MHC-BPS: MHC-binder prediction server for identifying peptides of flexible lengths from sequence-derived physicochemical properties

Major histocompatibility complex (MHC)-binding peptides are essential for antigen recognition by T-cell receptors and are being explored for vaccine design. Computational methods have been developed for predicting MHC-binding peptides of fixed lengths, based on the training of relatively few non-binders. It is desirable to introduce methods applicable for peptides of flexible lengths and trained by using more diverse sets of non-binders. MHC-BPS is a web-based MHC-binder prediction server that uses support vector machines for predicting peptide binders of flexible lengths for 18 MHC class I and 12 class II alleles from sequence-derived physicochemical properties, which were trained by using 4,208∼3,252 binders and 234,333∼168,793 non-binders, and evaluated by an independent set of 545∼476 binders and 110,564∼84,430 non-binders. The binder prediction accuracies are 86∼99% for 25 and 70∼80% for five alleles, and the non-binder accuracies are 96∼99% for 30 alleles. A screening of HIV-1 genome identifies 0.01∼5% and 5∼8% of the constituent peptides as binders for 24 and 6 alleles, respectively, including 75∼100% of the known epitopes. This method correctly predicts 73.3% of the 15 newly published epitopes in the last 4 months of 2005. MHC-BPS is available at .Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Quantitative real-time polymerase chain reaction for determination of plasmid copy number in bacteria

A method for determination of plasmid copy number (PCN) in bacteria by real-time quantitative polymerase chain reaction (QPCR) was developed as an alternative to current PCN assays. Conventional methods for PCN estimation are generally not of high throughput, laborious, have low reproducibility, require large amounts of biological samples and are applicable only for a narrow dynamic range. Real-time QPCR, using the ABI Prism 7000, was able to sensitively detect the quantity of the pUC ori based plasmid, NS3, transformed into Escherichia coli host, DH5alpha, to be 411+/-6.1. The PCN of pBR322 plasmid DNA in DH5alpha was estimated to be 40+/-0.6 which is within its previously reported PCN range of approximately 30 to 70. QPCR was found to show good reproducibility and high sensitivity in detecting a two fold difference in template concentration, and a wide linear dynamic range covering 0.5 pg to 50 ng of DNA. PCNs of DH5alpha bearing plasmids pBR322 and NS3 computed from real-time QPCR assay were validated by that of agarose gel assay, and a marginal difference of only 13.0% and 10.7% was found for the two plasmids respectively. The QPCR assay was able to detect changes in PCN of plasmid producing DH5alpha during the course of a 2 l batch fermentation.     

棕色田鼠睾丸和附睾雌激素α受体表达的增龄变化

应用免疫组织化学方法系统研究了初生（1日龄）到成体（60日龄）5个发育阶段各6只棕色田鼠睾丸和附睾内雌激素受体α（ERα）的表达。结果发现：①在生殖细胞中,1日龄组幼鼠的生殖母细胞和支持细胞有微弱的ERa阳性表达,10日龄组精原细胞中ERa有弱表达,25日龄组精子细胞出现了较强ERα阳性表达,发育到45日龄时精子细胞ERα阳性表达最强,成体组中各级生精细胞中均有ERα阳性表达。②在间质细胞中,1日龄组间质前体细胞有ERα阳性表达,10日龄表达减弱,而到25日龄增强,至45日龄达到峰值,而成体又减弱。③附睾中,1日龄附睾上皮细胞有ERα阳性表达,10和25日龄附睾管类肌细胞出现ERα阳性表达,45日龄和成体附睾管上皮细胞和类肌细胞中均有ERα阳性表达。上述结果表明,ERα可能作为一种特异性受体在棕色田鼠睾丸发育过程中影响睾丸间质细胞雄激素的分泌,进而调节生精过程和精子的发育成熟。     

粗茎鳞毛蕨应用的研究

为开发利用粗茎鳞毛蕨(Dryopteris crassirhizoma Nakai)的药用和观赏价值、提高其质量和产量,对其进行了人工有性繁殖和复壮研究.在大批量人工有性育苗的基础上,予以分组复壮、对照栽培.筛选出了经济简便的技术路线,观察了形态发育与栽培条件的相关性.     

鼎湖山季风常绿阔叶林物种多样性指数空间分布特征

生态学模式和生态学过程都具有尺度效应,研究取样尺度与物种多样性之间的关系,探索物种多样性空间分布的内在机制有助于更好地理解植物群落结构及其组织方式.作者研究了鼎湖山季风常绿阔叶林20 ha样地中Simpson指数、Shannon-Weiner指数和Pielou均匀度指数在空间上的分布特征及其与取样尺度的关系,并采用方差和变异系数描述它们的空间变异特征.结果表明,这3种指数均表现出较强的区域性分布特征,且这种区域性特征与取样尺度有关.它们的方差随尺度的增加都表现出单峰分布的特征,在80 m×100 m尺度上达到最大值;而变异系数则随尺度的增加而减小,其中Shannon-Weiner指数和Pielou均匀度指数在＜20 m×25 m尺度上,其变异系数急剧减小,之后则较为平缓.本研究结果表明在分析鼎湖山季风常绿阔叶林20 ha样地物种多样性时应考虑尺度效应和取样区域.     

