Protein flexibility and intrinsic disorder

Comparisons were made among four categories of protein flexibility: (1) low-B-factor ordered regions, (2) high-B-factor ordered regions, (3) short disordered regions, and (4) long disordered regions. Amino acid compositions of the four categories were found to be significantly different from each other, with high-B-factor ordered and short disordered regions being the most similar pair. The high-B-factor (flexible) ordered regions are characterized by a higher average flexibility index, higher average hydrophilicity, higher average absolute net charge, and higher total charge than disordered regions. The low-B-factor regions are significantly enriched in hydrophobic residues and depleted in the total number of charged residues compared to the other three categories. We examined the predictability of the high-B-factor regions and developed a predictor that discriminates between regions of low and high B-factors. This predictor achieved an accuracy of 70% and a correlation of 0.43 with experimental data, outperforming the 64% accuracy and 0.32 correlation of predictors based solely on flexibility indices. To further clarify the differences between short disordered regions and ordered regions, a predictor of short disordered regions was developed. Its relatively high accuracy of 81% indicates considerable differences between ordered and disordered regions. The distinctive amino acid biases of high-B-factor ordered regions, short disordered regions, and long disordered regions indicate that the sequence determinants for these flexibility categories differ from one another, whereas the significantly-greater-than-chance predictability of these categories from sequence suggest that flexible ordered regions, short disorder, and long disorder are, to a significant degree, encoded at the primary structure level.     

吉林西部野生罗布麻生长季内土壤水盐变化趋势的研究

对吉林西部野生罗布麻分布区0~50 cm深度的土壤水盐变化趋势进行了研究,结果发现:土壤水分在水平格局的3个区有所不同,密集区和边缘区土壤水份含量和变化趋势相近,空白区土壤水份高于前两个区,垂直格局中,水份波动幅度随深度的增加而递减;土壤全盐量在水平格局的3个区含量不同,密集区边缘区空白区,在垂直格局中,密集区随深度增加,全盐量的波幅递减,边缘区和空白区是20~30 cm层含量高、波幅大,其它二层含量低波幅小;水平格局3个区的pH值是:密集区边缘区空白区,垂直格局中,密集和边缘两个区的20~30 cm层pH值高于其他两层,空白区pH值随深度增加呈递减趋势。正常生长的罗布麻土壤水份含量在9%~20%之间;全盐量在0.05%~0.25%之间;pH值在7.8~9.4之间。当生长季内大部分时间水份低于5%或高于21%、全盐量在0.35%以上、pH值高于9.8时,罗布麻不能生长。罗布麻根系发达,能贮存较多水分以应对干旱环境。该植物适于栽培在垄高为20~30 cm的环境中。苗期能耐受较高的全盐量和pH值,是一种适合于干旱盐碱环境的经济植物。     

Structural classification and prediction of reentrant regions in alpha-helical transmembrane proteins: application to complete genomes

Alongside the well-studied membrane spanning helices, alpha-helical transmembrane (TM) proteins contain several functionally and structurally important types of substructures. Here, existing 3D structures of transmembrane proteins have been used to define and study the concept of reentrant regions, i.e. membrane penetrating regions that enter and exit the membrane on the same side. We find that these regions can be divided into three distinct categories based on secondary structure motifs, namely long regions with a helix-coil-helix motif, regions of medium length with the structure helix-coil or coil-helix and regions of short to medium length consisting entirely of irregular secondary structure. The residues situated in reentrant regions are significantly smaller on average compared to other regions and reentrant regions can be detected in the inter-transmembrane loops with an accuracy of approximately 70% based on their amino acid composition. Using TOP-MOD, a novel method for predicting reentrant regions, we have scanned the genomes of Escherichia coli, Saccharomyces cerevisiae and Homo sapiens. The results suggest that more than 10% of transmembrane proteins contain reentrant regions and that the occurrence of reentrant regions increases linearly with the number of transmembrane regions. Reentrant regions seem to be most commonly found in channel proteins and least commonly in signal receptors.     

