An alternative approach to normalization and evaluation for gait patterns: Procrustes analysis applied to the cyclograms of sprinters and middle-distance runners

In order to compare gait patterns, a common procedure is to normalize strides both in time and magnitude. The stride duration is usually normalized to a time percentage before averaging curves. As the timing of event occurrences may shift across strides, the shape of the averaged curves is distorted and therefore the standard deviation is overvalued. Stride magnitude normalization is performed by means of dimensionless numbers. However, there is little agreement on which body size correction methods should be used. The Procrustes method describes curve shape and shape change in a mathematical and statistical framework, independently of time and size factors. The present study aims to explore how this technique may be used for time- and magnitude-stride normalization to reflect individual and group mean responses. The Procrustes method, which combines quantitative and visual features, is applied to the shape of the ankle and knee cyclograms. Superimposition of 25 cyclograms (10 for sprinters (SP) and 15 for middle-distance runners (MDR)) was supplemented by statistical procedures (principal component analysis, discriminant function) to extract the main key events, which vary according to the athletic specialities. In comparison with the MDR (poulaine-shaped cyclogram), the ovoid cyclogram of SP reveals the following gait indicators: a short braking phase, a rapid initial lower limb swing in the forward direction, a fast upward movement of the knee and ankle, and an active foot contact. The Procrustes approach could be used to describe other quasi-periodic movements through relative motion plots (e.g., cyclograms, angle-angle diagrams, phase plane portraits).     

Biosystematics of the aphid genus Cryptomyzus (Hornoptera, Aphididae): an electrophoretic analysis

The aphid genus Crypromyzus was studied using starch. el electrophoresis in order to establish differences between the various taxa and to estimate their paylogenetic relationships. A low degree of polymorphism and heterozyosity was observed. Taxa previously assumed to be homogeneous appeared to consist of different tost-secific forms. Polymorphism at the PGI locus was used to assess the degree of isolation. It was founf to range from complete separation to a reduction in gene flow. Three methods of estimating hylogenetic relationships were employed: the UPGMA clustering method using Nei's genetic distance; the Rogers distance together with the distance Wagner method and the independent allele model of Mickevich and Mitter (1981) combined with the Wagner parsimony method. The results of all three methods agree that several of the taxa are closely related but assign different lower branching points to the phylogenetic tree. The independent allele model is discussed in more detail because it is not often applied.     

Peptide substrate profiling defines fibroblast activation protein as an endopeptidase of strict Gly(2)-Pro(1)-cleaving specificity

Fibroblast activation protein (FAP) is a serine protease of undefined endopeptidase specificity implicated in tumorigenesis. To characterize FAP's P(4)-P(2)(') specificity, we synthesized intramolecularly quenched fluorescent substrate sets based on the FAP cleavage site in alpha(2)-antiplasmin (TSGP-NQ). FAP required substrates with Pro at P(1) and Gly or d-amino acids at P(2) and preferred small, uncharged amino acids at P(3), but tolerated most amino acids at P(4), P(1)(') and P(2)('). These substrate preferences allowed design of peptidyl-chloromethyl ketones that inhibited FAP, but not the related protease, dipeptidyl peptidase-4. Thus, FAP is a narrow specificity endopeptidase and this can be exploited for inhibitor design.     

Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data

SUMMARY: We introduce a novel Matlab toolbox for microarray data analysis. This toolbox uses normalization based upon a normally distributed background and differential gene expression based on five statistical measures. The objects in this toolbox are open source and can be implemented to suit your application. AVAILABILITY: MDAT v1.0 is a Matlab toolbox and requires Matlab to run. MDAT is freely available at http://microarray.omrf.org/publications/2004/knowlton/MDAT.zip.     

Three microarray platforms: an analysis of their concordance in profiling gene expression

Background

Bacillus cereus, Bacillus anthracis and Bacillus thuringiensis belong to the genetically close-knit Bacillus cereus sensu lato group, a family of rod-shaped Gram-positive bacteria. pAW63 is the first conjugative plasmid from the B. cereus group to be completely sequenced.

Results

The 71,777 bp nucleotide sequence of pAW63 reveals a modular structure, including a 42 kb tra region encoding homologs of the Type IV secretion systems components VirB11, VirB4 and VirD4, as well as homologs of Gram-positive conjugation genes from Enterococcus, Lactococcus, Listeria, Streptococcus and Staphylococcus species. It also firmly establishes the existence of a common backbone between pAW63, pXO2 from Bacillus anthracis and pBT9727 from the pathogenic Bacillus thuringiensis serovar konkukian strain 97-27. The alignment of these three plasmids highlights the presence of well conserved segments, in contrast to distinct regions of high sequence plastiCity. The study of their specific differences has provided a three-point reference framework that can be exploited to formulate solid hypotheses concerning the functionalities and the molecular evolution of these three closely related plasmids. This has provided insight into the chronology of their divergence, and led to the discovery of two Type II introns on pAW63, matching copies of the mobile element IS231L in different loci of pXO2 and pBT9727, and the identification on pXO2 of a 37 kb pathogeniCity island (PAI) containing the anthrax capsule genes.

