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Sample records for gene structure identification

  1. Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs.

    PubMed

    Moriya, Yuki; Yamada, Takuji; Okuda, Shujiro; Nakagawa, Zenichi; Kotera, Masaaki; Tokimatsu, Toshiaki; Kanehisa, Minoru; Goto, Susumu

    2016-03-28

    Although there are several databases that contain data on many metabolites and reactions in biochemical pathways, there is still a big gap in the numbers between experimentally identified enzymes and metabolites. It is supposed that many catalytic enzyme genes are still unknown. Although there are previous studies that estimate the number of candidate enzyme genes, these studies required some additional information aside from the structures of metabolites such as gene expression and order in the genome. In this study, we developed a novel method to identify a candidate enzyme gene of a reaction using the chemical structures of the substrate-product pair (reactant pair). The proposed method is based on a search for similar reactant pairs in a reference database and offers ortholog groups that possibly mediate the given reaction. We applied the proposed method to two experimentally validated reactions. As a result, we confirmed that the histidine transaminase was correctly identified. Although our method could not directly identify the asparagine oxo-acid transaminase, we successfully found the paralog gene most similar to the correct enzyme gene. We also applied our method to infer candidate enzyme genes in the mesaconate pathway. The advantage of our method lies in the prediction of possible genes for orphan enzyme reactions where any associated gene sequences are not determined yet. We believe that this approach will facilitate experimental identification of genes for orphan enzymes.

  2. Identification of the Arabidopsis CHL3 gene as the nitrate reductase structural gene NIA2.

    PubMed Central

    Wilkinson, J Q; Crawford, N M

    1991-01-01

    Chlorate, the chlorine analog of nitrate, is a herbicide that has been used to select mutants impaired in the process of nitrate assimilation. In Arabidopsis thaliana, mutations at any one of eight distinct loci confer resistance to chlorate. The molecular identities of the genes at these loci are not known; however, one of these loci--chl3--maps very near the nitrate reductase structural gene NIA2. Through the isolation, characterization, and genetic analysis of new chlorate-resistant mutants generated by gamma irradiation, we have been able to demonstrate that the CHL3 gene and the NIA2 gene are identical. Three new chlorate-resistant mutants were identified that had deletions of the entire NIA2 gene. These nia2 null mutants were viable and still retained 10% of wild-type nitrate reductase activity in the leaves of the plants. All three deletion mutations were found to be new alleles of chl3. Introduction of the NIA2 gene back into these chl3 mutants by Agrobacterium-mediated transformation partially complemented their mutant phenotype. From these data, we conclude that Arabidopsis has at least two functional nitrate reductase genes and that the NIA2 gene product accounts for the majority of the leaf nitrate reductase activity and chlorate sensitivity of Arabidopsis plants. PMID:1840922

  3. A scalable algorithm for structure identification of complex gene regulatory network from temporal expression data.

    PubMed

    Gui, Shupeng; Rice, Andrew P; Chen, Rui; Wu, Liang; Liu, Ji; Miao, Hongyu

    2017-01-31

    Gene regulatory interactions are of fundamental importance to various biological functions and processes. However, only a few previous computational studies have claimed success in revealing genome-wide regulatory landscapes from temporal gene expression data, especially for complex eukaryotes like human. Moreover, recent work suggests that these methods still suffer from the curse of dimensionality if a network size increases to 100 or higher. Here we present a novel scalable algorithm for identifying genome-wide gene regulatory network (GRN) structures, and we have verified the algorithm performances by extensive simulation studies based on the DREAM challenge benchmark data. The highlight of our method is that its superior performance does not degenerate even for a network size on the order of 10(4), and is thus readily applicable to large-scale complex networks. Such a breakthrough is achieved by considering both prior biological knowledge and multiple topological properties (i.e., sparsity and hub gene structure) of complex networks in the regularized formulation. We also validate and illustrate the application of our algorithm in practice using the time-course gene expression data from a study on human respiratory epithelial cells in response to influenza A virus (IAV) infection, as well as the CHIP-seq data from ENCODE on transcription factor (TF) and target gene interactions. An interesting finding, owing to the proposed algorithm, is that the biggest hub structures (e.g., top ten) in the GRN all center at some transcription factors in the context of epithelial cell infection by IAV. The proposed algorithm is the first scalable method for large complex network structure identification. The GRN structure identified by our algorithm could reveal possible biological links and help researchers to choose which gene functions to investigate in a biological event. The algorithm described in this article is implemented in MATLAB (Ⓡ) , and the source code is

  4. Identification and structure of the Rhizobium galegae common nodulation genes: evidence for horizontal gene transfer.

    PubMed

    Suominen, L; Roos, C; Lortet, G; Paulin, L; Lindström, K

    2001-06-01

    Rhizobia are soil bacteria able to fix atmospheric nitrogen in symbiosis with leguminous plants. In response to a signal cascade coded by genes of both symbiotic partners, a specific plant organ, the nodule, is formed. Rhizobial nodulation (nod) genes trigger nodule formation through the synthesis of Nod factors, a family of chitolipooligosaccharides that are specifically recognized by the host plant at the first stages of the nodulation process. Here, we present the organization and sequence of the common nod genes from Rhizobium galegae, a symbiotic member of the RHIZOBIACEAE: This species has an intriguing phylogenetic position, being symbiotic among pathogenic agrobacteria, which induce tumors instead of nodules in plant shoots or roots. This apparent incongruence raises special interest in the origin of the symbiotic apparatus of R. galegae. Our analysis of DNA sequence data indicated that the organization of the common nod gene region of R. galegae was similar to that of Sinorhizobium meliloti and Rhizobium leguminosarum, with nodIJ downstream of nodABC and the regulatory nodD gene closely linked to the common nod operon. Moreover, phylogenetic analyses of the nod gene sequences showed a close relationship especially between the common nodA sequences of R. galegae, S. meliloti, and R. leguminosarum biovars viciae and trifolii. This relationship in structure and sequence contrasts with the phylogeny based on 16S rRNA, which groups R. galegae close to agrobacteria and separate from most other rhizobia. The topology of the nodA tree was similar to that of the corresponding host plant tree. Taken together, these observations indicate that lateral nod gene transfer occurred from fast-growing rhizobia toward agrobacteria, after which the symbiotic apparatus evolved under host plant constraint.

  5. A Metastate HMM with Application to Gene Structure Identification in Eukaryotes

    NASA Astrophysics Data System (ADS)

    Winters-Hilt, Stephen; Baribault, Carl

    2010-12-01

    We introduce a generalized-clique hidden Markov model (HMM) and apply it to gene finding in eukaryotes ( C. elegans). We demonstrate a HMM structure identification platform that is novel and robustly-performing in a number of ways. The generalized clique HMM begins by enlarging the primitive hidden states associated with the individual base labels (as exon, intron, or junk) to substrings of primitive hidden states, or footprint states, having a minimal length greater than the footprint state length. The emissions are likewise expanded to higher order in the fundamental joint probability that is the basis of the generalized-clique, or "metastate", HMM. We then consider application to eukaryotic gene finding and show how such a metastate HMM improves the strength of coding/noncoding-transition contributions to gene-structure identification. We will describe situations where the coding/noncoding-transition modeling can effectively recapture the exon and intron heavy tail distribution modeling capability as well as manage the exon-start needle-in-the-haystack problem. In analysis of the C. elegans genome we show that the sensitivity and specificity (SN,SP) results for both the individual-state and full-exon predictions are greatly enhanced over the standard HMM when using the generalized-clique HMM.

  6. Computational identification and structural analysis of deleterious functional SNPs in MLL gene causing acute leukemia.

    PubMed

    George Priya Doss, C; Rajasekaran, R; Sethumadhavan, Rao

    2010-09-01

    A promising application of the huge amounts of data from the Human Genome Project currently available offers new opportunities for identifying the genetic predisposition and developing a better understanding of complex diseases such as cancers. The main focus of cancer genetics is the study of mutations that are causally implicated in tumorigenesis. The identification of such causal mutations does not only provide insight into cancer biology but also presents anticancer therapeutic targets and diagnostic markers. In this study, we evaluated the Single Nucleotide Polymorphisms (SNPs) that can alter the expression and the function in MLL gene through computational methods. We applied an evolutionary perspective to screen the SNPs using a sequence homologybased SIFT tool, suggested that 10 non-synonymous SNPs (nsSNPs) (50%) were found to be deleterious. Structure based approach PolyPhen server suggested that 5 nsSNPS (25%) may disrupt protein function and structure. PupaSuite tool predicted the phenotypic effect of SNPs on the structure and function of the affected protein. Structure analysis was carried out with the major mutations that occurred in the native protein coded by MLL gene is at amino acid positions Q1198P and K1203Q. The solvent accessibility results showed that 7 residues changed from exposed state in the native type protein to buried state in Q1198P mutant protein and remained unchanged in the case of K1203Q. From the overall results obtained, nsSNP with id (rs1784246) at the amino acid position Q1198P could be considered as deleterious mutation in the acute leukemia caused by MLL gene.

  7. The use of R-looping for structural gene identification and mRNA purification.

    PubMed Central

    Woolford, J L; Rosbash, M

    1979-01-01

    A method is presented for the purification of mRNAs and the identification of structural gene sequences in recombinant DNA molecules. RNA is hybridized to double-stranded linear DNA such that R-loops are formed between most DNAs and their complementary RNA sequences. These R-loops are purified from unhybridized RNAs by gel filtration chromatography in the presence of a high concentration of salt. The complementary RNAs are released from the R-loops by heating, and are assayed by gel electrophoresis or cell free translation to determine their purity and to identify the proteins for which they code. We have demonstrated that recombinant DNAs containing sequences for abundant or moderately abundant mRNAs of Saccharomyces cerevisiae can be identified by this means. Images PMID:379820

  8. yrGATE: a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes.

    PubMed

    Wilkerson, Matthew D; Schlueter, Shannon D; Brendel, Volker

    2006-01-01

    Your Gene structure Annotation Tool for Eukaryotes (yrGATE) provides an Annotation Tool and Community Utilities for worldwide web-based community genome and gene annotation. Annotators can evaluate gene structure evidence derived from multiple sources to create gene structure annotations. Administrators regulate the acceptance of annotations into published gene sets. yrGATE is designed to facilitate rapid and accurate annotation of emerging genomes as well as to confirm, refine, or correct currently published annotations. yrGATE is highly portable and supports different standard input and output formats. The yrGATE software and usage cases are available at http://www.plantgdb.org/prj/yrGATE.

  9. yrGATE: a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes

    PubMed Central

    Wilkerson, Matthew D; Schlueter, Shannon D; Brendel, Volker

    2006-01-01

    Your Gene structure Annotation Tool for Eukaryotes (yrGATE) provides an Annotation Tool and Community Utilities for worldwide web-based community genome and gene annotation. Annotators can evaluate gene structure evidence derived from multiple sources to create gene structure annotations. Administrators regulate the acceptance of annotations into published gene sets. yrGATE is designed to facilitate rapid and accurate annotation of emerging genomes as well as to confirm, refine, or correct currently published annotations. yrGATE is highly portable and supports different standard input and output formats. The yrGATE software and usage cases are available at . PMID:16859520

  10. The structure of the human peripherin gene (PRPH) and identification of potential regulatory elements

    SciTech Connect

    Foley, J.; Ley, C.A.; Parysek, L.M.

    1994-07-15

    The authors determined the complete nucleotide sequence of the coding region of the human peripherin gene (PRPH), as well as 742 bp 5{prime} to the cap site and 584 bp 3{prime} to the stop codon, and compared its structure and sequence to the rat and mouse genes. The overall structure of 9 exons separated by 8 introns is conserved among these three mammalian species. The nucleotide sequences of the human peripherin gene exons were 90% identical to the rat gene sequences, and the predicted human peripherin protein differed from rat peripherin at only 18 of 475 amino acid residues. Comparison of the 5{prime} flanking regions of the human peripherin gene and rodent genes revealed extensive areas of high homology. Additional conserved segments were found in introns 1 and 2. Within the 5{prime} region, potential regulatory sequences, including a nerve growth factor negative regulatory element, a Hox protein binding site, and a heat shock element, were identified in all peripherin genes. The positional conservation of each element suggests that they may be important in the tissue-specific, developmental-specific, and injury-specific expression of the peripherin gene. 24 refs., 2 figs., 1 tab.

  11. Identification of human gene structure using linear discriminant functions and dynamic programming

    SciTech Connect

    Solovyev, V.V.; Salamov, A.A.; Lawrence, C.B.

    1995-12-31

    Development of advanced technique to identify gene structure is one of the main challenges of the Human Genome Project. Discriminant analysis was applied to the construction of recognition functions for various components of gene structure. Linear discriminant functions for splice sites, 5{prime}-coding, internal exon, and Y-coding region recognition have been developed. A gene structure prediction system FGENE has been developed based on the exon recognition functions. We compute a graph of mutual compatibility of different exons and present a gene structure models as paths of this directed acyclic graph. For an optimal model selection we apply a variant of dynamic programming algorithm to search for the path in the graph with the maximal value of the corresponding discriminant functions. Prediction by FGENE for 185 complete human gene sequences has 81% exact exon recognition accuracy and 91% accuracy at the level of individual exon nucleotides with the correlation coefficient (C) equals 0.90. Testing FGENE on 35 genes not used in the development of discriminant functions shows 71% accuracy of exact exon prediction and 89% at the nucleotide level (C=0.86). FGENE compares very favorably with the other programs currently used to predict protein-coding regions. Analysis of uncharacterized human sequences based on our methods for splice site (HSPL, RNASPL), internal exons (HEXON), all type of exons (FEXH) and human (FGENEH) and bacterial (CDSB) gene structure prediction and recognition of human and bacterial sequences (HBR) (to test a library for E. coli contamination) is available through the University of Houston, Weizmann Institute of Science network server and a WWW page of the Human Genome Center at Baylor College of Medicine.

  12. Identification of the structural gene for dipeptidyl aminopeptidase yscV (DAP2) of Saccharomyces cerevisiae.

    PubMed Central

    Suárez Rendueles, P; Wolf, D H

    1987-01-01

    Mutants of Saccharomyces cerevisiae lacking dipeptidyl aminopeptidase yscV were isolated from a strain already defective in dipeptidyl aminopeptidase yscIV, an enzyme with overlapping substrate specificity. The mutants were identified by a staining technique with the chromogenic substrate Ala-Pro-4-methoxy-beta-naphthylamide to screen colonies for the absence of the enzyme. One of the mutants had a thermolabile activity, indicating that it contained a structural gene mutation. The 53 mutants analyzed fell into one complementation group that corresponded to the yscV structural gene, DAP2. The defect segregated 2:2 in meiotic tetrads, indicating a single chromosomal gene mutation, which was shown to be recessive. Diploids heterozygous for DAP2 displayed gene dosage effects with respect to yscV enzyme activity. The absence of dipeptidyl aminopeptidase yscV or the combined loss of both dipeptidyl aminopeptidases yscIV and yscV did not affect mitotic growth under rich or poor growth conditions. In contrast to the dipeptidyl aminopeptidase yscIV lesion (ste13), which leads to alpha sterility because strains secrete incompletely processed forms of the alpha-factor pheromone, the dipeptidyl aminopeptidase yscV lesion did not affect mating, and strains produced fully active alpha-factor pheromone. dap2 mutants did not show any obvious phenotype under a variety of conditions tested. PMID:3305478

  13. Overview of PSB track on gene structure identification in large-scale genomic sequence

    SciTech Connect

    Uberbacher, E.C.; Xu, Y.

