绿脓杆菌外膜蛋白OprF的生物信息学分析

[目的]利用生物信息学方法预测绿脓杆菌外膜蛋白OprF的理化性质、高级结构和细胞表位。[方法]采用在线软件预测OprF蛋白的理化性质;Signal P 4.1软件预测OprF信号肽序列;利用TMHMM软件预测ACFA蛋白跨膜结构;SOPMA服务器预测蛋白的二级结构;Swiss-Model程序预测OprF三维结构;综合ABCpred与Bepi Pred方案预测OprF的B细胞表位;运用神经网络法预测OprF的CTL表位;使用MHC-Ⅱ类分子结合肽程序预测OprF的Th细胞表位。[结果]OprF为亲水性蛋白;1~24位氨基酸为信号肽序列;存在多个酶切位点;无跨膜结构并定位于细胞膜外;二级结构中含无规则卷曲34.36%、α-螺旋31.90%、β-转角11.66%、β-片层22.09%;并可能存在3个B细胞表位、2个CTL表位、4个Th细胞表位。[结论]系统分析了OprF蛋白的理化性质、信号肽、跨膜结构、二级与三级结构,以及B、T细胞抗原表位。     

具有抗氧化活性的酸性菟丝子多糖H2的研究

从药用植物菟丝子 (CuscutachinensisLam .)的种子中经碱液提取所得的粗多糖CHC ,经进一步分离纯化得一酸性纯多糖H2 ,其分子量大于 1.0× 10 6,利用化学方法和光谱分析方法对其结构进行了研究。多糖H2由 1,6_linked_β_DGalp、1,4_linked_β_DGalp、1,4_linked_β_DGalA和 1,2or 4_linked_β_L_Rhap构成主链 ,并在部分1,6_linked_β_DGalp残基的O_3位和 1,2or 4_linked_β_L_Rhap残基的O_4或O_2形成分枝点 ,以末端半乳糖构成末端。侧链由末端半乳糖 ,1,6_linked_β_DGalp、1,4_linked_β_DGalp和 1,3,6_linked_β_DGalp残基构成 ,连接于主链的1,6_linked_β_DGalp残基的O_3位。阿拉伯糖残基 1,5_linkedAra、1,3,5_linkedAra、末端Ara以及末端鼠李糖残基存在于多糖分子H2的外周 ,连接于侧链和主链的 1,6_linked_β_DGalp残基的O_3位。此外 ,药理研究结果显示 ,H2能减少自由基引起的对大鼠成嗜铬细胞瘤PC12神经细胞系的损伤 ,明显提高细胞的存活率     

猪水疱病病毒外壳蛋白的二级结构和抗原表位预测

以SVDV外壳蛋白基因序列为基础,采用Chou-Fasman法、Garnier-Robson 法和Karplus-Schulz法预测蛋白质的二级结构;按Kyte-Doolittle方案、Emini方案和Jameson-Wolf方案预测SVDV外壳蛋白的B细胞表位。预测结果表明,SVDV外壳蛋白的二级结构较为复杂,含有较多的转角和无规则卷曲等柔性区域以及α-螺旋和β-折叠区段;SVDV外壳蛋白的VP1、VP2和VP3上均有多个区域为B细胞优势表位,其中,VP1蛋白的B细胞表位优势区域比VP2和VP3蛋白的多,与已鉴定的B细胞表位相比较,该方法预测的结果有较高的准确度。为实验确定SVDV外壳蛋白的B细胞表位和反向疫苗学设计提供理论基础。     

小鼠可溶性ST2二级结构及B细胞表位的预测

目的:预测小鼠可溶性ST2的二级结构及B细胞表位。方法:采用SOPMA法预测小鼠可溶性ST2的二级结构;借助ProScale、Bcepred服务器,分析小鼠可溶性ST2的亲水性、可及性和柔韧性,并结合二级结构特征,预测小鼠可溶性ST2的B细胞表位。结果:小鼠可溶性ST2的二级结构由α螺旋(12.46%%)、无规卷曲(50.15%%)、β折叠(32.64%)和β转角(4.75%)组成。其B细胞表位可能位于N端第24～34、37～50、59～89、110～118、128～137、177～186、267～288和318～333氨基酸区段。结论:预测结果将有助于确定小鼠可溶性ST2的B细胞表位,为研制抗小鼠可溶性ST2抗体提供理论依据。     

