Reverse vaccinology and genomics

The genomic revolution has had a dramatic effect on our ability to find new vaccine targets and develop effective vaccines.     

Why testing improves memory: mediator effectiveness hypothesis

A wealth of research has established that practice tests improve memory for the tested material. Although the benefits of practice tests are well documented, the mechanisms underlying testing effects are not well understood. We propose the mediator effectiveness hypothesis, which states that more-effective mediators (that is, information linking cues to targets) are generated during practice involving tests with restudy versus during restudy only. Effective mediators must be retrievable at time of test and must elicit the target response. We evaluated these two components of mediator effectiveness for learning foreign language translations during practice involving either test-restudy or restudy only. Supporting the mediator effectiveness hypothesis, test-restudy practice resulted in mediators that were more likely to be retrieved and more likely to elicit targets on a final test.     

度量生物性状广义相关系数的抽样分布及假设检验

【目的】完善生物性状非线性相关性的广义相关系数理论体系,为实际育种工作提供一套完整的理论体系。【方法】采用构造综合指标,借助于一元线性回归模型,对度量生物性状线性、非线性相关性的广义相关系数的抽样分布及假设检验问题进行研究。【结果】该广义相关系数服从F分布或t分布,可用F检验或者t检验对该相关系数与0之间的差异显著性进行检验。【结论】建立的广义相关系数检验方法计算简单、无信息损失,线性与非线性广义相关系数的定义、性质、抽样分布及假设检验问题都予以解决,丰富了多元统计学内容。     

用春小麦株高性状自交后代遗传变异推导和检验多基因假说

遗传变异的研究是数量遗传学研究的重点.多基因假说是数量遗传学的基础,其要点是＂各基因的作用是累加的＂.在加性遗传模式和符合孟德尔定律（符合分离定律和独立分配定律、没有连锁遗传和基因互作）的条件下,采用双单倍体技术分析遗传变异的＂累加性＂,得到2个结论：①用遗传距离表示F2遗传变异的大小,推导多基因假说的＂累加性＂符合＂代数和＂（A=B＋C）.②用遗传方差表示F2遗传变异的大小,推导多基因假说的＂累加性＂符合＂平方和＂（∑a2=∑b2＋∑c2）.t-测验表明2个结论都是正确的.以多基因假说为基础提出加性遗传模式,加性遗传模式的重点是不同等位基因间的作用是＂代数和＂,不是＂平方和＂.用遗传方差表示F2遗传变异的大小,不符合加性遗传模式,不符合多基因假说.     

中国粮食增长因素分析及其统计假设检验

结合中国1983～2006年粮食生产相关统计数据,构建了相应的计量模型,并消除模型存在的序列相关性.结果表明,在农业生产过程中,化肥施用量、播种面积、成灾面积对粮食增长具有显著的影响,而农业劳动就业人数对粮食生产不具有影响力.     

Mechanism of transmitter release: voltage hypothesis and calcium hypothesis

The calcium hypothesis of synaptic transmission has been challenged by experimental results using the crayfish neuromuscular junction that suggest that presynaptic depolarization can trigger transmitter release directly without calcium influx. Results from electrophysiological experiments using the same preparation do not support this voltage hypothesis, but are consistent with the calcium hypothesis. Voltage may modulate, but not elicit, transmitter release.     

以牛亚科家畜线粒体细胞色素b基因全序列检验分子钟假说

在测定牛亚科家畜6个物种线粒体细胞色素b(Cyt b)基因全序列的基础上,以非参数检验法检验分子钟假说,提出肯定或否定分子钟假说的部分客观资料.结果表明,6个牛种的Cyt b基因全序列长度都是1140bp,牛种间序列的碱基组成差异较小,碱基替代以转换为主,转换/颠换比为5.4.基于核苷酸序列和氨基酸相对速率检验结果表明,牛种内序列的进化全部接受分子钟假说;牛种问大多数序列的进化接受分子钟假说,少数序列的进化拒绝分子钟假说.与基于氨基酸序列的检验结果相比较,基于核苷酸序列的检验结果更易于拒绝分子钟假说.进而推论,接受或者拒绝分子钟假说与所检测物种之间亲缘关系的远近无明显的相关性,分子钟假说在一定的物种范围内是成立的;对于长期进化而言,既无核苷酸序列亦无氨基酸序列以绝对恒定的速率变化,分子钟不具有通用性.     

Comparative genomics of the eukaryotes

A comparative analysis of the genomes of Drosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae-and the proteins they are predicted to encode-was undertaken in the context of cellular, developmental, and evolutionary processes. The nonredundant protein sets of flies and worms are similar in size and are only twice that of yeast, but different gene families are expanded in each genome, and the multidomain proteins and signaling pathways of the fly and worm are far more complex than those of yeast. The fly has orthologs to 177 of the 289 human disease genes examined and provides the foundation for rapid analysis of some of the basic processes involved in human disease.     

Phylogenomics: intersection of evolution and genomics

Much has been gained from genomic and evolutionary studies of species. Combining the perspectives of these different approaches suggests that an integrated phylogenomic approach will be beneficial.     