    1998-12-31

    The recent funding of more than a dozen major genome centers to begin community-wide high-throughput sequencing of the human genome has created a significant new challenge for the computational analysis of DNA sequence and the prediction of gene structure and function. It has been estimated that on average from 1996 to 2003, approximately 2 million bases of newly finished DNA sequence will be produced every day and be made available on the Internet and in central databases. The finished (fully assembled) sequence generated each day will represent approximately 75 new genes (and their respective proteins), and many times this number will be represented in partially completed sequences. The information contained in these is of immeasurable value to medical research, biotechnology, the pharmaceutical industry and researchers in a host of fields ranging from microorganism metabolism, to structural biology, to bioremediation. Sequencing of microorganisms and other model organisms is also ramping up at a very rapid rate. The genomes for yeast and several microorganisms such as H. influenza have recently been fully sequenced, although the significance of many genes remains to be determined.

  14. Structure of the human histamine H3 receptor gene (HRH3) and identification of naturally occurring variations.

    PubMed

    Wiedemann, P; Bönisch, H; Oerters, F; Brüss, M

    2002-04-01

    Neurotransmitter release is modulated by presynaptic histamine H(3) receptors located on histaminergic, noradrenergic and other nonhistaminergic neurons of the central and peripheral nervous system. Here, we report the determination of the structure of the human histamine H(3) receptor gene (HRH3) and the identification of a missense mutation (Ala280Val) in a patient with Shy-Drager syndrome. The coding region of the gene consists of three exons interrupted by two introns of approximately 1 kb in size. Exon boundaries only partly correspond to transmembrane domain organization. The homozygous Ala280Val variation in the third intracellular loop of the histamine H(3) receptor of a patient with Shy-Drager syndrome may be related to the etiology of the illness due to altered norepinephrine release. Furthermore, knowledge of the gene structure allows the verification of alternative splicing of the receptor. The corresponding histamine H(3) receptor isoforms as reported for the guinea pig and rat histamine H(3) receptor in different brain regions are not found in the human brain.

  15. Force Identification from Structural Response

    DTIC Science & Technology

    1999-12-01

    Jan 1986. 20. Distefano, Nestor, and Amitav Rath , (1975). "System Identification in Nonlinear Structural Seismic Dynamics." Computer Methods ill...response identification. Distefano and Rath (1975) presented methods of identification for the determination of nonlinear parameters associated with

  16. Identification and structural analysis of a ribosomal RNA gene promoter from Thiobacillus ferrooxidans.

    PubMed

    Takamiya, M; Salazar, O; Vargas, D; Jedlicki, E; Orellana, O

    1990-10-15

    The 5'-terminus of a rRNA operon (rrnT2) from Thiobacillus ferrooxidans was characterized. The rRNA promoters from this microorganism were identified by means of a functional assay in Escherichia coli. DNA sequencing of the promoter region, upstream the 16 S rRNA gene, showed the presence of a consensus sequence for bacterial ribosomal promoters. Other features such as a 'discriminator' sequence, antiterminator elements and an upstream hexanucleotide common to several rRNA operons were also found. Two other putative transcription promoters were also identified.

  17. Auxin Response Factor Genes Repertoire in Mulberry: Identification, and Structural, Functional and Evolutionary Analyses

    PubMed Central

    Baranwal, Vinay Kumar; Negi, Nisha; Khurana, Paramjit

    2017-01-01

    Auxin Response Factors (ARFs) are at the core of the regulation mechanism for auxin-mediated responses, along with AUX/IAA proteins.They are critical in the auxin-mediated control of various biological responses including development and stress. A wild mulberry species genome has been sequenced and offers an opportunity to investigate this important gene family. A total of 17 ARFs have been identified from mulberry (Morus notabilis) which show a wide range of expression patterns. Of these 17 ARFs, 15 have strong acidic isoelectric point (pI) values and a molecular mass ranging from 52 kDa to 101 kDa. The putative promoters of these ARFs harbour cis motifs related to light-dependent responses, various stress responses and hormone regulations suggestive of their multifactorial regulation. The gene ontology terms for ARFs indicate their role in flower development, stress, root morphology and other such development and stress mitigation related activities. Conserved motif analysis showed the presence of all typical domains in all but four members that lack the PB1 domain and thus represent truncated ARFs. Expression analysis of these ARFs suggests their preferential expression in tissues ranging from leaf, root, winter bud, bark and male flowers. These ARFs showed differential expression in the leaf tissue of M. notabilis, Morus laevigata and Morus serrata. Insights gained from this analysis have implications in mulberry improvement programs. PMID:28841197

  18. Auxin Response Factor Genes Repertoire in Mulberry: Identification, and Structural, Functional and Evolutionary Analyses.

    PubMed

    Baranwal, Vinay Kumar; Negi, Nisha; Khurana, Paramjit

    2017-08-25

    Auxin Response Factors (ARFs) are at the core of the regulation mechanism for auxin-mediated responses, along with AUX/IAA proteins.They are critical in the auxin-mediated control of various biological responses including development and stress. A wild mulberry species genome has been sequenced and offers an opportunity to investigate this important gene family. A total of 17 ARFs have been identified from mulberry (Morus notabilis) which show a wide range of expression patterns. Of these 17 ARFs, 15 have strong acidic isoelectric point (pI) values and a molecular mass ranging from 52 kDa to 101 kDa. The putative promoters of these ARFs harbour cis motifs related to light-dependent responses, various stress responses and hormone regulations suggestive of their multifactorial regulation. The gene ontology terms for ARFs indicate their role in flower development, stress, root morphology and other such development and stress mitigation related activities. Conserved motif analysis showed the presence of all typical domains in all but four members that lack the PB1 domain and thus represent truncated ARFs. Expression analysis of these ARFs suggests their preferential expression in tissues ranging from leaf, root, winter bud, bark and male flowers. These ARFs showed differential expression in the leaf tissue of M. notabilis, Morus laevigata and Morus serrata. Insights gained from this analysis have implications in mulberry improvement programs.

  19. Differentially Coexpressed Disease Gene Identification Based on Gene Coexpression Network.

    PubMed

    Jiang, Xue; Zhang, Han; Quan, Xiongwen

    2016-01-01

    Screening disease-related genes by analyzing gene expression data has become a popular theme. Traditional disease-related gene selection methods always focus on identifying differentially expressed gene between case samples and a control group. These traditional methods may not fully consider the changes of interactions between genes at different cell states and the dynamic processes of gene expression levels during the disease progression. However, in order to understand the mechanism of disease, it is important to explore the dynamic changes of interactions between genes in biological networks at different cell states. In this study, we designed a novel framework to identify disease-related genes and developed a differentially coexpressed disease-related gene identification method based on gene coexpression network (DCGN) to screen differentially coexpressed genes. We firstly constructed phase-specific gene coexpression network using time-series gene expression data and defined the conception of differential coexpression of genes in coexpression network. Then, we designed two metrics to measure the value of gene differential coexpression according to the change of local topological structures between different phase-specific networks. Finally, we conducted meta-analysis of gene differential coexpression based on the rank-product method. Experimental results demonstrated the feasibility and effectiveness of DCGN and the superior performance of DCGN over other popular disease-related gene selection methods through real-world gene expression data sets.

  20. Differentially Coexpressed Disease Gene Identification Based on Gene Coexpression Network

    PubMed Central

    Quan, Xiongwen

    2016-01-01

    Screening disease-related genes by analyzing gene expression data has become a popular theme. Traditional disease-related gene selection methods always focus on identifying differentially expressed gene between case samples and a control group. These traditional methods may not fully consider the changes of interactions between genes at different cell states and the dynamic processes of gene expression levels during the disease progression. However, in order to understand the mechanism of disease, it is important to explore the dynamic changes of interactions between genes in biological networks at different cell states. In this study, we designed a novel framework to identify disease-related genes and developed a differentially coexpressed disease-related gene identification method based on gene coexpression network (DCGN) to screen differentially coexpressed genes. We firstly constructed phase-specific gene coexpression network using time-series gene expression data and defined the conception of differential coexpression of genes in coexpression network. Then, we designed two metrics to measure the value of gene differential coexpression according to the change of local topological structures between different phase-specific networks. Finally, we conducted meta-analysis of gene differential coexpression based on the rank-product method. Experimental results demonstrated the feasibility and effectiveness of DCGN and the superior performance of DCGN over other popular disease-related gene selection methods through real-world gene expression data sets. PMID:28042568

  1. Identification and Characterization of MAE1, the Saccharomyces cerevisiae Structural Gene Encoding Mitochondrial Malic Enzyme

    PubMed Central

    Boles, Eckhard; de Jong-Gubbels, Patricia; Pronk, Jack T.

    1998-01-01

    Pyruvate, a precursor for several amino acids, can be synthesized from phosphoenolpyruvate by pyruvate kinase. Nevertheless, pyk1 pyk2 mutants of Saccharomyces cerevisiae devoid of pyruvate kinase activity grew normally on ethanol in defined media, indicating the presence of an alternative route for pyruvate synthesis. A candidate for this role is malic enzyme, which catalyzes the oxidative decarboxylation of malate to pyruvate. Disruption of open reading frame YKL029c, which is homologous to malic enzyme genes from other organisms, abolished malic enzyme activity in extracts of glucose-grown cells. Conversely, overexpression of YKL029c/MAE1 from the MET25 promoter resulted in an up to 33-fold increase of malic enzyme activity. Growth studies with mutants demonstrated that presence of either Pyk1p or Mae1p is required for growth on ethanol. Mutants lacking both enzymes could be rescued by addition of alanine or pyruvate to ethanol cultures. Disruption of MAE1 alone did not result in a clear phenotype. Regulation of MAE1 was studied by determining enzyme activities and MAE1 mRNA levels in wild-type cultures and by measuring β-galactosidase activities in a strain carrying a MAE1::lacZ fusion. Both in shake flask cultures and in carbon-limited chemostat cultures, MAE1 was constitutively expressed. A three- to fourfold induction was observed during anaerobic growth on glucose. Subcellular fractionation experiments indicated that malic enzyme in S. cerevisiae is a mitochondrial enzyme. Its regulation and localization suggest a role in the provision of intramitochondrial NADPH or pyruvate under anaerobic growth conditions. However, since null mutants could still grow anaerobically, this function is apparently not essential. PMID:9603875

  2. The structure of the presenilin 1 (S182) gene and identification of six novel mutations in early onset AD families.

    PubMed

    1995-10-01

    Genetic linkage studies place a gene causing early onset familial Alzheimer's disease (FAD) on chromosome 14q24.3 (refs 1-4). Five mutations within the S182 (Presenilin 1: PS-1) gene, which maps to this region, have recently been reported in several early onset FAD kindreds. We have localized the PS-1 gene to a 75 kb region and present the structure of this gene, evidence for alternative splicing and describe six novel mutations in early onset FAD pedigrees all of which alter residues conserved in the STM2 (Presenilin 2: PS-2) gene.

  3. Identification of Mating Type Genes in the Bipolar Basidiomycetous Yeast Rhodosporidium toruloides: First Insight into the MAT Locus Structure of the Sporidiobolales▿ †

    PubMed Central

    Coelho, Marco A.; Rosa, André; Rodrigues, Nádia; Fonseca, Álvaro; Gonçalves, Paula

    2008-01-01

    Rhodosporidium toruloides is a heterothallic, bipolar, red yeast that belongs to the Sporidiobolales, an order within a major lineage of basidiomycetes, the Pucciniomycotina. In contrast to other basidiomycetes, considerably less is known about the nature of the mating type (MAT) loci that control sexual reproduction in this lineage. Three genes (RHA1, RHA2, and RHA3) encoding precursors of the MAT A1 pheromone (rhodotorucine A) were previously identified and formed the basis for a genome walking approach that led to the identification of additional MAT genes in complementary mating strains of R. toruloides. Two mating type-specific alleles encoding a p21-activated kinase (PAK; Ste20 homolog) were found between the RHA2 and RHA3 genes, and identification in MAT A2 strains of a gene encoding a presumptive pheromone precursor enabled prediction of the structure of rhodotorucine a. In addition, a putative pheromone receptor gene (STE3 homolog) was identified upstream of RHA1. Analyses of genomic data from two closely related species, Sporobolomyces roseus and Sporidiobolus salmonicolor, identified syntenic regions that contain homologs of all the above-mentioned genes. Notably, six novel pheromone precursor genes were uncovered, which encoded, similarly to the RHA genes, multiple tandem copies of the peptide moiety. This suggests that this structure, which is unique among fungal lipopeptide pheromones, seems to be prevalent in red yeasts. Species comparisons provided evidence for a large, multigenic MAT locus structure in the Sporidiobolales, but no putative homeodomain transcription factor genes (which are present in all basidiomycetous MAT loci characterized thus far) could be found in any of the three species in the vicinity of the MAT genes identified. PMID:18408057

  4. Identification and Characterization of Two Novel Methyltransferase Genes That Determine the Serotype 12-Specific Structure of Glycopeptidolipids of Mycobacterium intracellulare▿

    PubMed Central

    Nakata, Noboru; Fujiwara, Nagatoshi; Naka, Takashi; Yano, Ikuya; Kobayashi, Kazuo; Maeda, Shinji

    2008-01-01

    The Mycobacterium avium complex is distributed ubiquitously in the environment. It is an important cause of pulmonary and extrapulmonary diseases in humans and animals. The species in this complex produce polar glycopeptidolipids (GPLs); of particular interest is their serotype-specific antigenicity. Several reports have described that GPL structure may play an important role in bacterial physiology and pathogenesis and in the host immune response. Recently, we determined the complete structure of the GPL derived from Mycobacterium intracellulare serotype 7 and characterized the serotype 7 GPL-specific gene cluster. The structure of serotype 7 GPL closely resembles that of serotype 12 GPL, except for O methylation. In the present study, we isolated and characterized the serotype 12-specific gene cluster involved in glycosylation of the GPL. Ten open reading frames (ORFs) and one pseudogene were observed in the cluster. The genetic organization of the serotype 12-specific gene cluster resembles that of the serotype 7-specific gene cluster, but two novel ORFs (orfA and orfB) encoding putative methyltransferases are present in the cluster. Functional analyses revealed that orfA and orfB encode methyltransferases that synthesize O-methyl groups at the C-4 position in the rhamnose residue next to the terminal hexose and at the C-3 position in the terminal hexose, respectively. Our results show that these two methyltransferase genes determine the structural difference of serotype 12-specific GPL from serotype 7-specific GPL. PMID:18024513

  5. Force Identification from Structural Response

    DTIC Science & Technology

    1990-03-01

    Amitav Rath , (1975). "System Identification in Nonlinear Structural Seismic Dynamics." Computer Mechods in Applied Mechanics and Engineering, 5 (1975) 353...than linear models. Singh and Subramanian (1980) attacked the problem from a frequency response identification. Distefano and Rath (1975) presented

  6. Proteomic analysis and identification of the structural and regulatory proteins of the Rhodobacter capsulatus gene transfer agent.

    PubMed

    Chen, Frank; Spano, Anthony; Goodman, Benjamin E; Blasier, Kiev R; Sabat, Agnes; Jeffery, Erin; Norris, Andrew; Shabanowitz, Jeffrey; Hunt, Donald F; Lebedev, Nikolai

    2009-02-01

    The gene transfer agent of Rhodobacter capsulatus (GTA) is a unique phage-like particle that exchanges genetic information between members of this same species of bacterium. Besides being an excellent tool for genetic mapping, the GTA has a number of advantages for biotechnological and nanoengineering purposes. To facilitate the GTA purification and identify the proteins involved in GTA expression, assembly and regulation, in the present work we construct and transform into R. capsulatus Y262 a gene coding for a C-terminally His-tagged capsid protein. The constructed protein was expressed in the cells, assembled into chimeric GTA particles inside the cells and excreted from the cells into surrounding medium. Transmission electron micrographs of phosphotungstate-stained, NiNTA-purified chimeric GTA confirm that its structure is similar to normal GTA particles, with many particles composed both of a head and a tail. The mass spectrometric proteomic analysis of polypeptides present in the GTA recovered outside the cells shows that GTA is composed of at least 9 proteins represented in the GTA gene cluster including proteins coded for by Orf's 3, 5, 6-9, 11, 13, and 15.

