基于BB—SIR方法的结肠癌特征基因提取

结合复杂数据分析（Complex Data Analysis）理论和充分降维的思想，在有效提取结肠癌特征基因研究的基础上，建立结肠癌特征基因提取的BB-SIR模型。该模型方法简洁易懂且有较高的识别率。依据BB-SIR模型和所给数据找到了两个结肠癌亚型，并确定了该亚型的特征基因。实验结果表明，BB—SIR方法选出的特征基因能够识别出结肠癌亚型，并且识别正确率达到96％以上。     

欧洲病理基因研究网络（ERA-NET I）

欧洲研究经费的投入焦点已经转移以生物标记（biomarkers）的确认，因其不但将成为感染性疾病研究的新目标。也得借功能性基因之助发展出新的疫苗。目前已经有8个国家承诺以国内研究预算集资于ERA-NET的“病理基因”（Pathogenomics）计划。奥地利、芬兰、法国、德国、以色列、葡萄牙、斯洛伐克以及西班牙等国的科研单位与企业都可在2006年3月底之前共同申请这一计划的资助。该计划的主要目的在于统筹研究资源，如用以建立数据库、     

基因转移的研究进展

本文从新的思路上介绍了基因转移的研究进展,首先论述了有性杂交与基因交流和物种进化的关系,重点论述了非有性杂交条件下生物体间、生物体内的基因水平转移研究概况,并讨论了基因转移与生物进化,突变和生物工程的关系及存在的有关问题。     

基因疗法助胖老鼠"燃脂瘦身"

美国和瑞士科学家日前通过基因疗法,将老鼠体内储存脂肪的细胞转化为消耗能量的细胞,使老鼠的体重平均减少了四分之一。这可能为治疗肥胖症以及糖尿病等与肥胖相关的疾病提供一种新方法。英国《新科学家》杂志网站前些日报道,美、瑞科学家给有患糖尿病倾向的老鼠静脉注射一种名为腺毒素的病毒。这种病毒含有一种促使动物体内产生“瘦身蛋白”Leptin的基因。在静脉注射2到4天后,老鼠体内由肝脏合成的Lep tin含量比正常水平高出近5 0倍。两周后,老鼠的体重减少了2 0 7克到2 80克,食量也减少了三分之一。研究人员随后对老鼠体内的脂肪细胞进行…     

薄液膜表面蒸发对降液膜传热和传质的影响

对实验结果的分析和界面质扩散量级的估算表明，降液膜表面存在着可观的过度蒸发现象，理论分析指出：表面张力引发的“毛细诱导面蒸发”是这一过度蒸发的驱动力。通过关联实验数据，得到了“有效毛细半径”的表达式，将这一表达式与表面蒸发率的计算式结合得到了“毛细诱导界面蒸发”的计算式，并以此式完善了碑已地出的液膜临界热流率的预测式，对比表明，本预测式的相对偏差比已有的其他预测式的低得多。     

基于类别空间的基因选择

基因选择通常是在基因空间中进行的. 由于基因空间的维数(基因数目)比该空间中的样本数要多得多, 这种做法存在严重的维数发难(curse of dimensionality)问题, 其结果是在基因空间中所建立数据模型难于获得满意的精度, 基于所建立模型的基因选择结果可信度低. 如何对具有极少样本的极高维空间进行特征选择(基因选择)是一个极具挑战性的课题. 将基因空间变换为它的对偶空间, 称为类别空间, 从而空间的维数仅为基因空间中样本的类别数, 空间中的样本数则为基因空间的维数. 显然, 在类别空间中不存在任何维数发难现象; 提出了在类别空间中基于将不同的类尽可能分开的原则、并借助主分量分析的基于类别空间基因选择方法. 对真实基因数据的基因选择实验, 并通过Fisher指标、加权Fisher指标以及leave-one-out cross validation等可分性指标, 与其他两种基因选择方法进行了深入的比较, 结果表明该方法是十分有效的.     

转抗旱基因作物的研究进展

在烟草中已分别进行过与抗旱有拳甘露糖醇－１－磷酰脱氢酶基因,甜菜碱脱氢酶基因,二氢吡咯－５－羧酸酶基因,晚期胚胎发生丰富蛋白基因,海藻糖合成酶基因,过氧化物酶基因的转抗旱基因烟草的研究。转Ｍｎ－ＳＯＤ ｃＤＮＡ的转基因苜蓿,表现了较强抗寒性和抗旱性。     

德美科学家借助植物实验获得癌症研究新进展

德国和美国科学家日前联合进行了一项研究，成功地发现了发育基因“RAD51”在模式植物拟南芥中的特性机理。科学家说，由于该基因与遗传行为及肿瘤形成具有密切关系，因此新成果有望为人类征服癌症带来帮助。     