硫酸盐对厌氧消化产甲烷的影响

以杭州四堡污水处理厂厌氧活性污泥为接种源，以葡萄糖模拟合成废水为基质、硫酸钠为硫酸根源，研究了硫酸盐还原作用对产甲烷的影响。结果表明，批量试验中第一次添加基质后，不同硫酸盐浓度下，产甲烷量下降不明显，硫酸盐仅被还原一部分；第二次添加基质后，甲烷形成量显著降低，且硫酸盐浓度愈大，下降幅度也愈大。在多次添加基质过程中，硫酸盐抑制作用逐渐减小，但并不完全消除。在连续运行试验中，加入硫酸盐后，反应器运行即受到很大冲击，即使恢复到稳态运行后，ＣＯＤ去除率、甲烷形成量均达不到未加硫酸盐时的水平。用ＦｅＳＯ＿４代替Ｎａ＿２ＳＯ＿４消除硫酸盐还原产物游离性Ｓ￣（２－）后，ＣＯＤ去除率和产甲烷量有所上升。在未加硫酸盐时反应器底部有相当高浓度的丙酸，而加入硫酸盐后丙酸和丁酸浓度显著下降．     

Serial-choice reaction time: inadequacies of the information hypothesis

The results of an experiment on serial-choice reaction time, specifically designed as a critical test of the Information Hypothesis, lead to rejection of the hypothesis; information is found to be neither a necessary nor a sufficient condition to account for the data. Where previously information had been interpreted as a determinant of reaction time, it was usually confounded with the probability of nonrepetition of a signal. Thus, to the extent that this confounding is present in previous experiments, the inference attributing an increase in reaction time to an increase in information is logically invalid.     

The impact of structural genomics: expectations and outcomes

Structural genomics (SG) projects aim to expand our structural knowledge of biological macromolecules while lowering the average costs of structure determination. We quantitatively analyzed the novelty, cost, and impact of structures solved by SG centers, and we contrast these results with traditional structural biology. The first structure identified in a protein family enables inference of the fold and of ancient relationships to other proteins; in the year ending 31 January 2005, about half of such structures were solved at a SG center rather than in a traditional laboratory. Furthermore, the cost of solving a structure at the most efficient SG center in the United States has dropped to one-quarter of the estimated cost of solving a structure by traditional methods. However, the efficiency of the top structural biology laboratories-even though they work on very challenging structures-is comparable to that of SG centers; moreover, traditional structural biology papers are cited significantly more often, suggesting greater current impact.     

Chemical messengers in development: a hypothesis

The hypothesis that physiological and developmental regulatory mechanisms are similar has been presented. Well-known developmental systems chosen illustrate the capability of the model to suggest a simple mechanism underlying the effects on development of a diverse group of chemicals. This hypothesis might be applied to other systems including the induction of the lens, limb regeneration, and the induction of the head of hydra (124). I have proposed this hypothesis not only because it permits consideration of a complex and varied array of experimental observations as reflections of a simple basic biochemical mechanism, but because recent technical advances in instrumentation and methods allow it to be directly tested. The fluorescent antibody method for the cytochemical measurement of cyclic nucleotides provides a means for investigating changes in the concentrations of cyclic nucleotides in developing cells and could also be used to detect neurotransmitters in developing cells. Similarly, the scanning electron microscope in the emitted x-ray mode provides a method for measuring changes in the content and distribution of cations within developing cells. The hypothesis presented here suggests pleasing asceticism on the part of eukaryotes. It suggests that simple derivatives of metabolites, including neurotransmitters and cyclic nucleotides, are linked together as regulatory molecules throughout the eukaryotes. The neurotransmitters are suggested to have a more general role in information transmission in eukaryotes than is generally accepted. They are hypothesized to have progressed during evolution from being intracellular messengers to a role as intercellular messengers for the relatively slow communication of developmental informatbn; and, finally, this process has culminated with their participation in the rapid intercellular communication mediated by nerves. The thought that the complex pictures of physiological regulation and of the construction of a complex multicellular organism like man might be painted with so few colors is quite satisfying.     

Depressive disorders: toward a unified hypothesis

Our scientific understanding of psychiatric syndromes, including the phenomena of depression, has been hampered because of: (i) the use of metapsychological concepts that are difficult to test; (ii) methodological and linguistic barriers that prevent communication among psychoanalysts, behaviorists, experimental psychologists, and psychiatrists; and (iii) the reluctance of psychiatrists to accept animal models as possible approximations of certain aspects of human psychopathology. We have attempted to demonstrate that the animal models simulate some of the central features of clinical depression (for example, helplessness and object loss), thereby allowing one to rigorously investigate them from developmental, behavioral, and biochemical perspectives. The object loss model, as a concrete version of a metapsychological-psychoanalytic concept, has enabled primatologists to study the disruption of an attachment bond. The behavioral model accommodates this concept to a broader generalization: loss of reinforcement or loss of control over reinforcement. We have reviewed the evidence that these processes involve the diencephalic centers of reward or reinforcement, thereby permitting integration of the psychoanalytical and behavioral formulations with the biochemical hypotheses. Also, we have presented data strongly suggesting that the breaking of an attachment bond in the primate represents significant loss of reinforcement that induces helplessness and disrupts motivated behavior. Finally, we have argued that the depressive syndrome could be caused by interactions of genetic, chemical, developmental, and interpersonal factors, all of which impinge on the diencephalic centers of reinforcement.