人白细胞介素-36受体拮抗剂的二级结构及B细胞表位的预测

[目的]预测人白细胞介素-36受体拮抗剂(interleukin-36 receptor antagonist,IL-36Ra)蛋白的特性及其B细胞抗原表位。[方法]以人IL-36Ra基因序列为基础,应用Expasy工具中Prot Param程序分析人IL-36Ra蛋白的氨基酸组成、理化性质和二级结构;采用Prot Scale网络服务器预测亲水性和柔韧性;采用Emini和Kolaskar方案分析其可及性。结合其二级结构的特性,进一步预测IL-36Ra的B细胞抗原表位。[结果]人IL-36Ra的二级结构主要由无规则卷曲(44.52%)、β折叠(30.97%)、α-螺旋(18.06%)和β-转角(6.45%)组成。IL-36Ra蛋白肽链的36-37、72-79、91-96、103-110、126-130和134-138区段为B细胞表位区域的可能性较大。[结论]该研究采用多参数方案综合预测人IL-36Ra蛋白的二级结构和B细胞表位,为深入鉴定IL-36Ra的抗原表位及试验方法探索其单克隆抗体奠定了理论基础。     

SARS病毒M蛋白的二级结构和B细胞表位预测

以SARS病毒基因组序列为基础,采用GarnierRobson方法、ChouFasman方法和KarplusSchulz方法预测蛋白质的二级结构;按KyteDoolittle方案、Emini方案和JamesonWolf方案预测SARS病毒M蛋白的B细胞表位。预测结果表明,在SARS病毒M蛋白N端第11～20、27～36区段和第133～141区段可能是α螺旋中心;M蛋白分子N端第20～27、34～37,44～56,61～64,70～76,79～97,117～132,142～147,165～176区段和第216～221区段可能是β折叠中心。在M蛋白N端第5～6、40～44、105～107、112～116、189～190、202～203区段和第210～215区段具有较柔软的结构,有可能进行一定幅度的摆动或折叠而形成较复杂的三级结构。SARS病毒M蛋白N端第1～15、37～47、99～120、181～192区段和第196～215区段内或附近很可能是B细胞表位优势区域。以蛋白质的二级结构预测作为辅助手段,用抗原指数,亲水性参数和可及性参数预测SARS冠状病毒M蛋白的B细胞表位,为实验确定SARS病毒M蛋白的B细胞表位和免疫识别研究奠定了基础 。     

A型肉毒毒素Hc片段B细胞表位预测

应用4种参数和方法对A型肉毒毒素Hc片段进行综合分析,包括亲水性参数、可及性参数、抗原性参数和二级结构预测等方法,预测A型肉毒毒素Hc片段(BoNT/A-Hc)氨基酸序列的B细胞表位,结果显示B细胞表位可能位于其Hc片段残基第37-42、294-300、355-359、400-411等区域内或附近.分析预测结果将有助于确定BoNT/A-Hc的B细胞表位.     

肽链及蛋白质N-末端羰酰荧光衍生物的形成

短肽及胰岛素的N-末端经Dixpn转氨后具有荧光发色性质,其激发与发射波长随肽链氨基酸残基的种类和数量的不同而有差异,其范围大约为Ex 312—333nm;Em 398—408nm;量子产率为0.020—0.03.荧光发色团的基本化学结构可能是N-末端α-羰酰基及其相连的酰胺基,并且N-末端第二及第三位氨基酸残基对其荧光性质有影响.在碱性溶液中(pH>9.0)它的荧光强度降低,但在NaCl溶液中随盐浓度的增加而增强.在不同浓度的CuHCl溶液中,羰酰三肽的荧光强度变化随其氨基酸残基的种类和构型的不同而有差异.以上结果提示;α-羰酰荧光衍生物可能作为蛋白及肽N-末端的荧光探剂,可能成为研究蛋白和肽结构与功能的一种手段.     

