Data exploration tools for the Gene Ontology database

MOTIVATION: To improve the ability of biologists (both researchers and students) to ask biologically interesting questions of the Gene Ontology (GO) database and to explore the ontologies by seeing large portions of the ontology graphs in context, along with details of individual terms in the ontologies. RESULTS: GoGet and GoView are two new tools built as part of an extensible web application system based on Java 2 Enterprise Edition technology. GoGet has a user interface that enables users to ask biologically interesting questions, such as (1) What are the DNA binding proteins involved in DNA repair, but not in DNA replication? and (2) Of the terms containing the word triphosphatase, which have associated gene products from mouse, but not fruit fly? The results of such queries can be viewed in a collapsed tabular format that eases the burden of getting through large tables of data. GoView enables users to explore the large directed acyclic graph structure of the ontologies in the GO database. The two tools are coordinated, so that results from queries in GoGet can be visualized in GoView in the ontology in which they appear, and explorations started from GoView can request details of gene product associations to appear in a result table in GoGet. AVAILABILITY: Free access to the GoGet query tool and free download of the GoView ontology viewer are provided to all users at http://db.math.macalester.edu/goproject. In addition, source code for the GoView tool is also available from this site, along with a user manual for both tools.     

Modelling expected trout ranges under current and future water temperature regimes in the Eastern Cape,South Africa

Different values have resulted in conflicts between anglers and conservation lobbies in the management of trout in South Africa. Key to the conflict is the demarcation of boundaries to areas in which brown trout Salmo trutta and rainbow trout Oncorhynchus mykiss currently occur, or are likely to establish following stocking for angling. To provide a longer-term perspective on these areas, we developed models to link salmonid biological thermal thresholds to elevation. These, when applied spatially using a digital elevation model with a probability of occurrence model, provided the basis for estimating potentially available thermal habitat for these two cold water species. Here, we acknowledge that other variables (stocking history; river connectivity) also play a role in understanding trout distributions. Using a simple scenario of an increase in mean daily water temperatures of 2 °C, we demonstrated that both brown and rainbow trout are likely to exhibit considerable range reductions in the future. Because it is possible that these range restrictions will result in an increasing desire to introduce trout into areas above their current distribution limits for the maintenance of angling opportunities, conservation managers should prioritise these areas, with management interventions seeking to understand what will help to limit introductions.     

东北小鲵中枢神经系统形态学与组织学初步研究

本文应用脊椎动物神经标本制作法和HE染色法,对东北小鲵中枢神经系统的外部形态和组织学结构进行了初步研究,描述了东北小鲵神经系统形态和组织学结构的特点,并与无尾两栖类和爬行类相对比,探讨了有尾两栖类的进化地位。结果表明:与无尾两栖类(如蛙)相比,东北小鲵中枢神经系统中,大脑半球较小,结构较为原始,小脑结构简单,是两栖类中较为原始的类群。此外,东北小鲵开始具有了臂神经丛和骶神经丛,但没有爬行类的发达,可作为两栖类向爬行类进化的证据之一。     

Characterization of microsatellite DNA markers in a critically endangered species,Mekong giant catfish,Pangasianodon gigas

Microsatellite DNA markers for a critically endangered Mekong giant catfish (Pangasianodon gigas Roberts and Vidthayanon, 1991) were developed from fin clips collected from captive fish using (GT)₁₅ probe. The number of alleles per locus ranged from two to four. The expected heterozygosities ranged from 0.13 to 0.68. Also, these primers were successfully amplified in four closely related species, Pangasius bocourti, Pangasius conchophilus, Pangasius larnaudii and Pangasius sanitwongsei with the number of alleles per locus ranged from 1 to 13, 1 to 16, 1 to 12 and 1 to 4, respectively. These markers should prove to be very useful for the evaluation of genetic diversity for this species and other related Pangasius species.     

利用恒河婴猴模型对肠道病毒71型传播感染特征的生物学分析

本文在前期工作基础上,进一步对肠道病毒71型(EV71)从恒河婴猴的感染个体向其他未感染个体传播的可能性及相关生物学特性做了初步分析.通过喷雾形式经呼吸道感染1~2月龄恒河婴猴(A组);在观察临床症状同时,于感染后第7天,取该组动物粪便处理后,将上清液以喷雾形式经呼吸道感染新的婴猴个体(B组),随后对该次代感染个体进行...     

Soil inorganic carbon storage pattern in China

Soils with pedogenic carbonate cover about 30% (3.44 × 10⁶ km²) of China, mainly across its arid and semiarid regions in the Northwest. Based on the second national soil survey (1979–1992), total soil inorganic carbon (SIC) storage in China was estimated to be 53.3±6.3 PgC (1 Pg=10¹⁵ g) to the depth investigated to 2 m. Soil inorganic carbon storages were 4.6, 10.6, 11.1, and 20.8 Pg for the depth ranges of 0–0.1, 0.1–0.3, 0.3–0.5, and 0.5–1 m, respectively. Stocks for 0.1, 0.3, 0.5, and 1 m of depth accounted for 8.7%, 28.7%, 49.6%, and 88.9% of total SIC, respectively. In contrast with soil organic carbon (SOC) storage, which is highest under 500–800 mm yr⁻¹ of mean precipitation, SIC storage peaks where mean precipitation is <400 mm yr⁻¹. The amount and vertical distribution of SIC was related to climate and land cover type. Content of SIC in each incremental horizon was positively related with mean annual temperature and negatively related with mean annual precipitation, with the magnitude of SIC content across land cover types showing the following order: desert, grassland >shrubland, cropland >marsh, forest, meadow. Densities of SIC increased generally with depth in all ecosystem types with the exception of deserts and marshes where it peaked in intermediate layers (0.1–0.3 m for first and 0.3–0.5 m for latter). Being an abundant component of soil carbon stocks in China, SIC dynamics and the process involved in its accumulation or loss from soils require a better understanding.     

甘薯愈伤组织中的淀粉酶

从甘薯愈伤组织和块根可溶性提取物中淀粉酶的非变性凝胶电泳和活性染色发现 ,愈伤组织和块根的淀粉酶完全不同。前者有 4种不同大小的淀粉酶 (2种α 淀粉酶和 2种 β 淀粉酶 ) ,而后者只有一种 (β 淀粉酶 ) ;其次 ,块根 β 淀粉酶对EDTA和 β 巯基乙醇都不敏感 ,而愈伤组织的淀粉酶对EDTA和 β 巯基乙醇都敏感。这些结果表明甘薯愈伤组织中不仅淀粉酶同工酶的数量多 ,而且包括α和 β两种类型。     

川芎嗪对Aβ25-35诱导体外大鼠海马神经元细胞凋亡的影响

本文通过Aβ25-35诱导体外原代培养的SD乳大鼠海马神经元,建立Aβ毒性损伤细胞模型,结合AnnexinV-FITC/PI荧光双染法流式细胞术、MTT比色法、实时荧光定量PCR及Western blot方法检测川芎嗪(tetrameth-ylpyrazine,TMP)对原代培养的海马神经元细胞活性、早期凋亡率和Bax、Bcl-2基因表达的影响。结果显示川芎嗪高、中剂量可明显增强细胞活性,增加神经元细胞的存活率(P<0.01),可显著抑制海马神经元细胞早期凋亡(P<0.01),抑制凋亡蛋白Bax的表达(P<0.01),增强抗凋亡蛋白bcl-2的表达(P<0.01)。川芎嗪可通过调节Bax/Bcl-2平衡抵抗Aβ25-35诱导的海马神经元凋亡,降低Aβ的神经元毒性,对海马神经元损伤有明显的保护作用。