Genomic overview of serine proteases

Serine proteases (SP) are peptidases with a uniquely activated serine residue in the substrate-binding pocket. They represent about 0.6% of all proteins in the human genome. SP are involved in many vital functions such as digestion, blood clotting, fibrinolysis, fertilization, and complement activation and are related to many diseases including cancer, arthritis, and emphysema. In this study, we performed a genomic analysis of human serine proteases utilizing different databases, primarily that of MEROPS. SP are distributed along all human chromosomes except 18 and Y with the highest density (23 genes) on chromosome 19. They are either randomly located within the genome or occur in clusters. We identified a number of SP clusters, the largest being the kallikrein cluster on chromosome 19q13.4 which is formed of 15 adjacent genes. Other clusters are located on chromosomes 19p13, 16p13, 14q11, 13q35, 11q22, and 7q35. Genes of each cluster tend to be of comparable sizes and to be transcribed in the same direction. The members of some clusters are sometimes functionally related, e.g., the involvement of many kallikreins in endocrine-related malignancies and the hematopoietic cluster on chromosome 14. It is hypothesized that members of some clusters are under common regulatory mechanisms and might be involved in cascade enzymatic pathways. Several functional domains are found in SP, which reflect their functional diversity. Membrane-type SP tend to cluster in 3 chromosomes and have some common structural domains. Several databases are available for screening, structural and functional analysis of serine proteases. With the near completion of the Human Genome Project, research will be more focused on the interactions between SP and their involvement in pathophysiological processes.     

The Oompa-Loompas of the genome factories

Automation Technologies for Genome Characterization

edited by Tony J. Beugelsdijk, John Wiley and Sons, 1997. UK£55.00 hbk (xvi +306 pages) ISBN 0 471 12806 6     

Simulated distribution of vegetation types in response to climate change on the Tibetan Plateau

Abstract. Questions: What is the relationship between alpine vegetation patterns and climate? And how do alpine vegetation patterns respond to climate changes? Location: Tibetan Plateau, southwestern China. The total area is 2500000 km² with an average altitude over 4000 m. Methods: The geographic distribution of vegetation types on the Tibetan Plateau was simulated based on climatology using a small set of plant functional types (PFTs) embedded in the biogeochemistry‐biography model BIOME4. The paleoclimate for the early Holocene was used to explore the possibility of simulating past vegetation patterns. Changes in vegetation patterns were simulated assuming continuous exponential increase in atmospheric CO concentration, based on a transient ocean‐atmosphere simulation including sulfate aerosol effects during the 21st century. Results: Forest, shrub steppe, alpine steppe and alpine meadow extended while no desert vegetation developed under the warmer and humid climate of the early Holocene. In the future climate scenario, the simulated tree line is farther north in most sectors than at present. There are also major northward shifts of alpine meadows and a reduction in shrub‐dominated montane steppe. The boundary between montane desert and alpine desert will be farther to the south than today. The area of alpine desert would decrease, that of montane desert would increase. Conclusions: The outline of changes in vegetation distribution was captured with the simulation. Increased CO2 concentration would potentially lead to big changes in alpine ecosystems.     

Echinococcus granulosus:An Intraperitoneal Diffusion Chamber Model of Secondary Infection in Mice

Breijo, M., Spinelli, P., Sim, R.B., and Ferreira, A. M. 1998.Echinococcus granulosus:An intraperitoneal diffusion chamber model of secondary infection in mice.Experimental Parasitology90, 270–276. The present work describes a new experimental model of secondary infection which allows, through the recovery of the parasite together with its localin vivoenvironment, examination of the local nonadaptive immune response of the infected host and the differentiation of the parasite from protoscoleces to cysts. In this model we administered protoscoleces within silicone diffusion chambers, previously implanted into the peritoneal cavities of mice. The process of designing the model involved, first, determination of the optimal time postimplantation to infect the mice and, second, evaluation of the parasite's ability to establish infection within the chambers. The optimal time for infection was considered to be after the inflammation caused by implantation of the chambers had subsided. Our results showed that by day 20 postsurgery, three parameters used as indications of inflammation (complement C3, serum amyloid P protein, and polymorphonuclear cells in the peritoneum and in the chamber contents) had reverted to their normal levels. In our study of parasite differentiation, we found that 2–3% of the total number of parasites inoculated into the chambers were recovered as viable cysts after 100 days. Throughout the infection period, the population of parasites recovered was heterogeneous; certain parasite morphologies that have not been described previously were observed. In conclusion, the use of intraperitoneal diffusion chambers offers a potential tool for investigating thein vivodifferentiation process of secondary cysts ofEchinococcus granulosusin mice and the early local interactions between host and parasite during this process.     

