基于不同标度伪氨基酸组成预测脂肪酶的类型

从序列出发预测某蛋白质是否为脂肪酶以及属于哪种脂肪酶具有重要的理论和应用价值.提出了基于Z标度和T标度的伪氨基酸组成方法提取序列特征值,采用了k-近邻算法回答上述问题.经参数选择后,三种方法在各自最优运行参数下,其1倍交叉验证的结果为:对脂肪酶和非脂肪酶预测精度分别为92.8%、91.4%和91.3%;对脂肪酶类型预测的精度分别为92.3%、90.3%和89.7%.其中基于Z标度伪氨基酸组成效果最佳.基于T标度的次之,但均明显优于其他6种常见的特征值提取方法,并对其可能的原因进行了探讨.     

库姆塔格沙漠植被特征分析

沿7条考察路线布设了91个样地,对库姆塔格沙漠植物组成、群落结构及植被分布等特征进行调查分析。结果表明:(1)库姆塔格沙漠植物相对稀少,有23科73属109种植物,物种组成趋向于集中在少数大科中和单种属中,优势科属组成较少,植物区系的温带性质明显,并与古地中海成分关系密切。(2)库姆塔格荒漠植被类型较为丰富,拥有4种植被型17个植被群系。受干旱气候及古水系变化的影响,植被群落物种组成稀少,结构单调,在一定程度上反映了荒漠生态环境的严酷性。(3)库姆塔格荒漠植被分布格局受气候、水分条件的影响较大。沙漠南缘降水条件相对较好,植被分布由东到西随降水的递减而呈现减弱趋势,北缘植被则表现为随古水系的萎缩而减小;植被随海拔高度的分布则表现为随海拔由南到北逐级降低,气候愈为干燥,地表径流减少,植被分布更为稀少。     

Estimating contemporary early life-history dispersal in an estuarine fish: integrating molecular and otolith elemental approaches

Dispersal during the early life history of the anadromous rainbow smelt, Osmerus mordax , was examined using assignment testing and mixture analysis of multilocus genotypes and otolith elemental composition. Six spawning areas and associated estuarine nurseries were sampled throughout southeastern Newfoundland. Samples of adults and juveniles isolated by > 25 km displayed moderate genetic differentiation ( F _ST ~ 0.05), whereas nearby (< 25 km) spawning and nursery samples displayed low differentiation ( F _ST < 0.01). Self-assignment and mixture analysis of adult spawning samples supported the hypothesis of independence of isolated spawning locations (> 80% self-assignment) with nearby runs self-assigning at rates between 50 % and 70%. Assignment and mixture analysis of juveniles using adult baselines indicated high local recruitment at several locations (70–90%). Nearby (< 25 km) estuaries at the head of St Mary's Bay showed mixtures of individuals (i.e. 20–40% assignment to adjacent spawning location). Laser ablation inductively coupled mass spectrometry transects across otoliths of spawning adults of unknown dispersal history were used to estimate dispersal among estuaries across the first year of life. Single-element trends and multivariate discriminant function analysis (Sr:Ca and Ba:Ca) classified the majority of samples as estuarine suggesting limited movement between estuaries (< 0.5%). The mixtures of juveniles evident in the genetic data at nearby sites and a lack of evidence of straying in the otolith data support a hypothesis of selective mortality of immigrants. If indeed selective mortality of immigrants reduces the survivorship of dispersers, estimates of dispersal in marine environments that neglect survival may significantly overestimate gene flow.     

Birds are tracking climate warming, but not fast enough

Range shifts of many species are now documented as a response to global warming. But whether these observed changes are occurring fast enough remains uncertain and hardly quantifiable. Here, we developed a simple framework to measure change in community composition in response to climate warming. This framework is based on a community temperature index (CTI) that directly reflects, for a given species assemblage, the balance between low- and high-temperature dwelling species. Using data from the French breeding bird survey, we first found a strong increase in CTI over the last two decades revealing that birds are rapidly tracking climate warming. This increase corresponds to a 91 km northward shift in bird community composition, which is much higher than previous estimates based on changes in species range edges. During the same period, temperature increase corresponds to a 273 km northward shift in temperature. Change in community composition was thus insufficient to keep up with temperature increase: birds are lagging approximately 182 km behind climate warming. Our method is applicable to any taxa with large-scale survey data, using either abundance or occurrence data. This approach can be further used to test whether different delays are found across groups or in different land-use contexts.     

Microfungal biodeterioration of historic paper: Preliminary FTIR and microbiological analyses

Paper is subjected to numerous biodeterioration processes, which may cause the irreversible degradation of important documents and works of art. Many chemical and physical factors can affect these processes and their behaviour, and fungi seem to play a key role in biodeteriorating paper materials. This study is mainly aimed at verifying the presence of fungi in biodeteriorated 18th century etchings, and characterizing the paper surface by means of Fourier transform infrared (FTIR) spectroscopy and fluorescence under UV radiation. The laboratory tests highlight the presence of fungal entities from all the samples investigated. Specifically, 14 species were identified; three of them were never isolated from paper until now. Furthermore, the data gathered do not confirm the theory according to which there is a correspondence between fluorescence of the stains under UV radiation and the vitality of microfungi. Finally, possible correlations among paper composition (as determined by FTIR), mode of conservation and fungal attack are presented and discussed.     

