Prediction of methylated CpGs in DNA sequences using a support vector machine

DNA methylation plays a key role in the regulation of gene expression. The most common type of DNA modification consists of the methylation of cytosine in the CpG dinucleotide. At the present time, there is no method available for the prediction of DNA methylation sites. Therefore, in this study we have developed a support vector machine (SVM)-based method for the prediction of cytosine methylation in CpG dinucleotides. Initially a SVM module was developed from human data for the prediction of human-specific methylation sites. This module achieved a MCC and AUC of 0.501 and 0.814, respectively, when evaluated using a 5-fold cross-validation. The performance of this SVM-based module was better than the classifiers built using alternative machine learning and statistical algorithms including artificial neural networks, Bayesian statistics, and decision trees. Additional SVM modules were also developed based on mammalian- and vertebrate-specific methylation patterns. The SVM module based on human methylation patterns was used for genome-wide analysis of methylation sites. This analysis demonstrated that the percentage of methylated CpGs is higher in UTRs as compared to exonic and intronic regions of human genes. This method is available on line for public use under the name of Methylator at http://bio.dfci.harvard.edu/Methylator/.     

Structural characterization of proteins using residue environments

A primary challenge for structural genomics is the automated functional characterization of protein structures. We have developed a sequence-independent method called S-BLEST (Structure-Based Local Environment Search Tool) for the annotation of previously uncharacterized protein structures. S-BLEST encodes the local environment of an amino acid as a vector of structural property values. It has been applied to all amino acids in a nonredundant database of protein structures to generate a searchable structural resource. Given a query amino acid from an experimentally determined or modeled structure, S-BLEST quickly identifies similar amino acid environments using a K-nearest neighbor search. In addition, the method gives an estimation of the statistical significance of each result. We validated S-BLEST on X-ray crystal structures from the ASTRAL 40 nonredundant dataset. We then applied it to 86 crystallographically determined proteins in the protein data bank (PDB) with unknown function and with no significant sequence neighbors in the PDB. S-BLEST was able to associate 20 proteins with at least one local structural neighbor and identify the amino acid environments that are most similar between those neighbors.     

DOES GENETIC RELATEDNESS OF MATES INFLUENCE COMPETITIVE FERTILIZATION SUCCESS IN GUPPIES?

A growing number of studies highlight the nontransitive properties of ejaculates when they are in competition to fertilize a female's eggs. Increasingly, these studies suggest that postcopulatory processes act as a filter against sperm from closely related males or those with similar genotypes, limiting the deleterious effects of inbreeding on offspring fitness. We investigated the potential for such postcopulatory mechanisms of inbreeding avoidance in the guppy (Poecilia reticulata), a promiscuous livebearing fish. We used artificial insemination as a method of delivering to a female the combined ejaculates from a first cousin (relatedness coefficient r = 0.125) and an unrelated male. This method of sperm delivery controls behavioral processes of pre- and postcopulatory female choice, which can bias paternity toward unrelated males. Our genetic analysis revealed no effect of parental relatedness on paternity outcomes. The observed mean paternity share for related males (0.47) and associated variance did not differ significantly from an expected binomial distribution that assumes no biased use of sperm with respect to relatedness (0.5). Although our data provide no evidence for postcopulatory mechanisms of inbreeding avoidance, the ability of female guppies to influence ejaculate transfer and retention offers an alternative and easily testable mechanism of inbreeding avoidance in this species.     

基于表型性状和SSR分子标记的云南省水稻主要育成品种（系）的遗传相似性分析

为了揭示云南省水稻主要育成品种（系）的遗传相似性。本文利用株高等17个表型性状和48个微卫星（SSR）分子标记,对云南省18个育种部门（或课题组）60年代以来选育的40个品种（系）进行遗传相似性评价。结果显示表型遗传相似性低于DNA水平。40个品种（系）基于17个表型性状的平均遗传相似系数为0.244,籼型为0.289,粳型为0.309,籼粳亚种间为0.162;基于48个SSR分子标记的平均遗传相似系数为0.383,籼型为0.318,粳型为0.478,籼粳亚种间为0.267。48个SSR分子标记共检测到等位基因214个,每个标记2～8,平均4.458个;平均有效等位基因数为2.8336,变幅为1.1515～5.2981;多态性信息含量（PIC）平均值为0.6058,变幅为0.2118～0.8816;基因型多样性指数（H′）平均值为1.1328,变幅为0.3768～1.8087。RM84、RM249、RM152、RM222和RM528是评价云南省水稻选育品种（系）遗传相似性比较理想的SSR分子标记。聚类分析显示,云南省水稻主要选育品种（系）表现为亚种间遗传差异明显,亚种内遗传差异较小,粳型遗传相似性高于籼型。表明云南省选育的粳型品种（系）遗传多样性低,且同一育种部门（或育种人）选育的品种遗传相似度高。     

