Sensitive protein comparisons with profiles and hidden Markov models

Sequence database searches have become an important tool for the life sciences in general and for gene discovery-driven biotechnology in particular. Both the functional assignment of newly found proteins and the mining of genome databases for functional candidates are equally important tasks typically addressed by database searches. Sensitivity and reliability of the search methods are of crucial importance.The overall performance of sequence alignments and database searches can be enhanced considerably, when profiles or hidden Markov models (HMMs) derived from protein families are used as query objects instead of single sequences.This review discusses the concept of profiles, generalised profiles and profile-HMMs, the methods how they are constructed and the scope of possible applications in gene discovery and gene functional assignment.     

The use of the Mexican Hat and the Morlet wavelets for detection of ecological patterns

In this paper, we compare the relationship between scale and period in ecological pattern analysis and wavelet analysis. We also adapt a commonly used wavelet, the Morlet, to ecological pattern analysis. Using Monte Carlo assessments, we apply methods of statistical significance test to wavelet analysis for pattern analysis. In order to understand the inherent strength and weakness of the Morlet and the Mexican Hat wavelets, we also investigate and compare the properties of two frequently used wavelets by testing with field data and four artificial transects of different typical patterns which is often encountered in ecological research. It is shown that the Mexican Hat provides better detection and localization of patch and gap events over the Morlet, whereas the Morlet offers improved detection and localization of scale over the Mexican Hat. There is always a trade-off between the detection and localization of scale versus patch and gap events. Therefore, the best composite analysis is the combination of their advantages. The properties of wavelet in dealing with ecological data may be affected by characteristics intrinsic to wavelet itself. The peaks of different scales in isograms of wavelet power spectrum from the Mexican Hat may overlap with each other. Alternatively, these peaks of different scales in isograms of wavelet power spectrum may combine with each other unless the size of the analyzed scales is significantly different. These overlapping or combining lead to combining of peaks for different scales, or the masking of trough between peaks of different scales in the scalogram. Ecologists should combine all the information in scalogram and isograms of wavelet coefficient and wavelet power spectrum from different wavelets, which can provide us a broader view and precise pattern information.     

中沙、西沙群岛微型腹足类、双壳类表层沉积组合与环境意义

中沙、西沙群岛海底２１个表层沉积样中发现微型腹足类１７６种,微型双壳类４８种,形成３组合类型：水深０－６０ｍ为Ｔｒｉｃｏｌｉａ（Ｈｉｌｏａ）ｖａｒｉａｂｉｌｉｓ－Ｃａｄｅｌｌａ ｓｅｍｉｔｏｒｔａ组合,水深６０－１２０ｍ为Ｃｅｒｉｔｈｉｏｐｓｉｓ－Ｒｉｎｇｉｃｕｌａ－Ｖａｒｉｃｏｒｂｕｌａ组合,水深大于８００ｍ为Ａｎａｔｏｍｉａ－Ｇａｓｔｒｏｃｈａｅｎａ组合。腹足类、双壳类沉积组合包括原地理藏和异     

Characters of Leaf Epidermis and Their Systematic Significance in Menispermaceae

The epidermal characters of mature leaves of 29 genera, 50 species and 3 varieties (totally 56 samples) representing all the 5 tribes in the family Menispermaceae were examined under the light microscope. The main conclusions are as follows: (1) The shape of the epidermal cells is polygonal or irregular, and the anticlinal walls are straight or waved in the family. In some genera a special arrangement of epidermal cells is named as “rosette-cell arrangement" for the first time. The lower epidermal cells were found to have a papilla in Stephania, Diploclisia and Legnephora . (2) In some genera, the anticlinal walls are oblique, rather than perpendicular, to the surface. (3) The stomatal apparatuses, generally restricted to the lower surface of the leaves, were assigned to anomocytic, staurocytic, cyclocytic, anisocytic and actinocytic types, and their distribution on the epidermis may be of diffuse pattern or island congregating pattern. (4) The cells of both upper and lower epidermis in the tribe Pachygoneae and Fibraureae are generally polygonal with straight or arched anticlinal walls, and the stomatal apparatuses are usually staurocytic and actinocytic. The cyclocytic stomatal apparatus was found only in two genera of the tribe Pachygoneae. By contrast, the epidermal cells of the tribes Anomospermeae, Tinosporeae and Menispermeae are generally irregular with waved anticlinal walls, and the stomatal apparatuses are predominantly anomocytic. These correlated characters are of much significance in delimiting tribes within the Menispermaceae, and also provide evidence for studies on systematic relationships of several genera.     

