荞麦粉营养品质与加工特性研究

通过对荞麦粉营养品质和加工特性的测定分析,结果表明：荞麦粉必需氨基酸含量高,氨基酸组成优于小麦面粉,接近WHO／FAO建议模式;荞麦粉的淀粉酶活性远低于小麦粉,是荞麦粉粘度远大于小麦粉以及降落值(Falling number)远高于小麦粉的主要原因之一。营养成分在荞麦子粒的不同部位的分布很不均衡,外层麸粉的营养价值高于内层心粉,但内层心粉的加工性能优于外层麸粉。     

Using genetic algorithms to select most predictive protein features

Many important characteristics of proteins such as biochemical activity and subcellular localization present a challenge to machine-learning methods: it is often difficult to encode the appropriate input features at the residue level for the purpose of making a prediction for the entire protein. The problem is usually that the biophysics of the connection between a machine-learning method's input (sequence feature) and its output (observed phenomenon to be predicted) remains unknown; in other words, we may only know that a certain protein is an enzyme (output) without knowing which region may contain the active site residues (input). The goal then becomes to dissect a protein into a vast set of sequence-derived features and to correlate those features with the desired output. We introduce a framework that begins with a set of global sequence features and then vastly expands the feature space by generically encoding the coexistence of residue-based features. It is this combination of individual features, that is the step from the fractions of serine and buried (input space 20 + 2) to the fraction of buried serine (input space 20 * 2) that implicitly shifts the search space from global feature inputs to features that can capture very local evidence such as a the individual residues of a catalytic triad. The vast feature space created is explored by a genetic algorithm (GA) paired with neural networks and support vector machines. We find that the GA is critical for selecting combinations of features that are neither too general resulting in poor performance, nor too specific, leading to overtraining. The final framework manages to effectively sample a feature space that is far too large for exhaustive enumeration. We demonstrate the power of the concept by applying it to prediction of protein enzymatic activity.     

Brief communication: dental development and enamel thickness in the Lakonis Neanderthal molar

Developmental and structural affinities between modern human and Neanderthal dental remains continue to be a subject of debate as well as their utility for informing assessments of life history and taxonomy. Excavation of the Middle Paleolithic cave site Lakonis in southern Greece has yielded a lower third molar (LKH 1). Here, we detail the crown development and enamel thickness of the distal cusps of the LKH 1 specimen, which has been classified as a Neanderthal based on the presence of an anterior fovea and mid-trigonid crest. Crown formation was determined using standard histological techniques, and enamel thickness was measured from a virtual plane of section. Developmental differences include thinner cuspal enamel and a lower periodicity than modern humans. Crown formation in the LKH 1 hypoconid is estimated to be 2.6-2.7 years, which is shorter than modern human times. The LKH 1 hypoconid also shows a more rapid overall crown extension rate than modern humans. Relative enamel thickness was approximately half that of a modern human sample mean; enamel on the distal cusps of modern human third molars is extremely thick in absolute and relative terms. These findings are consistent with recent studies that demonstrate differences in crown development, tissue proportions, and enamel thickness between Neanderthals and modern humans. Although overlap in some developmental variables may be found, the results of this and other studies suggest that Neanderthal molars formed in shorter periods of time than modern humans, due in part to thinner enamel and faster crown extension rates.     

Discovering plant metabolic biomarkers for phenotype prediction using an untargeted approach

Biomarkers are used to predict phenotypical properties before these features become apparent and, therefore, are valuable tools for both fundamental and applied research. Diagnostic biomarkers have been discovered in medicine many decades ago and are now commonly applied. While this is routine in the field of medicine, it is of surprise that in agriculture this approach has never been investigated. Up to now, the prediction of phenotypes in plants was based on growing plants and assaying the organs of interest in a time intensive process. For the first time, we demonstrate in this study the application of metabolomics to predict agronomic important phenotypes of a crop plant that was grown in different environments. Our procedure consists of established techniques to screen untargeted for a large amount of metabolites in parallel, in combination with machine learning methods. By using this combination of metabolomics and biomathematical tools metabolites were identified that can be used as biomarkers to improve the prediction of traits. The predictive metabolites can be selected and used subsequently to develop fast, targeted and low‐cost diagnostic biomarker assays that can be implemented in breeding programs or quality assessment analysis. The identified metabolic biomarkers allow for the prediction of crop product quality. Furthermore, marker‐assisted selection can benefit from the discovery of metabolic biomarkers when other molecular markers come to its limitation. The described marker selection method was developed for potato tubers, but is generally applicable to any crop and trait as it functions independently of genomic information.     

