificial gene networks with biologically realistic in/out degree characteristics. 相似文献7.
Morgane Thomas-Chollier Valérie Ledent Luc Leyns Michel Vervoort 《BMC evolutionary biology》2010,10(1):73
Background
Hox and the closely-related ParaHox genes, which emerged prior to the divergence between cnidarians and bilaterians, are the most well-known members of the ancient genetic toolkit that controls embryonic development across all metazoans. Fundamental questions relative to their origin and evolutionary relationships remain however unresolved. We investigate here the evolution of metazoan Hox and ParaHox genes using the HoxPred program that allows the identification of Hox genes without the need of phylogenetic tree reconstructions. 相似文献8.
Sebastian Klaus Christoph D Schubart Bruno Streit Markus Pfenninger 《BMC evolutionary biology》2010,10(1):287
Background
The faunal and floral relationship of northward-drifting India with its neighboring continents is of general biogeographic interest as an important driver of regional biodiversity. However, direct biogeographic connectivity of India and Southeast Asia during the Cenozoic remains largely unexplored. We investigate timing, direction and mechanisms of faunal exchange between India and Southeast Asia, based on a molecular phylogeny, molecular clock-derived time estimates and biogeographic reconstructions of the Asian freshwater crab family Gecarcinucidae. 相似文献9.
Ernst Wellnhofer Leonid Goubergrits Ulrich Kertzscher Klaus Affeld 《Biomedical engineering online》2006,5(1):39-15
Background
Clinical studies suggest that local wall shear stress (WSS) patterns modulate the site and the progression of atherosclerotic lesions. Computational fluid dynamics (CFD) methods based on in-vivo three-dimensional vessel reconstructions have recently been shown to provide prognostically relevant WSS data. This approach is, however, complex and time-consuming. Methodological simplifications are desirable in porting this approach from bench to bedside. The impact of such simplifications on the accuracy of geometry and wall shear stress calculations has to be investigated. 相似文献10.
Background
Metabolic reconstructions contain detailed information about metabolic enzymes and their reactants and products. These networks can be used to infer functional associations between metabolic enzymes. Many methods are based on the number of metabolites shared by two enzymes, or the shortest path between two enzymes. Metabolite sharing can miss associations between non-consecutive enzymes in a serial pathway, and shortest-path algorithms are sensitive to high-degree metabolites such as water and ATP that create connections between enzymes with little functional similarity. 相似文献11.
Background
Advances in bioinformatic techniques and analyses have led to the availability of genome-scale metabolic reconstructions. The size and complexity of such networks often means that their potential behaviour can only be analysed with constraint-based methods. Whilst requiring minimal experimental data, such methods are unable to give insight into cellular substrate concentrations. Instead, the long-term goal of systems biology is to use kinetic modelling to characterize fully the mechanics of each enzymatic reaction, and to combine such knowledge to predict system behaviour. 相似文献12.
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13.
Background
As originally defined, orthologous genes implied a reflection of the history of the species. In recent years, many studies have examined the concordance between orthologous gene trees and species trees in bacteria. These studies have produced contradictory results that may have been influenced by orthologous gene misidentification and artefactual phylogenetic reconstructions. Here, using a method that allows the detection and exclusion of false positives during identification of orthologous genes, we address the question of whether putative orthologous genes within bacteria really reflect the history of the species. 相似文献14.
Richard A Notebaart Frank HJ van Enckevort Christof Francke Roland J Siezen Bas Teusink 《BMC bioinformatics》2006,7(1):296
Background
The genomic information of a species allows for the genome-scale reconstruction of its metabolic capacity. Such a metabolic reconstruction gives support to metabolic engineering, but also to integrative bioinformatics and visualization. Sequence-based automatic reconstructions require extensive manual curation, which can be very time-consuming. Therefore, we present a method to accelerate the time-consuming process of network reconstruction for a query species. The method exploits the availability of well-curated metabolic networks and uses high-resolution predictions of gene equivalency between species, allowing the transfer of gene-reaction associations from curated networks. 相似文献15.
