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The topological viewpoint on spaces of phenotypes presented in Stadler et al. (J Theor Biol 213:241–274, 2001) is revisited,
and a quantified version is proposed. While necessary probabilistic information can be encoded in a topological- like fashion,
it turns out that it is not reflected adequately by the concept of continuity. We propose alternative models, but the behavior
of maps make these models non-topological in fundamental ways. 相似文献
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Turner''s infantile phenotype is a term used to describe infants with stigmata suggestive of Turner''s syndrome. These include brawny oedema of the feet, loose neck folds, and a characteristic facies. Ten cases are described in this report. Four of these had a similar facial appearance and three had serous effusions. Two of the latter died and at necropsy no cardiac, vascular, or renal cause for the effusions was found, but the gonads in each were macroscopically reduced in size and microscopically were grossly abnormal. 相似文献
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小鼠发育代谢表型库(Mouse Developmental and Metabolic Phenotype Repository,MDMPR)是一个致力于小鼠资源和表型数据实时共享的开放性平台,它依托于科技部重点研发计划“发育编程及其代谢调节”专项项目“建立小鼠发育代谢表型库”。该项目预计在5年内完成500个发育代谢相关小鼠敲除模型的建立,并对其表型数据进行标准化的解析、建立表型数据库。MDMPR作为一个资源及数据集成的库,由多个子系统作为支撑,包括ES细胞数据库、项目管理系统、繁育管理系统、精子库管理系统、表型分析系统,信息化管理深入到项目中每个环节,从基因突变ES细胞制备、基因突变小鼠制备、小鼠繁育,精子冻存到最终的表型分析、数据处理及展示,保证了MDMPR产生数据的真实性及实时性。MDMPR除了不断地推进项目进行,增加自身产生的数据外,也在积极的整合其他的资源及数据,如人特异性基因敲除ES细胞库、蛋白相互作用数据库(STRING)、核心转录调节环路(dbCoRc)和Enhancer-Indel数据库,今后还将进一步整合,帮助发育代谢及其他领域的研究人员能够一站式的获取所需资源和数据、加快研究进程,最终服务于全人类的医疗事业。 相似文献
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Background
Metagenomics can reveal the vast majority of microbes that have been missed by traditional cultivation-based methods. Due to its extremely wide range of application areas, fast metagenome sequencing simulation systems with high fidelity are in great demand to facilitate the development and comparison of metagenomics analysis tools.Results
We present here a customizable metagenome simulation system: NeSSM (Next-generation Sequencing Simulator for Metagenomics). Combining complete genomes currently available, a community composition table, and sequencing parameters, it can simulate metagenome sequencing better than existing systems. Sequencing error models based on the explicit distribution of errors at each base and sequencing coverage bias are incorporated in the simulation. In order to improve the fidelity of simulation, tools are provided by NeSSM to estimate the sequencing error models, sequencing coverage bias and the community composition directly from existing metagenome sequencing data. Currently, NeSSM supports single-end and pair-end sequencing for both 454 and Illumina platforms. In addition, a GPU (graphics processing units) version of NeSSM is also developed to accelerate the simulation. By comparing the simulated sequencing data from NeSSM with experimental metagenome sequencing data, we have demonstrated that NeSSM performs better in many aspects than existing popular metagenome simulators, such as MetaSim, GemSIM and Grinder. The GPU version of NeSSM is more than one-order of magnitude faster than MetaSim.Conclusions
NeSSM is a fast simulation system for high-throughput metagenome sequencing. It can be helpful to develop tools and evaluate strategies for metagenomics analysis and it’s freely available for academic users at http://cbb.sjtu.edu.cn/~ccwei/pub/software/NeSSM.php. 相似文献7.
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Mabee PM Ashburner M Cronk Q Gkoutos GV Haendel M Segerdell E Mungall C Westerfield M 《Trends in ecology & evolution》2007,22(7):345-350
Understanding the developmental and genetic underpinnings of particular evolutionary changes has been hindered by inadequate databases of evolutionary anatomy and by the lack of a computational approach to identify underlying candidate genes and regulators. By contrast, model organism studies have been enhanced by ontologies shared among genomic databases. Here, we suggest that evolutionary and genomics databases can be developed to exchange and use information through shared phenotype and anatomy ontologies. This would facilitate computing on evolutionary questions pertaining to the genetic basis of evolutionary change, the genetic and developmental bases of correlated characters and independent evolution, biomedical parallels to evolutionary change, and the ecological and paleontological correlates of particular types of change in genes, gene networks and developmental pathways. 相似文献
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A. Aguilera 《Genetics》1994,136(1):87-91
Yeast mutants unable to grow in the presence of 3% formamide have been isolated in parallel with mutants sensitive to either 37° or 6% ethanol. The number of formamide-sensitive mutations that affect different genes that can be identified from yeast cells is at least as large as the number of thermosensitive or ethanol-sensitive mutations. These mutations are of two types: those that are sensitive to formamide, temperature and/or ethanol simultaneously; and those that are specific for formamide sensitivity and show no temperature or ethanol sensitivity phenotype. Those genes susceptible to giving rise to formamide-sensitive alleles include the structural gene for DNA ligase, CDC9, and the structural gene for arginine permease, CAN1. The results indicate that formamide sensitivity can be used as a novel conditional phenotype for mutations on both essential and nonessential genes. This work also confirms that ethanol-sensitivity can be used as a conditional phenotype to identify mutations in at least as many genes as those susceptible to temperature or formamide sensitive mutations. 相似文献
