单点交叉多子代遗传算法

在现有文献研究的基础上,对传统遗传算法作了进一步研究,依据生物进化理论,提出了一种单点交叉多子代遗传算法,并给出了多子代的产生方法.单点交叉多子代遗传算法所产生的子代个体数量与传统遗传算法相比明显增多,这样不但可增大产生更优秀个体的可能性,而且使得种群竞争更激烈,故可使传统遗传算法的性能得到更好的改善.4个测试函数的测试结果表明,本文给出的单点交叉多子代遗传算法比传统遗传算法的运算速度明显提高,迭代次数明显减少,从而验证了本文提出的单点交叉多子代遗传算法的有效性。     

实数遗传算法的改进研究

在现有文献研究的基础上,对实数遗传算法又作了进一步研究,提出了一种改进算法．该算法不仅可快速产生初始种群,而且实现了子代种群的产生在优化方向上进行,提高了算法的搜索能力,克服了子代个体位置限制的不足,有利于保持种群的多样性,提高了避免未成熟收敛于局部最优解的能力．     

基于混合遗传算法的偶极子源定位的仿真计算

首先提出一种新的混合遗传算法。在基于实数编码的基础上,通过嵌入一个最速下降算子,结合遗传算法和最速下降法两者的优点,并引入模拟退火的思想,即可改善原算法的局部搜索能力,又能进一步提高优化效率。为了验证算法的可行性,通过对脑电偶极子源定位的仿真计算,证明所提出的新算法与其它优化算法相比,在达到最优解的效率上有了明显的提高。     

基于混合适传算法的偶极子源定位的仿真计算’

首先提出一种新的混合遗传算法。在基于实数编码的基础上,通过嵌入一个最速下降算子,结合遗传算法和最速下降法两者的优点,并引入模拟退火的思想,即可改善原算法的局部搜索能力,又能进一步提高优化效率。为了验证算法的可行性,通过对脑电偶极子源定位的仿真计算,证明所提出的新算法与其它优化算法相比,在达到最优解的效率上有了明显的提高。     

遗传算法的一种改进进化策略

在现有文献研究的基础上,对传统遗传算法的进化策略又作了进一步研究,提出了一种改进的进化策略.该进化策略保留了交叉产生个体中的精英个体,克服了传统遗传算法中交叉得到的优秀个体有可能在变异过程中遭到破坏而不能生存的不足;另外,在交叉中,交叉概率取1,使父代种群中所有个体均参与交叉操作,由于交叉产生的个体数增多,增大产生更优秀个体的可能性,因而可使遗传算法的性能得到更好的改善.通过4个测试函数的测试计算,结果表明,本文给出的改进进化策略比传统遗传算法进化策略的运算速度明显提高,迭代次数明显减少,从而验证了本文提出的改进进化策略的有效性.     

遗传算法在转录因子结合位点识别中的应用

遗传算法是模拟生物进化过程的计算模型,是一种全局优化搜索算法。将遗传算法与转录因子结合位点识别问题相结合的新方法,以一致性序列模型作为保守motif的描述模型,通过对motif序列与待测序列的比对问题进行编码,将其转化成搜索空间中的优化问题,利用遗传算法来搜索最优解,预测转录因子的结合位点。实验结果表明,这种新的方法是有效的,它在占用少量内存的情况下能够准确地识别出待测转录因子结合位点。     

基于投影寻踪的城市生态系统健康评价

掌握城市生态系统的健康水平,对城市实施可持续发展具有重要意义.采用一种新型的多指标数据处理方法-投影寻踪模型,选取典型指标,利用基于实数编码遗传算法优化求取最佳投影方向,对广州市2000年、2005年的城市生态系统健康状况进行评价.评价结果表明:2000年,广州市对应的等级值为2.95,处于亚健康状态,符合其客观状况,该结果与采用模糊综合评价法所得结论一致;2005年,广州市对应的等级值为3.48,仍处于亚健康状态,但其等级值大于2000年的数值,等级值在增大,表明经过5a的建设,广州市的生态系统健康状况在不断好转.此外,与模糊综合评价法相比,该模型能精确地刻画出生态系统的具体健康水平,具有较高的评价精度和区分度.     