人白细胞介素-38的特性分析及B细胞表位的预测

目的:为进一步了解人白细胞介素(IL)-38蛋白质的特性和B细胞表位,从GenBank中查得其序列,用生物信息学等方法预测人IL-38蛋白质的二级结构等特性,并对其B细胞表位进行预测。方法:应用ProtParam tool、ProtScale、Emini和Kolaskar等程序或方法,对IL-38的组成、理化特性、亲水性、柔韧性和可及性等进行分析,以进一步预测其二级结构和抗原表位。结果:IL-38的二级结构主要由无规则卷曲(44.08%)和β-折叠(39.47%)组成。其B细胞表位可能位于第26-36、45-55、78-98和124-143等氨基酸区段。结论:首次利用生物信息学方法对IL-38基因及其蛋白质结构进行了分析和预测,预测结果将有助于确定IL-38的B细胞表位,为IL-38基因功能的深入研究及研制IL-38单克隆抗体提供了理论依据。     

埃及伊蚊表皮结构蛋白AaCPR100A的抗原表位的生物信息学预测

【目的】预测埃及伊蚊Aedes aegypti表皮结构蛋白AaCPR100A的抗原表位。【方法】通过DNAStar 8的Protean软件对埃及伊蚊表皮结构蛋白AACPR100A的二级结构和亲疏水性、表面可及性、柔韧性等特性进行分析,预测其潜在的B细胞抗原表位和潜在的T细胞抗原表位。【结果】AaCPR100A蛋白的二级结构以转角和不规则卷曲为主,表面可及性、柔韧性较强,存在7个潜在的B细胞抗原表位,位于18-29、32-42、47-82、87-98、111-178、194-248氨基酸残基或其附近,同时有11个潜在的T细胞抗原表位,位于20-24、35-39、44-48、51-53、79-82、103-106、109-112、146-148、150-152、185-203、224-235氨基酸残基或其附近。【结论】AaCPR100A蛋白潜在的B细胞抗原表位有7个,潜在的T细胞抗原表位有11个,综合后有3个潜在抗原表位,预测结果将为进一步研究AaCPR100A蛋白的免疫学特性和功能奠定基础,并为蚊虫的控制提供潜在的靶标。     

Old-field successional dynamics on the Inland Pampa,Argentina

Abstract. The first 10 yr of old-field successional dynamics on the Argentine Inland Pampa were studied on a series of adjacent plots established consecutively between 1978 and 1989. We examined differences in species abundance patterns among plots in order to detect the spatial and temporal variability of succession. Perennial grasses steadily increased in cover and replaced the dominant annual species after 5 yr. Pioneer dicots persisted in older seral stages with 20 — 23 species/plot. Overall, exotic species (mostly the grasses Lolium multiflorum and Cynodon dactylon) contributed much to the plant cover in these communities. Native grasses comprised 45 % of total cover at years 7 — 10 of succession, but occurred with less than 7 species/plot. Substantial variation was found in the successional pathway, which reflected the particular sequence from annual forbs to short-lived and perennial grasses in the various plots. The course of succession was apparently influenced by a 2-yr period of unusually high rainfall. Deyeuxia viridiflavescens, a native perennial grass virtually absent before the wet period, spread over the study area and dominated seral communities for 3 yr, irrespective of plot age. Climatic conditions thus affected the successional turnover of life forms by increasing the rate of colonization by perennial grasses. We further point out the constraints imposed on secondary succession by the life histories of ‘available’ species.     