Comparison of the amino acid sequence of the major immunogen from three serotypes of foot and mouth disease virus.

Cloned cDNA molecules from three serotypes of FMDV have been sequenced around the VP1-coding region. The predicted amino acid sequences for VP1 were compared with the published sequences and variable regions identified. The amino acid sequences were also analysed for hydrophilic regions. Two of the variable regions, numbered 129-160 and 193-204 overlapped hydrophilic regions, and were therefore identified as potentially immunogenic. These regions overlap regions shown by others to be immunogenic.     

Allotment of carbon is responsible for disorders in proteins

Sequence stretches in proteins that do not fold into a form are referred as disordered regions. Databases like Disport describe disordered regions in proteins and web servers like PrDOS and DisEMBL, facilitate the prediction of disordered regions. These studies are often based on residue level features. Here, we describe proteins with disordered regions using carbon content and distributions. The distribution pattern for proteins with disordered regions is different from those that do not show disordered regions.     

广州市不同城市化发展区域蝶类多样性

2005～2006年,对广州地区4个不同城市化发展区域(森林区、农田区、城市区、沿海湿地区)的蝶类进行6次调查,共统计到10科46属73种.森林区科、属、物种和个体数目都最多,沿海湿地区各项数量指标都最小,农田区的个体数量大于城市区,但科、属和物种数却与城市区差异不大.多样性分析结果表明,森林区的种类丰度、多样性指数最高,沿海湿地区的种类丰度和多样性指数最低;均匀度大小依次为沿海湿地区﹥农田区﹥森林区﹥城市区;优势度指数大小依次为沿海湿地区﹥城市区﹥农田区﹥森林区.相似性分析结果表明,森林区和农田区具有的相同物种数最多,相似性系数最高;沿海湿地区和森林区、农田区、城市区具有的相同物种数都较少,相似性系数也较低.     

Biogeographic distribution of the Phytoseiidae (Acari: Mesostigmata)

More than 1982 species in 90 genera were included in an analysis of the biogeography of the Phytoseiidae, a family of predatory mites. Seven biogeographic regions were taken into account: Nearctic, Neotropical, Ethiopian, West Palaearctic, East Palaearctic, Oriental, and Australasian. The number of species was particularly high in the Neotropical, Oriental, and West Palaearctic regions. These regions also present the highest levels of species endemism. The number of genera was quite similar in all regions except for the Neotropics, which also had a high level of endemism. The possible Gondwanian (Neotropical, Ethiopian, Australasian, and Oriental regions) origin of the Phytoseiidae, most probably in the Neotropics, and their possible radiation to Laurasia (Nearctic, West Palaearctic, and East Palaearctic regions) are discussed. The comparison between genera and species in the different biogeographic regions indicate the importance of both dispersal and vicariance events in the evolution of the group. Dispersal is assumed to have been most important between Neotropical and Nearctic regions and between East Palaearctic and Oriental regions, whereas vicariance could have been the dominating process between Australasian, Ethiopian, and Oriental regions, as well as between West and East Palaearctic regions. A parsimony analysis of endemicity showed the Neotropical and the Nearctic regions to be isolated from the other regions. This is certainly due to a diversification after the continents drifted apart and then a high dispersal between Nearctic and Neotropical regions. Different phylogenetic hypotheses and scenarios are proposed for each subfamily based on the results obtained and further investigations are proposed.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 845–856.     