  7. Identification of IFITM1 and IFITM3 in Goose: Gene Structure, Expression Patterns, and Immune Reponses against Tembusu Virus Infection.

    PubMed

    Wang, Anqi; Sun, Lipei; Wang, Mingshu; Jia, Renyong; Zhu, Dekang; Liu, Mafeng; Sun, Kunfeng; Yang, Qiao; Wu, Ying; Chen, Xiaoyue; Cheng, Anchun; Chen, Shun

    2017-01-01

    As interferon-stimulated genes (ISGs), interferon-inducible transmembrane proteins 1 and 3 (IFITM1 and IFITM3) can effectively inhibit the replication of multiple viruses. Here, goose IFITM1 and IFITM3 were cloned and identified for the first time. The two proteins share the same topological structure and several important sites critical for the antiviral functions in other species are conserved in the goose. Goose IFITM1 and IFITM3 are most closely related to their respective orthologs in ducks; these proteins exhibited high mRNA transcript levels in immune-related tissues, including the thymus, bursa of Fabricius, and Harderian gland, compared to other tissues. Moreover, goose IFITM1 was highly constitutively expressed in gastrointestinal tract tissues, while goose IFITM3 was expressed in respiratory organs. Furthermore, goose IFITM3 was activated in goose peripheral blood mononuclear cells (PBMCs) infected with Tembusu virus (TMUV) or treated with Toll-like receptors (TLRs) agonists, while only the R848 and Poly (I:C) agonists induced significant upregulation of goose IFITM1. Furthermore, goose IFITM1 and IFITM3 were upregulated in the sampled tissues, to some extent, after TMUV infection. Notably, significant upregulation of goose IFITM1 and IFITM3 was detected in the cecum and cecal tonsil, where TMUV was primarily distributed. These data provide new insights into the immune effectors in geese and promote our understanding of the role of IFITM1 and IFITM3 in the defense against TMUV.

  8. Identification of IFITM1 and IFITM3 in Goose: Gene Structure, Expression Patterns, and Immune Reponses against Tembusu Virus Infection

    PubMed Central

    Wang, Anqi; Sun, Lipei; Wang, Mingshu; Jia, Renyong; Zhu, Dekang; Sun, Kunfeng; Yang, Qiao; Wu, Ying; Chen, Xiaoyue

    2017-01-01

    As interferon-stimulated genes (ISGs), interferon-inducible transmembrane proteins 1 and 3 (IFITM1 and IFITM3) can effectively inhibit the replication of multiple viruses. Here, goose IFITM1 and IFITM3 were cloned and identified for the first time. The two proteins share the same topological structure and several important sites critical for the antiviral functions in other species are conserved in the goose. Goose IFITM1 and IFITM3 are most closely related to their respective orthologs in ducks; these proteins exhibited high mRNA transcript levels in immune-related tissues, including the thymus, bursa of Fabricius, and Harderian gland, compared to other tissues. Moreover, goose IFITM1 was highly constitutively expressed in gastrointestinal tract tissues, while goose IFITM3 was expressed in respiratory organs. Furthermore, goose IFITM3 was activated in goose peripheral blood mononuclear cells (PBMCs) infected with Tembusu virus (TMUV) or treated with Toll-like receptors (TLRs) agonists, while only the R848 and Poly (I:C) agonists induced significant upregulation of goose IFITM1. Furthermore, goose IFITM1 and IFITM3 were upregulated in the sampled tissues, to some extent, after TMUV infection. Notably, significant upregulation of goose IFITM1 and IFITM3 was detected in the cecum and cecal tonsil, where TMUV was primarily distributed. These data provide new insights into the immune effectors in geese and promote our understanding of the role of IFITM1 and IFITM3 in the defense against TMUV. PMID:28386554

  9. Identification of genes involved in the expression of atypical lipooligosaccharide structures from a second class of Haemophilus ducreyi.

    PubMed

    Post, Deborah M B; Munson, Robert S; Baker, Beth; Zhong, Huachun; Bozue, Joel A; Gibson, Bradford W

    2007-01-01

    Haemophilus ducreyi is a gram-negative bacterium that is the causative agent of chancroid. Strain 35000HP has been well characterized and is representative of the majority of H. ducreyi strains. Strain 35000HP produces a lipooligosaccharide (LOS) that contains D-glycero-D-manno-heptose in the main oligosaccharide chain extension; the lbgB gene has been shown to encode the DD-heptosyltransferase. The lbgB gene is found in a gene cluster together with the lbgA gene, which encodes for the galactosyltransferase I. These two genes are flanked by two housekeeping genes, rpmE and xthA, encoding the ribosomal protein L31 and the exonuclease III, respectively. Recently, a second group of H. ducreyi strains have been identified. Strain 33921, a representative of the class II strains, produces an LOS that lacks DD-heptose in the oligosaccharide portion of its LOS. To better understand the biosynthesis of the DD-heptose-deficient 33921 LOS, we cloned and sequenced the corresponding lbgAB genomic region from strain 33921. Similar to strain 35000HP, the 33921 genome contains xthA and rpmE. However, between these two genes we identified genes encoding two putative glycosyltransferases that were not highly homologous to the 35000HP lbgAB genes. In this study, we demonstrate that the product of one of these genes encodes a galactosyltransferase. In addition, dot blot hybridization determined that 3 of 35 strains tested had the atypical transferases present, as did 4 strains characterized as class II strains by other criterion. These data indicate that the lbgAB genes can serve as one indicator of the classification of H. ducreyi strains.

  10. A genetic ensemble approach for gene-gene interaction identification

    PubMed Central

    2010-01-01

    Background It has now become clear that gene-gene interactions and gene-environment interactions are ubiquitous and fundamental mechanisms for the development of complex diseases. Though a considerable effort has been put into developing statistical models and algorithmic strategies for identifying such interactions, the accurate identification of those genetic interactions has been proven to be very challenging. Methods In this paper, we propose a new approach for identifying such gene-gene and gene-environment interactions underlying complex diseases. This is a hybrid algorithm and it combines genetic algorithm (GA) and an ensemble of classifiers (called genetic ensemble). Using this approach, the original problem of SNP interaction identification is converted into a data mining problem of combinatorial feature selection. By collecting various single nucleotide polymorphisms (SNP) subsets as well as environmental factors generated in multiple GA runs, patterns of gene-gene and gene-environment interactions can be extracted using a simple combinatorial ranking method. Also considered in this study is the idea of combining identification results obtained from multiple algorithms. A novel formula based on pairwise double fault is designed to quantify the degree of complementarity. Conclusions Our simulation study demonstrates that the proposed genetic ensemble algorithm has comparable identification power to Multifactor Dimensionality Reduction (MDR) and is slightly better than Polymorphism Interaction Analysis (PIA), which are the two most popular methods for gene-gene interaction identification. More importantly, the identification results generated by using our genetic ensemble algorithm are highly complementary to those obtained by PIA and MDR. Experimental results from our simulation studies and real world data application also confirm the effectiveness of the proposed genetic ensemble algorithm, as well as the potential benefits of combining identification

  11. Structural system identification: Structural dynamics model validation

    SciTech Connect

    Red-Horse, J.R.

    1997-04-01

    Structural system identification is concerned with the development of systematic procedures and tools for developing predictive analytical models based on a physical structure`s dynamic response characteristics. It is a multidisciplinary process that involves the ability (1) to define high fidelity physics-based analysis models, (2) to acquire accurate test-derived information for physical specimens using diagnostic experiments, (3) to validate the numerical simulation model by reconciling differences that inevitably exist between the analysis model and the experimental data, and (4) to quantify uncertainties in the final system models and subsequent numerical simulations. The goal of this project was to develop structural system identification techniques and software suitable for both research and production applications in code and model validation.

  12. Structural System Identification Technology Verification

    DTIC Science & Technology

    1981-11-01

    USAAVRADCOM-TR-81-D-28Q V󈧄 ADA1091 81 LEI STRUCTURAL SYSTEM IDENTIFICATION TECHNOLOGY VERIFICATION \\ N. Giansante, A. Berman, W. o. Flannelly, E...release; distribution unlimited. Prepared for APPLIED TECHNOLOGY LABORATORY U. S. ARMY RESEARCH AND TECHNOLOGY LABORATORIES (AVRADCOM) S Fort Eustis...Va. 23604 4-J" APPLI ED TECHNOLOGY LABORATORY POSITION STATEMENT The Applied Technology Laboratory has been involved in the development of the Struc

  13. Genomic Structure and Identification of Novel Mutations in Usherin, the Gene Responsible for Usher Syndrome Type IIa

    PubMed Central

    Weston, M. D.; Eudy, J. D.; Fujita, S.; Yao, S.-F.; Usami, S.; Cremers, C.; Greenburg, J.; Ramesar, R.; Martini, A.; Moller, C.; Smith, R. J.; Sumegi, J.; Kimberling, William J.

    2000-01-01

    Usher syndrome type IIa (USHIIa) is an autosomal recessive disorder characterized by moderate to severe sensorineural hearing loss and progressive retinitis pigmentosa. This disorder maps to human chromosome 1q41. Recently, mutations in USHIIa patients were identified in a novel gene isolated from this chromosomal region. The USH2A gene encodes a protein with a predicted molecular weight of 171.5 kD and possesses laminin epidermal growth factor as well as fibronectin type III domains. These domains are observed in other protein components of the basal lamina and extracellular matrixes; they may also be observed in cell-adhesion molecules. The intron/exon organization of the gene whose protein we name “Usherin” was determined by direct sequencing of PCR products and cloned genomic DNA with cDNA-specific primers. The gene is encoded by 21 exons and spans a minimum of 105 kb. A mutation search of 57 independent USHIIa probands was performed with a combination of direct sequencing and heteroduplex analysis of PCR-amplified exons. Fifteen new mutations were found. Of 114 independent USH2A alleles, 58 harbored probable pathologic mutations. Ten cases of USHIIa were true homozygotes and 10 were compound heterozygotes; 18 heterozygotes with only one identifiable mutation were observed. Sixty-five percent (38/58) of cases had at least one mutation, and 51% (58/114) of the total number of possible mutations were identified. The allele 2299delG (previously reported as 2314delG) was the most frequent mutant allele observed (16%; 31/192). Three new missense mutations (C319Y, N346H, and C419F) were discovered; all were restricted to the previously unreported laminin domain VI region of Usherin. The possible significance of this domain, known to be necessary for laminin network assembly, is discussed in the context of domain VI mutations from other proteins. PMID:10729113

  14. Identification of genetic variation and haplotype structure of the canine ABCA4 gene for retinal disease association studies

    PubMed Central

    Zangerl, B.; Lindauer, S. J.; Acland, G. M.; Aguirre, G. D.

    2010-01-01

    Over 200 mutations in the retina specific member of the ATP-binding cassette transporter super-family (ABCA4) have been associated with a diverse group of human retinal diseases. The disease mechanisms, and genotype–phenotype associations, nonetheless, remain elusive in many cases. As orthologous genes are commonly mutated in canine models of human blinding disorders, canine ABCA4 appears to be an ideal candidate gene to identify and study sequence changes in dogs affected by various forms of inherited retinal degeneration. However, the size of the gene and lack of haplotype assignment significantly limit targeted association and/or linkage approaches. This study assessed the naturally observed sequence diversity of ABCA4 in the dog, identifying 80% of novel variations. While none of the observed polymorphisms have been associated with blinding disorders to date, breed and potentially disease specific haplotypes have been identified. Moreover, a tag SNP map of 17 (15) markers has been established that accurately predicts common ABCA4 haplotypes (frequency > 5%) explaining >85% (>80%) of the observed genetic diversity and will considerably advance future studies. Our sequence analysis of the complete canine ABCA4 coding region will clearly provide a baseline and tools for future association studies and comparative genomics to further delineate the role of ABCA4 in canine blinding disorders. PMID:20661590

  15. Identification of Essential Genes in the Salmonella Phage SPN3US Reveals Novel Insights into Giant Phage Head Structure and Assembly.

    PubMed

    Thomas, Julie A; Benítez Quintana, Andrea Denisse; Bosch, Martine A; Coll De Peña, Adriana; Aguilera, Elizabeth; Coulibaly, Assitan; Wu, Weimin; Osier, Michael V; Hudson, André O; Weintraub, Susan T; Black, Lindsay W

    2016-11-15

    Giant tailed bacterial viruses, or phages, such as Pseudomonas aeruginosa phage ϕKZ, have long genomes packaged into large, atypical virions. Many aspects of ϕKZ and related phage biology are poorly understood, mostly due to the fact that the functions of the majority of their proteins are unknown. We hypothesized that the Salmonella enterica phage SPN3US could be a useful model phage to address this gap in knowledge. The 240-kb SPN3US genome shares a core set of 91 genes with ϕKZ and related phages, ∼61 of which are virion genes, consistent with the expectation that virion complexity is an ancient, conserved feature. Nucleotide sequencing of 18 mutants enabled assignment of 13 genes as essential, information which could not have been determined by sequence-based searches for 11 genes. Proteome analyses of two SPN3US virion protein mutants with knockouts in 64 and 241 provided new insight into the composition and assembly of giant phage heads. The 64 mutant analyses revealed all the genetic determinants required for assembly of the SPN3US head and a likely head-tail joining role for gp64, and its homologs in related phages, due to the tailless-particle phenotype produced. Analyses of the mutation in 241, which encodes an RNA polymerase β subunit, revealed that without this subunit, no other subunits are assembled into the head, and enabled identification of a "missing" β' subunit domain. These findings support SPN3US as an excellent model for giant phage research, laying the groundwork for future analyses of their highly unusual virions, host interactions, and evolution. In recent years, there has been a paradigm shift in virology with the realization that extremely large viruses infecting prokaryotes (giant phages) can be found in many environments. A group of phages related to the prototype giant phage ϕKZ are of great interest due to their virions being among the most complex of prokaryotic viruses and their potential for biocontrol and phage therapy

  16. Identification of Essential Genes in the Salmonella Phage SPN3US Reveals Novel Insights into Giant Phage Head Structure and Assembly

    PubMed Central

    Benítez Quintana, Andrea Denisse; Bosch, Martine A.; Coll De Peña, Adriana; Aguilera, Elizabeth; Coulibaly, Assitan; Wu, Weimin; Osier, Michael V.; Hudson, André O.; Weintraub, Susan T.; Black, Lindsay W.

    2016-01-01

    ABSTRACT Giant tailed bacterial viruses, or phages, such as Pseudomonas aeruginosa phage ϕKZ, have long genomes packaged into large, atypical virions. Many aspects of ϕKZ and related phage biology are poorly understood, mostly due to the fact that the functions of the majority of their proteins are unknown. We hypothesized that the Salmonella enterica phage SPN3US could be a useful model phage to address this gap in knowledge. The 240-kb SPN3US genome shares a core set of 91 genes with ϕKZ and related phages, ∼61 of which are virion genes, consistent with the expectation that virion complexity is an ancient, conserved feature. Nucleotide sequencing of 18 mutants enabled assignment of 13 genes as essential, information which could not have been determined by sequence-based searches for 11 genes. Proteome analyses of two SPN3US virion protein mutants with knockouts in 64 and 241 provided new insight into the composition and assembly of giant phage heads. The 64 mutant analyses revealed all the genetic determinants required for assembly of the SPN3US head and a likely head-tail joining role for gp64, and its homologs in related phages, due to the tailless-particle phenotype produced. Analyses of the mutation in 241, which encodes an RNA polymerase β subunit, revealed that without this subunit, no other subunits are assembled into the head, and enabled identification of a “missing” β′ subunit domain. These findings support SPN3US as an excellent model for giant phage research, laying the groundwork for future analyses of their highly unusual virions, host interactions, and evolution. IMPORTANCE In recent years, there has been a paradigm shift in virology with the realization that extremely large viruses infecting prokaryotes (giant phages) can be found in many environments. A group of phages related to the prototype giant phage ϕKZ are of great interest due to their virions being among the most complex of prokaryotic viruses and their potential for

  17. Computational identification of new structured cis-regulatory elements in the 3'-untranslated region of human protein coding genes.

