Clustering cancer gene expression data: a comparative study

Background  

The use of clustering methods for the discovery of cancer subtypes has drawn a great deal of attention in the scientific community. While bioinformaticians have proposed new clustering methods that take advantage of characteristics of the gene expression data, the medical community has a preference for using "classic" clustering methods. There have been no studies thus far performing a large-scale evaluation of different clustering methods in this context.     

Functional correlation between habitat use and leg morphology in birds (Aves)

Many of the morphological features of animals are considered to be adaptations to the habitat that the animals utilize. The habitats utilized by birds vary, perhaps more than for any other group of vertebrates. Here, we study possible adaptations in the morphology of the skeletal elements of the hind limbs to the habitat of birds. Measurements of the lengths of the femur, tibiotarsus and tarsometatarsus of 323 bird species from 74 families are used together with body mass data, taken from the literature. The species are separated into six habitat groups on the basis of literature data on leg use. A discriminant analysis of the groups based on leg morphology shows that swimming birds, wading birds and ground living species are more easily identified than other birds. Furthermore, functional predictions are made for each group based on ecological and mechanical considerations. The groups were tested for deviation from the norm for all birds for three indices of size- and leg-length-independent measures of the bones and for a size-independent-index of leg length. Several of the groups deviate significantly from the norm for one or more of the indices used, suggesting habitat-related adaptations in the leg morphology of birds. The results indicate that stability is an important factor affecting the leg morphology of primarily long-legged birds. The femur seems to be more important than previously thought because several of the groups have high femur indices, suggesting a positive selection pressure on this bone. On a general basis, the results suggest that the effect of leg length should be taken into consideration when discussing adaptations of mass-independent lengths of the long bones of the legs of birds.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 79, 461–484.     

三种啮齿类动物非酒精性脂肪肝形成及机制探讨

目的 分析物种差异对NAFLD模型复制的影响,探讨不同鼠种NAFLD形成及其机制.方法 长爪沙鼠、SD大鼠、ICR小鼠各20只,按种属随机分为对照组及模型组,对照组给予普通饲料,模型组给予高脂饲料.16周后,观察肝脏HE及Mallory三色染色病理变化,计算肝指数,检测血清血脂(CHO、TG、LDL-c、HDL-c)、肝功能(GOP、GPT)及肝组织中抗氧化酶(SOD、GSH-PX、CAT)活性及羟脯氨酸(Hyp)、丙二醛(MDA)、游离脂肪酸(FFA)水平.结果 与对照组比较,各模型组:沙鼠Hyp、CHO、TG、LDL-c、HDL-c、肝指数、GOP、GPT、MDA、FFA均升高,SOD、GSH-PX、CAT活性降低(P＜0.05,P＜0.01),肝脏出现纤维化;大鼠CHO、肝指数、GOP、GPT、FFA、SOD活性升高,MDA含量、GSH-PX、CAT活性降低(P ＜0.05,P＜0.01),有局灶性脂肪肝炎;小鼠CHO、LDL-c、HDL-c、肝指数、CAT活性升高,MDA含量降低(P ＜0.05,P＜0.01),肝脏病理正常.结论 三种动物在脂质代谢、肝功能、氧化应激等方面有显著的差异,并形成了不同的NAFLD模型:沙鼠形成伴高TG、CHO血症的肝纤维化模型、大鼠形成伴高CHO血症的局灶性脂肪肝炎模型、小鼠形成高胆固醇血症模型但肝脏未发生明显的病理改变.     