Conclusion

The complete sequence determination of pAW63 has led to a functional map of the plasmid yielding insights into its conjugative apparatus, which includes T4SS-like components, as well as its resemblance to other large plasmids of Gram-positive bacteria. Of particular interest is the extensive homology shared between pAW63 and pXO2, the second virulence plasmid of B. anthracis, as well as pBT9727 from the pathogenic strain B. thuringiensis serovar konkukian strain 97-27.     

松毛虫赤眼蜂一氧化氮合酶基因的克隆、原核表达及在不同滞育阶段的表达谱分析

【目的】本研究旨在克隆松毛虫赤眼蜂Trichogramma dendrolimi一氧化氮合酶(NOS)基因,表达其编码蛋白,并探究其在松毛虫赤眼蜂滞育过程中的表达模式,为松毛虫赤眼蜂滞育研究提供新依据。【方法】通过转录组数据分析获得松毛虫赤眼蜂一氧化氮合酶基因TdNOS cDNA序列,使用qPCR方法检测其在松毛虫赤眼蜂不同滞育阶段预蛹和蛹中的表达量。使用RT-PCR方法扩增TdNOS cDNA序列并通过生物信息学方法分析其序列特征。构建TdNOS的原核表达载体,利用大肠杆菌Escherichia coli表达系统表达重组TdNOS蛋白,通过Ni-NTA琼脂糖亲和层析纯化,并用于制备多克隆抗体。利用Western blot进一步检测TdNOS在松毛虫赤眼蜂不同滞育阶段的表达量。通过质谱鉴定纯化的目标蛋白。【结果】qPCR分析表明,TdNOS在松毛虫赤眼蜂滞育解除后蛹期的相对表达量显著高于其他阶段的。克隆获得松毛虫赤眼蜂TdNOS cDNA序列(GenBank登录号:MN650600),开放阅读框(ORF)序列长1 014 bp,编码337个氨基酸,无信号肽序列,不含跨膜结构,预测有33...     

A thermocline as an obstacle to the spread of water mites (Acari: Hydrachnidia) across the lake profile

The aim of the study was to determine whether a thermocline may constitute a barrier discouraging vertical migration of water mites. The research was carried out in May, June, July, and August 1999 in Lake Lubie, and a total of 3252 water mites (1880 females and 1178 males) belonging to 29 species were collected. A strong negative correlation was observed between the drop in temperature in the thermocline and the abundance and number of water mite species living beneath the thermocline. The negative correlation resulted from a considerable limitation of vertical migration of water mites by factors such as: low temperature below the thermocline, large difference between temperatures above and below the thermocline, and considerable thickness of the thermocline. During summer season, lower layers of the lake were increasingly penetrated by water mites as the temperatures above and below the thermocline were becoming more uniform. Lake species displayed the greatest ability to penetrate lower water layers and were present below the thermocline during the whole study period; moreover, their numbers were quite steady. On the contrary, the species, which are characteristic for small water bodies, crossed the thermocline in comparatively large numbers in June when the thermocline was of the lowest thickness.     

Two-dimensional electrophoretic profiling of normal human kidney glomerulus proteome and construction of an extensible markup language (XML)-based database

To contribute to physiology and pathophysiology of the glomerulus of human kidney, we have launched a proteomic study of human glomerulus, and compiled a profile of proteins expressed in the glomerulus of normal human kidney by two-dimensional gel electrophoresis (2-DE) and identification with matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) and/or liquid chromatography-tandem mass spectrometry (LC-MS/MS). Kidney cortices with normal appearance were obtained from patients under surgical nephrectomy due to renal tumor, and glomeruli were highly purified by a standard sieving method followed by picking-up under a phase-contrast microscope. The glomerular proteins were separated by 2-DE with 24 cm immobilized pH gradient strips in the 3-10 range in the first dimension and 26 x 20 cm sodium dodecyl sulfate polyacrylamide electrophoresis gels of 12.5% in the second dimension. Gels were silver-stained, and valid spots were processed for identification through an integrated robotic system that consisted of a spot picker, an in-gel digester, and a MALDI-TOF MS and / or a LC-MS/MS. From 2-DE gel images of glomeruli of four subjects with no apparent pathologic manifestations, a synthetic gel image of normal glomerular proteins was created. The synthetic gel image contained 1713 valid spots, of which 1559 spots were commonly observed in the respective 2-DE gels. Among the 1559 spots, 347 protein spots, representing 212 proteins, have so far been identified, and used for the construction of an extensible markup language (XML)-based database. The database is deposited on a web site (http://www.sw.nec.co.jp/bio/rd/hgldb/index.html) in a form accessible to researchers to contribute to proteomic studies of human glomerulus in health and disease.     

