Methionine oxidation perturbs the structural core of the prion protein and suggests a generic misfolding pathway

Oxidative stress and misfolding of the prion protein (PrP(C)) are fundamental to prion diseases. We have therefore probed the effect of oxidation on the structure and stability of PrP(C). Urea unfolding studies indicate that H(2)O(2) oxidation reduces the thermodynamic stability of PrP(C) by as much as 9 kJ/mol. (1)H-(15)N NMR studies indicate methionine oxidation perturbs key hydrophobic residues on one face of helix-C as follows: Met-205, Val-209, and Met-212 together with residues Val-160 and Tyr-156. These hydrophobic residues pack together and form the structured core of the protein, stabilizing its ternary structure. Copper-catalyzed oxidation of PrP(C) causes a more significant alteration of the structure, generating a monomeric molten globule species that retains its native helical content. Further copper-catalyzed oxidation promotes extended β-strand structures that lack a cooperative fold. This transition from the helical molten globule to β-conformation has striking similarities to a misfolding intermediate generated at low pH. PrP may therefore share a generic misfolding pathway to amyloid fibers, irrespective of the conditions promoting misfolding. Our observations support the hypothesis that oxidation of PrP destabilizes the native fold of PrP(C), facilitating the transition to PrP(Sc). This study gives a structural and thermodynamic explanation for the high levels of oxidized methionine in scrapie isolates.     

滇池北部湖区浮游植物时空格局及相关环境因子

为研究滇池北部湖区浮游植物的时空格局,探讨影响格局形成的关键影响因子,2008年12月至2009年6月,在滇池北部湖区选择6个点位,共开展了24次采样,调查并分析了浮游植物群落及其相关理化参数。通过比对滇池全湖周年监测数据,研究发现,北部湖区叶绿素a浓度从12月中旬开始下降,2月中旬降至最低值26.5μg/L,5月中旬达到最大值530.5μg/L。调查期间共鉴定出浮游植物74属97种,其中绿藻53种,蓝藻20种,硅藻17种,隐藻2种,金藻2种,甲藻1种,裸藻2种。蓝藻生物量在12月、3月至6月期间占优势,12月份优势种为绿色微囊藻(Microcystis viridis),3月至5月为水华束丝藻(Aphanizomenonflos-aquae),6月为惠氏微囊藻(Microcystis wesenbergii)。硅藻在1月占优势,优势种为颗粒直链藻最窄变种(Melosira granulata var.angustissima)。研究结果表明,水温高于14℃以上,微囊藻生物量迅速增加;束丝藻生物量随温度增加而增加,高于22℃时迅速减少。北部湖区6个点位浮游植物的空间差异显著,D1、D4号点微囊藻、束丝藻生物量显著高于其他四个点(P<0.01),D2、D5号点广缘小环藻生物量显著高于其他四个点(P<0.01)。研究结果显示,在富营养化严重的滇池北部湖区,水温可能为影响浮游植物种类组成及生物量的关键因子,浮游植物水平分布的差异主要由气象因素和水体营养盐共同决定。     

湖北九宫山成熟常绿落叶阔叶混交林3种优势种的邻域效应研究

以最近邻株距离统计研究了湖北九宫山成熟常绿落叶阔叶混交林3种优势种青冈栎(Cyclobalanopsis glauca)、甜槠(Castanopsis eyrei)和短柄枹栎(Quercus serrata var.brevipetiolata)的邻域效应,进而探讨了局域尺度上的竞争/帮促关系与物种共存格局.结果显示,青冈栎、甜槠和短柄枹栎的最近邻株距离不存在下限;青冈栎的胸径大小与其种内最近邻株距离存在正相关(p=0.029),甜槠的胸径大小与种内、种间最近邻株距离均无相关性(p≥0.360),而短柄枹栎的胸径大小与种间最近邻株距离为负相关(p=0.040);3树种中任意一个的种内与种间最近邻株距离都没有显著差异(p≥0.122).这些结果表明,九宫山成熟常绿落叶阔叶混交林内邻域尺度上的竞争排斥并未充分激化,但是青冈栎的种内竞争仍然在起作用,而甜槠的竞争效应不明显,短柄枹栎则依赖种间帮促甚于相互竞争.同种和异种之间的排斥效果没有差异表明局域尺度的物种共存格局可能出于随机过程而非负密度制约过程.     

Bayesian estimation of species richness from quadrat sampling data in the presence of prior information

We consider the problem of estimating the number of species of an animal community. It is assumed that it is possible to draw up a list of species liable to be present in this community. Data are collected from quadrat sampling. Models considered in this article separate the assumptions related to the experimental protocol and those related to the spatial distribution of species in the quadrats. Our parameterization enables us to incorporate prior information on the presence, detectability, and spatial density of species. Moreover, we elaborate procedures to build the prior distributions on these parameters from information furnished by external data. A simulation study is carried out to examine the influence of different priors on the performances of our estimator. We illustrate our approach by estimating the number of nesting bird species in a forest.     

