基于自适应遗传算法的特征基因选择

提出了一种基于自适应遗传算法的特征基因选择方法,首先建立一个基于Bhattacharyya距离的基因差异度模型,根据支持向量机(SVM)分类器的分类准确率选择出一个候选特征基因子集,然后利用自适应遗传算法搜索出一组最优特征基因组合,有效避免了遗传算法早熟收敛的缺陷,提高了全局寻优能力.对结肠癌基因表达谱数据进行仿真实验...     

Prioritizing natural-selection signals from the deep-sequencing genomic data suggests multi-variant adaptation in Tibetan highlanders

Human genetic adaptation to high altitudes (>2500 m) has been extensively studied over the last few years, but few functional adaptive genetic variants have been identified, largely owing to the lack of deep-genome sequencing data available to previous studies. Here, we build a list of putative adaptive variants, including 63 missense, 7 loss-of-function, 1,298 evolutionarily conserved variants and 509 expression quantitative traits loci. Notably, the top signal of selection is located in TMEM247, a transmembrane protein-coding gene. The Tibetan version of TMEM247 harbors one high-frequency (76.3%) missense variant, rs116983452 (c.248C > T; p.Ala83Val), with the T allele derived from archaic ancestry and carried by >94% of Tibetans but absent or in low frequencies (<3%) in non-Tibetan populations. The rs116983452-T is strongly and positively correlated with altitude and significantly associated with reduced hemoglobin concentration (p = 5.78 × 10⁻⁵), red blood cell count (p = 5.72 × 10⁻⁷) and hematocrit (p = 2.57 × 10⁻⁶). In particular, TMEM247-rs116983452 shows greater effect size and better predicts the phenotypic outcome than any EPAS1 variants in association with adaptive traits in Tibetans. Modeling the interaction between TMEM247-rs116983452 and EPAS1 variants indicates weak but statistically significant epistatic effects. Our results support that multiple variants may jointly deliver the fitness of the Tibetans on the plateau, where a complex model is needed to elucidate the adaptive evolution mechanism.     

Genomic diversity and post-admixture adaptation in the Uyghurs

Population admixture results in genome-wide combinations of genetic variants derived from different ancestral populations of distinct ancestry, thus providing a unique opportunity for understanding the genetic determinants of phenotypic variation in humans. Here, we used whole-genome sequencing of 92 individuals with high coverage (30–60×) to systematically investigate genomic diversity in the Uyghurs living in Xinjiang, China (XJU), an admixed population of both European-like and East-Asian-like ancestry. The XJU population shows greater genetic diversity, especially a higher proportion of rare variants, compared with their ancestral source populations, corresponding to greater phenotypic diversity of XJU. Admixture-induced functional variants in EDAR were associated with the diversity of facial morphology in XJU. Interestingly, the interaction of functional variants between SLC24A5 and OCA2 likely influences the diversity of skin pigmentation. Notably, selection has seemingly been relaxed or canceled in several genes with significantly biased ancestry, such as HERC2–OCA2. Moreover, signatures of post-admixture adaptation in XJU were identified, including genes related to metabolism (e.g. CYP2D6), digestion (e.g. COL11A1), olfactory perception (e.g. ANO2) and immunity (e.g. HLA). Our results demonstrated population admixture as a driving force, locally or globally, in shaping human genetic and phenotypic diversity as well as in adaptive evolution.     

Adaptive evolution and selection of stress-resistant Saccharomyces cerevisiae for very high-gravity bioethanol fermentation