DNA计算机的研究和展望

DNA计算机是计算机科学和分子生物学互相结合、互相渗透而产生的新兴交叉研究领域.目前已取得较大进展.DNA计算机是以编码的DNA序列为运算对象,通过分子生物学的运算操作以解决复杂的数学难题.DNA计算机的重要特点是信息容量的巨量性和密集性,和处理操作的高度并行性,通过强力搜索策略迅速得出正确的答案,从而使其运算速度大大超过常规计算机的计算速度.介绍了DNA计算机的近期进展和工作原理及其分子生物学的运算操作过程.并对DNA计算机的未来发展前景及在生物信息学中的意义,进行了分析和讨论.     

遗传算法在蛋白质结构预测中的应用

遗传算法(geneticalgorithm,GA)作为一种自适应启发式概率性迭代式全局搜索算法,具有不依赖于问题模型的特性、全局最优性、隐含并行性、高效性、解决不同非线性问题的鲁棒性特点,目前已经广泛应用于自动控制、机器人学、计算机科学、模式识别、模糊人工神经和工程优化等设计领域。本文首先介绍了GA的基本原理,即搜索的基本过程;随后总结了GA与传统算法相比所具有的优点;第三部分则分别综述了GA在蛋白质结构预测中主要使用的模型、设计和执行策略,以及使用GA与其他算法相互结合预测蛋白质结构的研究进展;最后提出了作者对GA研究中存在问题的认识和研究展望。     

基于GES机制遗传算法构建基因调控网络

目的：基因调控网络在药物研发与疾病防治方面有重要的生物学意义。目前基于芯片数据构建网络的方法普遍效率不高,准确度较低,为此提出了一种新的高效调控网络结构预测算法。方法：提出了一种基于贪婪等价搜索机制的遗传算法构建基因调控网络模型。通过引入遗传算法的多点并行性,使得算法易于摆脱局部最优。通过编码网络结构作为遗传算法的染色体和设计基于GES机制的变异算子,使网络的进化过程基于马尔科夫等价空间而不是有向无环图空间。结果：通过对标准网络ASIA和酵母调控网络的预测,与近期Xue-wen Chen等提出的Order K2算法进行了比较,在网络构建准确率上获得了更佳的结果。与标准遗传算法比较下在执行效率上大大提高。结论：提出的算法在网络结构预测准确率上相对于最近提出的Order K2算法在准确率上效果更佳,并且相较标准遗传算法网络在进化过程上效率更高。     

A Genetic Algorithm Approach to the Scheduling of FMSs with Multiple Routes

Usually, most of the typical job shop scheduling approaches deal with the processing sequence of parts in a fixed routing condition. In this paper, we suggest a genetic algorithm (GA) to solve the job-sequencing problem for a production shop that is characterized by flexible routing and flexible machines. This means that all parts, of all part types, can be processed through alternative routings. Also, there can be several machines for each machine type. To solve these general scheduling problems, a genetic algorithm approach is proposed and the concepts of virtual and real operations are introduced. Chromosome coding and genetic operators of GAs are defined during the problem solving. A minimum weighted tardiness objective function is used to define code fitness, which is used for selecting species and producing a new generation of codes. Finally, several experimental results are given.     

Feedback regulation of GA5 expression and metabolic engineering of gibberellin levels in Arabidopsis.

The gibberellin (GA) 20-oxidase encoded by the GA5 gene of Arabidopsis directs GA biosynthesis to active GAs, whereas that encoded by the P16 gene of pumpkin endosperm leads to biosynthesis of inactive GAs. Negative feedback regulation of GA5 expression was demonstrated in stems of Arabidopsis by bioactive GAs but not by inactive GA. In transgenic Arabidopsis plants overexpressing P16, there was a severe reduction in the amounts of C20-GA intermediates, accumulation of large amounts of inactive GA25 and GA17, a reduction in GA4 content, and a small increase in GA1. However, due to feedback regulation, expression of GA5 and GA4, the gene coding for the subsequent 3beta-hydroxylase, was greatly increased to compensate for the effects of the P16 transgene. Consequently, stem height was only slightly reduced in the transgenic plants.     

