油橄榄种质资源分类及品种鉴定研究进展

油橄榄的种类和品种的鉴定是油橄榄种质资源研究和新品种保护的基础。本文主要从形态学标记、细胞学标记、生化标记和DNA标记4个方面对油橄榄的鉴定进行了阐述及评价以及重点对几种主要的分子标记进行的比较。此外,本文还对油橄榄品种鉴定方法的发展趋势进行了展望。     

口腔细胞单细胞凝胶电泳

彗星测试被广泛应用在DNA损伤之生物监测最常用之人类细胞为淋巴细胞。但是现在有急切需要去发展可从正常志愿者采集而侵入性较低之人类细胞。此文章描述如何发展口腔细胞彗星测试及其应用。结果显示口腔细胞彗星测试是可行的并有潜质在生物监测及营养研究中取代淋巴细胞。     

基于多基因组合选择模型的结肠癌特征基因选取

通过基因的Bhattacharyya距离指标过滤掉大部分无关基因,然后探索性的提出了一种建立多基因组合选择模型的统计方法.从候选特征基因中选取了8个可能的结肠癌特征基因集合,判别分析的结果证明了该方法的可行性.     

Aligning DNA Sequences to Minimize the Change in Protein

We study an alignment model for coding DNA sequences recently proposed by J. Hein that takes into account both DNA and protein information, and attempts to minimize the total amount of evolution at both DNA and protein levels. Assuming that the gap penalty function is affine, we design a quadratic time dynamic programming algorithm for the model. Although the algorithm theoretically solves an open question of Hein, its running time is impractical because of the large constant factor embedded in the quadratic time complexity function. We therefore consider a mild simplification named Context-free Codon Alignment of Hein's model and present a much more efficient algorithm for the simplified model. The algorithms have been implemented and tested on both real and simulated sequences, and it is found that they produce almost identical alignments in most cases. Furthermore, we extend our model and design a heuristic algorithm to handle frame-shift errors and overlapping frames in coding regions.     

Statistical inference for DNA sequences of promoters: a non-stationary qualitative model

ABSTRACT

Gene promoters have variable repartition of AGCT nucleotides according to some probabilistic behaviours essentially depending on their position in a string. The paper aims to provide a model for this configuration. With this model we derive non-uniform confidence bounds for those probability distributions in the strings. A uniform bound deriving from previous works in Wu and Zhao [Inference of trends in time series. J R Stat Soc B. 2007;69:391–410] is more demanding for the model. A data-based study allows to clarify our suggestions and open the way for applications in molecular biology.     

The Levels of Cortisol,Oxidative Stress,and DNA Damage in the Victims of Childhood Sexual Abuse: A Preliminary Study

In this study we aimed to investigate serum cortisol, oxidative stress, and DNA damage in children who are sexual abuse victims. The study included 38 children who sustained child sexual abuse and 38 age- and gender-matched children who did not have a history of trauma. Cortisol levels reflecting the status of the hypothalamic-pituitary-adrenal axis, anti-oxidant enzymes glutathione peroxidase, superoxide dismutase, natural anti-oxidant coenzyme Q, and 8-hydroxy-2-deoxyguanosine as the indicator of DNA damage were analyzed in serum samples using the enzyme linked immunosorbent assay method. Cortisol levels were significantly higher in the child sexual abuse group compared to the control group. There were no significant differences between the groups in terms of oxidative stress and DNA damage. Cortisol and 8-hydroxy-2-deoxyguanosine levels decreased as the time elapsed since the sexual abuse increased. Coenzyme Q level was lower in victims who sustained multiple assaults than in the victims of a single assault. Cortisol and superoxide dismutase levels were lower in the victims of familial sexual abuse. Decreases in cortisol and 8-hydroxy-2-deoxyguanosine levels as time elapsed may be an adaptation to the toxic effects of high cortisol levels over a prolonged period of time. Child sexual abuse did not result in oxidative stress and DNA damage; however, some features of sexual abuse raised the level of oxidative stress.     

A Bayesian approach to inference about a change point model with application to DNA copy number experimental data

In this paper, we study the change-point inference problem motivated by the genomic data that were collected for the purpose of monitoring DNA copy number changes. DNA copy number changes or copy number variations (CNVs) correspond to chromosomal aberrations and signify abnormality of a cell. Cancer development or other related diseases are usually relevant to DNA copy number changes on the genome. There are inherited random noises in such data, therefore, there is a need to employ an appropriate statistical model for identifying statistically significant DNA copy number changes. This type of statistical inference is evidently crucial in cancer researches, clinical diagnostic applications, and other related genomic researches. For the high-throughput genomic data resulting from DNA copy number experiments, a mean and variance change point model (MVCM) for detecting the CNVs is appropriate. We propose to use a Bayesian approach to study the MVCM for the cases of one change and propose to use a sliding window to search for all CNVs on a given chromosome. We carry out simulation studies to evaluate the estimate of the locus of the DNA copy number change using the derived posterior probability. These simulation results show that the approach is suitable for identifying copy number changes. The approach is also illustrated on several chromosomes from nine fibroblast cancer cell line data (array-based comparative genomic hybridization data). All DNA copy number aberrations that have been identified and verified by karyotyping are detected by our approach on these cell lines.     

从海鱼加工下脚料中提取核酸的试验(Ⅰ) --原料中核酸含量的测定

采用定磷法测定了海鱼加工下脚料中核酸含量。试验表明从鱼白中分离得到核酸,远比其他下脚料容易,在样品预处理过程中,低温抽提法比索氏油提器法造成核酸损失要小。     

Exordium for DNA Codes

We describe how deletion-correcting codes may be enhanced to yield codes with double-strand DNA-sequence codewords. This enhancement involves abstractions of the pertinent aspects of DNA; it nevertheless ensures specificity of binding for all pairs of single strands derived from its codewords—the key desideratum of DNA codes– i.e. with binding feasible only between reverse complementary strands. We defer discussing the combinatorial-optimization superincumbencies of code construction. Generalization of deletion similarity to an optimal sequence-alignment score could readily effect advantageous improvements (Kaderali, Master's Thesis, Informatics, U. Köln, 2001) but would render the combinatorics opaque. We mention motivating applications of DNA codes.     

Some Results on the Control of the False Discovery Rate under Dependence

Abstract.  Controlling the false discovery rate (FDR) is a powerful approach to multiple testing, with procedures developed with applications in many areas. Dependence among the test statistics is a common problem, and many attempts have been made to extend the procedures. In this paper, we show that a certain degree of dependence is allowed among the test statistics, when the number of tests is large, with no need for any correction. We then suggest a way to conservatively estimate the proportion of false nulls, both under dependence and independence, and discuss the advantages of using such estimators when controlling the FDR.