Seeding tallgrass prairie in monospecific patches promotes native species establishment and cover

In tallgrass prairie reconstruction, the way desired seeds are arranged on the landscape may affect species establishment, species persistence, and the establishment and persistence of undesired (nonseeded) species from the local propagule pool. To test effects of species seeding pattern on how grasslands develop spatially, we seeded 20—4 × 4–m bare soil plots with 16 tallgrass prairie species. Treatment plots were divided into 16—1 × 1–m subplots, 64—0.5 × 0.5–m subplots, 256—0.25 × 0.25–m subplots, or 1,024—0.125 × 0.125–m subplots. Each species was hand broadcast into separate subplots (1 m² total area/species) within each plot. An additional treatment included uniformly mixing and broadcasting all seeds across a plot. We recorded species cover at the 0.125 × 0.125–m scale within each plot at the beginning of the second and third growing seasons. While species persistence was greatest within plots seeded with larger subplots, plots with smaller subplots were more spatially diverse and less occupied by nonseeded species over time than larger subplot and mixed plots. As is common in reconstruction efforts, establishment was variable among species and seeding with monospecific subplots enhanced colonization of desired rhizomatous species (e.g., Heliopsis helianthoides, Monarda fistulosa, Elymus virginicus) into unoccupied locations at the expense of species from the local propagule pool. Results suggest that seeding species in smaller, monospecific patches could result in grasslands with a more balanced native species composition than those established with a seed mixture approach.     

Comparative analysis of the floristic richness of alpine communities in the Caucasus and the Central Alps

Abstract. Species richness of selected alpine plant communities in the Teberda Biosphere Reserve (Northwestern Caucasus) and the Davos area (Central Alps) was compared in series of plots from 0.0025 to 100 m². Communities developing under similar ecological conditions and with similar syntaxonomic positions were compared in order to estimate the role of recent environment versus regional historical factors in determining plant community structure and diversity. The floristic richness of the Caucasian and Alpic fens was very similar. The Grasslands and Meadows were quite similar as to floristic richness for plots > 25 cm × 25 cm, but the Caucasian communities had fewer species in smaller plots. The Lichen heath at Teberda was richer than the Caricetum curvulae cetrarietosum for all plot sizes, except the two smallest ones. On the other hand, the plots of the Salix Snowbed community were richer in species than the Caucasian snowbeds for all plot sizes. The Rhododendron Shrubland plots were very similar as to floristic richness in larger plots (4 — 100 m²). Generally, most Alpic communities near Davos were richer in species at small plot sizes than the corresponding communities from Teberda. Caucasian communities were floristically less similar to each other — and thus more discrete — than the Alpic ones. The possible role of different factors controlling floristic richness of the communities is discussed. Our results suggest that recent ecological conditions have a big influence on local floristic diversity and may lead to high similarities between ecologically similar communities from different regions. In addition, the general floristic richness of a regions as well as island effects should be taken into account.     

Temperature dependence of the photosynthetic activities in the thylakoid membranes from the blue-green alga Anacystis nidulans

The photosynthetic electron transport and phosphorylation reactions were measured in the room temperature region in the thylakoid membranes prepared from the blue-green alga, Anacystis nidulans. The Arrhenius plot of the Hill reaction with 2,6-dichlorophenolindophenol showed a distinct break of straight lines at 21°C in the membranes from cells grown at 38°C, and at 12°C in those from cells grown at 28°C. The Arrhenius plot of the Hill reaction with ferricyanide showed a break at 13°C in the membranes from cells grown at 38°C, and at 7°C in those from cells grown at 28°C. On the other hand, the Arrhenius plot of the System I reaction with methylviologen as an electron acceptor and 2,6-dichlorophenolindophenol and ascorbate as an electron donor system was composed of a straight line in the membranes from cells grown at 28°C as well as at 38°C. The Arrhenius plot of the System II reaction measured by the ferricyanide reduction mediated by silicotungstate in the presence of 3-(3′,4′-dichlorophenyl)-1,1-dimethylurea also showed a break at 11°C in the membranes from cells grown at 38°C.The Arrhenius plot of the phosphorylation mediated by N-methylphenazonium methylsulfate showed a break at 21°C in the membranes from cells grown at 38°C and at 12°C in those from cells grown at 28°C. The Arrhenius plot of the phosphorylation mediated by the System I reaction showed a break at 24°C in the membranes from cells grown at 38°C.The characteristic features in the Arrhenius plots of the photosynthetic electron transport and phosphorylation reactions are discussed in terms of the transition of physical phase of the thylakoid membrane lipids.     