Species identity and phylogenetic relationship of the pearl oysters in Pinctada Röding, 1798 based on ITS sequence analysis

Analysis of ITS 1 and ITS 2 sequences in the pearl oysters Pinctada albina, Pinctada chemnitzi, Pinctada fucata, Pinctada fucata martensii, Pinctada imbricata, Pinctada margaritifera, Pinctada maxima, Pinctada nigra and Pinctada radiata was carried out. Homogeneity test of substitution patterns suggests that GC contents are highest in P. margaritifera and P. maxima and chromosomal rearrangements occurred in P. chemnitzi. These observations indicate that P. margaritifera and P. maxima are primitive species and P. chemnitzi is a recent species. Phylogenetic analysis shows that the pearl oysters studied constitute three clades with P. margaritifera and P. maxima forming the basal clade, congruent with results revealed by the substitution pattern test. The second clade consists of P. fucata, P. fucata martensii and P. imbricata. Low genetic distances among these taxa indicate that they may be conspecific. The remaining species make up the third clade and low genetic divergence between P. albina and P. nigra suggests that they may represent the same species. The ITS 1 sequence of P. radiata in GenBank is almost identical to that of P. chemnitzi determined in the present study and we suspect that the specimen used for the P. radiata sequence was misidentified.     

CRF receptors in the rodent and human cardiovascular systems: species differences

CRF has powerful receptor-mediated cardiovascular actions. To evaluate the precise distribution of CRF receptors, in vitro CRF receptor autoradiography with ¹²⁵I-[Tyr⁰, Glu¹, Nle¹⁷]-sauvagine or [¹²⁵I]-antisauvagine-30 was performed in the rodent and human cardiovascular system. An extremely high density of CRF₂ receptors was detected with both tracers in vessels of rodent lung, intestine, pancreas, mesenterium, kidney, urinary bladder, testis, heart, brain, and in heart muscle. In humans, CRF₂ receptors were detected with ¹²⁵I- antisauvagine-30 at low levels in vessels of kidneys, intestine, urinary bladder, testis, heart and in heart muscle, while only heart vessels were detected with ¹²⁵I-[Tyr⁰, Glu¹, Nle¹⁷]-sauvagine. This is the first extensive morphological study reporting the extremely wide distribution of CRF₂ receptors in the rodent cardiovascular system and a more limited expression in man, suggesting a species-selective CRF receptor expression.     

alpha-Lactalbumin species variation, HAMLET formation, and tumor cell death

HAMLET (human alpha-lactalbumin made lethal to tumor cells) is a tumoricidal complex of apo alpha-lactalbumin and oleic acid, formed in casein after low pH treatment of human milk. This study examined if HAMLET-like complexes are present in casein from different species and if isolated alpha-lactalbumin from those species can form such complexes with oleic acid. Casein from human, bovine, equine, and porcine milk was separated by ion exchange chromatography and active complexes were only found in human casein. This was not explained by alpha-lactalbumin sequence variation, as purified bovine, equine, porcine, and caprine alpha-lactalbumins formed complexes with oleic acid with biological activity similar to HAMLET. We conclude that structural variation of alpha-lactalbumins does not preclude the formation of HAMLET-like complexes and that natural HAMLET formation in casein was unique to human milk, which also showed the highest oleic acid content.     

利用16SrDNA建立种特异性PCR快速检测鸭疫里默氏菌

鸭疫里默氏菌感染是危害养鸭业的主要疾病,用表型指标鉴定鸭疫里默氏菌存在不足,因此有必要建立检测该菌的种特异性PCR法。利用已登录的鸭疫里默氏菌、大肠杆菌、沙门氏菌、多杀性巴氏杆菌的16S rDNA基因序列,设计了一对鸭疫里默氏菌16S rDNA基因的特异性引物190f和843r,分别以基因组DNA和菌落提取液为模板,从1-19型鸭疫里默氏菌参考菌株和代表亚型、变异株和可能新型的国内分离株共26株细菌中均扩增出大小为654bp的特异性片段,而扩增鸭大肠杆菌、鸭沙门氏菌和禽多杀性巴氏杆菌等感染鸭的常见细菌的结果均呈阴性。分别将鸭疫里默氏菌基因组DNA和菌落提取液进行10倍梯度稀释,基因组DNA的最小检出量为50pg,菌落最小检出量为15CFU／mL。结果说明,该PCR法具有较好的特异性和敏感性,可用于快速鉴定鸭疫里默氏菌。     

Microbial diversity in natural environments: focusing on fundamental questions

Interactions with Gijs Kuenen and other Dutch scientists have led my lab to fundamental insights into the composition, structure and function of a hot spring cyanobacterial mat community that should influence our thinking about all microbial communities. By focusing on the distribution of molecular sequence variants of predominant mat phototrophs, we have discovered that small-scale sequence variation can be ecologically meaningful. By applying novel cultivation approaches, we have been able to obtain genetically relevant community members and thus to test the hypothesis that closely related sequence variants arose via adaptive evolutionary radiation. By applying the analytical tools of organic geochemistry we have gained insight into the metabolisms of major phototrophic members of the mat community as well as interactions between phototrophic guilds. These observations challenge traditional paradigms about prokaryotic species and cause us to consider evolutionary ecology theory as we develop genome-based methods for high-resolution analysis of the species-like fundamental units comprising microbial communities, and for investigating how such units coordinate the physiological activities within guilds of the community.