Skeletal structure and progression of growth anomalies in Porites australiensis in Okinawa, Japan

Growth anomalies (GAs), one of the diseases recently reported for scleractinian corals, are characterized by an abnormal skeletal structure and reduced zooxanthella density. The pathological characteristics of GAs were studied in colonies of Porites australiensis on a reef in Kayo, Okinawa, Japan. Corallites in the GA region lost the skeletal architecture characteristic of P. australiensis, and polyp density had decreased in the GAs due to enlargement of both calices and the coenosteum. The gross productivity of isolated GA samples was lower than in healthy samples and decreased to almost 0 within 11 d after isolation. However, when GA samples were brought into contact with healthy-looking samples from the same colony, they fused and both the GA and healthy regions grew. Healthy samples fused with GA samples grew more slowly than those fused with healthy samples. For in situ GAs surrounded by healthy tissue, tissue death usually started at the center of the GA, probably due to a deficiency in the translocated energy supply from the surrounding tissue. The total area of the GA region and the dead area increased at a rate of 5.3 ± 2.9 cm2 yr-1. These results suggest that GA regions are maintained by energy supplies from surrounding healthy tissues and that GAs may have a negative impact on host corals.     

Role of gibberellins during arbuscular mycorrhizal formation in tomato: new insights revealed by endogenous quantification and genetic analysis of their metabolism in mycorrhizal roots

Gibberellins (GAs) are key regulators of plant growth and development and recent studies suggest also a role during arbuscular mycorrhizal (AM) formation. Here, complementary approaches have been used to obtain a clearer picture that correlates AM fungal development inside roots with GA metabolism. An extensive analysis of genes associated with GA metabolism as well as a quantification of GA content in roots was made. Application of GA₃ and its biosynthesis inhibitor prohexadione calcium (PrCa) combined with a GA‐constitutive response mutant (procera) were used to determine whether fungal colonization is altered by the level of these hormones or by changes in the GA‐signaling pathway. The increased levels of specific GAs from the 13‐hydroxylation pathway in mycorrhizal roots correlate closely with the increased expression of genes coding enzymes from the GA biosynthetic trail. The imbalance of GAs in tomato roots caused by exogenous applications of GA₃ or PrCa affects arbuscules in both negative and positive ways, respectively. In addition, procera plants were adversely affected by the mycorrhization process. Our findings demonstrate that an imbalance in favor of an increased amount of GAs negatively affects the frequency of mycorrhization and particularly the arbuscular abundance in tomato mycorrhizal roots and the results point out that AM formation is associated with a change in the 13‐hydroxylation pathway of GAs.     

Correlation of Endogenous Gibberellic Acid with Initiation of Mango Shoot Growth

Stems of mango (Mangifera indica L.) rest in a nongrowing, dormant state for much of the year. Ephemeral flushes of vegetative or reproductive shoot growth are periodically evoked in apical or lateral buds of these resting stems. The initiation of shoot growth is postulated to be primarily regulated by a critical ratio of root-produced cytokinins, which accumulate in buds and by leaf-produced auxin, which decreases in synthesis and transport over time. Exogenously applied gibberellic acid (GA3) delays initiation of bud break but does not determine whether the resulting flush of growth is vegetative or reproductive. We tested the hypothesis that endogenous GA3, which influences release of these resting buds, may decrease in stem tips or leaves with increasing age of mango stems. GA3 and several other GAs in stem tip buds and leaves were identified and quantified in stems of different ages. The major endogenous GAs found in apical buds and leaves of vegetative mango stems were early 13-hydroxylation pathway gibberellins: GA1, epi-GA1, GA3, GA19, GA20, and GA29, as identified by gas chromatography-mass spectrometry (GC-MS). A novel but unidentified GA-like compound was also present. The most abundant GAs in apical stem buds were GA3 and GA19. Contrary to the hypothesis, the concentration of GA3 increased within buds with increasing age of the stems. The concentrations of other GAs in buds were variable. The concentration of GA3 did not change significantly with age in leaves, whereas that of most of the other GAs declined. GA1 levels were greatest in leaves of elongating shoots. These results are consistent with the concept that rapid shoot growth is associated with synthesis of GAs leading to GA1. The role of GA3 in delaying bud break in mango is not known, but it is proposed that it may enhance or maintain the synthesis or activity of endogenous auxin. It, thereby, maintains a high auxin/cytokinin ratio similar to responses to GA3 that maintain apical dominance in other plant species.     