促红细胞生成素基因表达载体的构建及其在CHO细胞中表达的研究

用从基因文库中所克隆的促红细胞生成素（ＥＰＯ）基因组基因,构建了３种由不同启动子调控的表达载体——ｐＯＰ１３／ＥＰＯ,ｐＲＳＶ／ＥＰＯ,ｐＣＭＶ／ＥＰＯ,在这３个表达载体的构建过程中对基因的转录起始效率、内含子的剪接、５′非翻译区和３′非翻译区对基因表达的影响等因素都加以考虑．用脂质体转染法分别将上述３个载体导入ＣＨＯ细胞,经瞬时表达,用ＥＬＩＳＡ方法检测,表达量分别为１９０ｍＩＵ／ｍｌ、１６０ｍＩＵ／ｍｌ、４４７ｍＩＵ／ｍｌ．用表达载体ｐＯＰ１３／ＥＰＯ转染ＣＨＯ－Ｋ１２细胞,在４００μｇ／ｍｌ的Ｇ４１８浓度下筛选稳定表达细胞克隆,获得了表达量约为１６０ＩＵ／１０６细胞（４８ｈ）的Ｃ１０细胞株．表达产物经Ｗｅｓｔｅｒｎｂｌｏｔ检测发现了ＥＰＯ阳性条带．用ＴＦ－１细胞对ＥＰＯ进行了生物活性检测,初步证实所表达的ＥＰＯ有生物活性．     

Allosteric repression: An Analysis

A kinetic analysis of repression is presented based on the accepted sequence of molecular events and the assumption that the co-repressor-repressor interaction involves an allosteric transition. This leads to an expression which relates the two experimentally accessible variables—enzyme and signal—when the system is operating in vivo. A suitable plot allows the estimation of a coefficient, h_max, which is related to the number of protomers, n, of the oligomeric repressor protein. This parameter is similar to but distinct from a Hill coefficient for allosteric inhibitions. Two examples from the literature are analysed in terms of the model.     

Nucleotide, dinucleotide and trinucleotide frequencies explain patterns observed in chaos game representations of DNA sequences.

The chaos game representation (CGR) is a scatter plot derived from a DNA sequence, with each point of the plot corresponding to one base of the sequence. If the DNA sequence were a random collection of bases, the CGR would be a uniformly filled square; conversely, any patterns visible in the CGR represent some pattern (information) in the DNA sequence. In this paper, patterns previously observed in a variety of DNA sequences are explained solely in terms of nucleotide, dinucleotide and trinucleotide frequencies.     

采伐干扰对华北落叶松细根生物量空间异质性的影响

以华北落叶松天然林为研究对象,选择采伐干扰林分(样地A)和未采伐干扰林分(样地B),利用根钻法分3层(0—10cm,10—20cm,20—30cm)获取各径级细根(≤1mm、1—2mm、2—5mm3级活细根,≤2mm死亡细根)生物量数据。采用地统计学变异函数和经典统计相结合的数据分析方法对采伐干扰造成的细根生物量空间异质性的变化进行定量研究。主要研究结果如下:采伐干扰林分样地A各经级细根生物量均值减少;同一土层相同径级细根生物量样地A与样地B相比差异显著(P<0.05);不同土层的细根生物量异质性具有显著差别(P<0.05)。0—10cm土层,未采伐干扰林分≤1mm细根生物量呈现较明显的空间自相关变异,采伐干扰林分则表现为随机性变异特征,采伐干扰导致≤1mm细根生物量空间分布特征更加复杂(分维数D=1.978);10—20cm土层,采伐干扰林分各径级细根生物量异质性程度明显降低,只有未采伐干扰林分的5.4%—88.9%。20—30cm土层,未采伐干扰林分≤1mm细根生物量在较小尺度范围(<2.9m)表现出明显的空间自相关变异(结构方差比86.1%),受采伐干扰林分各径级细根生物量异质性程度只有未采伐干扰林分的8.9%—45.9%,且呈现随机性变异。各径级细根生物量空间异质性的垂直分异均表现为随土层深度的增加异质性强度明显降低。     

