Comparison of Algorithms for Prediction of Protein Structural Features from Evolutionary Data

Proteins have many functions and predicting these is still one of the major challenges in theoretical biophysics and bioinformatics. Foremost amongst these functions is the need to fold correctly thereby allowing the other genetically dictated tasks that the protein has to carry out to proceed efficiently. In this work, some earlier algorithms for predicting protein domain folds are revisited and they are compared with more recently developed methods. In dealing with intractable problems such as fold prediction, when different algorithms show convergence onto the same result there is every reason to take all algorithms into account such that a consensus result can be arrived at. In this work it is shown that the application of different algorithms in protein structure prediction leads to results that do not converge as such but rather they collude in a striking and useful way that has never been considered before.     

演化计算的应用研究

介绍了演化计算的基本思想、特点及主要分支。在统一的枢架下给出了演化算法的设计方法和基本结构,并给出了演化计算在旅行商问题中的应用。最后讨论了演化计算的发展前景。     

Evolutionary Engineering Improves Tolerance for Replacement Jet Fuels in Saccharomyces cerevisiae

Monoterpenes are liquid hydrocarbons with applications ranging from flavor and fragrance to replacement jet fuel. Their toxicity, however, presents a major challenge for microbial synthesis. Here we evolved limonene-tolerant Saccharomyces cerevisiae strains and sequenced six strains across the 200-generation evolutionary time course. Mutations were found in the tricalbin proteins Tcb2p and Tcb3p. Genomic reconstruction in the parent strain showed that truncation of a single protein (tTcb3p^1-989), but not its complete deletion, was sufficient to recover the evolved phenotype improving limonene fitness 9-fold. tTcb3p^1-989 increased tolerance toward two other monoterpenes (β-pinene and myrcene) 11- and 8-fold, respectively, and tolerance toward the biojet fuel blend AMJ-700t (10% cymene, 50% limonene, 40% farnesene) 4-fold. tTcb3p^1-989 is the first example of successful engineering of phase tolerance and creates opportunities for production of the highly toxic C₁₀ alkenes in yeast.     

Evolutionary Engineering of Saccharomyces cerevisiae for Anaerobic Growth on Xylose

Xylose utilization is of commercial interest for efficient conversion of abundant plant material to ethanol. Perhaps the most important ethanol-producing organism, Saccharomyces cerevisiae, however, is incapable of xylose utilization. While S. cerevisiae strains have been metabolically engineered to utilize xylose, none of the recombinant strains or any other naturally occurring yeast has been able to grow anaerobically on xylose. Starting with the recombinant S. cerevisiae strain TMB3001 that overexpresses the xylose utilization pathway from Pichia stipitis, in this study we developed a selection procedure for the evolution of strains that are capable of anaerobic growth on xylose alone. Selection was successful only when organisms were first selected for efficient aerobic growth on xylose alone and then slowly adapted to microaerobic conditions and finally anaerobic conditions, which indicated that multiple mutations were necessary. After a total of 460 generations or 266 days of selection, the culture reproduced stably under anaerobic conditions on xylose and consisted primarily of two subpopulations with distinct phenotypes. Clones in the larger subpopulation grew anaerobically on xylose and utilized both xylose and glucose simultaneously in batch culture, but they exhibited impaired growth on glucose. Surprisingly, clones in the smaller subpopulation were incapable of anaerobic growth on xylose. However, as a consequence of their improved xylose catabolism, these clones produced up to 19% more ethanol than the parental TMB3001 strain produced under process-like conditions from a mixture of glucose and xylose.     

全局转录调控及其在代谢工程中的应用

全局转录调控是一种全新的改进细胞表型的定向进化方法,通过error-prone PCR、DNA shuffling等技术对细胞中的σ因子和其他转录元件进行多轮突变修饰,改变RNA聚合酶的转录效率和对启动子的亲和能力,使细胞的转录在整体水平上发生改变,导致许多由多种基因控制的细胞表型得以改进。全局转录调控可以对代谢途径快速优化,在代谢工程中已被成功地应用于各种代谢产物的生物合成中。随着全局转录调控理论的不断完善,其应用前景也将越来越广阔。     

激光在医学中的应用

本文叙述了几种激光器的优点及其在医学中的应用。它们在治疗过程中的应用方法有很多种,并且还存在有更多种类的激光器,这里选择叙述的是医生和专家常应用的。随着科技的发展,激光技术在医学中的应用将会越来越成熟,旧的激光器也将会被淘汰,越来越先进的激光器一定会问世。本文还将叙述激光的基本理论,以及不同手术中所采用的激光应用技术。     

Prospects for the Application of Methods of Evolutionary Biology in Oncology

Journal of Evolutionary Biochemistry and Physiology - Oncological diseases is the second leading cause of death among noninfectious diseases in Russia and worldwide. Evolutionary medicine is a...     

