基于转录组的不同火龙果品种抗性差异分析

不同的品种抗性不同,为进一步探究不同火龙果品种之间的抗性差异,为后续火龙果抗性育种提供参考,该研究利用Illumina HiSeq 2000测序平台对'普通白肉'(BR)和'厄瓜多尔黄龙'(EY)两个品种进行转录组测序分析,并参考GO Ontology、KEGG等公共数据库对差异表达基因进行功能分类与富集分析.结果表明...     

应用CGH数据和树模型探索癌症的发病机理

比较基因组杂交技术(comparative genomic hybridization, CGH)主要用于检测肿瘤的染色体缺失和扩嘱, 迄今已积累了大量的实验数据, 为全基因组分析肿瘤的发生机制提供了可能。树模型在生物信息学领域通常被用于研究生物形成和进化的历史, 物种之间的进化关系常以系统发生树来表示。树模型同样可以作为一种有力的生物信息学工具来分析CGH数据, 探索癌症的发病机理。文中介绍了两种常见的树模型—— 分支树和距离树, 详细叙述了重建树模型的基本原理和方法, 分析了创建树模型时要注意的几个技术问题, 并对其在肿瘤研究中的应用进行了回顾和总结。肿瘤的树状模型作为单路径线性模型的泛化, 克服了以往单路径线性模型的缺点, 理论上能更加精确地概括到肿脉的多基因、多路径、多阶段的发生发展模式, 从不同角度探讨肿瘤发生发展的分子机制。该模型除可用于分析肿瘤的CGH数据外, 还可用于分析其他多种类型的数据, 包括微阵列CGH(array-CGH)技术等产生的高分辨率数据。     

A gall-inducing arthropod drives declines in canopy tree photosynthesis

Mature forest canopies sustain an enormous diversity of herbivorous arthropods; however, with the exception of species that exhibit large-scale outbreaks, canopy arthropods are thought to have relatively little influence on overall forest productivity. Diminutive gall-inducing mites (Acari; Eriophyoidae) are ubiquitous in forest canopies and are almost always highly host specific, but despite their pervasive occurrence, the impacts of these obligate parasites on canopy physiology have not been examined. We have documented large declines in photosynthetic capacity (approx. 60%) and stomatal conductance (approx. 50%) in canopy leaves of mature sugar maple (Acer saccharum) trees frequently galled by the maple spindle gall mite Vasates aceriscrumena. Remarkably, such large impacts occurred at very low levels of galling, with the presence of only a few galls (occupying approx. 1% of leaf area) compromising gas-exchange across the entire leaf. In contrast to these extreme impacts on the leaves of adult trees, galls had no detectible effect on the gas-exchange of maple saplings, implying large ontogenetic differences in host tolerance to mite galling. We also found a significant negative correlation between canopy tree radial increment growth and levels of mite galling. Increased galling levels and higher physiological susceptibility in older canopy trees thus suggest that gall-inducing mites may be major drivers of “age-dependent” reductions in the physiological performance and growth of older trees.     

Microbial control of arthropod pests of tropical tree fruits

A multitude of insects and mites attack fruit crops throughout the tropics. The traditional method for controlling most of these pests is the application of chemical pesticides. Growing concern on the negative environmental effects has encouraged the development of alternatives. Inundatively and inoculatively applied microbial control agents (virus, bacteria, fungi, and entomopathogenic nematodes) have been developed as alternative control methods of a wide variety of arthropods including tropical fruit pests. The majority of the research and applications in tropical fruit agroecosystems has been conducted in citrus, banana, coconut, and mango. Successful microbial control initiatives of citrus pests and mites have been reported. Microbial control of arthropod pests of banana includes banana weevil, Cosmopolites sordidus Germar (Coleoptera: Curculionidae) (with EPNs and fungi) among others Oryctes rhinoceros (L.) is one of the most important pests of coconut and one of the most successful uses of non-occluded virus for classical biological control. Key pests of mango that have been controlled with microbial control agents include fruit flies (Diptera: Tephritidae) (with EPNs and fungi), and other pests. Also successful is the microbial control of arthropod pests of guava, papaya and pineapple. The challenge towards a broader application of entomopathogens is the development of successful combinations of entomopathogens, predators, and parasitoids along with other interventions to produce effective and sustainable pest management.     

Preprocessing of tandem mass spectrometric data based on decision tree classification

In this study, we present a preprocessing method for quadrupole time-of-flight （Q-TOF） tandem mass spectra to increase the accuracy of database searching for peptide （protein） identification. Based on the natural isotopic information inherent in tandem mass spectra, we construct a decision tree after feature selection to classify the noise and ion peaks in tandem spectra. Furthermore, we recognize overlapping peaks to find the monoisotopic masses of ions for the following identification process. The experimental results show that this preprocessing method increases the search speed and the reliability of peptide identification.     