日本发现可预测抗癌剂效果的基因

日本札幌医科大学及其附属癌症研究所最近发现一种能预测抗癌剂疗效的基因 ,这种基因在抗癌剂发挥作用时会出现异常。这一研究成果有助于根据不同患者的癌症特征选择药物进行个性化医疗。抗癌剂的效果因人而异 ,用在有些人身上效果明显 ,但同时会殃及正常细胞 ,引起腹泻、骨髓功能下降等症状 ;抗癌剂对另外一些患者却没有任何疗效 ,只有明显的副作用。因此科学家一直在进行研究 ,希望能事先预测抗癌剂的疗效 ,以便因人施药。据日本《朝日新闻》报道 ,研究小组以 16 0位直肠癌和口腔癌等患者的癌组织为对象进行实验。他们发现 ,若抗癌剂对癌…     

美科学家发现关键致癌基因

美国科学家在前些时候出版的《自然》杂志上报告说，他们发现了一种导致癌症的关键基因。它不仅本身能使正常细胞发生癌变，而且还可以使其他致癌基因发挥作用。     

Automatic prediction of protein function

Most methods annotating protein function utilise sequence homology to proteins of experimentally known function. Such a homology-based annotation transfer is problematic and limited in scope. Therefore, computational biologists have begun to develop ab initio methods that predict aspects of function, including subcellular localization, post-translational modifications, functional type and protein-protein interactions. For the first two cases, the most accurate approaches rely on identifying short signalling motifs, while the most general methods utilise tools of artificial intelligence. An outstanding new method predicts classes of cellular function directly from sequence. Similarly, promising methods have been developed predicting protein-protein interaction partners at acceptable levels of accuracy for some pairs in entire proteomes. No matter how difficult the task, successes over the last few years have clearly paved the way for ab initio prediction of protein function.Received 26 March 2003; received after revision 15 May 2003; accepted 12 June 2003     

Current topics in genome evolution: Molecular mechanisms of new gene formation

Comparative genome analyses reveal that most functional domains of human genes have homologs in widely divergent species. These shared functional domains, however, are differentially shuffled among evolutionary lineages to produce an increasing number of domain architectures. Combined with duplication and adaptive evolution, domain shuffling is responsible for the great phenotypic complexity of higher eukaryotes. Although the domain-shuffling hypothesis is generally accepted, determining the molecular mechanisms that lead to domain shuffling and novel gene creation has been challenging, as sequence features accompanying the formation of known genes have been obscured by accumulated mutations. The growing availability of genome sequences and EST databases allows us to study the characteristics of newly emerged genes. Here we review recent genome-wide DNA and EST analyses, and discuss the three major molecular mechanisms of gene formation: (1) atypical spicing, both within and between genes, followed by adaptation, (2) tandem and interspersed segmental duplications, and (3) retrotransposition events. Received 18 October 2006; received after revision 18 November 2006; accepted 28 November 2006     

Transformation: a tool for studying fungal pathogens of plants

Plant diseases caused by plant pathogenic fungi continuously threaten the sustainability of global crop production. An effective way to study the disease-causing mechanisms of these organisms is to disrupt their genes, in both a targeted and random manner, so as to isolate mutants exhibiting altered virulence. Although a number of techniques have been employed for such an analysis, those based on transformation are by far the most commonly used. In filamentous fungi, the introduction of DNA by transformation typically results in either the heterologous (illegitimate) integration or the homologous integration of the transforming DNA into the target genome. Homologous integration permits a targeted gene disruption by replacing the wild-type allele on the genome with a mutant allele on transforming DNA. This process has been widely used to determine the role of newly isolated fungal genes in pathogenicity. The heterologous integration of transforming DNA causes a random process of gene disruption (insertional mutagenesis) and has led to the isolation of many fungal mutants defective in pathogenicity. A big advantage of insertional mutagenesis over the more traditional chemical or radiation mutagenesis procedures is that the mutated gene is tagged by transforming DNA and can subsequently be cloned using the transforming DNA. The application of various transformation-based techniques for fungal gene manipulation and how they have increased our understanding and appreciation of some of the most serious plant pathogenic fungi are discussed. Received 9 May 2001; received after revision 2 July 2001; accepted 3 July 2001     

Distribution of tightened end fragments of globular proteins statistically matches that of topohydrophobic positions: towards an efficient punctuation of protein folding?

Using a set of 372 proteins representative of a variety of 56 distinct globular folds, a statistical correlation was observed between two recently revealed features of protein structures: tightened end fragments or 'closed loops', i. e. sequence fragments that are able in three-dimensional (3D) space to nearly close their ends (a current parameter of polymer physics), and 'topohydrophobic positions', i. e. positions always occupied in 3D space by strong hydrophobic amino acids for all members of a fold family. Indeed, in sequence space, the distribution of preferred lengths for tightened end fragments and that for topohydrophobic separation match. In addition to this statistically significant similarity, the extremities of these 'closed loops' may be preferentially occupied by topohydrophobic positions, as observed on a random sample of various folds. This observation may be of special interest for sequence comparison of distantly related proteins. It is also important for the ab initio prediction of protein folds, considering the remarkable topological properties of topohydrophobic positions and their paramount importance within folding nuclei. Consequently, topohydrophobic positions locking the 'closed loops' belong to the deep cores of protein domains and might have a key role in the folding process. Received 1 February 2001; accepted 7 February 2001     