Ground State Robustness as an Evolutionary Design Principle in Signaling Networks

The ability of an organism to survive depends on its capability to adapt to external conditions. In addition to metabolic versatility and efficient replication, reliable signal transduction is essential. As signaling systems are under permanent evolutionary pressure one may assume that their structure reflects certain functional properties. However, despite promising theoretical studies in recent years, the selective forces which shape signaling network topologies in general remain unclear. Here, we propose prevention of autoactivation as one possible evolutionary design principle. A generic framework for continuous kinetic models is used to derive topological implications of demanding a dynamically stable ground state in signaling systems. To this end graph theoretical methods are applied. The index of the underlying digraph is shown to be a key topological property which determines the so-called kinetic ground state (or off-state) robustness. The kinetic robustness depends solely on the composition of the subdigraph with the strongly connected components, which comprise all positive feedbacks in the network. The component with the highest index in the feedback family is shown to dominate the kinetic robustness of the whole network, whereas relative size and girth of these motifs are emphasized as important determinants of the component index. Moreover, depending on topological features, the maintenance of robustness differs when networks are faced with structural perturbations. This structural off-state robustness, defined as the average kinetic robustness of a network''s neighborhood, turns out to be useful since some structural features are neutral towards kinetic robustness, but show up to be supporting against structural perturbations. Among these are a low connectivity, a high divergence and a low path sum. All results are tested against real signaling networks obtained from databases. The analysis suggests that ground state robustness may serve as a rationale for some structural peculiarities found in intracellular signaling networks.     

基因枪法在水稻工程育种中的应用

至今,基因枪法以其实用性和有效性应用于水稻工程育种已有十几年,本文阐述了其在水稻工程育种的六个主要领域的应用现状,同时评价了外源基因在转基因水稻中的稳定性和对转基因水稻主要农艺性状的影响。当然,基因枪法的转化效率还有待提高,随着转不同基因的工程水稻的日益增多,进一步的安全性试验显得十分必要,它是转基因水稻商品化的前提。     

胁迫诱导型启动子在植物抗逆基因工程中的应用

在抗逆基因工程中,大多采用的是组成型表达启动子,组成型表达启动子驱动外源抗逆基因表达虽然可以提高转基因植物的抗逆性,但会导致转基因植株生长迟缓或不育;而胁迫诱导型启动子则可提高转基因植物的抗逆性,不影响其正常生长发育,所以,胁迫诱导型启动子已逐渐用于植物抗逆基因工程。本文介绍不同胁迫诱导型启动子在植物抗逆基因工程中的应用。     

The Evolutionary Design of Error-Rates, and the Fast Fixation Enigma

Genetic and non-genetic error-rates are analyzed in parallel for a lower and a higher organism (E. coli and man, respectively). From the comparison of mutation with fixation rates, contrasting proposals are made, concerning the arrangement of error-rates in the two organisms. In E. coli, reproduction is very conservative, but genetic variability is high within populations. Most mutations are discarded by selection, yet single mutational variants of a gene have, on average, little impact on fitness. In man, the mutation rate per generation is high, the variability generated in the population is comparatively low, and most mutations are fixed by drift rather than selection. The variants of a gene are in general more deleterious than in E. coli. There is a discrepancy in the published mutation rates: the rate of mutation fixations in human populations is twice or four times higher than the individual rate of mutation production, a feature which is not consistent with current population genetics models. Two, not mutually exclusive, hypotheses may explain this fast fixation enigma: (i) Mutation rates have substantially decreased in recent human evolution and (ii) A substantial fraction of the fixed mutations were generated in a process – such as gene conversion – that violates the principle of independence of mutation events.     