Background
Increasingly, metabolite and reaction information is organized in the form of genome-scale metabolic reconstructions that describe the reaction stoichiometry, directionality, and gene to protein to reaction associations. A key bottleneck in the pace of reconstruction of new, high-quality metabolic models is the inability to directly make use of metabolite/reaction information from biological databases or other models due to incompatibilities in content representation (i.e., metabolites with multiple names across databases and models), stoichiometric errors such as elemental or charge imbalances, and incomplete atomistic detail (e.g., use of generic R-group or non-explicit specification of stereo-specificity). 相似文献16.
Background
The cytoplasmic ribosomal small subunit (SSU, 18S) ribosomal RNA (rRNA) is the most frequently-used gene for molecular phylogenetic studies. However, information regarding its secondary structure is neglected in most phylogenetic analyses. Incorporation of this information is essential in order to apply specific rRNA evolutionary models to overcome the problem of co-evolution of paired sites, which violates the basic assumption of the independent evolution of sites made by most phylogenetic methods. Information about secondary structure also supports the process of aligning rRNA sequences across taxa. Both aspects have been shown to increase the accuracy of phylogenetic reconstructions within various taxa. 相似文献17.
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18.
New insights into the tonoplast architecture of plant vacuoles and vacuolar dynamics during osmotic stress 总被引:1,自引:0,他引:1
Background
The vegetative plant vacuole occupies >90% of the volume in mature plant cells. Vacuoles play fundamental roles in adjusting cellular homeostasis and allowing cell growth. The composition of the vacuole and the regulation of its volume depend on the coordinated activities of the transporters and channels localized in the membrane (named tonoplast) surrounding the vacuole. While the tonoplast protein complexes are well studied, the tonoplast itself is less well described. To extend our knowledge of how the vacuole folds inside the plant cell, we present three-dimensional reconstructions of vacuoles from tobacco suspension cells expressing the tonoplast aquaporin fusion gene BobTIP26-1::gfp. 相似文献19.
Chih-Hung Lin Chung-Jan Kang Chung-Kan Tsao Christopher Glenn Wallace Li-Yu Lee Chien-Yu Lin Hung-Ming Wang Shu-Hang Ng Tzu-Chen Yen Chun-Ta Liao 《PloS one》2014,9(4)
Background
The fibula osteoseptocutaneous free flap is generally used for segmental mandibular reconstructions following resection of oral cavity squamous cell carcinoma (OSCC). However, less complex reconstructions may be feasible for patients with predicted poor survival. Herein, we sought to identify the main risk factors (RFs) associated with poor prognosis in OSCC patients undergoing segmental mandibulectomy to help decide between fibular and non-fibular reconstructions.Methods
Between 1996 and 2011, we examined the 5-year control, distant metastases, and survival rates in 310 consecutive, previously untreated patients with primary OSCC who underwent segmental mandibulectomy.Results
Margin status was the only independent RF for 5-year local control. Level IV/V metastases, extracapsular spread, and tumor depth ≥15 mm were independent RFs for poor 5-year survival. In the entire study cohort, 23% of the patients had 2 or 3 adverse RFs; such a high-risk group was characterized by a poor prognosis and may be suitable for non-fibular reconstructions. Overall, 70% of the study patients were cT1-4N0, cT1N2, cT2N1, or had tumor depth <15 mm; less than 5% of patients in this subgroup had 2 or 3 adverse RFs and were thus candidates for fibular reconstructions. Among the remaining 30% of patients who showed both advanced clinical stage (cT2N2, cT3-4N1-2) and tumor depth ≥15 mm, 70% exhibited 2 or 3 adverse RFs.Conclusions
Level IV/V metastases, extracapsular spread, and tumor depth ≥15 mm were independent predictors of poor prognosis in OSCC patients undergoing segmental mandibulectomy. The preoperative or intraoperative identification of adverse RFs may help decide between fibular and non-fibular mandibular reconstruction. High-risk patients bearing 2 or 3 adverse RFs have poor prognosis and should not be considered as candidates for fibular reconstructions. 相似文献20.
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