基于质谱技术的计算蛋白质组学研究

蛋白质组是继人类基因组计划完成之后又一新兴的生命科学研究对象，蛋白质组学研究细胞或组织内所有表达的蛋白质．生物质谱技术已为蛋白质组学研究产生了大规模的质谱数据；而如何从这些数据中提取和发现有关蛋白质组的重要生物学知识为计算蛋白质组学的研究提出了重大需求，如蛋白质鉴定、翻译后修饰、定量分析，以及疾病模式的发现等．本文研究了如何应用计算技术来解决蛋白质组学研究中质谱信息处理的这几个关键问题．     

污染胁迫下的蛋白质组学研究

近年来,以双向电泳技术、生物质谱和生物信息学为核心的蛋白质组学技术飞速发展,其大规模高通量的特点,使得这项技术逐渐在环境科学领域,尤其是对污染胁迫下差异蛋白表达和污染物特异性的生物标志物的筛选研究中得到了广泛的应用。本文简要介绍了蛋白质组学的基本概念和技术方法,对蛋白质组学在微生物、植物和动物对于无机污染物和有机污染物胁迫的响应机制和分子生物标志物探究等方面的研究进展进行了概述,并对蛋白质组学技术今后在生态环境领域的需求、应用与发展进行了展望。     

胎儿宫内发育迟缓疾病标志物的初步研究

目的筛选胎儿宫内发育迟缓大鼠血清中差异表达的蛋白质，寻找与胎儿宫内发育迟缓相关的疾病标志物。方法收集大鼠疾病正常组、IUGR组血浆各3例；TCA法沉淀血清蛋白，建立疾病组和正常组蛋白质的双向凝胶电泳图谱；ImageMaster分析软件分析差异蛋白质；飞行时间质谱（MALDI—TOF—MS）获得差异蛋白肽指纹图谱，MASCOT引擎搜索蛋白质种类。结果鉴定出个差异蛋白点3个，分别为：IGF—I、IGF-Ⅱ、IGFBP-3。结论IGF—I、IGF-II、IGFBP-3，可能是胎儿宫内发育迟缓疾病诊断的生物标志物。     

抑郁模型大鼠海马突触的差异蛋白质组学分析

目的通过抑郁模型大鼠海马突触的差异蛋白质组学分析，为抑郁症发病机制研究提供依据。方法根据糖水消耗基线值将40只健康雄性Sprague—Dawley大鼠随机分为慢性轻度不可预见性应激组和对照组（每组20只）。通过CUMS实验模式建立大鼠抑郁模型后，运用蔗糖密度梯度离心法提取两组大鼠的海马突触并用透射电镜进行检测。采用传统的双向凝胶电泳和基质辅助激光解析电离飞行时间串联质谱进行差异蛋白质组学分析。结果在行为学评价中CUMS组大鼠糖水消耗量和偏好度均降低（P〈0．01），表明大鼠抑郁模型建立成功。通过结合双向凝胶电泳和质谱分析，共得到6个在CUMS组表达上调和10个在CUMS组表达下调的蛋白质，这些蛋白质的功能主要归为四类，即囊泡调节／递质释放／信号转导、能量代谢、细胞骨架、物质代谢。结论通过对抑郁模型大鼠海马突触的比较蛋白质组学分析及后续的蛋白质功能预测，发现了一些与突触传导功能障碍可能相关的蛋白质，从而为抑郁症发病机制的研究提供了有价值的线索。     

中国科学院上海有机化学研究所生命有机国家重点实验室——生物合成课题组

作为药物发展的主要来源，天然产物在人类与各类疾病的斗争史上发挥了至关重要的作用。近年来随着基因组学和蛋白质组学研究的深入，我们可以运用分子遗传学的原理和技术，特异性地对天然产物的生物合成途径进行合理修饰来获得基因重组菌株，生物合成所需要的抗生素及其类似物（代谢工程，Metabolic Engineering）；或者从基因水平对天然产物的生物合成途径进行重组，建立结构复杂的天然产物类似物库，     

