Hierarchy of protein loop-lock structures: a new server for the decomposition of a protein structure into a set of closed loops

HoPLLS (Hierarchy of protein loop-lock structures) (http://leah.haifa.ac.il/~skogan/Apache/mydata1/main.html) is a web server that identifies closed loops - a structural basis for protein domain hierarchy. The server is based on the loop-and-lock theory for structural organisation of natural proteins. We describe this web server, the algorithms for the decomposition of a 3D protein into loops and the results of scientific investigations into a structural "alphabet" of loops and locks.Comment: 11 pages, 4 figure

An Iterative Projective Clustering Method

AbstractIn this article we offer an algorithm recurrently divides a dataset by search of partitions via one dimensional subspace discovered by means of optimizing of a projected pursuit function. Aiming to assess the model order a resampling technique is employed. For each number of clusters, bounded by a predefined limit, samples from the projected data are drawn and clustered through the EM algorithm. Further, the basis cumulative histogram of the projected data is approximated by means of the GMM histograms constructed using the samples’ partitions. The saturation order of this approximation process, at what time the components’ amount increases, is recognized as the “true” components’ number. Afterward the whole data is clustered and the densest cluster is omitted. The process is repeated while waiting for the true number of clusters equals one. Numerical experiments demonstrate the high ability of the proposed method

Physical mapping integrated with syntenic analysis to characterize the gene space of the long arm of wheat chromosome 1A

Background: Bread wheat (Triticum aestivum L.) is one of the most important crops worldwide and its production faces pressing challenges, the solution of which demands genome information. However, the large, highly repetitive hexaploid wheat genome has been considered intractable to standard sequencing approaches. Therefore the International Wheat Genome Sequencing Consortium (IWGSC) proposes to map and sequence the genome on a chromosome-by-chromosome basis. Methodology/Principal Findings: We have constructed a physical map of the long arm of bread wheat chromosome 1A using chromosome-specific BAC libraries by High Information Content Fingerprinting (HICF). Two alternative methods (FPC and LTC) were used to assemble the fingerprints into a high-resolution physical map of the chromosome arm. A total of 365 molecular markers were added to the map, in addition to 1122 putative unique transcripts that were identified by microarray hybridization. The final map consists of 1180 FPC based or 583 LTC based contigs. Conclusions/Significance: The physical map presented here marks an important step forward in mapping of hexaploid bread wheat. The map is orders of magnitude more detailed than previously available maps of this chromosome, and the assignment of over a thousand putative expressed gene sequences to specific map locations will greatly assist future functional studies. This map will be an essential tool for future sequencing of and positional cloning within chromosome 1A

第840回千葉医学会整形外科例会 25.

Phylogenetic tree of 47 species. (PDF 15 kb

Physical Mapping of Bread Wheat Chromosome 5A: An Integrated Approach

The huge size, redundancy, and highly repetitive nature of the bread wheat [Triticum aestivum (L.)] genome, makes it among the most difficult species to be sequenced. To overcome these limitations, a strategy based on the separation of individual chromosomes or chromosome arms and the subsequent production of physical maps was established within the frame of the International Wheat Genome Sequence Consortium (IWGSC). A total of 95,812 bacterial artificial chromosome (BAC) clones of short-arm chromosome 5A (5AS) and long-arm chromosome 5A (5AL) arm-specific BAC libraries were fingerprinted and assembled into contigs by complementary analytical approaches based on the FingerPrinted Contig (FPC) and Linear Topological Contig (LTC) tools. Combined anchoring approaches based on polymerase chain reaction (PCR) marker screening, microarray, and sequence homology searches applied to several genomic tools (i. e., genetic maps, deletion bin map, neighbor maps, BAC end sequences (BESs), genome zipper, and chromosome survey sequences) allowed the development of a high-quality physical map with an anchored physical coverage of 75% for 5AS and 53% for 5AL with high portions (64 and 48%, respectively) of contigs ordered along the chromosome. In the genome of grasses, Brachypodium [Brachypodium distachyon (L.) Beauv.], rice (Oryza sativa L.), and sorghum [Sorghum bicolor (L.) Moench] homologs of genes on wheat chromosome 5A were separated into syntenic blocks on different chromosomes as a result of translocations and inversions during evolution. The physical map presented represents an essential resource for fine genetic mapping and map-based cloning of agronomically relevant traits and a reference for the 5A sequencing projects

LTC: a novel algorithm to improve the efficiency of contig assembly for physical mapping in complex genomes

<p>Abstract</p> <p>Background</p> <p>Physical maps are the substrate of genome sequencing and map-based cloning and their construction relies on the accurate assembly of BAC clones into large contigs that are then anchored to genetic maps with molecular markers. High Information Content Fingerprinting has become the method of choice for large and repetitive genomes such as those of maize, barley, and wheat. However, the high level of repeated DNA present in these genomes requires the application of very stringent criteria to ensure a reliable assembly with the FingerPrinted Contig (FPC) software, which often results in short contig lengths (of 3-5 clones before merging) as well as an unreliable assembly in some difficult regions. Difficulties can originate from a non-linear topological structure of clone overlaps, low power of clone ordering algorithms, and the absence of tools to identify sources of gaps in Minimal Tiling Paths (MTPs).</p> <p>Results</p> <p>To address these problems, we propose a novel approach that: (i) reduces the rate of false connections and Q-clones by using a new cutoff calculation method; (ii) obtains reliable clusters robust to the exclusion of single clone or clone overlap; (iii) explores the topological contig structure by considering contigs as networks of clones connected by significant overlaps; (iv) performs iterative clone clustering combined with ordering and order verification using re-sampling methods; and (v) uses global optimization methods for clone ordering and Band Map construction. The elements of this new analytical framework called Linear Topological Contig (LTC) were applied on datasets used previously for the construction of the physical map of wheat chromosome 3B with FPC. The performance of LTC vs. FPC was compared also on the simulated BAC libraries based on the known genome sequences for chromosome 1 of rice and chromosome 1 of maize.</p> <p>Conclusions</p> <p>The results show that compared to other methods, LTC enables the construction of highly reliable and longer contigs (5-12 clones before merging), the detection of "weak" connections in contigs and their "repair", and the elongation of contigs obtained by other assembly methods.</p