Molecular orientation distributions in a biaxially oriented poly(L-lactic acid) film determined by polarized Raman spectroscopy

Molecular orientation distributions in the crystalline and amorphous regions of a biaxially oriented poly(L-lactic acid) film were analyzed fully by polarized Raman spectroscopy. Raman bands at 926 and 875 cm(-1) were chosen for the determination of the most probable molecular orientation distribution functions for the crystalline and amorphous regions in the film. It was revealed that the PLLA molecules were oriented biaxially in both the crystalline and amorphous regions. The orientation distribution normal to the film surface was found to be broader in the amorphous regions than in the crystalline regions. Furthermore, a predominant unidirectional molecular orientation was observed in the crystalline regions, whereas the molecular orientation distribution in the amorphous regions was isotropic in the plane parallel to the film surface. The different behavior of the crystalline and amorphous regions suggests that each region underwent different deformation mechanisms during the film formation.     

Is it possible to predict amyloidogenic regions from sequence alone?

Identification of potentially amyloidogenic regions in polypeptide chains is very important because the amyloid fibril formation can be induced in most normal proteins. In our work we suggest a new method to detect amyloidogenic regions in protein sequence. It is based on the assumption that packing is tight inside an amyloid and therefore regions which could potentially pack well would have a tendency to form amyloids. This means that the regions with strong expected packing of residues would be responsible for the amyloid formation. We use this property to identify potentially amyloidogenic regions in proteins basing on their amino acid sequences only. Our predictions are consistent with known disease-related amyloidogenic regions for 8 of 11 amyloid-forming proteins and peptides in which the positions of amyloidogenic regions have been revealed experimentally. Predictions of the regions which are responsible for the formation of amyloid fibrils in proteins unrelated to disease have been also done.     

Correlation approach to identify coding regions in DNA sequences.

Recently, it was observed that noncoding regions of DNA sequences possess long-range power-law correlations, whereas coding regions typically display only short-range correlations. We develop an algorithm based on this finding that enables investigators to perform a statistical analysis on long DNA sequences to locate possible coding regions. The algorithm is particularly successful in predicting the location of lengthy coding regions. For example, for the complete genome of yeast chromosome III (315,344 nucleotides), at least 82% of the predictions correspond to putative coding regions; the algorithm correctly identified all coding regions larger than 3000 nucleotides, 92% of coding regions between 2000 and 3000 nucleotides long, and 79% of coding regions between 1000 and 2000 nucleotides. The predictive ability of this new algorithm supports the claim that there is a fundamental difference in the correlation property between coding and noncoding sequences. This algorithm, which is not species-dependent, can be implemented with other techniques for rapidly and accurately locating relatively long coding regions in genomic sequences.     

A mosaic pattern characterizes the evolution of the avian brain

Diversity in vertebrate brain size and composition is thought to arise from either developmental constraints that cause coordinated changes between brain regions or a mosaic model, whereby changes in individual brain regions are independent of changes in other brain regions. These two mechanisms were tested in birds using multiple regression analyses. Across 13 orders, significant correlations were present between some brain regions, but not all. Most of the correlated changes reflect the connectivity between different brain components, such that regions with the most interconnections are correlated with one another but not other brain regions. Whether mosaic changes are characteristic of brain regions or systems in birds, however, to our knowledge, remains to be investigated.     

Relationship between microRNA genes incidence and cancer-associated genomic regions in canine tumors: a comprehensive bioinformatics study

The role of microRNAs (miRNAs) in human cancer biology has been confirmed on a genome-wide scale through the high incidence of these genes in cancer-associated regions. We analyzed the association between canine miRNA genes and cancer-associated regions (deleted and amplified regions) using previously published array of comparative genomic hybridization data on 268 canine cancer samples—comprising osteosarcoma, breast cancer, leukemia, and colorectal cancer. We also assessed this relationship apropos the incidence of miRNA genes in the CpG islands of the canine genome assembly. The association was evaluated using the mixed-effects Poisson regression analysis. Our analyses revealed that 135 miRNA genes were exactly located in the aberrated regions: 77 (57 %) in the loss and 58 (43 %) in amplified regions. Our findings indicated that the miRNA genes were located more frequently in the deleted regions as well as in the CpG islands than in all other regions. Additionally, with the exception of leukemia, the amplified regions significantly contained higher numbers of miRNA genes than did all the other regions.     