遗传多样性上限假说所揭示的进化历程

作为生物进化的两个主流理论, 中性学说和现代达尔文进化理论相对系统地揭示了进化机理和历程, 但也都有缺陷, 比如对某些重大进化现象如遗传等距离和重叠位点(Overlap sites)的忽视, 对复杂性的视而不见, 对遗传多样性的片面解读, 以及与化石证据相悖等。遗传多样性上限假说(Maximum genetic diversity hypothesis, MGD)通过对遗传等距离现象的重新解读, 给出了复杂性的量化定义和可操作研究手段, 提出了重叠特征和遗传多样性具有上限等结论。它对人猿分类关系和现代人多地区起源的分子解读结论, 与独立的化石证据契合度较高, 重新肯定了中国在人类发展中的关键作用, 点出了流行分子结论的荒谬在于误用了极限距离。该理论同时对复杂性状和复杂疾病的遗传机制研究具有指导意义。文章对多种酵母、鱼类、灵长类的细胞色素c进行序列比对, 独立验证了MGD假说的部分论断, 并解释了重叠位点在遗传距离计算上的重要意义。MGD假说中的上限或最佳平衡概念, 与传统国学和中医阴阳中庸思想对宇宙基本规律的描述是一脉相承的。     

基于结构方程模型的吴起县农业生态经济系统耦合关系

基于2008年吴起县农户调查资料,利用结构方程模型对吴起县农业生态经济系统耦合关系进行了分析.结果表明：具有相关关系的农业资源和产业态势对系统耦合有一定影响,其影响系数分别为0.14和1.00;农业资源与产业态势之间的相关系数为-0.11,说明吴起县的产业发展并非建立在对农业资源有效利用基础之上,农业资源对经济效益的变化没有直接作用;产业的发展主要建立在对农业资源之外的能量和物质的开发利用上,导致产业态势对经济效益的直接路径系数为-2.95,总的路径系数仅为0.23.从农业生态系统与经济系统的关系及其耦合的角度看,目前研究区农业系统建立在不稳定的、较少依赖于本系统资源的耦合态势下,即在农业生态经济系统良性耦合机制的建立与形成过程中潜伏了较大危机.为此,需要提高牧草等农业资源的利用率,发展林草及其相关产业.     

Prediction and analysis of protein methylarginine and methyllysine based on Multisequence features

Protein methylation, one of the most important post-translational modifications, typically takes place on arginine or lysine residue. The reversible modification involves a series of basic cellular processes. Identification of methyl proteins with their sites will facilitate the understanding of the molecular mechanism of methylation. Besides the experimental methods, computational predictions of methylated sites are much more desirable for their convenience and fast speed. Here, we propose a method dedicated to predicting methylated sites of proteins. Feature selection was made on sequence conservation, physicochemical/biochemical properties, and structural disorder by applying maximum relevance minimum redundancy and incremental feature selection methods. The prediction models were built according to nearest the neighbor algorithm and evaluated by the jackknife cross-validation. We built 11 and 9 predictors for methylarginine and methyllysine, respectively, and integrated them to predict methylated sites. As a result, the average prediction accuracies are 74.25%, 77.02% for methylarginine and methyllysine training sets, respectively. Feature analysis suggested evolutionary information, and physicochemical/biochemical properties play important roles in the recognition of methylated sites. These findings may provide valuable information for exploiting the mechanisms of methylation. Our method may serve as a useful tool for biologists to find the potential methylated sites of proteins.     

浙江省木本植物区系特征及其与引种驯化的关系

本文对浙江省木本植物区系特征进行分析,探讨该省木本植物区系与引种驯化的关系,旨在为园林工作者更好地开展引种驯化工作、切实提高引种成功率提供参考。