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。     

高寒草地甘肃臭草根系分形结构的坡向差异性

根系分形结构是植物根系构型应对环境异质性的表型可塑性结果, 可反映植物对生长环境的适应策略。利用ArcGIS建立研究区域的数字高程模型, 并提取坡向数据, 采用全根挖掘和Win-RHIZO根系分析仪相结合的方法, 研究了祁连山北坡高寒退化草地不同坡向甘肃臭草(Melica przewalskyi)的根系分形结构。结果表明: 随着坡向由北坡向东坡、西坡、南坡转变, 草地群落的密度、高度和土壤含水量逐渐减小, 甘肃臭草种群的密度、高度以及根系分形丰度呈逐渐增大的趋势、分形维数逐渐减小; 不同坡向甘肃臭草根系分形维数和分形丰度间的相关性存在差异(p < 0.05), 南坡和北坡甘肃臭草根系分形维数分形丰度之间存在极显著负相关关系(p < 0.01), 东坡和西坡之间存在显著负相关关系(p < 0.05), 甘肃臭草根系分形维数和分形丰度存在着“此消彼长”的权衡关系; 随着坡向由北坡向东坡、西坡、南坡转变, 甘肃臭草根系分形维数和分形丰度回归方程的标准化主轴(SMA)斜率逐渐增大(p < 0.05), 说明在干旱的南坡, 根系所开发利用的相同体积的土壤内, 根系分支更少、更稀疏。不同坡向甘肃臭草合理权衡根系分形维数和分形丰度的资源配置模式, 体现了植物根系构型构建的资源投资权衡机制。     

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.     

脓疮草复合体的生物学特性研究

通过野外和移栽实验观测,对脓疮草复合体（Ｐａｎｚｅｒｉａｎ ｌａｎａｔａ ｃｏｍｐｌｅｘ）居群进行了生物学特性研究。结果表明：浓疮草复合体居群在生活史方面无明显差异,移栽的１０个复合体居群生活史十分 相似：脓疮草复合本的花量大,花期可达３个月左右,花为雌雄异熟,以异花授粉为主,自交（同株异花授粉）亲合;叶裂程度、花萼裂片宽窄等性状,在天然居群中是连续变化的,而且移栽后可逆性较大,性状不稳定。     

上海郊区人群的体质特征和遗传关系

本项研究收集了上海郊区的 13个具有明显方言差异的人群的各类人类遗传学数据 5 3项进行聚类分析 ,发现黄浦江以东的人群相对较纯 ,而黄浦江以西的则较混杂 ,两组群体都分别可以聚成较远的 3类。由此认为上海郊区的人群大致有 3种起源 ,上海奉贤区金汇镇和闵行区马桥镇为代表的居民与南方土著民族较近 ,崇明县、嘉定区、浦东新区和南汇区的居民与北方民族较近 ,而奉贤区的头桥镇、金山区、青浦区的朱家角和商榻、松江区天马山等地的居民又是另一类。这与历史记载他们的不同来源有关。