    PubMed

    Chen, Xiaowei Sylvia; Brown, Chris M

    2012-10-01

    Messenger ribonucleic acids (RNAs) contain a large number of cis-regulatory RNA elements that function in many types of post-transcriptional regulation. These cis-regulatory elements are often characterized by conserved structures and/or sequences. Although some classes are well known, given the wide range of RNA-interacting proteins in eukaryotes, it is likely that many new classes of cis-regulatory elements are yet to be discovered. An approach to this is to use computational methods that have the advantage of analysing genomic data, particularly comparative data on a large scale. In this study, a set of structural discovery algorithms was applied followed by support vector machine (SVM) classification. We trained a new classification model (CisRNA-SVM) on a set of known structured cis-regulatory elements from 3'-untranslated regions (UTRs) and successfully distinguished these and groups of cis-regulatory elements not been strained on from control genomic and shuffled sequences. The new method outperformed previous methods in classification of cis-regulatory RNA elements. This model was then used to predict new elements from cross-species conserved regions of human 3'-UTRs. Clustering of these elements identified new classes of potential cis-regulatory elements. The model, training and testing sets and novel human predictions are available at: http://mRNA.otago.ac.nz/CisRNA-SVM.

  18. Disease gene identification strategies for exome sequencing

    PubMed Central

    Gilissen, Christian; Hoischen, Alexander; Brunner, Han G; Veltman, Joris A

    2012-01-01

    Next generation sequencing can be used to search for Mendelian disease genes in an unbiased manner by sequencing the entire protein-coding sequence, known as the exome, or even the entire human genome. Identifying the pathogenic mutation amongst thousands to millions of genomic variants is a major challenge, and novel variant prioritization strategies are required. The choice of these strategies depends on the availability of well-phenotyped patients and family members, the mode of inheritance, the severity of the disease and its population frequency. In this review, we discuss the current strategies for Mendelian disease gene identification by exome resequencing. We conclude that exome strategies are successful and identify new Mendelian disease genes in approximately 60% of the projects. Improvements in bioinformatics as well as in sequencing technology will likely increase the success rate even further. Exome sequencing is likely to become the most commonly used tool for Mendelian disease gene identification for the coming years. PMID:22258526

  19. Genetic structure and diversity among sheep breeds in the United States: identification of the major gene pools.

    PubMed

    Blackburn, H D; Paiva, S R; Wildeus, S; Getz, W; Waldron, D; Stobart, R; Bixby, D; Purdy, P H; Welsh, C; Spiller, S; Brown, M

    2011-08-01

    Understanding existing levels of genetic diversity of sheep breeds facilitates in situ and ex situ conservation activities. A comprehensive evaluation of US sheep breeds has not been previously performed; therefore, we evaluated the genetic diversity among and within 28 US sheep breeds. Both major and minor breeds were included in the analysis and consisted of 666 animals from 222 producers located in 38 states. The level of within-breed genetic diversity was variable and not dependent upon status of a breed as a major or minor breed. Bayesian cluster analysis indicated the breeds were grouped more by physiological differences (meat vs. wool production) rather than geographic origin. Results suggest several actionable items to improve in situ and ex situ conservation. The results clearly identify breeds in need of increased in situ and ex situ management (e.g., Hog Island and Karakul) and allow several suggestions for in situ management of flocks. Conversely, several of the breeds appear genetically similar and therefore require less emphasis on collecting germplasm samples for the gene bank. Commercially important breeds (e.g., Rambouillet and Suffolk) were found to have substantial variation, which should enable breeders to proceed, unencumbered by genetic diversity concerns, with selection strategies that maximize profit.

  20. System Identification Tools for Control Structure Interaction

    DTIC Science & Technology

    1990-01-01

    DT! FILE COPY AL-TR-89-054 AD: 00 Final Report System Identification Tools for O for the period - September 1988 to Control Structure Interaction May...Classification) System Identification Tools for Control Structure Interaction (U) 12. PERSONAL AUTHOR(S) Kosut, Robert L.; Kabuli, Guntekin M. 13a. TYPE OF...identification, dynamics, 22 01 system identification , robustness, dynamic modeling, robust 22 02 control design, control design procedure 19. ABSTRACT

  1. Identification of Adaptive Mutations in the Influenza A Virus Non-Structural 1 Gene That Increase Cytoplasmic Localization and Differentially Regulate Host Gene Expression

    PubMed Central

    Forbes, Nicole; Selman, Mohammed; Pelchat, Martin; Jia, Jian Jun; Stintzi, Alain; Brown, Earl G.

    2013-01-01

    The NS1 protein of influenza A virus (IAV) is a multifunctional virulence factor. We have previously characterized gain-of-function mutations in the NS1 protein arising from the experimental adaptation of the human isolate A/Hong Kong/1/1968(H3N2) (HK) to the mouse. The majority of these mouse adapted NS1 mutations were demonstrated to increase virulence, viral fitness, and interferon antagonism, but differ in binding to the post-transcriptional processing factor cleavage and polyadenylation specificity factor 30 (CPSF30). Because nuclear trafficking is a major genetic determinant of influenza virus host adaptation, we assessed subcellular localization and host gene expression of NS1 adaptive mutations. Recombinant HK viruses with adaptive mutations in the NS1 gene were assessed for NS1 protein subcellular localization in mouse and human cells using confocal microscopy and cellular fractionation. In human cells the HK wild-type (HK-wt) virus NS1 protein partitioned equivalently between the cytoplasm and nucleus but was defective in cytoplasmic localization in mouse cells. Several adaptive mutations increased the proportion of NS1 in the cytoplasm of mouse cells with the greatest effects for mutations M106I and D125G. The host gene expression profile of the adaptive mutants was determined by microarray analysis of infected mouse cells to show either high or low extents of host-gene regulation (HGR or LGR) phenotypes. While host genes were predominantly down regulated for the HGR group of mutants (D2N, V23A, F103L, M106I+L98S, L98S, M106V, and M106V+M124I), the LGR phenotype mutants (D125G, M106I, V180A, V226I, and R227K) were characterized by a predominant up regulation of host genes. CPSF30 binding affinity of NS1 mutants did not predict effects on host gene expression. To our knowledge this is the first report of roles of adaptive NS1 mutations that impact intracellular localization and regulation of host gene expression. PMID:24391972

  2. Familial identification: population structure and relationship distinguishability.

    PubMed

    Rohlfs, Rori V; Fullerton, Stephanie Malia; Weir, Bruce S

    2012-02-01

    With the expansion of offender/arrestee DNA profile databases, genetic forensic identification has become commonplace in the United States criminal justice system. Implementation of familial searching has been proposed to extend forensic identification to family members of individuals with profiles in offender/arrestee DNA databases. In familial searching, a partial genetic profile match between a database entrant and a crime scene sample is used to implicate genetic relatives of the database entrant as potential sources of the crime scene sample. In addition to concerns regarding civil liberties, familial searching poses unanswered statistical questions. In this study, we define confidence intervals on estimated likelihood ratios for familial identification. Using these confidence intervals, we consider familial searching in a structured population. We show that relatives and unrelated individuals from population samples with lower gene diversity over the loci considered are less distinguishable. We also consider cases where the most appropriate population sample for individuals considered is unknown. We find that as a less appropriate population sample, and thus allele frequency distribution, is assumed, relatives and unrelated individuals become more difficult to distinguish. In addition, we show that relationship distinguishability increases with the number of markers considered, but decreases for more distant genetic familial relationships. All of these results indicate that caution is warranted in the application of familial searching in structured populations, such as in the United States.

  3. Familial Identification: Population Structure and Relationship Distinguishability

    PubMed Central

    Rohlfs, Rori V.; Fullerton, Stephanie Malia; Weir, Bruce S.

    2012-01-01

    With the expansion of offender/arrestee DNA profile databases, genetic forensic identification has become commonplace in the United States criminal justice system. Implementation of familial searching has been proposed to extend forensic identification to family members of individuals with profiles in offender/arrestee DNA databases. In familial searching, a partial genetic profile match between a database entrant and a crime scene sample is used to implicate genetic relatives of the database entrant as potential sources of the crime scene sample. In addition to concerns regarding civil liberties, familial searching poses unanswered statistical questions. In this study, we define confidence intervals on estimated likelihood ratios for familial identification. Using these confidence intervals, we consider familial searching in a structured population. We show that relatives and unrelated individuals from population samples with lower gene diversity over the loci considered are less distinguishable. We also consider cases where the most appropriate population sample for individuals considered is unknown. We find that as a less appropriate population sample, and thus allele frequency distribution, is assumed, relatives and unrelated individuals become more difficult to distinguish. In addition, we show that relationship distinguishability increases with the number of markers considered, but decreases for more distant genetic familial relationships. All of these results indicate that caution is warranted in the application of familial searching in structured populations, such as in the United States. PMID:22346758

  4. Identification of Unannotated Small Genes in Salmonella.

    PubMed

    Baek, Jonghwan; Lee, Jiyoung; Yoon, Kihoon; Lee, Hyunwoo

    2017-03-10

    Increasing evidence indicates that many, if not all, small genes encoding proteins ≤100 aa are missing in annotations of bacterial genomes currently available. To uncover unannotated small genes in the model bacterium Salmonella enterica Typhimurium 14028s, we used the genomic technique ribosome profiling, which provides a snapshot of all mRNAs being translated (translatome) in a given growth condition. For comprehensive identification of unannotated small genes, we obtained Salmonella translatomes from four different growth conditions: LB, MOPS rich defined medium, and two infection-relevant conditions low Mg(2+) (10 µM) and low pH (5.8). To facilitate the identification of small genes, ribosome profiling data were analyzed in combination with in silico predicted putative open reading frames and transcriptome profiles. As a result, we uncovered 130 unannotated ORFs. Of them, 98% were small ORFs putatively encoding peptides/proteins ≤100 aa, and some of them were only expressed in the infection-relevant low Mg(2+) and/or low pH condition. We validated the expression of 25 of these ORFs by western blot, including the smallest, which encodes a peptide of 7 aa residues. Our results suggest that many sequenced bacterial genomes are underannotated with regard to small genes and their gene annotations need to be revised.

  5. Identification of Unannotated Small Genes in Salmonella

    PubMed Central

    Baek, Jonghwan; Lee, Jiyoung; Yoon, Kihoon; Lee, Hyunwoo

    2017-01-01

    Increasing evidence indicates that many, if not all, small genes encoding proteins ≤100 aa are missing in annotations of bacterial genomes currently available. To uncover unannotated small genes in the model bacterium Salmonella enterica Typhimurium 14028s, we used the genomic technique ribosome profiling, which provides a snapshot of all mRNAs being translated (translatome) in a given growth condition. For comprehensive identification of unannotated small genes, we obtained Salmonella translatomes from four different growth conditions: LB, MOPS rich defined medium, and two infection-relevant conditions low Mg2+ (10 µM) and low pH (5.8). To facilitate the identification of small genes, ribosome profiling data were analyzed in combination with in silico predicted putative open reading frames and transcriptome profiles. As a result, we uncovered 130 unannotated ORFs. Of them, 98% were small ORFs putatively encoding peptides/proteins ≤100 aa, and some of them were only expressed in the infection-relevant low Mg2+ and/or low pH condition. We validated the expression of 25 of these ORFs by western blot, including the smallest, which encodes a peptide of 7 aa residues. Our results suggest that many sequenced bacterial genomes are underannotated with regard to small genes and their gene annotations need to be revised. PMID:28122954

  6. Structural Aspects of System Identification

    NASA Technical Reports Server (NTRS)

    Glover, Keith

    1973-01-01

    The problem of identifying linear dynamical systems is studied by considering structural and deterministic properties of linear systems that have an impact on stochastic identification algorithms. In particular considered is parametrization of linear systems so that there is a unique solution and all systems in appropriate class can be represented. It is assumed that a parametrization of system matrices has been established from a priori knowledge of the system, and the question is considered of when the unknown parameters of this system can be identified from input/output observations. It is assumed that the transfer function can be asymptotically identified, and the conditions are derived for the local, global and partial identifiability of the parametrization. Then it is shown that, with the right formulation, identifiability in the presence of feedback can be treated in the same way. Similarly the identifiability of parametrizations of systems driven by unobserved white noise is considered using the results from the theory of spectral factorization.

  7. Identification of the transcriptional unit, structural organization, and promoter sequence of the human sex-determining region Y (SRY) gene, using a reverse genetic approach

    SciTech Connect

    Hua Su; Lau, Y.F.C. )

    1993-01-01

    Using a simple strategy involving cosmid-mediated gene transfer, cDNA library construction, and molecular characterization techniques, the authors have determined the transcriptional unit, structural organization, and promoter sequence of the human sex-determining region Y (SRY) gene, the putative testis-determining factor (TDF) gene on the human Y chromosome. By this approach, a recombinant cosmid harboring the human SRY sequence was isolated and transfected to appropriate tissue-cultured cells. Recombinant cDNA clones were isolated from a cDNA library constructed from poly (A) + RNA of the transfected cells. Comparative studies between the respective cDNAs and the genomic cosmid have provided information regarding the organization of the SRY gene and its mRNAs. The results indicate that the human SRY gene is an intronless gene, produces transcripts of 1.1 kb, and possesses promoter activities in the transfected cells at approximately 310 bp of its upstream sequences. 57 refs., 5 figs.

  8. Structural system identification of a composite shell

    SciTech Connect

    Red-Horse, J.R.; Carne, T.G.; James, G.H.; Witkowski, W.R.

    1991-01-01

    Structural system identification is undergoing a period of renewed interest. Probabilistic approaches to physical parameter identification in analysis finite element models make uncertainty in test results an important issue. In this paper, we investigate this issue with a simple, though in many ways representative, structural system. The results of two modal parameter identification techniques are compared and uncertainty estimates, both through bias and random errors, are quantified. The importance of the interaction between test and analysis is also highlighted. 25 refs.

  9. Structural system identification of a composite shell

    SciTech Connect

    Red-Horse, J.R.; Carne, T.G.; James, G.H.; Witkowski, W.R.

    1991-12-31

    Structural system identification is undergoing a period of renewed interest. Probabilistic approaches to physical parameter identification in analysis finite element models make uncertainty in test results an important issue. In this paper, we investigate this issue with a simple, though in many ways representative, structural system. The results of two modal parameter identification techniques are compared and uncertainty estimates, both through bias and random errors, are quantified. The importance of the interaction between test and analysis is also highlighted. 25 refs.

  10. Gene expression complex networks: synthesis, identification, and analysis.

    PubMed

    Lopes, Fabrício M; Cesar, Roberto M; Costa, Luciano Da F

    2011-10-01

    method was sensitive to average degree variation, decreasing its network recovery rate with the increase of . The signal size was important for the inference method to get better accuracy in the network identification rate, presenting very good results with small expression profiles. However, the adopted inference method was not sensible to recognize distinct structures of interaction among genes, presenting a similar behavior when applied to different network topologies. In summary, the proposed framework, though simple, was adequate for the validation of the inferred networks by identifying some properties of the evaluated method, which can be extended to other inference methods.