BackgroundIn industrial yeasts, selection and breeding for resistance to multiple stresses is a focus of current research. The objective of this study was to investigate the tolerance to multiple stresses of Saccharomyces cerevisiae obtained through an adaptive laboratory evolution strategy involving a repeated liquid nitrogen freeze–thaw process coupled with multi-stress shock selection. We also assessed the related resistance mechanisms and very high-gravity (VHG) bioethanol production of this strain.ResultsElite S. cerevisiae strain YF10-5, exhibiting improved VHG fermentation capacity and stress resistance to osmotic pressure and ethanol, was isolated following ten consecutive rounds of liquid nitrogen freeze–thaw treatment followed by plate screening under osmotic and ethanol stress. The ethanol yield of YF10-5 was 16% higher than that of the parent strain during 35% (w/v) glucose fermentation. Furthermore, there was upregulation of three genes (HSP26, HSP30, and HSP104) encoding heat-shock proteins involved in the stress response, one gene (TPS1) involved in the synthesis of trehalose, and three genes (ADH1, HXK1, and PFK1) involved in ethanol metabolism and intracellular trehalose accumulation in YF10-5 yeast cells, indicating increased stress tolerance and fermentative capacity. YF10-5 also showed excellent fermentation performance during the simultaneous saccharification and fermentation of VHG sweet potato mash, producing 13.40% (w/v) ethanol, which corresponded to 93.95% of the theoretical ethanol yield.ConclusionsA multiple-stress-tolerant yeast clone was obtained using adaptive evolution by a freeze–thaw method coupled with stress shock selection. The selected robust yeast strain exhibits potential for bioethanol production through VHG fermentation.How to cite: Zhang Q, Jin Y, Fang Y, et al. Adaptive evolution and selection of stress-resistant Saccharomyces cerevisiae for very high gravity bioethanol fermentation. Electron J Biotechnol 2019;41. https://doi.org/10.1016/j.ejbt.2019.06.003     

De novo assembly of a Tibetan genome and identification of novel structural variants associated with high-altitude adaptation

Structural variants (SVs) may play important roles in human adaptation to extreme environments such as high altitude but have been under-investigated. Here, combining long-read sequencing with multiple scaffolding techniques, we assembled a high-quality Tibetan genome (ZF1), with a contig N50 length of 24.57 mega-base pairs (Mb) and a scaffold N50 length of 58.80 Mb. The ZF1 assembly filled 80 remaining N-gaps (0.25 Mb in total length) in the reference human genome (GRCh38). Markedly, we detected 17 900 SVs, among which the ZF1-specific SVs are enriched in GTPase activity that is required for activation of the hypoxic pathway. Further population analysis uncovered a 163-bp intronic deletion in the MKL1 gene showing large divergence between highland Tibetans and lowland Han Chinese. This deletion is significantly associated with lower systolic pulmonary arterial pressure, one of the key adaptive physiological traits in Tibetans. Moreover, with the use of the high-quality de novo assembly, we observed a much higher rate of genome-wide archaic hominid (Altai Neanderthal and Denisovan) shared non-reference sequences in ZF1 (1.32%–1.53%) compared to other East Asian genomes (0.70%–0.98%), reflecting a unique genomic composition of Tibetans. One such archaic hominid shared sequence—a 662-bp intronic insertion in the SCUBE2 gene—is enriched and associated with better lung function (the FEV1/FVC ratio) in Tibetans. Collectively, we generated the first high-resolution Tibetan reference genome, and the identified SVs may serve as valuable resources for future evolutionary and medical studies.     

A family of proportionate normalized subband adaptive filter algorithms

In this paper, the concept of proportionate adaptation is extended to the normalized subband adaptive filter (NSAF), and seven proportionate normalized subband adaptive filter algorithms are established. The proposed algorithms are proportionate normalized subband adaptive filter (PNSAF), μ‐law PNSAF (MPNSAF), improved PNSAF (IPNSAF), the improved IPNSAF (IIPNSAF), the set-membership IPNSAF (SM-IPNSAF), the selective partial update IPNSAF (SPU-IPNSAF), and SM-SPU-IPNSAF which are suitable for sparse system identification in network echo cancellation. When the impulse response of the echo path is sparse, the PNSAF has initial faster convergence than NSAF but slows down dramatically after initial convergence. The MPNSAF algorithm has fast convergence speed during the whole adaptation. The IPNSAF algorithm is suitable for both sparse and dispersive impulse responses. The SM-IPNSAF exhibits good performance with significant reduction in the overall computational complexity compared with the ordinary IPNSAF. In SPU-IPNSAF, the filter coefficients are partially updated rather than the entire filter at every adaptation. In SM-SPU-IPNSAF algorithm, the concepts of SM and SPU are combined which leads to a reduction in computational complexity. The simulation results show good performance of the proposed algorithms.     