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We study the phenotype allocation problem for the stochastic evolution of a multitype population in a random environment. Our underlying model is a multitype Galton–Watson branching process in a random environment. In the multitype branching model, different types denote different phenotypes of offspring, and offspring distributions denote the allocation strategies. Two possible optimization targets are considered: the long-term growth rate of the population conditioned on nonextinction, and the extinction probability of the lineage. In a simple and biologically motivated case, we derive an explicit formula for the long-term growth rate using the random Perron–Frobenius theorem, and we give an approximation to the extinction probability by a method similar to that developed by Wilkinson. Then we obtain the optimal strategies that maximize the long-term growth rate or minimize the approximate extinction probability, respectively, in a numerical example. It turns out that different optimality criteria can lead to different strategies. 相似文献
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Inheritance of Pattern: Analysis from Phenotype to Gene 总被引:1,自引:0,他引:1
The form and pattern of multicellular organisms are developmentalphenotypes. They are long term processes rather than staticstructures. They involve myriad events at multiple locations.The efficient encoding of such phenotypes is analyzed here intwo stages. First, the complex developmental behavior is brokendown so it can be accounted for by cell or tissue rules. Themost effective rules have the instantaneous character foundin time-based differential equations. When integrated over timeand space, the rules produce the behavior. Second, the cytologicaland nuclear basis of the rules is sought. One thus studies acomplex phenotype in terms of its successive antecedent causes,refining understanding as one gets closer to the genome. The approach is applied here to phyllotactic (leaf placement)patterns. Leaves may be alternating in a plane, whorled, orin a helical arrangement. In all three cases a new leaf formsas an arc-like bulge at a site apical to a small number of neighboringleaves. The leaf-forming sites are irregularities in the patternof cellulose reinforcement in the surface of the apical dome.Two organ-level rules combine to produce new leaf sites. First,each established leaf develops a single reinforcement field,with gently curved reinforcement lines, on the region of thedome just above the leaf. Second, where parts of two or threesuch fields abut on the dome they combine to make the irregularityfor the next leaf. Hence a given reinforcement pattern on thedome produces a leaf; the action of the leaves in turn reestablishesthe reinforcement pattern. The cellular basis of generatinga reinforcement field appears to be a cytoskeletal responseto excessive stretch, brought on by rapid growth of adjacentleaf bases. The large scale patterns are thus traceable to cytoskeletalphenomena and from there to genes involving microtubular behavior. 相似文献
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《Cell cycle (Georgetown, Tex.)》2013,12(3):195-197
Recently, we have shown that small cell lung cancer (SCLC) is dependent on activation of the Hedgehog signaling, an embryonic pathway implicated in development, morphogenesis and the regulation of stem cell fates. These findings form the framework for an emerging view of cancer as a process of aberrant organogenesis in which progenitor/ stem cells escape dependence on niche signaling through mutation in genes such as Ptch, or through persistent activation of progenitor cell pathways. Interestingly, the normally quiescent airway epithelial compartment uses the Hh pathway to repopulate itself when challenged by injury. How Hh signaling works to promote the malignant phenotype promises to be as important biologically as the promise of Hh pathway inhibitors are clinically.Key wordsCancer, Hedgehog signaling, Morphogenesis, Stem cells 相似文献
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已知一种药物可用于治疗某疾病,则该药物可能对与该疾病具有相似表型的其他疾病有疗效。因此,大规模地计算疾病表型相似性可辅助发现的疾病新的治疗方法。我们从OMIM下载了3742种疾病的表型信息,从Mesh词库下载13721个关联解剖学和疾病症状的注释词。我们将以上的Mesh词逐一在3742种疾病的表型信息文本中搜索,得到每种疾病涉及的Mesh词汇列表,进而基于语义分析的方法系统地计算了疾病表型的两两相似性矩阵。我们发现疾病关联生物通路最多的有肿瘤生物通路,胰岛素信号通路,肥大心肌病通路和细胞粘附通路等。随疾病对表型相似度的增加,其更涉及相同KEGG生物通路的概率亦增加,证明了本文方法的可靠性。疾病表型相似性可作为疾病在基因水平相似性的补充,有望为药物发现研究提供一条新途径。 相似文献
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The key pathogenic event in prion disease involves misfolding and aggregation of the cellular prion protein (PrP). Beyond this fundamental observation, the mechanism by which PrP misfolding in neurons leads to injury and death remains enigmatic. Prion toxicity may come about by perverting the normal function of PrP. If so, understanding the normal function of PrP may help to elucidate the molecular mechansim of prion disease. Ablation of the Prnp gene, which encodes PrP, was instrumental for determining that the continuous production of PrP is essential for replicating prion infectivity. Since the structure of PrP has not provided any hints to its possible function, and there is no obvious phenotype in PrP KO mice, studies of PrP function have often relied on intuition and serendipity. Here, we enumerate the multitude of phenotypes described in PrP deficient mice, many of which manifest themselves only upon physiological challenge. We discuss the pleiotropic phenotypes of PrP deficient mice in relation to the possible normal function of PrP. The critical question remains open: which of these phenotypes are primary effects of PrP deletion and what do they tell us about the function of PrP?Key Words: transmissible spongiform encephalopathy, amyloid, PrP 相似文献