新版“生物信息学工具箱”发布

美国MathWorks公司近日发布了新版的Bioinformatics Toolbox for MATLAB（MATLAB生物信息学工具箱），新版“工具箱”将更好地帮助科学家从事药物、遗传工程、基因组学、蛋白质组学等研究。     

嗜酸氧化亚铁硫杆菌蛋白质组研究进展

嗜酸氧化亚铁硫杆菌在生物湿法冶金中具有广泛的应用前景.随着At.f菌分离与鉴定技术和基因组研究的深入,At.f菌的研究已进入蛋白质组水平.本文较详细地归纳总结了嗜酸氧化亚铁硫杆菌蛋白质组研究的最新进展,指出了未来的发展方向.     

运用生物大分子检测环境质量变异的研究进展

以DNA和蛋白质等生物大分子作为生物标志物在环境监测中应用广泛。本文在总结前人工作的基础上，根据前人的经验，对某些现存问题提出一些看法及可能的解决方案。     

表观遗传基因沉默研究新进展

美国弗吉尼亚联邦大学Massey癌症中心的研究人员确定出了一种蛋白质在血红蛋白基因沉默中的作用。这种蛋白将可能成为在分子水平上治疗遗传性血液疾病如镰刀细胞贫血症和β-地中海贫血症的一个非常有潜力的靶标。这项研究的结果公布在4月的PNAS（美国科学院院刊）中。研究人员首次发现蛋白质MBD2蛋白通过甲基化作用（DNA的一种化学修饰过程）介导胎儿gamma球蛋白基因沉默。     

后基因组时代的结构生物学及蛋白质和药物分子设计

人类基因组计划完成之后分子生物的重点将从基因组转到蛋白质组。在后基因组时代结构生物学将十分重要它既要回答生命过程中的重大基础理论问题，又与重要疾病治疗，蛋白质工程，药物设计，抗体设计，疫苗设计密切相关。     

Implications of toxins in the ecology and evolution of plant pathogenic microorganisms: Bacteria

This review attempts to rationalise what is known about bacterial phytotoxins and associate it with the ecology and possible evolution of the producing organisms. Study of non-toxin producing variants gives insight into the ecological role of the toxin. Elucidation of chemical structures of phytotoxins has shown that many exist as families of analogous compounds. Studies on the variation of chemical structures and how they are distributed across species and genera can lead to development of hypotheses on evolutionary relationships. Knowledge on biosynthetic pathways to tosins allows recognition of specific enzymatic steps involved in developing the characteristic features of the structures. Phytotoxins often have a potent biochemical activity, and in some cases the producing organism has associated mechanisms to prevent action of the toxin upon itself; in such cases toxigenesis is clearly not a chance event. The various aspects of bacterial toxigenesis indicate that bacterial phytotoxins are special secondary metabolic products that play beneficial roles to the producing organisms in their various ecological niches.     

Inherent properties and statistics with individual particles in quantum mechanics

This paper puts forward the hypothesis that the distinctive features of quantum statistics are exclusively determined by the nature of the properties it describes. In particular, all statistically relevant properties of identical quantum particles in many-particle systems are conjectured to be irreducible, ‘inherent’ properties only belonging to the whole system. This allows one to explain quantum statistics without endorsing the ‘Received View’ that particles are non-individuals, or postulating that quantum systems obey peculiar probability distributions, or assuming that there are primitive restrictions on the range of states accessible to such systems. With this, the need for an unambiguously metaphysical explanation of certain physical facts is acknowledged and satisfied.     

Instar-specific defensive secretions of stink bugs (Heteroptera: Pentatomidae)

Defensive secretions (allomones) from first-instar nymphs of stink bugs in the subfamily Pentatominae contain (E)-4-oxo-2-decenal as a major constituent, whereas this compound is absent from later instars. In contrast, first instars ofEdessa meditabunda (Edessinae) produce allomones like those of later instars. The C₆ and C₈ (E)-4-oxo-2-alkenals are common, characteristic exocrine compounds of nymphal and adult Heteroptera, but (E)-4-oxo-2-decenal is previously unknown as a major natural product for which a biological role has yet to be established.     