绒山羊表达红色荧光及转胰岛素样生长因子Ⅰ基因体细胞核移植胚胎的制备

利用含有红色荧光和Neor基因双选择标记的IGF1毛囊特异表达载体pCDsR-KI转染绒山羊胎儿成纤维细胞,经G418筛选获得具有红色荧光的IGF1转基因细胞.核移植操作前,通过比较卵母细胞体外成熟培养不同时间的成熟率以及核与极体的距离,确定20h为绒山羊卵母细胞的最佳成熟时间.比较了不同激活方法和培养体系对孤雌胚激活效率和孤雌胚早期发育的影响,结果表明：IA23187＋6-DMAP组的激活效率和囊胚率（88.7%＆21.6%）均稍高于乙醇＋6-DMAP组（86.4%＆20.4%）,但二组相应数据之间差异均不显著（P〉0.05）,选择前者作为转基因核移植胚的激活方案;SOFaa和CR1aa两种体外培养体系中,孤雌胚卵裂率（86.8%vs83.9%）和囊胚率（23.1%vs17.2%）均差异不显著（P〉0.05）,选择结果较好的SOFaa组.比较了不同电融合参数的融合效果,结果表明：190V/mm处理组结果（62.4%）显著高于130V/mm（32.8%）和200V/mm（42.9%）组（P〈0.05）.通过T-SCNT获得转基因重构胚胎203枚,48h卵裂率为79.3%（161/203）,第7~9天囊胚发育率为15.3%（31/203）.所得到的31枚囊胚中,较强表达红色荧光蛋白的囊胚数为17枚（阳性率为54.8%）.随机挑选两枚红色荧光囊胚以PCR法进行鉴定,结果全部为转基因阳性.以上结果显示：（i）表达载体的红色荧光蛋白和Neor基因可以正常表达可获取转基因细胞和阳性转基因胚胎;（ii）所制备转基因囊胚仍有部分不表达红色荧光蛋白,说明即使选择转基因阳性细胞进行核移植所得囊胚也并非全部为转基因阳性,在囊胚期进一步筛选是必要的;（iii）通过TSCNT操作及优化,成功获得了表达红色荧光并同时转有IGF1基因的绒山羊胚胎,为绒山羊的转基因研究提供基础数据.     

ERK通路在脑缺血及缺血预处理沙土鼠海马神经元中的作用

目的：探讨细胞外信号调节激酶（ERK）通路在脑缺血及缺血预处理海马神经元中的作用。方法：雄性蒙古沙土鼠,随机分为假手术组（SH）、缺血/再灌注组（I/R）、缺血预处理组（IP）、PD98059组（PD）、溶剂对照组（VE组）、PD98059复合IP组（PIP）,每组按再灌注15 min、2 h、4 h、6 h、1 d、3 d、5 d及7 d又分8个亚组。建立前脑缺血再灌注损伤模型,观察对行为学、组织学、p-ERK、HSP70、Fos及NF-κB表达的影响。结果：IP组鼠探索活动、CA1区凋亡神经元数及NF-κB阳性神经元数较I/R组明显减少（P〈0.05）,CA1区Fos阳性神经元数、HSP70及CA3/DG区p-ERK表达水平较I/R组明显增加（P〈0.05）。PD组再灌注各点Fos阳性神经元数较I/R组明显减少（P〈0.05）。再灌注1 d、3 d凋亡神经元数较I/R组明显增多（P〈0.05）。PIP组各观察指标介于IP组及IR组间。结论：ERK通路在缺血后海马CA3/DG区的激活可能与该区的缺血耐受有关 诱导CA1区神经元Fos、HSP70表达,减少NF-κB生成是缺血预处理神经元保护作用的分子机制之一。     

Translocation of Amyloid Precursor Protein C-terminal Fragment(s) to the Nucleus Precedes Neuronal Death due to Thiamine Deficiency-induced Mild Impairment of Oxidative Metabolism

Thiamine deficiency (TD) is a model of neurodegeneration induced by mild impairment of oxidative metabolism. TD produces time-dependent glial activation, inflammation, oxidative stress, altered metabolism of amyloid precursor protein (APP), exacerbation of plaque formation from APP, and finally, selective neuron death in specific brain regions. The sub-medial thalamic nucleus (SmTN) is the most sensitive region to TD. Alteration in APP metabolism and nuclear translocation of carboxy-terminal fragments (CTF) of APP has been implicated in neuron death in other models of neurodegeneration. These experiments tested whether TD causes translocation of CTF into the nucleus of neurons in the SmTN that are destined to die after 9 days of TD by examining overlapping immunoreactivity (IR) of antibody APP 369 with either Alz90, 6E10 or 4G8 epitopes in the nuclei of the neurons in the SmTN. TD caused the accumulation of the CTF of APP in nuclei of SmTN neurons within 3 days of TD. These changes did not occur in the cortex which is spared in TD. Western blot analysis of nuclear fractions revealed a significant (61%; P < 0.026) increase in CTF 12 levels in TD SmTN (2.08 +/- 0.56) compared to control SmTN (1.29 +/- 0.41). Although TD increased CTF 15 levels in TD SmTN (1.95 +/- 0.73) compared to control SmTN (0.62 +/- 0.52) by 214%; P < 0.665 and decreased the full-length holo-APP levels in TD SmTN (0.32 +/- 0.30) compared to control SmTN (0.47 +/- 0.18) by 34%; P < 0.753, the differences were statistically insignificant. TD did not alter CTF 15 or CTF 12 levels in cortex. These findings demonstrate that changes in APP metabolism occur in early stages of TD, and they may play an important role in TD-induced selective neuronal loss.     

中国沼石蛾科五新种记述(昆虫纲,毛翅目)

记述沼石蛾科5新种:挪氏长须沼石蛾Nothopsyche nozakii Yang et Leng,sp.nov.、史氏弧缘沼石蛾Anabolia schmidi Leng et Yang,sp.nov.、云南弧缘沼石蛾Anabolia yunnanensis Leng et Yang,sp.nov.、中华多斑沼石蛾Lenarchus sinensis Yang et Leng,sp.nov.和浙江沼石蛾Limnephilus zhejiangensis Leng et Yang,sp.nov..新种模式标本保存于南京农业大学昆虫标本室.