舞草侧生小叶旋转的生态意义感性运动还是防御行为?

舞草复叶的运动兼具昼夜节律性和次昼夜节律性(周期<24 h),两者运动机制显著不同.舞草侧生小叶叶枕运动细胞呈环状排列,协调可逆的体积变化形成侧生小叶的旋转运动.侧生小叶叶枕可对多种环境因子进行响应,但生态功能不明.对舞草侧生小叶叶枕解剖学、电生理学、细胞生物学等研究进行整合,结合最新的植物行为学、动物行为学及生物力学...     

Chemical constituents of Physochlaina physaloides (L.) G. Don (Solanaceae)

The study of the whole plants of Physochlaina physaloides (L.) G. Don. has led to the isolation of eight alkaloids (1–6, 18, and 25), fourteen flavonoids (9, 11–17, and 19–24), two coumarins (7 and 10), one iridoid (8). The structures of these compounds were identified spectroscopically, and nuclear magnetic resonance (NMR) data were compared with previously reported data. This is the first study to describe the isolation and identification of compounds 1–3, 7, and 10–25 in P. physaloides. The chemotaxonomic significance of these compounds in the genus Physochlaina and its closely related genera was discussed.     

Chemical constituents of sponge Pseudoceratina sp. and their chemotaxonomic significance

The chemical investigation of Pseudoceratina sp. led to the isolation of six compounds including tyrosine brominated isoxazoline alkaloids (1 and 2), polyketide (3), and 5α,8α-epidioxysterols (4–6). The structures of these compounds were identified by comparison of NMR and MS spectroscopic data with those previously reported. Compounds 3–6 were isolated for the first time from sponges of the genus Pseudoceratina. The chemotaxonomic significance of these compounds was discussed.     

Vernoguinamide: A new ceramide and other compounds from the root of Vernonia guineensis Benth. and their chemophenetic significance

The chemical investigation of the roots of Vernonia guineensis Benth. (Asteraceae) resulted in the isolation of a new ceramide, named vernoguinamide (1), together with fifteen known compounds, including three anthraquinones, physion (2), erythroglaucin (3) and emodin (4), three triterpenoids, hop-17(21)-en-3β-yl acetate (5), lupeol (6) and betulinic acid (7), six steroids, vernoguinoside A (8), vernoguinoside (9), β-sitosterol 3-O-β-D-glucoside (10), stigmasterol 3-O-β-D-glucoside (11), stigmasterol (12) and β-sitosterol (13) and three fatty acid derivatives, tetracosanoic acid (14), tricosanic acid (15) and arachidic acid glycerol ester (16). The structure of the new compound as well as those of the known compounds were established by spectrometric analysis including HRESI-MS, 1D and 2D-NMR and by comparison with the previously reported data. Among these compounds, the anthraquinones 2–4 and the triterpene 5 were isolated for the first time from Vernonia genus and compounds 6, 7 and 14–16 were extracted for the first time from the species. The isolated compounds were tested for their antibacterial activity and 3, 8 and 9 were the most active compounds against the tested bacteria. Furthermore, the chemophenetic relationships of the isolated compounds and their significance were also discussed.     

New polyacetylene and other compounds from Bupleurum chinense and their chemotaxonomic significance

Here, we isolated a new polyacetylene, (2Z,8E)-heptadecadiene-10-oxo-4,6-diyn-1-ol (1), an oxylipin (2), eight phenolic compounds (3–10), and 15 saponins (11–25) from the roots of Bupleurum chinense. We elucidated their structures by analysis of 1D and 2D-NMR spectroscopic data and mass spectrometry, and by comparison with those of related metabolites. This is the first report of the presence of compounds 2 and 6 in the Bupleurum spp.. Chemotaxonomic significance of these compounds is described herein.