  11. Structure of the human glucokinase gene and identification of a missense mutation in a Japanese patient with early-onset non-insulin-dependent diabetes mellitus

    SciTech Connect

    Sakura, Hiroshi; Eto, Kazuhiro; Ueno, Hirohisa; Yazaki, Yoshio; Kadowaki, Takashi ); Kadowaki, Hiroko; Simokawa, Kotaro; Akanuma, Yasuo ); Koda, Naoya; Fukushima, Yoshimitsu )

    1992-12-01

    Glucokinase is thought to play a glucose-sensor role in the pancreas, and abnormalities in its structure, function, and regulation can induce diabetes. The authors isolated the human glucokinase gene, and determined its genomic structure including exon-intron boundaries. Structure of the glucokinase gene in human was very similar to that in rat. Then, by screening Japanese diabetic patients using polymerase chain reaction - single strand conformation polymorphism (PCR-SSCP) and direct-sequencing strategies, they identified a missense mutation substituting ariginine (AGG) for glycine (GGG) at position 261 in exon 7 of the glucokinase gene in a patient with early-onset non-insulin-dependent diabetes (NIDDM). 12 refs., 3 figs., 2 tabs.

  12. The gene identification problem: An overview for developers

    SciTech Connect

    Fickett, J.W.

    1995-03-27

    The gene identification problem is the problem of interpreting nucleotide sequences by computer, in order to provide tentative annotation on the location, structure, and functional class of protein-coding genes. This problem is of self-evident importance, and is far from being fully solved, particularly for higher eukaryotes, Thus it is not surprising that the number of algorithm and software developers working in this area is rapidly increasing. The present paper is an overview of the field, with an emphasis on eukaryotes, for such developers.

  13. Nucleotide sequence of a Pseudomonas denitrificans 5.4-kilobase DNA fragment containing five cob genes and identification of structural genes encoding S-adenosyl-L-methionine: uroporphyrinogen III methyltransferase and cobyrinic acid a,c-diamide synthase.

    PubMed Central

    Crouzet, J; Cauchois, L; Blanche, F; Debussche, L; Thibaut, D; Rouyez, M C; Rigault, S; Mayaux, J F; Cameron, B

    1990-01-01

    A 5.4-kilobase DNA fragment carrying Pseudomonas denitrificans cob genes has been sequenced. The nucleotide sequence and genetic analysis revealed that this fragment carries five different cob genes (cobA to cobE). Four of these genes present the characteristics of translationally coupled genes. cobA has been identified as the structural gene of S-adenosyl-L-methionine:uroporphyrinogen III methyltransferase (SUMT) because the encoded protein has the same NH2 terminus and molecular weight as those determined for the purified SUMT. For the same reasons the cobB gene was shown to be the structural gene for cobyrinic acid a,c-diamide synthase. Genetic and biochemical data concerning cobC and cobD mutants suggest that the products of these genes are involved in the conversion of cobyric acid to cobinamide. PMID:2211520

  14. Analysis of the S-locus structure in Prunus armeniaca L. Identification of S-haplotype specific S-RNase and F-box genes.

    PubMed

    Romero, C; Vilanova, S; Burgos, L; Martínez-Calvo, J; Vicente, M; Llácer, G; Badenes, M L

    2004-09-01

    The gametophytic self-incompatibility (GSI) system in Rosaceae has been proposed to be controlled by two genes located in the S -locusan S-RNase and a recently described pollen expressed S -haplotype specific F-box gene (SFB). However, in apricot (Prunus armeniaca L.) these genes had not been identified yet. We have sequenced 21 kb in total of the S -locus region in 3 different apricot S -haplotypes. These fragments contain genes homologous to the S-RNase and F-box genes found in other Prunus species, preserving their basic gene structure features and defined amino acid domains. The physical distance between the F-box and the S-RNase genes was determined exactly in the S2-haplotype (2.9 kb) and inferred approximately in the S 1-haplotype (< 49 kb) confirming that these genes are linked. Sequence analysis of the 5' flanking regions indicates the presence of a conserved region upstream of the putative TATA box in the S-RNase gene. The three identified S-RNase alleles (S1, S2 and S4) had a high allelic sequence diversity (75.3 amino acid identity), and the apricot F-box allelic variants (SFB1, SFB2 and SFB4) were also highly haplotype-specific (79.4 amino acid identity). Organ specific-expression was also studied, revealing that S1- and S2-RNases are expressed in style tissues, but not in pollen or leaves. In contrast, SFB1 and SFB2 are only expressed in pollen, but not in styles or leaves. Taken together, these results support these genes as candidates for the pistil and pollen S-determinants of GSI in apricot.

  15. Recovery of Dominant, Autosomal Flightless Mutants of Drosophila Melanogaster and Identification of a New Gene Required for Normal Muscle Structure and Function

    PubMed Central

    Cripps, R. M.; Ball, E.; Stark, M.; Lawn, A.; Sparrow, J. C.

    1994-01-01

    To identify further mutations affecting muscle function and development in Drosophila melanogaster we recovered 22 autosomal dominant flightless mutations. From these we have isolated eight viable and lethal alleles of the muscle myosin heavy chain gene, and seven viable alleles of the indirect flight muscle (IFM)-specific Act88F actin gene. The Mhc mutations display a variety of phenotypic effects, ranging from reductions in myosin heavy chain content in the indirect flight muscles only, to reductions in the levels of this protein in other muscles. The Act88F mutations range from those which produce no stable actin and have severely abnormal myofibrillar structure, to those which accumulate apparently normal levels of actin in the flight muscles but which still have abnormal myofibrils and fly very poorly. We also recovered two recessive flightless mutants on the third chromosome. The remaining five dominant flightless mutations are all lethal alleles of a gene named lethal(3)Laker. The Laker alleles have been characterized and the gene located in polytene bands 62A10,B1-62B2,4. Laker is a previously unidentified locus which is haplo-insufficient for flight. In addition, adult wild-type heterozygotes and the lethal larval trans-heterozygotes show abnormalities of muscle structure indicating that the Laker gene product is an important component of muscle. PMID:8056306

  16. Identification of large space structures - Overview

    NASA Technical Reports Server (NTRS)

    Denman, Eugene; Juang, Jer-Nan; Junkins, John; Kamat, Manohar; Hasselman, T. K.

    1988-01-01

    The system identification process presently discussed for the case of large space structures uses the observed input to a system and its observed response, or output, to derive an analytical model of the system which can then be used to predict its response to future inputs. Due to their size and complexity, as well as the intrinsic difficulty of identifying the environment in which they function, large space structures will require vast amounts of information, encompassing both experimental and analytical data for identification. A status evaluation is made of the structural system identification literature to date.

  17. Identification of the transcriptional unit, structural organization, and promoter sequence of the human sex-determining region Y (SRY) gene, using a reverse genetic approach.

    PubMed Central

    Su, H; Lau, Y F

    1993-01-01

    Using a simple strategy involving cosmid-mediated gene transfer, cDNA library construction, and molecular characterization techniques, we have determined the transcriptional unit, structural organization, and promoter sequence of the human sex-determining region Y (SRY) gene, the putative testis-determining factor (TDF) gene on the human Y chromosome. By this approach, a recombinant cosmid harboring the human SRY sequence was isolated and transfected to appropriate tissue-cultured cells. Recombinant cDNA clones were isolated from a cDNA library constructed from poly (A) + RNA of the transfected cells. Comparative studies between the respective cDNAs and the genomic cosmid have provided information regarding the organization of the SRY gene and its mRNAs. The results indicate that the human SRY gene is an intronless gene, produces transcripts of 1.1 kb, and possesses promoter activities in the transfected cells at approximately 310 bp of its upstream sequences. Images Figure 1 Figure 2 Figure 4 Figure 5 PMID:8434602

  18. Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification

    SciTech Connect

    Hyatt, Philip Douglas; Chen, Gwo-Liang; Larimer, Frank W; LoCascio, Philip F; Hauser, Loren John; Land, Miriam L

    2010-01-01

    Background The quality of automated gene prediction in microbial organisms has improved steadily over the past decade, but there is still room for improvement. Increasing the number of correct identifications, both of genes and of the translation initiation sites for each gene, and reducing the overall number of false positives, are all desirable goals. Results With our years of experience in manually curating genomes for the Joint Genome Institute, we developed a new gene prediction algorithm called Prodigal (PROkaryotic DYnamic programming Gene-finding ALgorithm). With Prodigal, we focused specifically on the three goals of improved gene structure prediction, improved translation initiation site recognition, and reduced false positives. We compared the results of Prodigal to existing gene-finding methods to demonstrate that it met each of these objectives. Conclusion We built a fast, lightweight, open source gene prediction program called Prodigal (http://compbio.ornl.gov/prodigal/). Prodigal achieved good results compared to existing methods, and we believe it will be a valuable asset to automated microbial annotation pipelines.

  19. Identification of a biologically active, small, secreted peptide in Arabidopsis by in silico gene screening, followed by LC-MS-based structure analysis.

    PubMed

    Ohyama, Kentaro; Ogawa, Mari; Matsubayashi, Yoshikatsu

    2008-07-01

    Peptidomics is a challenging field in which to create a link between genomic information and biological function through biochemical analysis of expressed peptides, including precise identification of post-translational modifications and proteolytic processing. We found that secreted peptides in Arabidopsis plants diffuse into the medium of whole-plant submerged cultures, and can be effectively identified by o-chlorophenol extraction followed by LC-MS analysis. Using this system, we first confirmed that a 12-amino-acid mature CLE44 peptide accumulated at a considerable level in the culture medium of transgenic plants overexpressing CLE44. Next, using an in silico approach, we identified a novel gene family encoding small secreted peptides that exhibit significant sequence similarity within the C-terminal short conserved domain. We determined that the mature peptide encoded by At1g47485, a member of this gene family, is a 15-amino-acid peptide containing two hydroxyproline residues derived from the conserved domain. This peptide, which we have named CEP1, is mainly expressed in the lateral root primordia and, when overexpressed or externally applied, significantly arrests root growth. CEP1 is a candidate for a novel peptide plant hormone.

  20. Identification of the Orthopoxvirus p4c Gene, Which Encodes a Structural Protein That Directs Intracellular Mature Virus Particles into A-Type Inclusions

    PubMed Central

    McKelvey, Terry A.; Andrews, Stanley C.; Miller, Sara E.; Ray, Caroline A.; Pickup, David J.

    2002-01-01

    The orthopoxvirus gene p4c has been identified in the genome of the vaccinia virus strain Western Reserve. This gene encodes the 58-kDa structural protein P4c present on the surfaces of the intracellular mature virus (IMV) particles. The gene is disrupted in the genome of cowpox virus Brighton Red (BR), demonstrating that although the P4c protein may be advantageous for virus replication in vivo, it is not essential for virus replication in vitro. Complementation and recombination analyses with the p4c gene have shown that the P4c protein is required to direct the IMV into the A-type inclusions (ATIs) produced by cowpox virus BR. The p4c gene is highly conserved among most members of the orthopoxvirus genus, including viruses that produce ATIs, such as cowpox, ectromelia, and raccoonpox viruses, as well as those such as variola, monkeypox, vaccinia, and camelpox viruses, which do not. The conservation of the p4c gene among the orthopoxviruses, irrespective of their capacities to produce ATIs, suggests that the P4c protein provides functions in addition to that of directing IMV into ATIs. These findings, and the presence of the P4c protein in IMV but not extracellular enveloped virus (D. Ulaeto, D. Grosenbach, and D. E. Hruby, J. Virol. 70:3372-3377, 1996), suggest a model in which the P4c protein may play a role in the retrograde movement of IMV particles, thereby contributing to the retention of IMV particles within the cytoplasm and within ATIs when they are present. In this way, the P4c protein may affect both viral morphogenesis and processes of virus dissemination. PMID:12388681

  1. Molecular identification of aiiA homologous gene from endophytic Enterobacter species and in silico analysis of putative tertiary structure of AHL-lactonase.

    PubMed

    Rajesh, P S; Rai, V Ravishankar

    2014-01-03

    The aiiA homologous gene known to encode AHL- lactonase enzyme which hydrolyze the N-acylhomoserine lactone (AHL) quorum sensing signaling molecules produced by Gram negative bacteria. In this study, the degradation of AHL molecules was determined by cell-free lysate of endophytic Enterobacter species. The percentage of quorum quenching was confirmed and quantified by HPLC method (p<0.0001). Amplification and sequence BLAST analysis showed the presence of aiiA homologous gene in endophytic Enterobacter asburiae VT65, Enterobacter aerogenes VT66 and Enterobacter ludwigii VT70 strains. Sequence alignment analysis revealed the presence of two zinc binding sites, "HXHXDH" motif as well as tyrosine residue at the position 194. Based on known template available at Swiss-Model, putative tertiary structure of AHL-lactonase was constructed. The result showed that novel endophytic strains of Enterobacter genera encode the novel aiiA homologous gene and its structural importance for future study. Copyright © 2013 Elsevier Inc. All rights reserved.

  2. Identification of 31 novel mutations in the F8 gene in Spanish hemophilia A patients: structural analysis of 20 missense mutations suggests new intermolecular binding sites

    PubMed Central

    Venceslá, Adoración; Corral-Rodríguez, María Ángeles; Baena, Manel; Cornet, Mónica; Domènech, Montserrat; Baiget, Montserrat; Fuentes-Prior, Pablo

    2008-01-01

    Hemophilia A (HA) is an X-linked bleeding disorder caused by a wide variety of mutations in the factor 8 (F8) gene, leading to absent or deficient factor VIII (FVIII). We analyzed the F8 gene of 267 unrelated Spanish patients with HA. After excluding patients with the common intron-1 and intron-22 inversions and large deletions, we detected 137 individuals with small mutations, 31 of which had not been reported previously. Eleven of these were nonsense, frameshift, and splicing mutations, whereas 20 were missense changes. We assessed the impact of the 20 substitutions based on currently available information about FV and FVIII structure and function relationship, including previously reported results of replacements at these and topologically equivalent positions. Although most changes are likely to cause gross structural perturbations and concomitant cofactor instability, p.Ala375Ser is predicted to affect cofactor activation. Finally, 3 further mutations (p.Pro64Arg, p.Gly494Val, and p.Asp2267Gly) appear to affect cofactor interactions with its carrier protein, von Willebrand factor, with the scavenger receptor low-density lipoprotein receptor–related protein (LRP), and/or with the substrate of the FVIIIapi•FIXa (Xase) complex, factor X. Characterization of these novel mutations is important for adequate genetic counseling in HA families, but also contributes to a better understanding of FVIII structure-function relationship. PMID:18184865

  3. Identification and characteristics of the structural gene for the Drosophila eye colour mutant sepia, encoding PDA synthase, a member of the Omega class glutathione S-transferases

    PubMed Central

    Kim, Jaekwang; Suh, Hyunsuk; Kim, Songhee; Kim, Kiyoung; Ahn, Chiyoung; Yim, Jeongbin

    2006-01-01

    The eye colour mutant sepia (se1) is defective in PDA {6-acetyl-2-amino-3,7,8,9-tetrahydro-4H-pyrimido[4,5-b]-[1,4]diazepin-4-one or pyrimidodiazepine} synthase involved in the conversion of 6-PTP (2-amino-4-oxo-6-pyruvoyl-5,6,7,8-tetrahydropteridine; also known as 6-pyruvoyltetrahydropterin) into PDA, a key intermediate in drosopterin biosynthesis. However, the identity of the gene encoding this enzyme, as well as its molecular properties, have not yet been established. Here, we identify and characterize the gene encoding PDA synthase and show that it is the structural gene for sepia. Based on previously reported information [Wiederrecht, Paton and Brown (1984) J. Biol. Chem. 259, 2195–2200; Wiederrecht and Brown (1984) J. Biol. Chem. 259, 14121–14127; Andres (1945) Drosoph. Inf. Serv. 19, 45; Ingham, Pinchin, Howard and Ish-Horowicz (1985) Genetics 111, 463–486; Howard, Ingham and Rushlow (1988) Genes Dev. 2, 1037–1046], we isolated five candidate genes predicted to encode GSTs (glutathione S-transferases) from the presumed sepia locus (region 66D5 on chromosome 3L). All cloned and expressed candidates exhibited relatively high thiol transferase and dehydroascorbate reductase activities and low activity towards 1-chloro-2,4-dinitrobenzene, characteristic of Omega class GSTs, whereas only CG6781 catalysed the synthesis of PDA in vitro. The molecular mass of recombinant CG6781 was estimated to be 28 kDa by SDS/PAGE and 56 kDa by gel filtration, indicating that it is a homodimer under native conditions. Sequencing of the genomic region spanning CG6781 revealed that the se1 allele has a frameshift mutation from ‘AAGAA’ to ‘GTG’ at nt 190–194, and that this generates a premature stop codon. Expression of the CG6781 open reading frame in an se1 background rescued the eye colour defect as well as PDA synthase activity and drosopterins content. The extent of rescue was dependent on the dosage of transgenic CG6781. In conclusion, we have discovered a

  4. Structural damage assessment as an identification problem

    NASA Technical Reports Server (NTRS)

    Hajela, Prabhat; Soeiro, F. J.

