Towards precise classification of cancers based on robust gene functional expression profiles

Background

Despite the continuous production of genome sequence for a number of organisms, reliable, comprehensive, and cost effective gene prediction remains problematic. This is particularly true for genomes for which there is not a large collection of known gene sequences, such as the recently published chicken genome. We used the chicken sequence to test comparative and homology-based gene-finding methods followed by experimental validation as an effective genome annotation method.

Results

We performed experimental evaluation by RT-PCR of three different computational gene finders, Ensembl, SGP2 and TWINSCAN, applied to the chicken genome. A Venn diagram was computed and each component of it was evaluated. The results showed that de novo comparative methods can identify up to about 700 chicken genes with no previous evidence of expression, and can correctly extend about 40% of homology-based predictions at the 5' end.

Conclusions

De novo comparative gene prediction followed by experimental verification is effective at enhancing the annotation of the newly sequenced genomes provided by standard homology-based methods.     

The induction of trehalose and glycerol in Saccharomyces cerevisiae in response to various stresses

Trehalose and glycerol have been implicated as potential stress protectants that accumulate in yeasts during various stress conditions. We investigated the levels of glycerol and trehalose and the expression profiles of genes involved in their metabolism to determine their involvement in the response of Saccharomyces cerevisiae XQ1 to thermal, sorbitol and ethanol stresses. The results showed that the genes involved in the synthesis and degradation of trehalose and glycerol were stress induced, and that trehalose and glycerol were synthesized simultaneously during the initial stages (a sensitive response period) of diverse stress treatments. Trehalose accumulated markedly under heat treatment, but not under sorbitol or ethanol stress, whereas glycerol accumulated strikingly under sorbitol stress conditions. Interestingly, extracellular trehalose seemed to be involved in protecting cells from damage under unfavorable conditions. Moreover, our results suggest that the stress-activated futile ATP cycles of trehalose and glycerol turnover are of general importance during cellular stress adaptation.     

Architecture and function of the lophophore in the problematic brachiopod Heliomedusa orienta (Early Cambrian, South China)

The detailed structure of the lophophore is a key diagnostic character in the definition of higher brachiopod taxa. The problematic Heliomedusa orienta Sun and Hou, from the Lower Cambrian Chengjiang Lagerstätte of Yunnan, southwestern China, has a well-preserved lophophore, which is unlike that of any known extant or extinct brachiopods. Based on a comparative study of lophophore disposition in H. orienta and the extant discinid Pelagodiscus atlanticus, the in- and excurrent pattern and shell orientation of H. orienta are described and discussed. Reconstructions of lophophore shape and function are based on numerous specimens and comparison with P. atlanticus. The lophophore is composed of a pair of lophophoral arms that freely arch posteriorly rather than coiling anteriorly as commonly seen in fossil and recent lingulids. The lophophore is attached to the dorsal lobe of the mantle; it has neither calcareous nor chitinous supporting structures, and is disposed symmetrically on either side of the valve midline. The mouth can be inferred to be located at the base of the two brachial tubes, slightly posterior to the anterodorsal projection of the body wall. The lophophoral arms bear laterofrontal tentacles with a double row of cilia along their lateral edge, as in extant lingulid brachiopods. The main brachial axes are also ciliated, which presumably facilitated transport of mucous-bound nutrient particles to the mouth. The unique organization of the lophophore in Heliomedusa is not like any known fossil and living brachiopods. This clearly demonstrates that H. orienta is not a member of any crown group. It is here considered as a member of the brachiopod stem group, which challenges recent interpretations of a close discinid affinity.     

Synthesis, structures and DNA binding of ternary transition metal complexes M(II)L with the 2,2′-bipyridylamine (L = p-aminobenzenecarboxylic acid, M = Ni, Cu and Zn)

New ternary transition metal complexes of formulations [Ni(bpa)(p-AB)Cl]_n · 3nH₂O (bpa = 2,2′-bipyridylamine, p-AB = aminobenzenecarboxylic acid) (1), [Cu(bpa)(p-AB)Cl] · H₂O (2), [Zn(bpa)(p-AB)₂] · H₂O (3) are prepared, their structural features are characterized by crystal structural studies, and their DNA binding propensity has been evaluated by fluorescence and viscosity method. In complex 2 and 3, both bpa and p-AB act as the bidentate N and O-donor ligand, respectively. While in complex 1, p-AB acts as a rare tridentate ligand. In the packing pattern of each complex, π-π interaction in their solid state is also described. The complexes show the competitive inhibition of ethidium binding to DNA, and the DNA binding propensity can be reflected as the relative order: 1 > 2 > 3.     