Spasmin-like proteins in various ciliates revealed by antibody to purified spasmins ofCarchesium polypinum

Summary It was found that some ciliates,Stentor, Spirostomum andBlepharisma, which can contract rapidly like the stalks of Vorticellidae, have Ca²⁺-binding proteins that are very similar to spasmins, in the immunological sense. The presence of spasmins in other Protozoa and in some Metazoa was also investigated.     

Partial sequence of the gene for a serine protease from a halophilic archaeumhaloferax mediterranei R4, and nucleotide sequences of 16S rRNA encoding genes from several halophilic archaea

A part of the gene coding for a halophilic serine protease from a halophilic archaeumHaloferax mediterranei R4 was amplified by PCR and its 672 nucleotide sequence was determined. Tentative translation to the amino acid sequence suggested that the enzyme was quite similar to halolysin produced by another halophilic archaeum strain 172P1. Nucleotide sequences of 16S rRNA encoding genes from 9 halophilic archaea were determined. Alignment of 19 sequences known so far showed that there are more than 20 positions carrying bases or deletions specific for each halobacterial genus:Halobacterium, Haloarcula, Haloferax, andHalococcus.     

Anthelmintic activity of a benzimidazoline compound in sheep by abomasal infusion

Summary In vitro and in vivo data on the benzimidazoline compound indicate anthelmintic potential when introduced directly into the abomasum.     

Cognition wars

In what kinds of physical systems can cognition be realized? There are currently competing answers among scientists and theorists of cognition. There are many plant scientists who maintain that cognition can be realized in plants. There are biological scientists who maintain that cognition is materially realized in bacteria. In this paper, I will present the basis for such claims and evaluate them and discuss the future for theories of the metaphysical basis of cognition in the cognitive sciences.     

Mating attempts between the Scarlet Tiger Moth,Callimorpha dominula L., and the Cinnabar Moth,Tyria jacobaeae L. (Lepidoptera: Arctiidae), involve a common sex pheromone composition

It has been suggested that a common sex pheromone composition may account for interspecific sexual interactions observed with certain moths in the Arctiidae. In this study, it is demonstrated that the sex pheromones released by females of the Scarlet Tiger Moth,Callimorpha dominula L., and the Cinnabar Moth,Tyria jacobaeae L., have similar activities and elute at the same retention time on analysis by coupled gas chromatography (GC)-electrophysiology with males from each species. Peak enhancement on GC, chiral GC and coupled GC-mass spectrometry using authentic compounds show that the sex pheromone for bothC. dominula andT. jacobaeae is (3Z,6Z,9S,10R)-9,10-epoxyheneicosa-3,6-diene.     

Phenology of fruit and leaf production by ‘strangler’ figs on Barro Colorado Island,Panamá

Summary Fruit and leaf initiation by 26 trees representing five stranglerFicus species in the subgenusUrostigma were monitored for 5–8 years in a seasonal lowland forest of central Panamá. Individual trees of each species initiated fruit in synchronized crops. High variation in the number of crops, intervals between crops and dates of crop initiation indicate that these species, like species in the subgenusPharmacosycea, initiate fruit crops the year around. Nevertheless, mean crop initiation dates for four of five species fell within the four-month dry season. Similarly, all species produced new leaf flushes throughout the year, however, mean leaf flush dates of all species fell within the first three months of the dry season.     

Phytotoxins as potential herbicides

Phytotoxins are produced in various culture media by many fungi that are pathogenic to weeds. These phytotoxins belong to a wide array of chemical substances including sesquiterpenoids, sesterterpenoids, diketopiperazines, peptides, spirocyclic lactams, isocoumarins, and polyketides. In most cases, the phytotoxin belongs to a family of related compounds produced by the fungus. These related compounds may or may not be phytotoxins. Phytotoxin production, in some cases, is optimized by the addition of a host extract to the culture medium. Biological activity is usually observed in a range of concentrations from 10^–3 to 10^–6 M. The concept of using these molecules, derivatives thereof, or related compounds as herbicides should be explored.