非生物胁迫对烟草悬浮细胞胞内和胞外ATP水平的影响

以烟草悬浮细胞BY-2(Nicotiana tabacum ‘Bright Yellow-2’)为材料,研究了NaCl、PEG(6000)、低温3种非生物胁迫对细胞内ATP(intracellular ATP,iATP)和细胞外ATP(extracellular ATP,eATP)水平的影响。结果显示：50～200 mmol·L^-1 NaCl处理导致烟草悬浮细胞膜通透性显著增加(P<0.05),100和200 mmol·L^-1 NaCl处理时iATP和eATP水平显著降低(P<0.05)。随着PEG质量浓度的增加(50、100、200 g·L^-1),烟草悬浮细胞膜通透性和eATP水平逐渐增加,其中在200 g·L^-1 PEG处理时eATP水平显著增加至对照的3.4倍(P<0.05),而iATP水平则在200 g·L^-1 PEG处理时显著降低至对照的0.5倍(P<0.05)。0～10℃低温处理后,烟草悬浮细胞膜通透性和iATP水平呈不同程度增加,其中0℃处...     

南水北调中线水源区弃耕地草本植被演替初步研究

以南水北调中线水源区不同年限的退耕弃荒地为研究对象,分析了其草本植被恢复阶段的群落学特征,用聚类分析和极点排序的方法对各群落类型进行了划分,探讨了其自然演替规律,并对弃耕地植被恢复的一般机理进行了初步探讨。结果表明,草本植被恢复演替过程可明显分为以下几个阶段：荠菜(Capsella bursa—pastoris) 铁苋菜(Acalypha australis) 小白酒草(Conyza canadensis)群落(退耕1年);小白酒草(Conyza canadensis) 灰绿藜(Chenopodium glaucum)群落(退耕2年);艾蒿(Artemisia argyi) 小白酒草(Conyza canadensis) 猪毛蒿(Artemisia scoparia)群落(退耕3～6年);白茅(Imperata cylindrica) 牛尾蒿(Arternisia subdigitata) 野艾蒿(Artemisia lavandulaefolia) 狗尾草(Setaria viridis)群落(退耕7～12年^ )。退耕3年时群落已经趋于稳定,草本植被基本上得到恢复。     

The impact of uncertainty on phytoremediation project costs

Pollution of the environment by metals and organic contaminants is an intractable global problem, with cleanup costs running into billions of dollars using current engineering technologies. The availability of alternative, cheap and effective technologies would significantly improve the prospects of cleaning-up metal contaminated sites. Phytoremediation has been proposed as an economical and 'green' method of exploiting plants to extract or degrade the contaminants in the soil. To date, the majority of phytoremediation efforts have been directed at leaping the biological biochemical and agronomic hurdles to deliver a working technology, with scant attention to the economic outlook other than simple estimates of the cost advantages ofphytoremediation over other techniques. In this paper we use a deterministic actauarial model to show that uncertainty in project success (the possibility that full clean up may not be realized) may significantly increase the perceived costs of remediation works for decision-makers.     

整合现代教育技术与建构主义学习理论的基因组学创新教学模式

为了克服传统教学方式的各种弊端, 作为广东省分子生物学精品课程体系建设的内容之一, 对当今生命科学研究的热点领域—— 基因组学的教学模式进行了改革, 其中包括采用外国原版教材、进行双语教学以及以建构主义为指导的专题讨论教学法与多媒体辅助教学。在考试形式和实验教学方面, 则采用了多元化考核方式和增添了设计性实验。通过对基因组学教学的改革, 逐步完善了现代分子生物学课程体系的建设。     

功能基因组学的研究内容与方法

基因组学的研究已从结构基因组学转向功能基因组学.综述了功能基因组学研究的内容和方法,主要包括应用微点阵、基因表达系列分析(SAGE)、蛋白质组、生物信息学等方法来研究基因组表达概况、基因组多样性、模式生物体等.