    1989-01-01

    Damage assessment of structural assemblies is treated as an identification problem. A brief review of identification methods is first presented with particular focus on the output error approach. The use of numerical optimization methods in identifying the location and extent of damage in structures is studied. The influence of damage on eigenmode shapes and static displacements is explored as a means of formulating a measure of damage in the structure. Preliminary results obtained in this study are presented and special attention is directed at the shortcomings associated with the nonlinear programming approach to solving the optimization problem.

  5. Identification of Large Space Structures on Orbit

    DTIC Science & Technology

    1986-09-01

    Anderson, M.S. and Greene , W.H.,"Continuurn Models for Beam and Plate-like Lattice Structures," ALAA J., vol. 16, No. 12, 1978, pp. 1219-1228. 43. Noor...Identification, Advances and Caes Studies, Edited by R. K. Mehra and D. G. Lain- iotis, Academic PRess, 1976. Ljung, L., T. Soderatrom and Gustavsson ...Ljung, L., I. Gustavsson and T. Soderstrom, "Identification of Linear, Multivariable Sys- tem Operating Under Linear Feedback Control", IEEE Trans

  6. Biochemical and molecular characterization of GALT gene from Indian galactosemia patients: identification of 10 novel mutations and their structural and functional implications.

    PubMed

    Singh, Ramandeep; Thapa, Babu R; Kaur, Gurjit; Prasad, Rajendra

    2012-12-24

    Classical Galactosemia is an autosomal recessive disorder of galactose metabolism caused by severe reduction or absence of the galactose-1-phosphate uridyl transferase (GALT) enzyme. Till date, no reports are available on clinical and molecular spectrum of galactosemia from Indian population. The characterization of underlying GALT gene lesions was performed in 55 unrelated galactosemia patients. The GALT mutational spectrum comprised 16 distinct mutations including 10 previously unreported mutations. N314D was the most common mutation with a frequency of 40% followed by Q188R at 2.7%. The novel GALT gene mutations included 6 missense mutations viz. Y89H, Q103R, P166A, S181F, K285R, R333L; one nonsense mutation, S307X and 3 silent mutations--Q103Q, K210K and H319H. The functional significance of the novel GALT missense mutations was investigated using SNPs&GO and SIFT tools. Further, modeling studies using 3D models of mutant and wild type GALT proteins revealed mutations to exert their effects at the molecular level by altering H-bonds, salt bridges, secondary structure or surface features. The study highlighted the heterogeneity of classical galactosemia in the Indian population and also emphasizes the importance of GALT gene analysis in diagnosis of galactosemia. It also revealed that the Indian GALT mutational profile differs significantly from other populations studied.

  7. Identification of three somatostatin genes in lampreys.

    PubMed

    Tostivint, Hervé; Dettaï, Agnès; Quan, Feng B; Ravi, Vydianathan; Tay, Boon-Hui; Rodicio, Maria Celina; Mazan, Sylvie; Venkatesh, Byrappa; Kenigfest, Natalia B

    2016-10-01

    Somatostatins (SSs) are a structurally diverse family of neuropeptides that play important roles in the regulation of growth, development and metabolism in vertebrates. It has been recently proposed that the common ancestor of gnathostomes possessed three SS genes, namely SS1, SS2 and SS5. SS1 and SS2 are still present in most extant gnathostome species investigated so far while SS5 primarily occurs in chondrichthyes, actinopterygians and actinistia but not in tetrapods. Very little is known about the repertoire of SSs in cyclostomes, which are extant jawless vertebrates. In the present study, we report the cloning of the cDNAs encoding three distinct lamprey SS variants that we call SSa, SSb and SSc. SSa and SSb correspond to the two SS variants previously characterized in lamprey, while SSc appears to be a totally novel one. SSa exhibits the same sequence as gnathostome SS1. SSb differs from SSa by only one substitution (Thr(12)→Ser). SSc exhibits a totally unique structure (ANCRMFYWKTMAAC) that shares only 50% identity with SSa and SSb. SSa, SSb and SSc precursors do not exhibit any appreciable sequence similarity outside the C-terminal region containing the SS sequence. Phylogenetic analyses failed to clearly assign orthology relationships between lamprey and gnathostome SS genes. Synteny analysis suggests that the SSc gene arose before the split of the three gnathostome genes SS1, SS2 and SS5. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. Molecular identification of the chitinase genes in Plasmodium relictum.

    PubMed

    Garcia-Longoria, Luz; Hellgren, Olof; Bensch, Staffan

    2014-06-18

    Malaria parasites need to synthesize chitinase in order to go through the peritrophic membrane, which is created around the mosquito midgut, to complete its life cycle. In mammalian malaria species, the chitinase gene comprises either a large or a short copy. In the avian malaria parasites Plasmodium gallinaceum both copies are present, suggesting that a gene duplication in the ancestor to these extant species preceded the loss of either the long or the short copy in Plasmodium parasites of mammals. Plasmodium gallinaceum is not the most widespread and harmful parasite of birds. This study is the first to search for and identify the chitinase gene in one of the most prevalent avian malaria parasites, Plasmodium relictum. Both copies of P. gallinaceum chitinase were used as reference sequences for primer design. Different sequences of Plasmodium spp. were used to build the phylogenetic tree of chitinase gene. The gene encoding for chitinase was identified in isolates of two mitochondrial lineages of P. relictum (SGS1 and GRW4). The chitinase found in these two lineages consists both of the long (PrCHT1) and the short (PrCHT2) copy. The genetic differences found in the long copy of the chitinase gene between SGS1 and GRW4 were higher than the difference observed for the cytochrome b gene. The identification of both copies in P. relictum sheds light on the phylogenetic relationship of the chitinase gene in the genus Plasmodium. Due to its high variability, the chitinase gene could be used to study the genetic population structure in isolates from different host species and geographic regions.

  9. Data identification for improving gene network inference using computational algebra.

    PubMed

    Dimitrova, Elena; Stigler, Brandilyn

    2014-11-01

    Identification of models of gene regulatory networks is sensitive to the amount of data used as input. Considering the substantial costs in conducting experiments, it is of value to have an estimate of the amount of data required to infer the network structure. To minimize wasted resources, it is also beneficial to know which data are necessary to identify the network. Knowledge of the data and knowledge of the terms in polynomial models are often required a priori in model identification. In applications, it is unlikely that the structure of a polynomial model will be known, which may force data sets to be unnecessarily large in order to identify a model. Furthermore, none of the known results provides any strategy for constructing data sets to uniquely identify a model. We provide a specialization of an existing criterion for deciding when a set of data points identifies a minimal polynomial model when its monomial terms have been specified. Then, we relax the requirement of the knowledge of the monomials and present results for model identification given only the data. Finally, we present a method for constructing data sets that identify minimal polynomial models.

  10. Machine learning for autonomous crystal structure identification.

    PubMed

    Reinhart, Wesley F; Long, Andrew W; Howard, Michael P; Ferguson, Andrew L; Panagiotopoulos, Athanassios Z

    2017-07-21

    We present a machine learning technique to discover and distinguish relevant ordered structures from molecular simulation snapshots or particle tracking data. Unlike other popular methods for structural identification, our technique requires no a priori description of the target structures. Instead, we use nonlinear manifold learning to infer structural relationships between particles according to the topology of their local environment. This graph-based approach yields unbiased structural information which allows us to quantify the crystalline character of particles near defects, grain boundaries, and interfaces. We demonstrate the method by classifying particles in a simulation of colloidal crystallization, and show that our method identifies structural features that are missed by standard techniques.

  11. Identification of Complex Carbon Nanotube Structures

    NASA Technical Reports Server (NTRS)

    Han, Jie; Saini, Subhash (Technical Monitor)

    1998-01-01

    A variety of complex carbon nanotube (CNT) structures have been observed experimentally. These include sharp bends, branches, tori, and helices. They are believed to be formed by using topological defects such as pentagons and heptagons to connect different CNT. The effects of type, number, and arrangement (separation and orientation) of defects on atomic structures and energetics of complex CNT are investigated using topology, quantum mechanics and molecular mechanics calculations. Energetically stable models are derived for identification of observed complex CNT structures.

  12. Structural health monitoring using parameter identification methods

    NASA Astrophysics Data System (ADS)

    Liu, Pengxiang; Rao, Vittal S.

    2000-06-01

    A structural health monitoring method for determination of damages in structural system is developed using state variable model. A time-domain identification method, the subspace system identification algorithm, is first applied to get a state-space model of the structure. The identified state-space model is then transformed to two special realization forms, for determination of the equation of motion of multiple- degrees-freedom of the structure. The parameters of equation of motion, mass and stiffness matrices or damage indices are used to determine the location and extent of the damage. This method is also extended for the health monitoring of substructural system. Unlike the health monitoring of the whole structure, the health monitoring of substructure uses localized parameter identification which only involves the measurement of substructure parameters. Using this method, the number of unknown parameters and the computational requirement for each identification can be significantly reduced, hence the accuracy of estimation can be improved. Illustrative cases studies using both numerical and experimental structures are presented.

  13. Identification of Cancer Related Genes Using a Comprehensive Map of Human Gene Expression.

    PubMed

    Torrente, Aurora; Lukk, Margus; Xue, Vincent; Parkinson, Helen; Rung, Johan; Brazma, Alvis

    2016-01-01

    Rapid accumulation and availability of gene expression datasets in public repositories have enabled large-scale meta-analyses of combined data. The richness of cross-experiment data has provided new biological insights, including identification of new cancer genes. In this study, we compiled a human gene expression dataset from ∼40,000 publicly available Affymetrix HG-U133Plus2 arrays. After strict quality control and data normalisation the data was quantified in an expression matrix of ∼20,000 genes and ∼28,000 samples. To enable different ways of sample grouping, existing annotations where subjected to systematic ontology assisted categorisation and manual curation. Groups like normal tissues, neoplasmic tissues, cell lines, homoeotic cells and incompletely differentiated cells were created. Unsupervised analysis of the data confirmed global structure of expression consistent with earlier analysis but with more details revealed due to increased resolution. A suitable mixed-effects linear model was used to further investigate gene expression in solid tissue tumours, and to compare these with the respective healthy solid tissues. The analysis identified 1,285 genes with systematic expression change in cancer. The list is significantly enriched with known cancer genes from large, public, peer-reviewed databases, whereas the remaining ones are proposed as new cancer gene candidates. The compiled dataset is publicly available in the ArrayExpress Archive. It contains the most diverse collection of biological samples, making it the largest systematically annotated gene expression dataset of its kind in the public domain.

  14. The identification of wadB, a new glycosyltransferase gene, confirms the branched structure and the role in virulence of the lipopolysaccharide core of Brucella abortus.

    PubMed

    Gil-Ramírez, Yolanda; Conde-Álvarez, Raquel; Palacios-Chaves, Leyre; Zúñiga-Ripa, Amaia; Grilló, María-Jesús; Arce-Gorvel, Vilma; Hanniffy, Sean; Moriyón, Ignacio; Iriarte, Maite

    2014-08-01

    Brucellosis is a worldwide extended zoonosis caused by Brucella spp. These gram-negative bacteria are not readily detected by innate immunity, a virulence-related property largely linked to their surface lipopolysaccharide (LPS). The role of the LPS lipid A and O-polysaccharide in virulence is well known. Moreover, mutation of the glycosyltransferase gene wadC of Brucella abortus, although not affecting O-polysaccharide assembly onto the lipid-A core section causes a core oligosaccharide defect that increases recognition by innate immunity. Here, we report on a second gene (wadB) encoding a LPS core glycosyltransferase not involved in the assembly of the O-polysaccharide-linked core section. As compared to wild-type B. abortus, a wadB mutant was sensitive to bactericidal peptides and non-immune serum, and was attenuated in mice and dendritic cells. These observations show that as WadC, WadB is also involved in the assembly of a branch of Brucella LPS core and support the concept that this LPS section is a virulence-related structure.

  15. Parameter identification of civil engineering structures

    NASA Technical Reports Server (NTRS)

    Juang, J. N.; Sun, C. T.

    1980-01-01

    This paper concerns the development of an identification method required in determining structural parameter variations for systems subjected to an extended exposure to the environment. The concept of structural identifiability of a large scale structural system in the absence of damping is presented. Three criteria are established indicating that a large number of system parameters (the coefficient parameters of the differential equations) can be identified by a few actuators and sensors. An eight-bay-fifteen-story frame structure is used as example. A simple model is employed for analyzing the dynamic response of the frame structure.

  16. [Hydrophidae identification through analysis on Cyt b gene barcode].

    PubMed

    Liao, Li-xi; Zeng, Ke-wu; Tu, Peng-fei

    2015-08-01

    Hydrophidae, one of the precious traditional Chinese medicines, is generally drily preserved to prevent corruption, but it is hard to identify the species of Hydrophidae through the appearance because of the change due to the drying process. The identification through analysis on gene barcode, a new technique in species identification, can avoid the problem. The gene barcodes of the 6 species of Hydrophidae like Lapemis hardwickii were aquired through DNA extraction and gene sequencing. These barcodes were then in sequence alignment and test the identification efficency by BLAST. Our results revealed that the barcode sequences performed high identification efficiency, and had obvious difference between intra- and inter-species. These all indicated that Cyt b DNA barcoding can confirm the Hydrophidae identification.