哺乳动物中的DNA主动去甲基化

DNA甲基化是一种相对稳定且可遗传的表观遗传标记,在植物和动物细胞中均发现有DNA主动去甲基化现象,其机制在植物中已基本得到阐释,但在哺乳动物中尚未鉴定出一种有效的DNA去甲基化酶,并且DNA主动去甲基化途径也存在争议。文章综合分析了近期的文献资料,阐述了哺乳动物中发生DNA主动去甲基化的时空特异性,并从细胞和组织特异性角度介绍DNA主动去甲基化的可能通路和机制,即5-甲基胞嘧啶的氧化作用、5-甲基胞嘧啶脱氨基以及DNA修复等,旨在为破译表观遗传重编程过程提供理论依据。     

诱导受体3（DcR3）在胆管癌中的表达及意义

目的:观察胆管癌组织及血清中诱导受体3(decoy receptor 3,DcR3)蛋白的表达及其临床价值。方法:采用免疫组化S-P法检测45例胆管癌、15例癌旁胆管正常组织中DcR3蛋白的表达,ELISA法检测31例胆管癌及18例胆道良性疾病患者和28例正常人外周血清中DcR3的水平。结果:45例胆管癌组织中DcR3阳性表达29例,阳性率为64.4%,胆管正常组织中无阳性表达。DcR3的表达与肿瘤临床分期、肿瘤浸润和转移有关(P<0.05)。胆管癌患者及胆管良性疾病患者血清DcR3水平分别为152.2535.94 pg/ml,98.35 14.27 pg/ml,均高于正常人。胆管癌患者与胆道良性疾病患者血清DcR3水平相比差异有显著性(P<0.01)。结论:DcR3在胆管癌组织中表达增高。DcR3的表达与胆管癌的发生、发展以及转移有关,可成为治疗胆管癌的一个新靶点。血清DcR3的检测对胆管癌的诊断有一定的临床价值。     

大蒜根系分泌物的化感作用

以苍山白蒜和蔡家坡紫蒜为材料,采用水培方法收集根系分泌物,研究了2个大蒜品种的根系分泌物对莴苣种子发芽和幼苗生长及对黄瓜枯萎病菌、西瓜枯萎病菌的化感效应.结果表明:2个大蒜品种的根系分泌物对莴苣种子发芽和幼苗生长均表现为低浓度(0.1、0.2 g·mL-1)促进、高浓度(0.4、0.6 g·mL-1)抑制,高浓度时蔡家坡紫蒜的抑制作用大于苍山白蒜;对黄瓜枯萎病菌和西瓜枯萎病菌的菌丝生长及孢子萌发均表现为抑制作用,随着根系分泌物浓度的提高,抑制作用增强,其中黄瓜枯萎病菌较敏感,且蔡家坡紫蒜的抑制作用大于苍山白蒜.     

酪酸梭菌活菌散在防治早产儿喂养不耐受方面的应用

目的观察和评价酪酸梭菌活菌散防治早产儿喂养不耐受的临床疗效。方法将56例早产儿随机分成观察组和对照组,观察组30例,对照组26例。对照组给予早产儿配方奶及部分肠外营养等常规治疗,观察组在常规治疗基础上同时添加酪酸梭菌活菌散。观察2组早产儿恢复出生体重、达到全胃肠喂养时间及发生喂养不耐受等情况。结果观察组早产儿恢复出生体重、达到全胃肠喂养时间明显短于对照组(P<0.01或P<0.05),喂养不耐受的发生率也显著少于对照组(P<0.05)。结论早产儿服用酪酸梭菌活菌散,对防治喂养不耐受具有积极的作用,能减少早产儿喂养过程中呕吐、胃潴留、腹胀的发生,促进患儿早期的生长发育,缩短达到全胃肠喂养的时间。     

白洋淀轮虫多样性及群落结构的初步研究

于2006年12月、2007年3～5月调查了白洋淀9个采样点的轮虫种类组成、数量及优势种,并对轮虫群落的多样性指数和群落相似性系数进行了测算,综合评价了白洋淀水质及富营养化状况.本次共发现轮虫41种,平均丰度为607～5024 ind./L,优势种为蒲达臂尾轮虫Brachionus budapesllensis、长肢多肢轮虫Polyarthra doli-choptera、角突臂尾轮虫B.angularis、矩形龟甲轮虫Keratella quadrata等,均为耐污性种类,各样点轮虫群落具较高相似性.从轮虫群落Margalef多样性指数看,白洋淀水质属中度污染和严重污染状况.