Scale-independent non-parametric multivariate tolerance regions and their application in medicine

Based on the principles introduced by TUKEY and FRASER , a method is proposed to construct non-parametric multivariate tolerance regions of irregular multiplanar shape. Contrary to the regions of corresponding shape as constructed by Tukey and Fraser, the tolerance regions constructed according to the proposed method can be shown to be invariant to linear scale transformations. In medical applications, where the concept of multivariate tolerance regions can be used to define “normal” regions for p ≦ 2 variables with measuring units generally differing from each other, the quality of scale-independency of the regions is essential. With reference to the method proposed, sample size determination and some important aspects of the use of multivariate tolerance regions are discussed.     

Comparative analysis of sequences at the 5' end of the human and mouse apolipoprotein B genes

A comparison was made between the DNA sequences in two regions of the mouse and the human apolipoprotein B genes: the 5'-flanking sequence and the region between the first exon and the second intron. Considerable homology was observed, particularly in the immediate 5' region and in the second intron. Because promoter and enhancer elements have been previously localized to these regions in the human apolipoprotein B gene, it is proposed that regions of conserved base sequence delineate binding regions for regulatory proteins. In some cases, contiguous regions of homology are longer than expected for regions designed as recognition sites for individual nuclear proteins, and may define regions recognizable by a cluster of interacting proteins. Both the human and mouse genes contain repetitive elements and a hypervariable dinucleotide repeat.     

Non-coding regions of the Ebola virus genome contain indispensable phylogenetic and evolutionary information

We compared the numbers of nucleotide substitutions occurring in the non-coding regions and coding regions of Ebola virus genomes and found that non-coding regions contain indispensable phylogenetic and evolutionary information. The omission of genetic data from non-coding regions can lead to unreliable phylogenies and inaccurate estimates of evolutionary parameters.     

Young but not relatively old retrotransposons are preferentially located in gene‐rich euchromatic regions in tomato (Solanum lycopersicum) plants

Long terminal repeat (LTR) retrotransposons are the major DNA components of flowering plants. They are generally enriched in pericentromeric heterochromatin regions of their host genomes, which could result from the preferential insertion of LTR retrotransposons and the low effectiveness of purifying selection in these regions. To estimate the relative importance of the actions of these two factors on their distribution pattern, the LTR retrotransposons in Solanum lycopersicum (tomato) plants were characterized at the genome level, and then the distribution of young elements was compared with that of relatively old elements. The current data show that old elements are mainly located in recombination‐suppressed heterochromatin regions, and that young elements are preferentially located in the gene‐rich euchromatic regions. Further analysis showed a negative correlation between the insertion time of LTR retrotransposons and the recombination rate. The data also showed there to be more solo LTRs in genic regions than in intergenic regions or in regions close to genes. These observations indicate that, unlike in many other plant genomes, the current LTR retrotransposons in tomatoes have a tendency to be preferentially located into euchromatic regions, probably caused by their severe suppression of activities in heterochromatic regions. These elements are apt to be maintained in heterochromatin regions, probably as a consequence of the pericentromeric effect in tomatoes. These results also indicate that local recombination rates and intensities of purifying selection in different genomic regions are largely responsible for structural variation and non‐random distribution of LTR retrotransposons in tomato plants.     

Two plus two does not equal three: statistical tests for multiple genome comparison

Gene clusters that span three or more chromosomal regions are of increasing importance, yet statistical tests to validate such clusters are in their infancy. Current approaches either conduct several pairwise comparisons or consider only the number of genes that occur in all of the regions. In this paper, we provide statistical tests for clusters spanning exactly three regions based on genome models of typical comparative genomics problems, including analysis of conserved linkage within multiple species and identification of large-scale duplications. Our tests are the first to combine evidence from genes shared among all three regions and genes shared between pairs of regions. We show that our tests of clusters spanning three regions are more sensitive than existing approaches, and can thus be used to identify more diverged homologous regions.