Production of pharmaceutical proteins in milk

There is every reason to expect that it will be possible within the next few years to begin to use farm animals to produce large quantities of some of the human proteins that are needed for the treatment of disease. Revolutionary new opportunities for the production of novel proteins in milk have been created by the development of methods for gene transfer. Exploitation of these opportunities depends upon selection and cloning of milk protein genes and identification of the sequences that govern tissue specific hormonally induced expression in the mammary gland. Studies with three genes, ovine -lactoglobulin, rat -casein and whey acidic protein of rat and mouse, suggest that they may all meet this requirement. Fragments of the ovine -lactoglobulin, murine whey acidic protein and rabbit -casein genes have directed production of novel proteins in the milk of transgenic mice, sheep, rabbits and pigs. The proteins were biologically active and usually co-migrated with authentic proteins. In early experiments, protein concentration was low, but our recent observations suggest that fusion genes containing genomic clones direct production of concentrations of protein that are suitable for commercial exploitation. In the longer term, two approaches may offer the potential of more reliable expression. Control elements capable of directing expression that is independent of site of insertion of the gene, but dependent on the number of copies of the gene, have been identified for a small number of genes. The availability of such elements for the milk protein genes would increase the reliability of gene expression considerably. Alternatively, targeted mutation of genes may allow the insertion of coding sequences within an existing gene so avoiding position effects.     

The genomic basis of the Williams – Beuren syndrome

The Williams-Beuren syndrome is a genomic disorder (prevalence: 1/7,500 to 1/20,000), caused by a hemizygous contiguous gene deletion on chromosome 7q11.23. Typical symptoms comprise supravalvular aortic stenosis, mental retardation, overfriendliness and visuospatial impairment. The common deletion sizes range of 1.5–1.8 mega base pairs (Mb), encompassing app. 28 genes. For a few genes, a genotype-phenotype correlation has been established. The best-explored gene within this region is the elastin gene; its haploinsufficiency causes arterial stenosis. The region of the Williams-Beuren syndrome consists of a single copy gene region (~1.2 Mb) flanked by repetitive sequences – Low Copy Repeats (LCR). The deletions arise as a consequence of misalignment of these repetitive sequences during meiosis and a following unequal crossing over due to high similarity of LCRs. This review presents an overview of the Williams-Beuren syndrome region considering the genomic assembly, chromosomal rearrangements and their mechanisms (i.e. deletions, duplications, inversions) and evolutionary and historical aspects. Received 11 July 2008; received after revision 15 October 2008; accepted 16 October 2008     

Where, when and how much: regulation of myelin proteolipid protein gene expression

The myelin proteolipid protein (PLP) gene (Plp) encodes the most abundant protein found in myelin from the central nervous system (CNS). Expression of the gene is regulated in a spatiotemporal manner with maximal levels of expression occurring in oligodendrocytes during the active myelination period of CNS development, although other cell types in the CNS as well as in the periphery can express the gene to a much lower degree. In oligodendrocytes, Plp gene expression is tightly regulated. Underexpression or overexpression of the gene has been shown to have adverse effects in humans and other vertebrates. In light of this strict control, this review provides an overview of the current knowledge of Plp gene regulation.Received 4 August 2003; received after revision 17 September 2003; accepted 24 September 2003     

The search for migraine genes: an overview of current knowledge

Migraine is a complex familial condition that imparts a significant burden on society. There is evidence for a role of genetic factors in migraine, and elucidating the genetic basis of this disabling condition remains the focus of much research. In this review we discuss results of genetic studies to date, from the discovery of the role of neural ion channel gene mutations in familial hemiplegic migraine (FHM) to linkage analyses and candidate gene studies in the more common forms of migraine. The success of FHM regarding discovery of genetic defects associated with the disorder remains elusive in common migraine, and causative genes have not yet been identified. Thus we suggest additional approaches for analysing the genetic basis of this disorder. The continuing search for migraine genes may aid in a greater understanding of the mechanisms that underlie the disorder and potentially lead to significant diagnostic and therapeutic applications. Received 16 December 2005; received after revision 9 October 2006; accepted 13 November 2006     

Phylogenetic origin of LI-cadherin revealed by protein and gene structure analysis

The intestine specific LI-cadherin differs in its overall structure from classical and desmosomal cadherins by the presence of seven instead of five cadherin repeats and a short cytoplasmic domain. Despite the low sequence similarity, a comparative protein structure analysis revealed that LI-cadherin may have originated from a five-repeat predecessor cadherin by a duplication of the first two aminoterminal repeats. To test this hypothesis, we cloned the murine LI-cadherin gene and compared its structure to that of other cadherins. The intron-exon organization, including the intron positions and phases, is perfectly conserved between repeats 3–7 of LI-cadherin and 1–5 of classical cadherins. Moreover, the genomic structure of the repeats 1–2 and 3–4 is identical for LI-cadherin and highly similar to that of the repeats 1–2 of classical cadherins. These findings strengthen our assumption that LI-cadherin originated from an ancestral cadherin with five domains by a partial gene duplication event.Received 22 December 2003; received after revision 9 February 2004; accepted 27 February 2004