Chemical composition and in vitro ruminal fermentation of common tree forages in the semi-arid rangelands of Swaziland

Browse plants play an important role in providing feed for livestock in semi-arid rangelands of Africa. Chemical composition and in vitro ruminal fermentation of leaves collected from Acacia burkei, Acacia tortilis, Acacia nilotica, Dichrostachys cinerea and Ehretia obtusifolia in communal grazing lands in the lowveld of Swaziland is presented. Leaves were collected from trees located on two soil types (i.e., lithosol and vertisol) in the communal land but it had no effect on the chemical composition of tree leaves. The NDFom and ADFom content were highest in D. cinerea and A. burkei and lowest in E. obtusifolia and A. nilotica. Crude protein (CP) contents ranged between 108 g/kg and 122 g/kg DM. D. cinerea had the highest Ca and Mg content, while A. tortilis had the lowest. There were marked variations in K level amongst browse species, with A. tortilis (9.1 g/kg DM) having the highest value. The P, Zn and Fe did not differ between browse species. Soil type and tree species interaction impacted in vitro fermentation parameters. Extent of fermentation, as measured by 48 h cumulative gas production, and organic matter degradability was highest in E. obtusifolia leaves and lowest in D. cinerea leaves within soil type. Fermentation efficiency, as measured by partitioning factors, was highest in A. nilotica leaves. Leaves of E. obtusifolia could be a valuable supplementary feedstuff for ruminant livestock due to its in vitro fermentation characteristics as well as low fibre and moderate CP levels.     

Seasonal and interannual variation of subtidal fish assemblages in Wakasa Bay with reference to the warming trend in the Sea of Japan

A bi-monthly underwater visual census was conducted in the subtidal habitat of Nagahama, Wakasa Bay, Sea of Japan, over 5 years from January 2002 to December 2006. A total of 83 fish species and 63,328 individuals were recorded over 120 1-h visual censuses composed of three 2 × 200 m transects. The number of both total individuals (abundance) and species (richness) were strongly correlated with the bottom-water temperature. Species richness was greatest in summer (July–September), with 10–20 species per 400 m², when the sea-bottom temperature was highest (24–28°C), and lowest in winter (January–March), with 1–8 species per 400 m², when the temperature was lowest (10–12°C). Five species, i.e., rockfish, Sebastes inermis, wrasse, Pseudolabrus sieboldi, two species of goby, Acentrogobius pflaumii and Tridentiger trigonocephalus, and pygmy filefish, Rudarius ercodes, were frequently observed and present in more than 200 of the total of 360 total transects. While the presence of most fish species was dependent on water temperature, some species were independent of water temperature, including anchovy, Engraulis japonicus, S. inermis, wasp fish, Hypodytes rubripinnis, A. pflaumii and pufferfish, Takifugu poecilonotus. Jack mackerel, Trachurus japonicus, was the most abundant fish, being most typically seen from spring through autumn, with a total of 21,850 individuals observed over the whole census period. Some species showed strong annual fluctuations in abundance. The interannual stability in fish abundance and species richness was probably because the fish assemblage was composed of a sufficiently large number of species, but with the number of each species fluctuating over time. A comparison of the present survey to one in 1970–72 revealed that over the last 30 years southern fish species have significantly increased whereas those indigenous to northern waters have decreased.

Diet composition in San Francisco Estuary striped bass: does trophic adaptability have its limits?

Trophic adaptability is a term used to describe feeding flexibility in fishes. Though a useful conceptual starting point, fishes often face constraints on their ability to switch prey that could limit feeding success even when prey switching is observed. We compared striped bass diet compositions summarized from previously published studies in California’s Sacramento-San Joaquin Delta during two time periods (1963–1964 and 2001–2003), which allowed us to evaluate trophic adaptability in San Francisco Estuary striped bass at multiple time scales, ranging from intra-annual to multidecadal. The Delta is the landward region of the San Francisco Estuary; over time between the study periods, the Delta underwent substantial changes in potential prey availability for striped bass. We found evidence for trophic adaptability in San Francisco Estuary (SFE) striped bass at all temporal scales examined. Despite this ability to adapt to changes in prey availability, the relative abundance and carrying capacity of young striped bass have declined. This decline has previously been associated with substantial declines in their dominant historical prey—mysid shrimp. Our results, coupled with these previous findings, indicate that trophic adaptability may have limited usefulness as a conceptual model to predict foraging success when other food web constraints are not considered. We speculate that this is particularly true in highly invaded ecosystems like the San Francisco Estuary because invading species often introduce substantial and permanent changes into food webs, decreasing the likelihood that a predator will find prey assemblages that fully replace historical prey assemblages.     

九种绢丝昆虫线粒体12S rRNA基因的序列特征和系统发育分析

为探讨鳞翅目中绢丝昆虫之间的系统发育关系和分子进化特征,本研究测定了中国柞蚕Antheraea pernyi野生型和放养型的线粒体12S rRNA基因的部分序列,结合来自GenBank数据库的17条序列,对总共9种绢丝昆虫（2科3属）的12S rRNA基因序列进行了分析。利用软件MEGA 3.1进行碱基组成、变异位点的统计和分子进化分析,分别用类平均聚类法（UPGMA）、邻接法（NJ）、最小进化法（ME）、最大简约法（MP）重建系统发生树。测定的中国柞蚕野生型的12S rRNA基因序列（427 bp）与放养型“豫早1号”的序列完全一致。序列对齐后共鉴定80个变异位点,50个简约信息位点。碱基组成分析显示在科属间具有明显差异,AT含量蚕蛾科高于大蚕蛾科;在A和T碱基的使用上,大蚕蛾科偏好使用T,而蚕蛾科则偏好使用A。与动物中常见的以转换为主的碱基替换模式不同,所分析的9种昆虫中除桑蚕属内部为转换与颠换基本一致外,其余物种间均是颠换多于转换。进化分析支持柞蚕属、樗蚕属和桑蚕属的单系。基于UPGMA法的进化树支持琥珀蚕是柞蚕属的较原始类型,而NJ、ME和MP法则支持印度柞蚕是较原始的类型,因此,柞蚕属种间的进化关系尚需进一步研究。