A long-term study of Pinus banksiana population dynamics

Abstract. The long-term population dynamics of a pure, naturally-established stand of Pinus banksiana (jack pine) in southeastern Manitoba, Canada is described. The study was initiated at stand age 15, when all 468 trees in a plot were mapped and their trunk diameter at breast height (DBH) measured. The plot was remeasured eight times — every five years (six years in one case) — and mortality and DBH changes recorded. Total mortality over the 41-yr study period was ca. 84 %. Mortality was initially very low, increased once the stand entered the self-thinning stage from ages 25–46, and declined at ages 46–56. Mortality was restricted to the smallest size classes throughout. The stand reached the self-thinning line at ca. age 30. The self-thinning slope was significantly less steep than the theoretically expected value of ?0.5. The distribution of DBH values was initially symmetric, showed increasing positive skewness during the period of highest mortality, and became symmetric again at later stages. Size (DBH) inequality was highest just prior to the onset of density-dependent mortality, and subsequently declined. Tree DBH values were positively autocorrelated both initially and at later stages of stand development, but were spatially independent during the period of highest density-dependent mortality. The stand initially had a strongly clumped pattern at all spatial scales. Patterns of mortality were non-random during stand development, however, resulting in increased spatial regularity over time. Mortality was initially restricted to high density patches of the stand, but occurred throughout the plot once the self-thinning line was reached. Mortality during the self-thinning stage deviated from random expectation at local spatial scales (1–2m radius), suggesting that individuals were competing with their immediate neighbours. It is argued that an integrated approach, incorporating both population size and spatial structures, is essential in improving our understanding of long-term plant population dynamics.     

Competition and body size in plants: the between-species trade-off for maximum potential versus minimum reproductive threshold size

Aims According to traditional theory, superior competitive ability in plants generally requires relatively large plant body size. Yet even within the most crowded vegetation, most resident species are relatively small; species size distributions are right-skewed at virtually every scale. We examine a potential explanation for this paradox: small species coexist with and outnumber large species because they have greater 'reproductive economy', i.e. they are better equipped—and hence more likely—to produce offspring despite severe size suppression from intense competition.Methods Randomly placed plots within old-field vegetation were surveyed across the growing season. Within each plot, the largest (MAX) and smallest (MIN) reproductive individuals of each resident species were collected for above-ground dry mass measurement. We tested three hypotheses: (i) smaller resident species (with smaller MAX size) have generally smaller reproductive threshold sizes; (ii) smaller resident species have greater 'reproductive economy', i.e. a smaller MIN relative to MAX reproductive plant size; and (iii) MIN size predicts plot occupancy (species abundance within the community) better than MAX size.Important findings The results supported the first and third, but not the second hypothesis. However, we could not reject the hypothesis that smaller species have greater reproductive economy, as it was not possible to record data for the largest potential plant size for each species—since even the largest (MAX) plants collected from our sampled plots were subjected to competition from neighbours under these natural field conditions. Importantly, contrary to conventional competition theory, more successful species (in terms of greater plot occupancy) had smaller minimum not larger (or smaller) maximum reproductive sizes. These results suggest that a small reproductive threshold size, commonly associated with relatively small potential body size, is generally more effective in transmitting genes into future generations when selection from neighbourhood crowding/competition is intense—at least within natural old-field vegetation. Accordingly, we propose a simple conceptual model that represents the basis for a fundamental paradigm shift in the predicted selection effects of crowding/competition on plant body size evolution.