Correlation of Endogenous Gibberellic Acid with Initiation of Mango Shoot Growth

Stems of mango (Mangifera indica L.) rest in a nongrowing, dormant state for much of the year. Ephemeral flushes of vegetative or reproductive shoot growth are periodically evoked in apical or lateral buds of these resting stems. The initiation of shoot growth is postulated to be primarily regulated by a critical ratio of root-produced cytokinins, which accumulate in buds and by leaf-produced auxin, which decreases in synthesis and transport over time. Exogenously applied gibberellic acid (GA3) delays initiation of bud break but does not determine whether the resulting flush of growth is vegetative or reproductive. We tested the hypothesis that endogenous GA3, which influences release of these resting buds, may decrease in stem tips or leaves with increasing age of mango stems. GA3 and several other GAs in stem tip buds and leaves were identified and quantified in stems of different ages. The major endogenous GAs found in apical buds and leaves of vegetative mango stems were early 13-hydroxylation pathway gibberellins: GA1, epi-GA1, GA3, GA19, GA20, and GA29, as identified by gas chromatography-mass spectrometry (GC-MS). A novel but unidentified GA-like compound was also present. The most abundant GAs in apical stem buds were GA3 and GA19. Contrary to the hypothesis, the concentration of GA3 increased within buds with increasing age of the stems. The concentrations of other GAs in buds were variable. The concentration of GA3 did not change significantly with age in leaves, whereas that of most of the other GAs declined. GA1 levels were greatest in leaves of elongating shoots. These results are consistent with the concept that rapid shoot growth is associated with synthesis of GAs leading to GA1. The role of GA3 in delaying bud break in mango is not known, but it is proposed that it may enhance or maintain the synthesis or activity of endogenous auxin. It, thereby, maintains a high auxin/cytokinin ratio similar to responses to GA3 that maintain apical dominance in other plant species.     

Tissue-specific localization of gibberellins and expression of gibberellin-biosynthetic and signaling genes in wood-forming tissues in aspen

Bioactive gibberellins (GAs) are known regulators of shoot growth and development in plants. In an attempt to identify where GAs are formed, we have analyzed the expression patterns of six GA biosynthesis genes and two genes with predicted roles in GA signaling and responses in relation to measured levels of GAs. The analysis was based on tangential sections, giving tissue-specific resolution across the cambial region of aspen trees (Populus tremula). Gibberellin quantification by GC/MS-SRM showed that the bioactive GA1 and GA4 were predominantly located in the zone of expansion of xylem cells. Based on co-localization of the expression of the late GA biosynthesis gene GA 20-oxidase 1 and bioactive GAs, we suggest that de novo GA biosynthesis occurs in the expanding xylem. However, expression levels of the first committed GA biosynthesis enzyme, ent-copalyl diphosphate synthase, were high in the phloem, suggesting that a GA precursor(s) may be transported to the xylem. The expression of the GA signaling and response genes DELLA-like1 and GIP-like1 coincided well with sites of high bioactive GA levels. We therefore suggest that the main role of GA during wood formation is to regulate early stages of xylem differentiation, including cell elongation.     

Distinct cell-specific expression patterns of early and late gibberellin biosynthetic genes during Arabidopsis seed germination

Gibberellins (GAs) are biosynthesized through a complex pathway that involves several classes of enzymes. To predict sites of individual GA biosynthetic steps, we studied cell type-specific expression of genes encoding early and late GA biosynthetic enzymes in germinating Arabidopsis seeds. We showed that expression of two genes, AtGA3ox1 and AtGA3ox2, encoding GA 3-oxidase, which catalyzes the terminal biosynthetic step, was mainly localized in the cortex and endodermis of embryo axes in germinating seeds. Because another GA biosynthetic gene, AtKO1, coding for ent-kaurene oxidase, exhibited a similar cell-specific expression pattern, we predicted that the synthesis of bioactive GAs from ent-kaurene oxidation occurs in the same cell types during seed germination. We also showed that the cortical cells expand during germination, suggesting a spatial correlation between GA production and response. However, promoter activity of the AtCPS1 gene, responsible for the first committed step in GA biosynthesis, was detected exclusively in the embryo provasculature in germinating seeds. When the AtCPS1 cDNA was expressed only in the cortex and endodermis of non-germinating ga1-3 seeds (deficient in AtCPS1) using the AtGA3ox2 promoter, germination was not as resistant to a GA biosynthesis inhibitor as expression in the provasculature. These results suggest that the biosynthesis of GAs during seed germination takes place in two separate locations with the early step occurring in the provasculature and the later steps in the cortex and endodermis. This implies that intercellular transport of an intermediate of the GA biosynthetic pathway is required to produce bioactive GAs.