长爪沙鼠线粒体DNA控制区全序列测定及分析

目的对长爪沙鼠线粒体DNA控制区全序列进行测定,并对其进行鉴定及进化分析。方法根据长爪沙鼠已知基因序列设计引物,采用PCR产物测序法,对所得的片段进行测序鉴定。结合已公布啮齿类动物D-loop区序列,分析其碱基组成、遗传距离、并基于最小进化法和UPGMA法构建系统进化树。结果获得长爪沙鼠D-loop区序列,其与家鼠、小家鼠和仓鼠平均同源性为58%;碱基组成分析显示,长爪沙鼠与啮齿类动物有相似的碱基组成和碱基偏离,其A-skew和G-skew分别为0.0047和-0.28。进化分析结果显示,长爪沙鼠与家鼠（0.35）、黑家鼠（0.38）和仓鼠（0.39）具有较近的遗传距离,其分化顺序为跳鼠、蔗鼠、长爪沙鼠、仓鼠、家鼠和小家鼠。结论本研究获得长爪沙鼠D-loop区全序列,确定了长爪沙鼠与仓鼠、家鼠、小家鼠及其它啮齿动物的进化关系,为长爪沙鼠进化研究、线粒体的结构和功能研究奠定基础。     

内蒙古大兴安岭森林可燃物燃烧释放PM2.5中水溶性离子排放特性

研究森林可燃物燃烧释放的细颗粒物(PM2.5)的排放因子对于揭示森林火灾对大气和生态系统的影响至关重要,而水溶性离子是细颗粒物的重要化学成分,对颗粒物的形成具有重要意义.利用自主设计的生物质燃烧系统,模拟内蒙古大兴安岭5种典型乔木(蒙古栎、白桦、兴安落叶松、黑桦、山杨)的3种组成部分(树干、树枝、树皮)及其地表死可燃物...     

Hierarchical analysis of variation in the mitochondrial 16S rRNA gene among Hymenoptera

Nucleotide sequences from a 434-bp region of the 16S rRNA gene were analyzed for 65 taxa of Hymenoptera (ants, bees, wasps, parasitoid wasps, sawflies) to examine the patterns of variation within the gene fragment and the taxonomic levels for which it shows maximum utility in phylogeny estimation. A hierarchical approach was adopted in the study through comparison of levels of sequence variation among taxa at different taxonomic levels. As previously reported for many holometabolous insects, the 16S data reported here for Hymenoptera are highly AT-rich and exhibit strong site-to-site variation in substitution rate. More precise estimates of the shape parameter (alpha) of the gamma distribution and the proportion of invariant sites were obtained in this study by employing a reference phylogeny and utilizing maximum-likelihood estimation. The effectiveness of this approach to recovering expected phylogenies of selected hymenopteran taxa has been tested against the use of maximum parsimony. This study finds that the 16S gene is most informative for phylogenetic analysis at two different levels: among closely related species or populations, and among tribes, subfamilies, and families. Maximization of the phylogenetic signal extracted from the 16S gene at higher taxonomic levels may require consideration of the base composition bias and the site-to-site rate variation in a maximum-likelihood framework.      

Mycotoxins of Alternaria alternata produced on ceiling tiles

The production of mycotoxins by Alternaria alternata in cellulosic ceiling tiles was examined with thin-layer chromatography and high-performance liquid chromatography procedures. Alternariol and alternariol monomethyl ether were found in ceiling tile extracts, whereas extracts of control rice cultures of all three isolates produced these mycotoxins plus altenuene and altertoxin I. Extensive fungal growth and mycotoxin production occurred in the ceiling tiles at relative humidities of 84–89% and 97%. Received 28 May 1997/ Accepted in revised form 06 October 1997     

Immunochemical identity of peroxisomal enoyl-CoA hydratase with the peroxisome-proliferation -associated 80,000 mol wt polypeptide in rat liver

