Identification of new human cadherin genes using a combination of protein motif search and gene finding methods

We have combined protein motif search and gene finding methods to identify genes encoding proteins containing specific domains. Particularly, we have focused on finding new human genes of the cadherin superfamily proteins, which represent a major group of cell-cell adhesion receptors contributing to embryonic neuronal morphogenesis. Models for three cadherin protein motifs were generated from over 100 already annotated cadherin domains and used to search the complete translated human genome. The genomic sequence regions containing motif "hits" were analyzed by eukaryotic GeneMark.hmm to identify the exon-intron structure of new genes. Three new genes CDH-J, PCDH-J and FAT-J were found. The predicted proteins PCDH-J and FAT-J were classified into protocadherin and FAT-like subfamilies, respectively, based on the number and organization of cadherin domains and presence of subfamily-specific conserved amino acid residues. Expression of FAT-J was shown in almost all tested tissues. The exon-intron organization of CDH-J was experimentally verified by PCR with specifically designed primers and its tissue-specific expression was demonstrated. The described methodology can be applied to discover new genes encoding proteins from families with well-characterized structural and functional domains.     

Crystallographic studies of quinol oxidation site inhibitors: a modified classification of inhibitors for the cytochrome bc(1) complex

Cytochrome bc(1) is an integral membrane protein complex essential for cellular respiration and photosynthesis; it couples electron transfer from quinol to cytochrome c to proton translocation across the membrane. Specific bc(1) inhibitors have not only played crucial roles in elucidating the mechanism of bc(1) function but have also provided leads for the development of novel antibiotics. Crystal structures of bovine bc(1) in complex with the specific Q(o) site inhibitors azoxystrobin, MOAS, myxothiazol, stigmatellin and 5-undecyl-6-hydroxy-4,7-dioxobenzothiazole were determined. Interactions, conformational changes and possible mechanisms of resistance, specific to each inhibitor, were defined. Residues and secondary structure elements that are capable of discriminating different classes of Q(o) site inhibitors were identified for the cytochrome b subunit. Directions in the displacement of the cd1 helix of cytochrome b subunit in response to various Q(o) site inhibitors were correlated to the binary conformational switch of the extrinsic domain of the iron-sulfur protein subunit. The new structural information, together with structures previously determined, provide a basis that, combined with biophysical and mutational data, suggest a modification to the existing classification of bc(1) inhibitors. bc(1) inhibitors are grouped into three classes: class P inhibitors bind to the Q(o) site, class N inhibitors bind to the Q(i) site and the class PN inhibitors target both sites. Class P contains two subgroups, Pm and Pf, that are distinct by their ability to induce mobile or fixed conformation of iron-sulfur protein.     

Expression of bioactive human M-CSF soluble receptor in transgenic tobacco plants

The cDNA encoding N-terminal three immunoglobin-like domains of human M-CSFR was linked to His-tag and endoplasmic reticulum retention sequence (KDEL) before being inserted into the genome of tobacco plant, Nicotiana tabacum cv. NC-89, by Agrobacterium tumefaciens-mediated transformation. The insertion and expression of target gene were confirmed by PCR, ELISA, and Western blot. The recombinant M-CSFsR reached a maximum expression level of 1.92% of total soluble protein in transgenic tobacco plant leaf tissues. The recombinant M-CSFsR could be purified through a one-step IMAC process and its bioactivity was confirmed by the inhibition of colony formation of J6-1 cells. The results suggested that we successfully expressed a high level of bioactive human M-CSFsR in tobacco plants.     