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Introduction: Wheat (Triticum aestivum L.) is the most widely cultivated crop on Earth, contributing about a fifth of the total calories consumed by humans. Consequently, wheat yields and production affect the global economy, and failed harvests can lead to social unrest. Breeders continuously strive to develop improved varieties by fine-tuning genetically complex yield and end-use quality parameters while maintaining stable yields and adapting the crop to regionally specific biotic and abiotic stresses. Rationale: Breeding efforts are limited by insufficient knowledge and understanding of wheat biology and the molecular basis of central agronomic traits. To meet the demands of human population growth, there is an urgent need for wheat research and breeding to accelerate genetic gain as well as to increase and protect wheat yield and quality traits. In other plant and animal species, access to a fully annotated and ordered genome sequence, including regulatory sequences and genome-diversity information, has promoted the development of systematic and more time-efficient approaches for the selection and understanding of important traits. Wheat has lagged behind, primarily owing to the challenges of assembling a genome that is more than five times as large as the human genome, polyploid, and complex, containing more than 85% repetitive DNA. To provide a foundation for improvement through molecular breeding, in 2005, the International Wheat Genome Sequencing Consortium set out to deliver a high-quality annotated reference genome sequence of bread wheat. Results: An annotated reference sequence representing the hexaploid bread wheat genome in the form of 21 chromosome-like sequence assemblies has now been delivered, giving access to 107,891 high-confidence genes, including their genomic context of regulatory sequences. This assembly enabled the discovery of tissue- and developmental stage–related gene coexpression networks using a transcriptome atlas representing all stages of wheat development. The dynamics of change in complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. Aspects of the future value of the annotated assembly for molecular breeding and research were exemplarily illustrated by resolving the genetic basis of a quantitative trait locus conferring resistance to abiotic stress and insect damage as well as by serving as the basis for genome editing of the flowering-time trait. Conclusion: This annotated reference sequence of wheat is a resource that can now drive disruptive innovation in wheat improvement, as this community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding. Importantly, the bioinformatics capacity developed for model-organism genomes will facilitate a better understanding of the wheat genome as a result of the high-quality chromosome-based genome assembly. By necessity, breeders work with the genome at the whole chromosome level, as each new cross involves the modification of genome-wide gene networks that control the expression of complex traits such as yield. With the annotated and ordered reference genome sequence in place, researchers and breeders can now easily access sequence-level information to precisely define the necessary changes in the genomes for breeding programs. This will be realized through the implementation of new DNA marker platforms and targeted breeding technologies, including genome editing

Data from: Triplet MaxCut: a new toolkit for rooted supertree

The rapid increase of molecular, as well as other types, of available classification data has created the need to combine this data into a unified hypothesis. Supertree methods are essential when amalgamating phylogenetic information from various, possibly conflicting, sources into a single tree. The goal of a supertree algorithm is to satisfy maximally each such source of information in the output tree. Triplets, rooted trees over three leaves, are the minimal piece of such information when dealing with rooted trees. Due to its fundamental role in phylogenetics, extensive effort has been dedicated to several aspects regarding triplets’ research. We have devised a new tool, Triplet MaxCut (TMC), performing various operations in rooted supertree, principally amalgamating rooted trees based on amalgamating rooted triplets. The utility and efficiency of the algorithm is demonstrated by both simulation study and four real data supertree inputs

Genetic diversity and stress of Ricotia lunaria in “Evolution Canyon

Abstract We examined the genetic diversity and divergence of Ricotia lunaria, a family relative species of Arabidopsis thaliana, sampled from 6 stations on 2 opposing slopes, the south-facing slope (&apos;&apos;African&apos;&apos; or AS) and north-facing slope (&apos;&apos;European&apos;&apos; or ES), separated on average by 200 m, at &apos;&apos;Evolution Canyon,&apos;&apos; Lower Nahal Oren, Mount Carmel, Israel, along a transect presenting sharply differing microclimates. The density of R. lunaria populations was slope specific: a higher density and smaller plants were observed on the AS. In addition, the density was positively correlated with annual plant cover. The interslope and intraslope genetic diversities of R. lunaria populations were examined using the amplified fragment length polymorphism (AFLP) technique with 5 primer pairs. Ricotia lunaria populations inhabiting the ES and AS differed, and among the 468 scored loci, 304 (65%) were polymorphic (at P ! 0.05 level). Polymorphism values obtained for AS and ES populations were similar (52% vs. 56%), but different loci were polymorphic in different populations; 40% of polymorphic loci were identical on both the ES and AS, 16% were polymorphic for the ES only, and 12% were polymorphic only for the AS. The AFLP results grouped the analyzed genotypes into 2 distinct clusters: one cluster included the plants belonging to the AS and the other included ES plants. The unbiased estimate of Nei genetic distances (D) indicated significantly higher interslope (D 5 0.124 ± 0.011) than intraslope (D 5 0.076 ± 0.015) differences (P , 0.001 in t-test). Correspondingly, mean intraslope gene flow was significantly higher than the interslope gene flow (2.9 ± 0.6 vs. 1.9 ± 0.2). Natural selection appears to adaptively diverge the plant ecotypes on the opposite slope, both phenotypically and genotypically. This includes significant divergence in flowering time likely to initiate incipient sympatric speciation