Adaptive synchronization of complex networks with general distributed update laws for coupling weights

This paper discusses adaptive synchronization control for complex networks interacted in an undirected weighted graph, and aims to provide a novel and general approach for the design of distributed update laws for adaptively adjusting coupling weights. The proposed updating laws are very general in the sense that they encompass most weight update laws reported in the literature as special cases, and also provide new insights in the analysis of network system evolution and graph weight convergence. We show a rigorous proof for the synchronization stability of the overall complex network to a synchronized state, and demonstrate the convergence of adaptive weights for each edge to some bounded constants. A detailed comparison with available results is provided to elaborate the new features and advantages of the proposed adaptive strategies as compared with conventional adaptive laws. The effectiveness of the proposed approach is also validated by several typical simulations.     

基因组视域下海洋渔业生物对胁迫环境的适应策略研究

海洋渔业(包括捕捞和养殖)提供的蛋白是全球人类膳食中重要的动物蛋白来源,同时海洋渔业也是众多国家国民生计的重要来源。我国是海洋渔业大国,确保海洋渔业可持续发展对维护我国食物及营养安全意义重大。近海生态系统是海洋渔业产出最为丰富的区域,在全球变暖背景下,近海过度开发、栖息地破坏以及陆源污染等,使我国渔业生物持续面临高胁迫环境,继而使海洋捕捞及海水养殖可持续发展面临巨大挑战。基因组等学科发展使得高胁迫环境下的海洋生物适应潜力的精准评估与预测成为可能。文章概述了我国渔业生物胁迫环境适应研究现状,以期明确海洋渔业生物环境适应进化研究的主要科学问题;并进一步提出未来研究建议,以促进我国海洋渔业生物资源与水产养殖精准化管理及产业健康、可持续发展。     

Rapid phenotypic evolution with shallow genomic differentiation during early stages of high elevation adaptation in Eurasian Tree Sparrows

Known as the ‘third polar region’, the Qinghai-Tibet Plateau represents one of the harshest highland environments in the world and yet a number of organisms thrive there. Previous studies of birds, animals and humans have focused on well-differentiated populations in later stages of phenotypic divergence. The adaptive processes during the initial phase of highland adaptation remain poorly understood. We studied a human commensal, the Eurasian Tree Sparrow, which has followed human agriculture to the Qinghai-Tibet Plateau. Despite strong phenotypic differentiation at multiple levels, in particular in muscle-related phenotypes, highland and lowland populations show shallow genomic divergence and the colonization event occurred within the past few thousand years. In a one-month acclimation experiment investigating phenotypic plasticity, we exposed adult lowland tree sparrows to a hypoxic environment and did not observe muscle changes. Through population genetic analyses, we identified a signature of polygenic adaptation, whereby shifts in allele frequencies are spread across multiple loci, many of which are associated with muscle-related processes. Our results reveal a case of positive selection in which polygenic adaptation appears to drive rapid phenotypic evolution, shedding light on early stages of adaptive evolution to a novel environment.     

Production of wheat-doubled haploids resistant to eyespot supported by marker-assisted selection

BackgroundWheat is one of the most important crops cultivated all over the world. New high-yielding cultivars that are more resistant to fungal diseases have been permanently developed. The present study aimed at the possibility of accelerating the process of breeding new cultivars, resistant to eyespot, by using doubled haploids (DH) system supported by marker-assisted selection.ResultsTwo highly resistant breeding lines (KBP 0916 and KBH 4942/05) carrying Pch1 gene were crossed with the elite wheat genotypes. Hybrid plants of early generations were analyzed using endopeptidase EpD1 and two SSR markers linked to the Pch1 locus. Selected homozygous and heterozygous genotypes for the Pch1-linked EpD1b allele were used to produce haploid plants. Molecular analyses were performed on haploids to identify plants possessing Pch1 gene. Chromosome doubling was performed only on haploid plants with Pch1 gene. Finally, 65 DH lines carrying eyespot resistance gene Pch1 and 30 lines without this gene were chosen for the eyespot resistance phenotyping in a field experiment.ConclusionsResults of the experiment confirmed higher resistance to eyespot of the genotypes with Pch1 in comparison to those without this gene. This indicates the efficiency of selection at the haploid level.How to cite: Wiśniewska H, Majka M, Kwiatek M, et al. Production of wheat doubled haploids resistant to eyespot supported by marker-assisted selection. Electron J Biotechnol 2019;37. https://doi.org/10.1016/j.ejbt.2018.10.003     