基于转录组数据的齿缘刺猎蝽微卫星分子标记开发

【目的】齿缘刺猎蝽Sclomina erinacea是我国猎蝽科天敌昆虫常见种类,其不同地理种群存在明显形态差异。本研究旨在利用已经获得的齿缘刺猎蝽转录组数据筛选微卫星位点,为齿缘刺猎蝽种群遗传多样性和遗传分化研究开发可靠的微卫星分子标记。【方法】基于高通量测序技术平台Illumina HiSeq^TM 2000获得齿缘刺猎蝽转录组数据(42 215条unigenes),利用MISA软件进行搜索发掘SSR标记;利用Primer Premier 3软件设计SSR引物,从中随机选取54对SSR引物,利用PCR技术在中国齿缘刺猎蝽9个地理种群上进行验证。【结果】利用MISA软件搜索到微卫星位点2 395个,它们分布在2 107条unigenes上,其主要重复类型是三核苷酸重复(占总SSR的44.43%),其次是二核苷酸重复(占总SSR的40.08%),再次是四核苷酸重复(占总SSR的12.94%)。利用Primer Premier 3 软件成功设计出2 000余对SSR引物。随机选取的54对引物对9个齿缘刺猎蝽不同地理种群进行的SSR位点PCR扩增结果表明,共有16对引物较好地扩增出目的片段。【结论】研究表明利用齿缘刺猎蝽转录组数据可以大量发掘微卫星分子标记。本研究为进一步开展齿缘刺猎蝽的种群遗传学研究奠定了基础。     

Examining the large-scale convergence of photosynthesis-weighted tree leaf temperatures through stable oxygen isotope analysis of multiple data sets

The idea that photosynthesis-weighted tree canopy leaf temperature (T(canδ)) can be resolved through analysis of oxygen isotope composition in tree wood cellulose (δ(18) O(wc)) has led to the observation of boreal-to-subtropical convergence of T(canδ) to c. 20°C. To further assess the validity of the large-scale convergence of T(canδ), we used the isotope approach to perform calculation of T(canδ) for independent δ(18) O(wc) data sets that have broad coverage of climates. For the boreal-to-subtropical data sets, we found that the deviation of T(canδ) from the growing season temperature systemically increases with the decreasing mean annual temperature. Across the whole data sets we calculated a mean T(canδ) of 19.48°C and an SD of 2.05°C, while for the tropical data set, the mean T(canδ) was 26.40 ± 1.03°C, significantly higher than the boreal-to-subtropical mean. Our study thus offers independent isotopic support for the concept that boreal-to-subtropical trees display conserved T(canδ) near 20°C. The isotopic analysis cannot distinguish between the possibility that leaf temperatures are generally elevated above ambient air temperatures in cooler environments and the possibility that leaf temperature equals air temperature, whereas the leaf/air temperature at which photosynthesis occurs has a weighted average of near 20°C in cooler environments. Future work will separate these potential explanations.     

A new geometric biclustering algorithm based on the Hough transform for analysis of large-scale microarray data

Biclustering is an important tool in microarray analysis when only a subset of genes co-regulates in a subset of conditions. Different from standard clustering analyses, biclustering performs simultaneous classification in both gene and condition directions in a microarray data matrix. However, the biclustering problem is inherently intractable and computationally complex. In this paper, we present a new biclustering algorithm based on the geometrical viewpoint of coherent gene expression profiles. In this method, we perform pattern identification based on the Hough transform in a column-pair space. The algorithm is especially suitable for the biclustering analysis of large-scale microarray data. Our studies show that the approach can discover significant biclusters with respect to the increased noise level and regulatory complexity. Furthermore, we also test the ability of our method to locate biologically verifiable biclusters within an annotated set of genes.     