  17. Prodigal: prokaryotic gene recognition and translation initiation site identification

    SciTech Connect

    Chen, Gwo-Liang; LoCascio, Philip F; Land, Miriam L; Larimer, Frank W; Hauser, Loren John

    2010-01-01

    The quality of automated gene prediction in microbial organisms has improved steadily over the past decade, but there is still room for improvement. Increasing the number of correct identifications, both of genes and of the translation initiation sites for each gene, and reducing the overall number of false positives, are all desirable goals. With our years of experience in manually curating genomes for the Joint Genome Institute, we developed a new gene prediction algorithm called Prodigal (PROkaryotic DYnamic programming Gene-finding ALgorithm). With Prodigal, we focused specifically on the three goals of improved gene structure prediction, improved translation initiation site recognition, and reduced false positives. We compared the results of Prodigal to existing gene-finding methods to demonstrate that it met each of these objectives. We built a fast, lightweight, open source gene prediction program called Prodigal http://compbio.ornl.gov/prodigal/. Prodigal achieved good results compared to existing methods, and we believe it will be a valuable asset to automated microbial annotation pipelines. The goals of Prodigal were to attain greater sensitivity in identifying existing genes, to predict translation initiation sites more accurately, and to minimize the number of false positive predictions. The results of Prodigal were compared to existing methods for both purely experimentally verified genes as well as curated Genbank files for a number of genomes. Prodigal's performance was found to be comparable or better to existing methods in the prediction of genes while also predicting fewer overall genes. In the prediction of translation initiation sites, Prodigal performed competitively with existing methods. Prodigal is currently already in use at many institutions, and it has been used to annotate all finished microbial genomes submitted to Genbank by DOE-JGI in 2008 and onward (a substantial percentage of the overall finished microbial genomes at NCBI). It is

  18. Identification of structural variation in mouse genomes

    PubMed Central

    Keane, Thomas M.; Wong, Kim; Adams, David J.; Flint, Jonathan; Reymond, Alexandre; Yalcin, Binnaz

    2014-01-01

    Structural variation is variation in structure of DNA regions affecting DNA sequence length and/or orientation. It generally includes deletions, insertions, copy-number gains, inversions, and transposable elements. Traditionally, the identification of structural variation in genomes has been challenging. However, with the recent advances in high-throughput DNA sequencing and paired-end mapping (PEM) methods, the ability to identify structural variation and their respective association to human diseases has improved considerably. In this review, we describe our current knowledge of structural variation in the mouse, one of the prime model systems for studying human diseases and mammalian biology. We further present the evolutionary implications of structural variation on transposable elements. We conclude with future directions on the study of structural variation in mouse genomes that will increase our understanding of molecular architecture and functional consequences of structural variation. PMID:25071822

  19. Single nucleotide polymorphism identification in candidate gene systems of obesity.

    PubMed

    Irizarry, K; Hu, G; Wong, M L; Licinio, J; Lee, C J

    2001-01-01

    We have constructed a large panel of single nucleotide polymorphisms (SNP) identified in 68 candidate genes for obesity. Our panel combines novel SNP identification methods based on EST data, with public SNP data from largescale genomic sequencing, to produce a total of 218 SNPs in the coding regions of obesity candidate genes, 178 SNPs in untranslated regions, and over 1000 intronic SNPs. These include new non-conservative amino acid changes in thyroid receptor beta, esterase D, acid phosphatase 1. Our data show evidence of negative selection among these polymorphisms implying functional impacts of the non-conservative mutations. Comparison of overlap between SNPs identified independently from EST data vs genomic sequencing indicate that together they may constitute about one half of the actual total number of amino acid polymorphisms in these genes that are common in the human population (defined here as a population allele frequency above 5%). We have analyzed our polymorphism panel to construct a database of detailed information about their location in the gene structure and effect on protein coding, available on the web at http://www.bioinformat ics.ucla.edu/snp/obesity. We believe this panel can serve as a valuable new resource for genetic and pharmacogenomic studies of the causes of obesity.

  20. Genome-wide identification and expression profiling of ankyrin-repeat gene family in maize.

    PubMed

    Jiang, Haiyang; Wu, Qingqing; Jin, Jing; Sheng, Lei; Yan, Hanwei; Cheng, Beijiu; Zhu, Suwen

    2013-09-01

    Members of the ankyrin repeats (ANK) gene family encode ANK domain that are common in diverse organisms and play important roles in cell growth and development, such as cell-cell signal transduction and cell cycle regulation. Recently, genome-wide identification and evolutionary analyses of the ANK gene family have been carried out in Arabidopsis and rice. However, little is known regarding the ANK genes in the entire maize genome. In this study, we described the identification and structural characterization of 71 ANK genes in maize (ZmANK). Then, comprehensive bioinformatics analyses of ZmANK genes family were performed including phylogenetic, domain and motif analysis, chromosomal localization, intron/exon structural patterns, gene duplications and expression profiling. Domain composition analyses showed that ZmANK genes formed ten subfamilies. Five tandem duplications and 14 segmental duplications were identified in ZmANK genes. Furthermore, we took comparative analysis of the total ANK gene family in Arabidopsis, rice and maize, ZmANKs were more closely paired with OsANKs than with AtANKs. At last, expression profile analyses were performed. Forty-one members of ZmANK genes held EST sequences records. Semi-quantitative expression and microarray data analysis of these 41 ZmANK genes demonstrated that ZmANK genes exhibit a various expression pattern, suggesting that functional diversification of ZmANK genes family. The results will present significant insights to explore ANK genes expression and function in future studies in maize.

  1. Global Identification of Disease Associated Genes in Fragile X Cells

    DTIC Science & Technology

    2016-08-01

    AWARD NUMBER: W81XWH-15-1-0204 TITLE: Global Identification of Disease-Associated Genes in Fragile X Cells PRINCIPAL INVESTIGATOR: Wenyi Feng...Global Identification of Disease-Associated Genes in Fragile X Cells 5a. CONTRACT NUMBER 5b. GRANT NUMBER W81XWH-15-1-0204 GRANT1171 2389...conflict. We have performed three biological replicate experiments to rigorously test if the Fragile X cell line produces more DSBs than the normal

  2. [Application of gene detection technology in food species identification].

    PubMed

    Chen, Ying; Wu, Yajun

    2011-07-01

    It is critical to determine the biological identity of all ingredients in food to ensure its safety and quality. Modern gene detection technology makes species identification in food more accurate, sensitive and rapid. A comprehensive review on its current applications in the last decade and the future perspective in food species identification is presented, including a brief introduction of gene detection methods, and their applications in plant-originated food, animal-originated food, high value-added food and highly processed food.

  3. Hierarchical Bayesian model updating for structural identification

    NASA Astrophysics Data System (ADS)

    Behmanesh, Iman; Moaveni, Babak; Lombaert, Geert; Papadimitriou, Costas

    2015-12-01

    A new probabilistic finite element (FE) model updating technique based on Hierarchical Bayesian modeling is proposed for identification of civil structural systems under changing ambient/environmental conditions. The performance of the proposed technique is investigated for (1) uncertainty quantification of model updating parameters, and (2) probabilistic damage identification of the structural systems. Accurate estimation of the uncertainty in modeling parameters such as mass or stiffness is a challenging task. Several Bayesian model updating frameworks have been proposed in the literature that can successfully provide the "parameter estimation uncertainty" of model parameters with the assumption that there is no underlying inherent variability in the updating parameters. However, this assumption may not be valid for civil structures where structural mass and stiffness have inherent variability due to different sources of uncertainty such as changing ambient temperature, temperature gradient, wind speed, and traffic loads. Hierarchical Bayesian model updating is capable of predicting the overall uncertainty/variability of updating parameters by assuming time-variability of the underlying linear system. A general solution based on Gibbs Sampler is proposed to estimate the joint probability distributions of the updating parameters. The performance of the proposed Hierarchical approach is evaluated numerically for uncertainty quantification and damage identification of a 3-story shear building model. Effects of modeling errors and incomplete modal data are considered in the numerical study.

  4. Crystal Structure of Mycobacterium tuberculosis H37Rv AldR (Rv2779c), a Regulator of the ald Gene: DNA BINDING AND IDENTIFICATION OF SMALL MOLECULE INHIBITORS.

    PubMed

    Dey, Abhishek; Shree, Sonal; Pandey, Sarvesh Kumar; Tripathi, Rama Pati; Ramachandran, Ravishankar

    2016-06-03

    Here we report the crystal structure of M. tuberculosis AldR (Rv2779c) showing that the N-terminal DNA-binding domains are swapped, forming a dimer, and four dimers are assembled into an octamer through crystal symmetry. The C-terminal domain is involved in oligomeric interactions that stabilize the oligomer, and it contains the effector-binding sites. The latter sites are 30-60% larger compared with homologs like MtbFFRP (Rv3291c) and can consequently accommodate larger molecules. MtbAldR binds to the region upstream to the ald gene that is highly up-regulated in nutrient-starved tuberculosis models and codes for l-alanine dehydrogenase (MtbAld; Rv2780). Further, the MtbAldR-DNA complex is inhibited upon binding of Ala, Tyr, Trp and Asp to the protein. Studies involving a ligand-binding site G131T mutant show that the mutant forms a DNA complex that cannot be inhibited by adding the amino acids. Comparative studies suggest that binding of the amino acids changes the relative spatial disposition of the DNA-binding domains and thereby disrupt the protein-DNA complex. Finally, we identified small molecules, including a tetrahydroquinoline carbonitrile derivative (S010-0261), that inhibit the MtbAldR-DNA complex. The latter molecules represent the very first inhibitors of a feast/famine regulatory protein from any source and set the stage for exploring MtbAldR as a potential anti-tuberculosis target.

  5. Molecular characterization of three NPY receptors (Y2, Y5 and Y7) in chickens: Gene structure, tissue expression, promoter identification, and functional analysis.

    PubMed

    He, Chen; Zhang, Jiannan; Gao, Shunyu; Meng, Fengyan; Bu, Guixian; Li, Juan; Wang, Yajun

    2016-09-15

    Six neuropeptide Y (NPY) receptors are suggested to mediate the biological actions of NPY, peptide YY (PYY), and pancreatic polypeptide (PP), such as food intake in birds, however, information regarding the structure and signaling of avian NPY receptors are rather limited. In this study, we investigated the gene structure, tissue expression and signaling property of three NPY receptors (cY2, cY5 and cY7) in chickens. The results showed that 1) cY2, cY5 and cY7 contain novel non-coding exons upstream of their start codon and alternative mRNA splicing in their 5'-UTR results in the formation of multiple transcript variants; 2) cY2, cY5 and cY7 transcripts were detected to be widely expressed in adult chicken tissues including various brain regions by RT-PCR, and their expression is controlled by a promoter(s) near exon 1, which display promoter activity in DF-1 cells as demonstrated by Dual-luciferase reporter assay; 3) cY2, cY5 and cY7 expressed in HEK293 cells were preferentially (or potently) activated by cNPY1-36 and cPYY1-37, but not by cPP1-36, and their activation led to the inhibition of cAMP/PKA signaling pathway and activation of MAPK/ERK signaling pathway, monitored by the cell-based luciferase reporter systems or western blots, indicating that the three NPY receptors are functional and capable of transmitting signals effectively. On the whole, our data establishes a molecular basis to elucidate the actions of three functional NPY receptors (cY2, cY5 and cY7) and their ligands in birds, which helps to uncover the conserved roles of these ligand-receptor pairs in vertebrates. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. Aquifer Structure Identification Using Stochastic Inversion

    SciTech Connect

    Harp, Dylan R; Dai, Zhenxue; Wolfsberg, Andrew V; Vrugt, Jasper A

    2008-01-01

    This study presents a stochastic inverse method for aquifer structure identification using sparse geophysical and hydraulic response data. The method is based on updating structure parameters from a transition probability model to iteratively modify the aquifer structure and parameter zonation. The method is extended to the adaptive parameterization of facies hydraulic parameters by including these parameters as optimization variables. The stochastic nature of the statistical structure parameters leads to nonconvex objective functions. A multi-method genetically adaptive evolutionary approach (AMALGAM-SO) was selected to perform the inversion given its search capabilities. Results are obtained as a probabilistic assessment of facies distribution based on indicator cokriging simulation of the optimized structural parameters. The method is illustrated by estimating the structure and facies hydraulic parameters of a synthetic example with a transient hydraulic response.

  7. Robust structural identification via polyhedral template matching

    NASA Astrophysics Data System (ADS)

    Mahler Larsen, Peter; Schmidt, Søren; Schiøtz, Jakob

    2016-06-01

    Successful scientific applications of large-scale molecular dynamics often rely on automated methods for identifying the local crystalline structure of condensed phases. Many existing methods for structural identification, such as common neighbour analysis, rely on interatomic distances (or thresholds thereof) to classify atomic structure. As a consequence they are sensitive to strain and thermal displacements, and preprocessing such as quenching or temporal averaging of the atomic positions is necessary to provide reliable identifications. We propose a new method, polyhedral template matching (PTM), which classifies structures according to the topology of the local atomic environment, without any ambiguity in the classification, and with greater reliability than e.g. common neighbour analysis in the presence of thermal fluctuations. We demonstrate that the method can reliably be used to identify structures even in simulations near the melting point, and that it can identify the most common ordered alloy structures as well. In addition, the method makes it easy to identify the local lattice orientation in polycrystalline samples, and to calculate the local strain tensor. An implementation is made available under a Free and Open Source Software license.

  8. Identification of Cancer Related Genes Using a Comprehensive Map of Human Gene Expression

    PubMed Central

    Lukk, Margus; Xue, Vincent; Parkinson, Helen; Rung, Johan; Brazma, Alvis

    2016-01-01

    Rapid accumulation and availability of gene expression datasets in public repositories have enabled large-scale meta-analyses of combined data. The richness of cross-experiment data has provided new biological insights, including identification of new cancer genes. In this study, we compiled a human gene expression dataset from ∼40,000 publicly available Affymetrix HG-U133Plus2 arrays. After strict quality control and data normalisation the data was quantified in an expression matrix of ∼20,000 genes and ∼28,000 samples. To enable different ways of sample grouping, existing annotations where subjected to systematic ontology assisted categorisation and manual curation. Groups like normal tissues, neoplasmic tissues, cell lines, homoeotic cells and incompletely differentiated cells were created. Unsupervised analysis of the data confirmed global structure of expression consistent with earlier analysis but with more details revealed due to increased resolution. A suitable mixed-effects linear model was used to further investigate gene expression in solid tissue tumours, and to compare these with the respective healthy solid tissues. The analysis identified 1,285 genes with systematic expression change in cancer. The list is significantly enriched with known cancer genes from large, public, peer-reviewed databases, whereas the remaining ones are proposed as new cancer gene candidates. The compiled dataset is publicly available in the ArrayExpress Archive. It contains the most diverse collection of biological samples, making it the largest systematically annotated gene expression dataset of its kind in the public domain. PMID:27322383

  9. Hemoglobin Pasadena: identification of the gene mutant by DNA analysis using synthetic DNA probes.

    PubMed

    Rahbar, S; Rosen, R; Nozari, G; Lee, T D; Asmerom, Y; Wallace, R B

    1988-03-01

    Hemoglobin Pasadena [beta 75(E19)Leu----Arg] was found in a boy who had an acute episode of anemia and rapid splenic enlargement. His father was the only other member of a large family with this hemoglobinopathy. We have used gene mapping techniques for direct identification of the beta-globin gene mutation. To correlate the DNA findings with the structural identification of this variant, we have also performed globin chain separation and analysis of the tryptic peptides using high performance liquid chromatography and secondary ion mass spectral analysis.