Avifauna response to hurricanes: regional changes in community similarity

Global climate models predict increases in the frequency and intensity of extreme climatic events such as hurricanes, which may abruptly alter ecological processes in forests and thus affect avian diversity. Developing appropriate conservation measures necessitates identifying patterns of avifauna response to hurricanes. We sought to answer two questions: (1) does avian diversity, measured as community similarity, abundance, and species richness, change in areas affected by hurricane compared with unaffected areas, and (2) what factors are associated with the change(s) in avian diversity? We used North American Breeding Bird Survey data, hurricane track information, and a time series of Landsat images in a repeated measures framework to answer these questions. Our results show a decrease in community similarity in the first posthurricane breeding season for all species as a group, and for species that nest in the midstory and canopy. We also found significant effects of hurricanes on abundance for species that breed in urban and woodland habitats, but not on the richness of any guild. In total, hurricanes produced regional changes in community similarity largely without significant loss of richness or overall avian abundance. We identified several potential mechanisms for these changes in avian diversity, including hurricane‐induced changes in forest habitat and the use of refugia by birds displaced from hurricane‐damaged forests. The prospect of increasing frequency and intensity of hurricanes is not likely to invoke a conservation crisis for birds provided we maintain sufficient forest habitat so that avifauna can respond to hurricanes by shifting to areas of suitable habitat.     

用胆固醇代谢的房室模型速率系数来分析动脉粥样硬化程度

理论上认为胆固醇逆向转运的速率与动脉粥样硬化程序呈负相关。但目前尚无完善的测试血浆脂蛋白－胆固醇体内代谢的方法。我们运用同位素＾３Ｈ－胆固醇示踪方法,建立房室模型,选取健康兔与ＡＳ兔对照,研究血浆脂蛋白转运胆固醇能力的差异,并结合ＡＳ兔主动脉斑块程度对比,结果验证了上述理论,此法如改用短半衰期同位素或稳定性同位素标记的胆固醇,就可用于人体,这可为临床判断ＡＳ程度提供一种无创性的新方法。     

Electrostatic recognition in substrate binding to serine proteases

Serine proteases of the Chymotrypsin family are structurally very similar but have very different substrate preferences. This study investigates a set of 9 different proteases of this family comprising proteases that prefer substrates containing positively charged amino acids, negatively charged amino acids, and uncharged amino acids with varying degree of specificity. Here, we show that differences in electrostatic substrate preferences can be predicted reliably by electrostatic molecular interaction fields employing customized GRID probes. Thus, we are able to directly link protease structures to their electrostatic substrate preferences. Additionally, we present a new metric that measures similarities in substrate preferences focusing only on electrostatics. It efficiently compares these electrostatic substrate preferences between different proteases. This new metric can be interpreted as the electrostatic part of our previously developed substrate similarity metric. Consequently, we suggest, that substrate recognition in terms of electrostatics and shape complementarity are rather orthogonal aspects of substrate recognition. This is in line with a 2‐step mechanism of protein‐protein recognition suggested in the literature.     

Versatile characterization of glycosylation modification in CTLA4-Ig fusion proteins by liquid chromatography-mass spectrometry

CTLA4-Ig is a highly glycosylated therapeutic fusion protein that contains multiple N- and O-glycosylation sites. Glycosylation plays a vital role in protein solubility, stability, serum half-life, activity, and immunogenicity. For a CTLA4-Ig biosimilar development program, comparative analytical data, especially the glycosylation data, can influence decisions about the type and amount of animal and clinical data needed to establish biosimilarity. Because of the limited clinical experience with biosimilars before approval, a comprehensive level of knowledge about the biosimilar candidates is needed to achieve subsequent development. Liquid chromatography-mass spectrometry (LC–MS) is a versatile technique for characterizing N- and O-glycosylation modification of recombinant therapeutic proteins, including 3 levels: intact protein analysis, peptide mapping analysis, and released glycans analysis. In this report, an in-depth characterization of glycosylation of a candidate biosimilar was carried out using a systematic approach: N- and O-linked glycans were identified and electron-transfer dissociation was then used to pinpoint the 4 occupied O-glycosylation sites for the first time. As the results show, the approach provides a set of routine tools that combine accurate intact mass measurement, peptide mapping, and released glycan profiling. This approach can be used to comprehensively research a candidate biosimilar Fc-fusion protein and provides a basis for future studies addressing the similarity of CTLA4-Ig biosimilars.     

补光对越冬灰仓鼠体重、主要器官指数及精子数量的影响

目的研究补光对灰仓鼠(Cricetulus migratorus)越冬时脏器器官的影响。方法室温下将其分为自然光照组和补充光照组,分别在第0、30、48和150天时测定动物的体重和脏器器官的重量,应用涂片法检查精子的数量。结果自然光照时,精子数量在冬至时变化不大,但冬至后第18天,灰仓鼠的睾丸系数降到最低值,精子数量仅为422枚,第150天时恢复到正常繁殖状态,精子数量达到7440枚。其他脏器指数在冬至时最高,第150天时最低。补充光照后,雌雄鼠体重高峰值时间均比自然光照组提前100 d,各器官指数变化与体重变化情况相类似,但睾丸和子宫系数维持稳定,精子数量未发现减少。结论在自然光照时越冬灰仓鼠的脏器指数逐渐下降,第150天时脏器指数达至最高值,睾丸指数在冬至后第18天下降到最低值,处于非繁殖状态。补充光照后,越冬灰仓鼠的精子数量和子宫指数变化不大,一直维持繁殖状态。