Effects of bird predation on arthropod abundance and tree growth across an elevational gradient

Considerable uncertainty surrounds the conditions under which birds can cause trophic cascades. In a three‐year experiment, we studied the direct and indirect effects of insectivorous birds on arthropod abundance, herbivory, and growth of striped maple Acer pensylvanicum saplings in a northern hardwood forest of central New Hampshire, USA. We manipulated bird predation by erecting exclosures around saplings and directly manipulated herbivory by removing herbivores. We also examined how climate modifies these interactions by replicating the experiment at three locations along an elevational gradient. Effects of bird predation were variable. Overall, mean arthropod biomass was 20% greater on saplings within bird exclosures than on controls (p<0.05). The mean biomass of leaf‐chewing herbivores, primarily Lepidoptera larvae, was 25% greater within exclosures but not statistically different from controls. To a lesser degree, mean herbivore damage to foliage within exclosures exceeded that of controls but differences were not significant. We also did not detect significant treatment effects on sapling shoot growth. The high understory vegetation density relative to bird abundance, and low rate of herbivory during the study (mean 5% leaf area removed, controls), may have limited the ability of birds to affect sapling growth. Climate effects operated at multiple scales, resulting in a complex interplay of interactions within the food web. Regional synchrony of climatic conditions resulted in annual fluctuations in herbivore abundance and tree growth that were shared across elevations. At the same time, local environmental variation resulted in site differences in the plant, herbivore, and bird communities. These patterns resulted in a mosaic of top–down strengths across time and space, suggesting an overall pattern of limited effects of birds on plant growth, possibly interspersed with hotspots of trophic cascades.     

基于家谱资料的死亡人数构成比的日节律

据 1 5 0 6～ 2 0 0 0年中国汉族某姓氏家谱资料 ,通过常规和圆形分析死亡人数构成比的日节律 ,发现男子死亡数构成比亥时、午时为高 ,卯时、辰时为低 ,最高值 (1 5 .0 9% )是最低值 (3 .47% )的 4.3 5倍 ,差异极显著 (P<0 .0 1 )。女子死亡数构成比亥时、巳时为高 ,卯时、寅时为低 ,最高值 (1 6 .0 8% )是最低值 (3 .5 5 % )的4.5 3倍 ,差异极显著。亥时是阴气盛极将衰、阳气将长 ,午时和巳时是阳气盛极将衰、阴气将长 ,可见阴阳二气的转换对死亡有催动作用。男子、女子数据合并 ,平均死亡高峰为 2 2时 5 8分。男子、女子昼、夜死亡数构成比均无甚差异 (P>0 .0 5 )。男子阳时、阴时死亡数构成比分别为 42 .6 5 %和 5 7.3 5 % ,差异极显著 ;女子分别为 46 .78%和 5 3 .2 2 % ,差异接近显著 (P=0 .1 0 )。男子最大时辰死亡数构成比 ,古代为亥时和午时的1 4.6 9% ,近现代为亥时的 1 5 .1 5 %。可见 ,在这两个时代中 ,男子时辰死亡数构成比无大的改变。女子最大时辰死亡数构成比 ,古代为亥时的 1 5 .5 1 % ,近现代仍为亥时的 1 7.2 1 % ,二时代女子的时辰死亡数构成比也无甚改变。死亡时辰 Y与死亡日 (农历初一至三十 ) X之间存在显著相关。男子和女子数据合并 ,Y=1 1 .0 95 1 0 .0 6 1 7X± 0 .443 (P=0     

COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas

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Of mites and millipedes: Recent progress in resolving the base of the arthropod tree

Deep‐level arthropod phylogeny has been in a state of upheaval ever since the emergence of molecular tree reconstruction approaches. While a consensus has settled in that hexapods are more closely related to crustaceans than to myriapods, the phylogenetic position of the latter has remained a matter of debate. Mitochondrial, nuclear, and genome‐scale studies have proposed rejecting the long‐standing superclade Mandibulata, which unites myriapods with insects and crustaceans, in favor of a clade that unites myriapods with chelicerates and has become known as Paradoxapoda or Myriochelata. Here we discuss the progress, problems, and prospects of arriving at the final arthropod tree.     

Individual tree context and contrast dictate tree physiological features and arthropod biodiversity patterns across multiple trophic levels

1. The present study tested the hypothesis that tree context (natural, semi-natural or planted) and contrast (height of surrounding vegetation) affect tree physiological characters (leaf size, nutrient content, and stress-related factors), and also alter the arthropod biodiversity patterns either directly or indirectly. 2. Arthropods were collected from tree canopies using chemical fogging from the ecologically important South African native tree Podocarpus elongatus. 3. Low contrast trees had significantly larger leaves than those in high contrast environments and harboured an overall higher richness, abundance, and biomass of arthropods, although this was guild-dependent. 4. Trees in natural contexts had less foliar δ¹³C, suffered less from artificial nitrogen enrichment, and harboured significantly higher herbivore and predator arthropod richness and unique assemblages, compared with planted trees. 5. Semi-natural trees supported natural levels of arthropod richness, although these were mostly generalist species. 6. Tree context and contrast can therefore dictate associated biota at multiple trophic levels and native trees may fail to maintain natural biodiversity in transformed landscapes.