Identification and characterization of piggyBac-like elements in the genome of domesticated silkworm, Bombyx mori

piggyBac is a short inverted terminal repeat (ITR) transposable element originally discovered in Trichoplusia ni. It is currently the preferred vector of choice for enhancer trapping, gene discovery and identifying gene function in insects and mammals. Many piggyBac-like sequences have been found in the genomes of phylogenetically species from fungi to mammals. We have identified 98 piggyBac-like sequences (BmPBLE1-98) from the genome data of domesticated silkworm (Bombyx mori) and 17 fragments from expressed sequence tags (ESTs). Most of the BmPBLE1-98 probably exist as fossils. A total of 21 BmPBLEs are flanked by ITRs and TTAA host dinucleotides, of which 5 contain a single ORF, implying that they may still be active. Interestingly, 16 BmPBLEs have CAC/GTG not CCC/GGG as the characteristic residues of ITRs, which is a surprising phenomenon first observed in the piggyBac families. Phylogenetic analysis indicates that many BmPBLEs have a close relation to mammals, especially to Homo sapiens, only a few being grouped with the T. ni piggyBac element. In addition, horizontal transfer was probably involved in the evolution of the piggyBac-like elements between B. mori and Daphnia pulicaria. The analysis of the BmPBLEs will contribute to our understanding of the characteristic of the piggyBac family and application of piggyBac in a wide range of insect species.     

A gradient analysis based on the buffer zones of urban landscape pattern of the constructed area in Guigang City, Guangxi, China

Over the last century urbanization on the landscape has increased and intensified. Urban development has a great impact on the environment at the local, regional and even global levels. As a driving force in global change, the need to understand the dynamics of urban pattern and its change in an accurate and efficient manner is ever more pressing. Based on aerial color infrared photography in 1985 and QuickBird satellite imagery in 2004 and according to the standard for plan and construction of city land use, the landscape of Guigang City was divided into 11 types. In the landscape classification maps, 31 buffer zones, each being 200 m wide, were divided. With the aid of GIS software ArcView 3.2 and landscape pattern analysis software FRAGSTATS 3.3, the landscape spatial patterns of each buffer zone were analyzed at the landscape level and class level. The landscape indices, such as patch size, patch fractal dimension, diversity index and evenness index, were calculated. The results indicated the following: The total area of the residential land and the communal land in 2004 covered 46.3% of the entire constructed area of Guigang City and the sum of the patch number of the two patch types occupied about 39.7% of the total patch number, while the percentages were respectively 48.2% and 45.4% in 1985. This showed that the mosaic landscape with the residential land and communal facilities land became increasingly unclear following urban development and landscape diversity. Based on the gradient analysis with the landscape-level index and the class-level index, there were two business and finance centers in the constructed area. One was located in the urban center with a range of 0.8 km; the other was from the 10^th to the 16^th zone. In each buffer zone, the mean patch size was larger and the landscape shape was more regular in 2004 than in 1985. Furthermore, the Shannon diversity index of each buffer zone rose in 2004 with patch richness and evenness increasing. The landscape index computed for the main landscape types (communal facilities land, industrial estate land, residential land and farmland) in the middle of the buffer zones clearly indicated the changes taking place in urbanization. The patch size and the patch number of industrial estate land and farmland also pointed to these changes, while communal facilities land and residential land assumed another similar tendency towards changes. In each gradient zone, industrial estate land had the most complex shape, the lowest area percentage of each zone and the biggest mean patch size, whereas communal facilities land and residential land were opposite to industrial estate land. Farmland had a steady percentage along the buffer zone and its continuous distribution had an important impact on the urban eco-environment. The question of how to relate the pattern of changing characteristics along the buffer zone to the urban ecological process and urban ecological planning remains to be studied further in the future.     

光系统II核心复合物的稳态荧光光谱(英文)

在 83K 和 160K 两个温度下,通过激发波长对荧光发射谱的影响研究了光系统II中核心复合物的荧光光谱特性。用不同波长的光激发,核心复合物的发射谱的最大发射峰值不变,用 480、489、495 和 507nm 的光分别激发核心复合物,其光谱最大峰值处的荧光强度随不同激发波长下β-胡萝卜素分子的吸收强度的增大而降低,在长波长区域光谱的变化依赖于首先被激发的色素分子。所以,激发波长的不同影响着核心复合物中能量传递的途径。通过高斯解析,分析出核心复合物中至少存在有 7组叶绿素a组分,它们是Chla660,Chla670,Chla680,Chla682,Chla684,Chla687和Chla690。