Using an evapo-transpiration model (ETpN) to predict the risk and expression of symptoms of pine wilt disease (PWD) across Europe

The pine wood nematode (PWN) Bursaphelenchus xylophilus is the causal agent of pine wilt disease (PWD), a xylem restricting disease of pine trees. PWN, a native of North America where it very rarely kills native pine trees, has spread internationally killing host trees in China, Japan, Korea, Taiwan and Portugal, with isolated incursions into Spain. Based on the locations where tree mortality has been recorded, it appears that pine trees growing in hot, dry conditions are more susceptible to pine wilt disease. This paper describes the ETpN model, an evapo-transpiration model (previously developed by Forest Research), which has been modified to incorporate the presence of PWN inside a tree and which predicts the regions of Europe that are likely to succumb to PWD. ETpN acts independently of the vector beetle (Monochamus spp.), predicting the likelihood of PWD on the assumption that a tree in a particular region has already been infested by the pine wood nematode. Different regions across Europe are included to investigate and demonstrate how different climates affect PWD incidence significantly. Simplified, “lite” and latency models have been developed to allow a non-specialist user to determine respectively the risk of PWD at a particular location and the likelihood of delays (latency) in expression of wilt symptoms.     

荒漠昆虫小胸鳖甲抗菌肽Attacin基因的克隆及低温表达模式分析

昆虫在低温冷驯化过程中会发生很多基因表达的改变, 从转录组层面上开展广泛的研究有助于全面认识昆虫对冷响应的分子机制。为了对荒漠昆虫小胸鳖甲Microdera punctipennis的 4℃低温转录组数据中一个上调表达的Attacin基因（MpAttacin1）进行深入了解并分析其对低温诱导的响应情况, 本研究通过生物信息学分析对该基因进行了鉴定, 并利用实时荧光定量PCR对其在低温下的mRNA水平进行了检测。结果表明： 获得的MpAttacin1 cDNA长度为523 bp, 包含一个456 bp的开放阅读框和67 bp的5′端非翻译区。MpAttacin1编码含有151个氨基酸残基的多肽, N端含有17个氨基酸的信号肽序列。同源性分析表明, 其氨基酸序列与其他鳞翅目、 双翅目和鞘翅目昆虫的抗菌肽Attacin具有30%~40%的一致性。以邻接法（neighbor-joining, NJ）构建的系统进化树表明, 小胸鳖甲Attacin1与其他鞘翅目昆虫的Attacin起源于共同的祖先, 属于Attacin_C超家族。实时荧光定量PCR分析结果显示, 在4℃与-4℃低温胁迫时, MpAttacin1基因的转录都呈现先升高后降低的应激反应趋势, 但在对低温的响应时间和强度上有所不同。在4℃处理5 h和9 h后, MpAttacin1的表达量分别为对照组的2.3和3.8倍, 而在-4℃处理7 h和9 h后, 分别为对照组的2.4和1.5倍。这些研究表明, 除已知的抗菌功能外, Attacin在昆虫的低温适应过程中可能也发挥着重要的作用。     

瓜实蝇嗅觉受体基因的克隆及表达谱分析

昆虫的嗅觉受体是一个高度变异的蛋白家族, 其中一类Or83b嗅觉受体在不同昆虫体内高度保守, 在昆虫的行为调控过程中起到十分重要的作用。为进一步探讨Or83b受体的功能, 本研究利用RT-PCR和RACE方法克隆获得瓜实蝇Bactrocera cucurbitae (Coquillett) Or83b-like受体的全长cDNA序列, 命名为BcucOr83b-like（GenBank登录号： HM745934）。测序结果表明, BcucOr83b-like开放阅读框全长1 422 bp,编码473个氨基酸残基。氨基酸序列比对表明, 此序列具有Or83b受体的典型特征, 序列中具有7个跨膜区和高度保守的C端区域。BcucOr83b-like与其他昆虫的Or83b具有较高的氨基酸序列一致性, 其中与桔小实蝇Bactrocera dorsalis（Hendel）Or83b的序列一致性高达99.6%。对该基因在瓜实蝇成虫不同组织和发育时期表达量的荧光定量PCR分析表明, BcucOr83b-like主要在瓜实蝇成虫触角中表达, 头部（去除触角）、 雌虫前足和翅中也有较高的表达; 瓜实蝇在各个发育时期的表达水平不同, 在刚羽化雌成虫中的表达量最高。本研究为深入研究瓜实蝇Or83b受体的功能提供了理论依据。