Genomic consequences of population decline in critically endangered pangolins and their demographic histories

Pangolins are among the most critically endangered animals due to heavy poaching and worldwide trafficking. However, their demographic histories and the genomic consequences of their recent population declines remain unknown. We generated high-quality de novo reference genomes for critically endangered Malayan (Manis javanica, MJ) and Chinese (M. pentadactyla, MP) pangolins and re-sequencing population genomic data from 74 MJs and 23 MPs. We recovered the population identities of illegally traded pangolins and previously unrecognized genetic populations that should be protected as evolutionarily distinct conservation units. Demographic reconstruction suggested environmental changes have resulted in a population size fluctuation of pangolins. Additionally, recent population size declines due to human activities have resulted in an increase in inbreeding and genetic load. Deleterious mutations were enriched in genes related to cancer/diseases and cholesterol homeostasis, which may have increased their susceptibility to diseases and decreased their survival potential to adapt to environmental changes and high-cholesterol diets. This comprehensive study provides not only high-quality pangolin reference genomes, but also valuable information concerning the driving factors of long-term population size fluctuations and the genomic impact of recent population size declines due to human activities, which is essential for pangolin conservation management and global action planning.     

中国省域科技创新效率演化及其影响因素研究

本文运用规模报酬可变的DEA模型测度2000-2007年中国省域科技创新效率并分析其收敛性和影响因素。研究发现:科技创新效率具周期性波动演化特点;东部省域科技创新效率高于中西部省域,西部省域科技创新效率提高快,赶上并超过了中部省域;西部省域科技创新效率具有绝对和条件收敛特征;全国和东中部省域科技创新效率条件收敛显著,绝对收敛特征不明显;考察期内工业结构、对外开放度、高等教育发展水平对科技创新效率具有正影响效应,而政府影响力具有负向作用。研究结果为国家及地区科技创新效率政策提供参考信息。     

A novel design method for optimal IIR system identification using opposition based harmony search algorithm

In this paper a population based evolutionary optimization methodology called Opposition based Harmony Search Algorithm (OHS) is applied for the optimization of system coefficients of adaptive infinite impulse response (IIR) system identification problem. The original Harmony Search (HS) algorithm is chosen as the parent one and opposition based approach is applied to it with an intention to exhibit accelerated near global convergence profile. During the initialization, for choosing the randomly generated population/solution opposite solutions are also considered and the fitter one is selected as apriori guess for having faster convergence profile. Each solution in Harmony Memory (HM) is generated on the basis of memory consideration rule, a pitch adjustment rule and a re-initialization process which gives the optimum result corresponding to the least error fitness in multidimensional search space. Incorporation of different control parameters in basic HS algorithm results in balancing of exploration and exploitation of search space. The proposed OHS based system identification approach has alleviated from inherent drawbacks of premature convergence and stagnation, unlike Genetic Algorithm (GA), Particle Swarm Optimization (PSO) and Differential Evolution (DE). The simulation results obtained for some well known benchmark examples justify the efficacy of the proposed OHS based system identification approach over GA, PSO and DE in terms of convergence speed, identifying the system plant coefficients and mean square error (MSE) fitness values produced for both same order and reduced order models of adaptive IIR filters.     

A single nucleotide mutation in the dual-oxidase 2 (DUOX2) gene causes some of the panda's unique metabolic phenotypes

The giant panda (Ailuropoda melanoleuca) is an iconic bear native to China, famous for eating almost exclusively bamboo. This unusual dietary behavior for a carnivore is enabled by several key adaptations including low physical activity, reduced organ sizes and hypothyroidism leading to lowered energy expenditure. These adaptive phenotypes have been hypothesized to arise from a panda-unique single-nucleotide mutation in the dual-oxidase 2 (DUOX2) gene, involved in thyroid hormone synthesis. To test this hypothesis, we created genome-edited mice carrying the same point mutation as the panda and investigated its effect on metabolic phenotype. Homozygous mice were 27% smaller than heterozygous and wild-type ones, had 13% lower body mass-adjusted food intake, 55% decreased physical activity, lower mass of kidneys (11%) and brain (5%), lower serum thyroxine (T4: 36%), decreased absolute (12%) and mass-adjusted (5%) daily energy expenditure, and altered gut microbiota. Supplementation with T4 reversed the effects of the mutation. This work uses a state-of-the-art genome editing approach to demonstrate the link between a single-nucleotide mutation in a key endocrine-related gene and profound adaptive changes in the metabolic phenotype, with great importance in ecology and evolution.     