Bone Histology Reveals a High Environmental and Metabolic Plasticity as a Successful Evolutionary Strategy in a Long-Lived Homeostatic Triassic Temnospondyl

Evolutionary stasis (long-term stability of morphology in an evolving lineage) is a pattern for which explanations are usually elusive. The Triassic tetrapod Gerrothorax pulcherrimus, a gill-bearing temnospondyl, survived for 35 million years in the Germanic Basin of Central Europe persisting throughout the dinosaur-dominated Late Triassic period. This evolutionary stasis coincides with the occurrence of this species in a wide range of habitats and environmental conditions. By the combination of palaeoecological and palaeohistological analyses, we found great ecological flexibility in G. pulcherrimus and present substantial evidence of developmental and metabolic plasticity despite the morphological stasis. We conclude that G. pulcherrimus could show the capacity to settle in water bodies too harsh or unpredictable for most other tetrapods. This would have been made possible by a unique life history strategy that involved a wide reaction norm, permitting adjustment to fluctuating conditions such as salinity and level of nutrients. Growth rate, duration of juvenile period, age at maturity, and life span were all subject to broad variation within specimens of G. pulcherrimus in one single lake and in between different lakes. In addition to providing a better understanding of fossil ecosystems, this study shows the potential of such a methodology to encourage palaeobiologists and evolutionary biologists to consider the mechanisms of variation in extant and fossil organisms by using a similar time-scope reference.     

在植物考据研究中应用进化思想的探讨

探讨了在植物考据研究中如何应用进化思想。我们认为在确定中国古籍文献中记载植物的学名时,对部分植物宜采用集合种（或复合种）的概念。     

Successful Application of Video-Projected Human Images for Signalling to Dogs

Dogs were tested (1) in a two‐way choice experiment, where the experimenter indicated a baited bowl by pointing; and (2) in a task where the owner was asked to command the dog to execute simple obedience tasks. In expt 1 dogs (n = 10) were tested at first in the presence of the experimenter (three dimensional condition, 3D), that was followed by a series of pointing trials when the life‐sized image of the experimenter was projected onto the wall by the means of a video‐projector (two dimensional condition, 2D). Dogs performed correctly more often than expected by chance in both 3D and 2D conditions. In expt 2 the commanding owner was either present in the room (3D), or her/his image was projected on the screen (2D), or only her/his voice was audible for the dog through a speaker (0D). The performance of the dogs (n = 10) decreased to great extent comparing the 3D and 0D condition, as the number of different actions the dogs obeyed was significantly less in the 0D condition. However, there was no difference in the number of different actions obeyed in the 3D and 2D conditions. Our results show that dogs readily obey life‐sized, interactive moving image in various communicative situtations. We suppose that the difference between 2D and 3D conditions can be attributed partially to the lack of some additional communicative signals as sounds (verbal cues) and odours (from the human), and to some changes in the context.     

联合细胞培养在组织工程血管化中的应用

自从1987年正式提出组织工程这一概念来以来,培养具有生物学活性组织器官替代物始终是组织工程学的发展方向。目前,虽然一些工程化组织如皮肤、软骨等已被成功构建,并应用于临床,但其他工程化组织如心脏、骨骼肌、肝脏等体积大、功能复杂,移植后难以及时建立血液供应。而及时建立的血管网络对组织器官的存活与功能实现至关重要。为此,国内外一些实验室采用联合细胞培养的方法,观察不同细胞间的相互作用对血管形成的影响。结果表明,联合细胞培养在血管的形成、稳定和成熟方面起着重要作用。     

基因工程在食品工业中的应用

阐述了基因工程的技术溯源,论述了基因工程在食品工业方面的应用,提出与生产实践相结合的实例;详细介绍了基因工程食品的由来,展望了基因工程技术在食品工业领域中的美好发展前景.     

植物糖基转移酶及其在代谢工程中的应用

糖基转移酶催化植物次生代谢物合成,在植物的生长发育过程以及代谢工程应用方面起着重要作用。该文介绍糖基转移酶的基本特性,总结近年来研究植物糖基转移酶基因的克隆与功能分析的方法,详细阐述了微生物中3个C-糖基转移酶基因（UrdGT2、gilGT和iroA）的克隆和功能研究,概括糖基转移酶在代谢工程的研究进展,并展望今后的研究趋势,为植物C-糖基转移酶的生物学功能研究和代谢应用方面提供有益帮助。     

共转化法及其在植物基因工程中的应用

共转化法是实现多基因在同一受体植株中转化的非常有效的方法.它在植物多基因代谢途径和获得去选择标记转基因植株研究中具有巨大的应用前景,现今已经形成以基因枪和农杆菌介导两大方法为主体的共转化系统.全面介绍了这两种方法在共转化研究中的应用进展,同时分析了转化过程中存在的问题和影响转化效率的因素.