Peroxisome proliferators, which induce proliferation of hepatic peroxisomes, have been shown previously to cause a marked increase in an 80,000 mol wt polypeptide predominantly in the light mitochondrial and microsomal fractions of liver of rodents. We now present evidence to show that this hepatic peroxisome-proliferation-associated polypeptide, referred to as polypeptide PPA-80, is immunochemically identical with the multifunctional peroxisome protein displaying heat-labile enoyl-CoA hydratase activity. This conclusion is based on the following observations: (a) the purified polypeptide PPA-80 and the heat- labile enoyl-CoA hydratase from livers of rats treated with the peroxisome proliferators Wy-14,643 {[4-chloro-6(2,3-xylidino)-2-pyrimidinylthio]acetic acid} exhibit identical minimum molecular weights of approximately 80,000 on SDS polyacrylamide gel electrophoresis; (b) these two proteins are immunochemically identical on the basis of ouchterlony double diffusion, immunotitration, rocket immunoelectrophoresis, and crossed immunoelectrophoresis analysis; and (c) the immunoprecipitates formed by antibodies to polypeptide PPA-80 when dissociated on a sephadex G-200 column yield enoyl-CoA hydratase activity. Whether the polypeptide PPA-80 exhibits the activity of other enzyme(s) of the peroxisomal β-oxidation system such as fatty acyl-CoA oxidase activity or displays immunochemical identity with such enzymes remains to be determined. The availability of antibodies to polypeptide PPA-80 and enoyl-CoA hydratase facilitated immunofluorescent and immunocytochemical localization of the polypeptide PPA- 80 and enoyl-CoA hydratase in the rat liver. The indirect immunofluorescent studies with these antibodies provided direct visual evidence for the marked induction of polypeptide PPA-80 and enoyl-CoA hydratase in the livers of rats treated with Wy-14,643. The present studies also provide immunocytochemical evidence for the localization of polypeptide PPA- 80 and the heat-labile enoyl-CoA hydratase in the peroxisome, but not in the mitochondria, of hepatic parenchymal cells. These studies, therefore, provide morphological evidence for the existence of fatty acyl-CoA oxidizing system in peroxisomes. An increase of polypeptide PPA-80 on SDS polyacrylamide gel electrophoretic analysis of the subcellular fractions of liver of rodents treated with lipid-lowering drugs should serve as a reliable and sensitive indicator of enhanced peroxisomal β- oxidation system.     

Water Flow in Wheat Seedlings after Small Water Deficits

Cultures of Scenedesmus obliquus when grown heterotrophically for 10 or 30 days without addition of fresh medium showed 85 and 98% loss of their photosynthetic capacity respectively. This loss in photosynthetic capacity was accompanied by an increase in quantum requirement. No major changes in the pigment amounts or types were detected which would explain the decay in photosynthetic capacity. Partial reactions mediated by photosystem II or I showed a more or less constant decay over a period of 30 days. Photosystem II reactions appeared less stable than those of photosystem I, decaying by 95% as compared with 70%, over this time period. The results of comparative studies on aged cells for their potential of cytochrome f photooxidation, fluorescence kinetics, 520 nm absorbance change and the variable influence of 3-(3,4-dichlorophenyl)-1,1-dimethylurea and 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone on the photosynthetic capacity of such cells, suggest that it is the inherent ability of the cells to photooxidize plastohydroquinone which is affected primarily. In addition, secondary changes were noted in the activity of reactions on the water-splitting side of photosystem II and in the P700 — plastocyanin — cytochrome f complex.     

Determinants of avian malaria prevalence in mountainous Transcaucasia

Deforestation, urban development, and global climate change can lead to dramatic changes of ecological communities and increase prevalence of infectious diseases at higher latitudes and altitudes. Identification of factors responsible for the prevalence of parasites is of crucial importance to understand the dynamics of parasite distribution in a changing environment. Mountain areas are especially suitable for studies of factors governing parasite distribution and prevalence due to heterogeneity of landscapes, climatic regimes, and other biotic and abiotic conditions. We examined 903 avian blood smears collected in mountains of Transcaucasia for prevalence of Haemoproteus and Plasmodium. We found that the haemoparasites prevalence differed among bird species and localities, highlighting the environmental components affecting disease distribution. The prevalence of both Haemoproteus and Plasmodium was significantly higher in males, adults, and migratory species than in females, juveniles, and resident species. Geographic Information System (GIS) and linear regression analyses revealed that elevation and monthly average precipitation were strongly correlated with proportion of infected birds with Plasmodium, indicating that the prevalence increased with increase of monthly average temperature and elevation. Birds from forested and high grassed areas were also more infected with avian haemosporidia. Our study provides baseline data for modelling of parasites distribution under global climate change scenarios, which is of great importance for monitoring and management of communities and environment for conservation and human health.