Single nucleotide polymorphisms in partial sequences of the gene encoding the large sub-units of ADP-glucose pyrophosphorylase within a representative collection of 10 Musa genotypes

BackgroundADP-glucose pyrophosphorylase (AGPase) is a rate-limiting enzyme catalyzing the first step in the starch biosynthesis pathway in higher plants. To date, there are no reported variants or isoforms of the AGPase enzyme in bananas (Musa spp. family Musaceae) as is the case of other plants. In this study, genomic DNA sequences homologous to the gene encoding one of the large subunits of the enzyme were amplified from 10 accessions of the genus Musa, including representatives of wild ancestors (AA and BB genomes), dessert bananas (AA, AAA, AB and AAB genomes), plantains (AAB genome) and cooking bananas (ABB and AAA genomes), and studied in order to find single nucleotide polymorphisms (SNP) base variations in Musa accessions.ResultsIn the 810-base pair amplicons of the AGPase large sub-unit (LSU) gene analyzed in ten Musa accessions, a total of 36 SNPs and insertions/deletions (indels) were found. The phylogenetic analysis revealed fifteen distinct haplotypes, which were grouped into four variants. Deep examination of SNPs in the 2nd exon in the LSU of AGPase showed that at seven locations, five SNPs altered their amino acid sequence.ConclusionsThis work reveals the possible number of AGPase enzyme isoforms and their molecular levels in banana. Molecular markers could be designed from SNPs present in these banana accessions. This information could be useful for the development of SNP-based molecular markers for Musa germplasm, and alteration of the allosteric properties of AGPase to increase the starch content and manipulate the starch quality of banana fruits.     

Kernel recursive generalized mixed norm algorithm

This work studies the problem of kernel adaptive filtering (KAF) for nonlinear signal processing under non-Gaussian noise environments. A new KAF algorithm, called kernel recursive generalized mixed norm (KRGMN), is derived by minimizing the generalized mixed norm (GMN) cost instead of the well-known mean square error (MSE). A single error norm such as l_p error norm can be used as a cost function in KAF to deal with non-Gaussian noises but it may exhibit slow convergence speed and poor misadjustments in some situations. To improve the convergence performance, the GMN cost is formed as a convex mixture of l_p and l_q norms to increase the convergence rate and substantially reduce the steady-state errors. The proposed KRGMN algorithm can solve efficiently the problems such as nonlinear channel equalization and system identification in non-Gaussian noises. Simulation results confirm the desirable performance of the new algorithm.     

Isolation and identification of a cellulolytic bacterium from the Tibetan pig's intestine and investigation of its cellulase production

BackgroundThe Tibetan pig is a pig breed with excellent grazing characteristics indigenous to the Qinghai–Tibet plateau in China. Under conditions of barn feeding, 90% of its diet consists of forage grass, which helps meet its nutritional needs. The present study aimed to isolate and identify a cellulolytic bacterium from the Tibetan pig's intestine and investigate cellulase production by this bacterium. The study purpose is to provide a basic theory for the research and development of herbivore characteristics and to identify a source of probiotics from the Tibetan pig.ResultsA cellulolytic bacterium was isolated from a Tibetan pig's intestine and identified based on morphological, physiological, and biochemical characteristics as well as 16S rRNA analysis; it was designated Bacillus subtilis BY-2. Examination of its growth characteristics showed that its growth curve entered the logarithmic phase after 8–12 h and the stable growth phase being between 20 and 40 h. The best carbon source for fermentation was 1% corn flour, while 2% peptone and yeast powder compound were the best nitrogen sources. The initial pH during fermentation was 5.5, with 4% inoculum, resulting in a high and stable amount of enzyme in 24–48 h.ConclusionsThe isolated BY-2 strain rapidly grew and produced cellulase. We believe that BY-2 cellulase can help overcome the shortage of endogenous animal cellulase, improve the utilization rate of roughage, and provide strain sources for research on porcine probiotics.