  10. Secondary structural entropy in RNA switch (Riboswitch) identification.

    PubMed

    Manzourolajdad, Amirhossein; Arnold, Jonathan

    2015-04-28

    RNA regulatory elements play a significant role in gene regulation. Riboswitches, a widespread group of regulatory RNAs, are vital components of many bacterial genomes. These regulatory elements generally function by forming a ligand-induced alternative fold that controls access to ribosome binding sites or other regulatory sites in RNA. Riboswitch-mediated mechanisms are ubiquitous across bacterial genomes. A typical class of riboswitch has its own unique structural and biological complexity, making de novo riboswitch identification a formidable task. Traditionally, riboswitches have been identified through comparative genomics based on sequence and structural homology. The limitations of structural-homology-based approaches, coupled with the assumption that there is a great diversity of undiscovered riboswitches, suggests the need for alternative methods for riboswitch identification, possibly based on features intrinsic to their structure. As of yet, no such reliable method has been proposed. We used structural entropy of riboswitch sequences as a measure of their secondary structural dynamics. Entropy values of a diverse set of riboswitches were compared to that of their mutants, their dinucleotide shuffles, and their reverse complement sequences under different stochastic context-free grammar folding models. Significance of our results was evaluated by comparison to other approaches, such as the base-pairing entropy and energy landscapes dynamics. Classifiers based on structural entropy optimized via sequence and structural features were devised as riboswitch identifiers and tested on Bacillus subtilis, Escherichia coli, and Synechococcus elongatus as an exploration of structural entropy based approaches. The unusually long untranslated region of the cotH in Bacillus subtilis, as well as upstream regions of certain genes, such as the sucC genes were associated with significant structural entropy values in genome-wide examinations. Various tests show that there

  11. Structure Identification Using High Resolution Mass ...

    EPA Pesticide Factsheets

    The iCSS CompTox Dashboard is a publicly accessible dashboard provided by the National Center for Computation Toxicology at the US-EPA. It serves a number of purposes, including providing a chemistry database underpinning many of our public-facing projects (e.g. ToxCast and ExpoCast). The available data and searches provide a valuable path to structure identification using mass spectrometry as the source data. With an underlying database of over 720,000 chemicals, the dashboard has already been used to assist in identifying chemicals present in house dust. This poster reviews the benefits of the EPA’s platform and underlying algorithms used for the purpose of compound identification using high-resolution mass spectrometry data. Standard approaches for both mass and formula lookup are available but the dashboard delivers a novel approach for hit ranking based on functional use of the chemicals. The focus on high-quality data, novel ranking approaches and integration to other resources of value to mass spectrometrists makes the CompTox Dashboard a valuable resource for the identification of environmental chemicals. This abstract does not reflect U.S. EPA policy poster presented at the Eastern Analytical Symposium (EAS) held in Somerset, NJ

  12. Missing gene identification using functional coherence scores

    PubMed Central

    Chitale, Meghana; Khan, Ishita K.; Kihara, Daisuke

    2016-01-01

    Reconstructing metabolic and signaling pathways is an effective way of interpreting a genome sequence. A challenge in a pathway reconstruction is that often genes in a pathway cannot be easily found, reflecting current imperfect information of the target organism. In this work, we developed a new method for finding missing genes, which integrates multiple features, including gene expression, phylogenetic profile, and function association scores. Particularly, for considering function association between candidate genes and neighboring proteins to the target missing gene in the network, we used Co-occurrence Association Score (CAS) and PubMed Association Score (PAS), which are designed for capturing functional coherence of proteins. We showed that adding CAS and PAS substantially improve the accuracy of identifying missing genes in the yeast enzyme-enzyme network compared to the cases when only the conventional features, gene expression, phylogenetic profile, were used. Finally, it was also demonstrated that the accuracy improves by considering indirect neighbors to the target enzyme position in the network using a proper network-topology-based weighting scheme. PMID:27552989

  13. Phosphate binding sites identification in protein structures

    PubMed Central

    Parca, Luca; Gherardini, Pier Federico; Helmer-Citterich, Manuela; Ausiello, Gabriele

    2011-01-01

    Nearly half of known protein structures interact with phosphate-containing ligands, such as nucleotides and other cofactors. Many methods have been developed for the identification of metal ions-binding sites and some for bigger ligands such as carbohydrates, but none is yet available for the prediction of phosphate-binding sites. Here we describe Pfinder, a method that predicts binding sites for phosphate groups, both in the form of ions or as parts of other non-peptide ligands, in proteins of known structure. Pfinder uses the Query3D local structural comparison algorithm to scan a protein structure for the presence of a number of structural motifs identified for their ability to bind the phosphate chemical group. Pfinder has been tested on a data set of 52 proteins for which both the apo and holo forms were available. We obtained at least one correct prediction in 63% of the holo structures and in 62% of the apo. The ability of Pfinder to recognize a phosphate-binding site in unbound protein structures makes it an ideal tool for functional annotation and for complementing docking and drug design methods. The Pfinder program is available at http://pdbfun.uniroma2.it/pfinder. PMID:20974634

  14. Identification and characterization of Nasonia Pax genes

    PubMed Central

    Keller, R. G.; Desplan, C.; Rosenberg, M. I.

    2010-01-01

    Pax genes are a group of critical developmental transcriptional regulators in both invertebrates and vertebrates, characterized by the presence of a paired DNA-binding domain. Pax proteins also often contain an octapeptide motif and a C-terminal homeodomain. The genome of Nasonia vitripennis (Hymenoptera) has recently become available, and analysis of this genome alongside Apis mellifera allowed us to contribute to the phylogeny of this gene family in insects. Nasonia, a parasitic wasp, has independently evolved a similar mode of development to that of the wellstudied Drosophila, making it an excellent model system for comparative studies of developmental gene networks. We report the characterization of the seven Nasonia Pax genes. We describe their genomic organization, and the embryonic expression of three of them, and uncover wider conservation of the octapeptide motif than previously described. PMID:20167022

  15. Identification of genes and gene products necessary for bacterial bioluminescence.

    PubMed

    Engebrecht, J; Silverman, M

    1984-07-01

    Expression of luminescence in Escherichia coli was recently achieved by cloning genes from the marine bacterium Vibrio fischeri. One DNA fragment on a hybrid plasmid encoded regulatory functions and enzymatic activities necessary for light production. We report the results of a genetic analysis to identify the luminescence genes (lux) that reside on this recombinant plasmid. lux gene mutations were generated by hydroxylamine treatment, and these mutations were ordered on a linear map by complementation in trans with a series of polar transposon insertions on other plasmids. lux genes were defined by complementation of lux gene defects on pairs of plasmids in trans in E. coli. Hybrid plasmids were also used to direct the synthesis of polypeptides in the E. coli minicell system. Seven lux genes and the corresponding gene products were identified from the complementation analysis and the minicell programing experiments. These genes, in the order of their position on a linear map, and the apparent molecular weights of the gene products are luxR (27,000), luxI (25,000), luxC (53,000), luxD (33,000), luxA (40,000), luxB (38,000), and luxE (42,000). From the luminescence phenotypes of E. coli containing mutant plasmids, functions were assigned to these genes: luxA, luxB, luxC, luxD, and luxE encode enzymes for light production and luxR and luxI encode regulatory functions.

  16. Bioinformatic identification of Ustilago maydis meiosis genes.

    PubMed

    Donaldson, Michael E; Saville, Barry J

    2008-08-01

    In the corn smut pathogen, Ustilago maydis, meiosis and teliospore germination are temporally linked. We review teliospore dormancy and germination in U. maydis and present an overview of meiosis in basidiomycetes. The relevant available expressed sequence tag data is discussed, the databases used in reciprocal best hit blastp analysis are presented and potential U. maydis meiosis genes are identified. The implications of identifying these genes are discussed and hypotheses are presented regarding the control of meiosis in U. maydis.

  17. Identification of essential genes for cancer immunotherapy.

    PubMed

    Patel, Shashank J; Sanjana, Neville E; Kishton, Rigel J; Eidizadeh, Arash; Vodnala, Suman K; Cam, Maggie; Gartner, Jared J; Jia, Li; Steinberg, Seth M; Yamamoto, Tori N; Merchant, Anand S; Mehta, Gautam U; Chichura, Anna; Shalem, Ophir; Tran, Eric; Eil, Robert; Sukumar, Madhusudhanan; Guijarro, Eva Perez; Day, Chi-Ping; Robbins, Paul; Feldman, Steve; Merlino, Glenn; Zhang, Feng; Restifo, Nicholas P

    2017-08-31

    Somatic gene mutations can alter the vulnerability of cancer cells to T-cell-based immunotherapies. Here we perturbed genes in human melanoma cells to mimic loss-of-function mutations involved in resistance to these therapies, by using a genome-scale CRISPR-Cas9 library that consisted of around 123,000 single-guide RNAs, and profiled genes whose loss in tumour cells impaired the effector function of CD8(+) T cells. The genes that were most enriched in the screen have key roles in antigen presentation and interferon-γ signalling, and correlate with cytolytic activity in patient tumours from The Cancer Genome Atlas. Among the genes validated using different cancer cell lines and antigens, we identified multiple loss-of-function mutations in APLNR, encoding the apelin receptor, in patient tumours that were refractory to immunotherapy. We show that APLNR interacts with JAK1, modulating interferon-γ responses in tumours, and that its functional loss reduces the efficacy of adoptive cell transfer and checkpoint blockade immunotherapies in mouse models. Our results link the loss of essential genes for the effector function of CD8(+) T cells with the resistance or non-responsiveness of cancer to immunotherapies.

  18. In silico identification and analysis of phytoene synthase genes in plants.

    PubMed

    Han, Y; Zheng, Q S; Wei, Y P; Chen, J; Liu, R; Wan, H J

    2015-08-14

    In this study, we examined phytoene synthetase (PSY), the first key limiting enzyme in the synthesis of carotenoids and catalyzing the formation of geranylgeranyl pyrophosphate in terpenoid biosynthesis. We used known amino acid sequences of the PSY gene in tomato plants to conduct a genome-wide search and identify putative candidates in 34 sequenced plants. A total of 101 homologous genes were identified. Phylogenetic analysis revealed that PSY evolved independently in algae as well as monocotyledonous and dicotyledonous plants. Our results showed that the amino acid structures exhibited 5 motifs (motifs 1 to 5) in algae and those in higher plants were highly conserved. The PSY gene structures showed that the number of intron in algae varied widely, while the number of introns in higher plants was 4 to 5. Identification of PSY genes in plants and the analysis of the gene structure may provide a theoretical basis for studying evolutionary relationships in future analyses.

  19. Identification of Actinobacillus actinomycetemcomitans by leukotoxin gene-specific hybridization and polymerase chain reaction assays.

    PubMed Central

    Tønjum, T; Haas, R

    1993-01-01

    Eleven strains of Actinobacillus actinomycetemcomitans isolated from cases of systemic infections, local abscesses, and periodontitis were identified by genetic assays using the leukotoxin gene as the target. We have developed a polymerase chain reaction (PCR) assay, based on the leukotoxin structural gene of this pathogen, which clearly identified all tested strains of A. actinomycetemcomitans and separated them from the closely related Haemophilus aphrophilus as well as other bacterial species. Furthermore, DNA-DNA hybridization was performed with the cloned partial leukotoxin structural gene (lktA) as a probe, which again clearly distinguished A. actinomycetemcomitans from H. aphrophilus, parts of the normal oral flora, and species harboring RTX (repeats in toxin) family-related cytotoxins. The PCR fragment amplified from the leukotoxin structural gene gave results similar to those given by the cloned leukotoxin gene when used as a probe in hybridization experiments. The hybridization and PCR assays described here are fundamental improvements for the identification of A. actinomycetemcomitans. Images PMID:8349764

  20. Genome-Wide Identification and Functional Classification of Tomato (Solanum lycopersicum) Aldehyde Dehydrogenase (ALDH) Gene Superfamily

    PubMed Central

    Lopez-Valverde, Francisco J.; Robles-Bolivar, Paula; Lima-Cabello, Elena; Gachomo, Emma W.; Kotchoni, Simeon O.

    2016-01-01

    Aldehyde dehydrogenases (ALDHs) is a protein superfamily that catalyzes the oxidation of aldehyde molecules into their corresponding non-toxic carboxylic acids, and responding to different environmental stresses, offering promising genetic approaches for improving plant adaptation. The aim of the current study is the functional analysis for systematic identification of S. lycopersicum ALDH gene superfamily. We performed genome-based ALDH genes identification and functional classification, phylogenetic relationship, structure and catalytic domains analysis, and microarray based gene expression. Twenty nine unique tomato ALDH sequences encoding 11 ALDH families were identified, including a unique member of the family 19 ALDH. Phylogenetic analysis revealed 13 groups, with a conserved relationship among ALDH families. Functional structure analysis of ALDH2 showed a catalytic mechanism involving Cys-Glu couple. However, the analysis of ALDH3 showed no functional gene duplication or potential neo-functionalities. Gene expression analysis reveals that particular ALDH genes might respond to wounding stress increasing the expression as ALDH2B7. Overall, this study reveals the complexity of S. lycopersicum ALDH gene superfamily and offers new insights into the structure-functional features and evolution of ALDH gene families in vascular plants. The functional characterization of ALDHs is valuable and promoting molecular breeding in tomato for the improvement of stress tolerance and signaling. PMID:27755582

  1. Genome-Wide Identification and Functional Classification of Tomato (Solanum lycopersicum) Aldehyde Dehydrogenase (ALDH) Gene Superfamily.

    PubMed

    Jimenez-Lopez, Jose C; Lopez-Valverde, Francisco J; Robles-Bolivar, Paula; Lima-Cabello, Elena; Gachomo, Emma W; Kotchoni, Simeon O

    2016-01-01

    Aldehyde dehydrogenases (ALDHs) is a protein superfamily that catalyzes the oxidation of aldehyde molecules into their corresponding non-toxic carboxylic acids, and responding to different environmental stresses, offering promising genetic approaches for improving plant adaptation. The aim of the current study is the functional analysis for systematic identification of S. lycopersicum ALDH gene superfamily. We performed genome-based ALDH genes identification and functional classification, phylogenetic relationship, structure and catalytic domains analysis, and microarray based gene expression. Twenty nine unique tomato ALDH sequences encoding 11 ALDH families were identified, including a unique member of the family 19 ALDH. Phylogenetic analysis revealed 13 groups, with a conserved relationship among ALDH families. Functional structure analysis of ALDH2 showed a catalytic mechanism involving Cys-Glu couple. However, the analysis of ALDH3 showed no functional gene duplication or potential neo-functionalities. Gene expression analysis reveals that particular ALDH genes might respond to wounding stress increasing the expression as ALDH2B7. Overall, this study reveals the complexity of S. lycopersicum ALDH gene superfamily and offers new insights into the structure-functional features and evolution of ALDH gene families in vascular plants. The functional characterization of ALDHs is valuable and promoting molecular breeding in tomato for the improvement of stress tolerance and signaling.

  2. Rotavirus gene structure and function.

    PubMed Central

    Estes, M K; Cohen, J

    1989-01-01

    Knowledge of the structure and function of the genes and proteins of the rotaviruses has expanded rapidly. Information obtained in the last 5 years has revealed unexpected and unique molecular properties of rotavirus proteins of general interest to virologists, biochemists, and cell biologists. Rotaviruses share some features of replication with reoviruses, yet antigenic and molecular properties of the outer capsid proteins, VP4 (a protein whose cleavage is required for infectivity, possibly by mediating fusion with the cell membrane) and VP7 (a glycoprotein), show more similarities with those of other viruses such as the orthomyxoviruses, paramyxoviruses, and alphaviruses. Rotavirus morphogenesis is a unique process, during which immature subviral particles bud through the membrane of the endoplasmic reticulum (ER). During this process, transiently enveloped particles form, the outer capsid proteins are assembled onto particles, and mature particles accumulate in the lumen of the ER. Two ER-specific viral glycoproteins are involved in virus maturation, and these glycoproteins have been shown to be useful models for studying protein targeting and retention in the ER and for studying mechanisms of virus budding. New ideas and approaches to understanding how each gene functions to replicate and assemble the segmented viral genome have emerged from knowledge of the primary structure of rotavirus genes and their proteins and from knowledge of the properties of domains on individual proteins. Localization of type-specific and cross-reactive neutralizing epitopes on the outer capsid proteins is becoming increasingly useful in dissecting the protective immune response, including evaluation of vaccine trials, with the practical possibility of enhancing the production of new, more effective vaccines. Finally, future analyses with recently characterized immunologic and gene probes and new animal models can be expected to provide a basic understanding of what regulates the

  3. Identification of the Genes Involved in the Biofilm-like Structures on Actinomyces oris K20, a Clinical Isolate from an Apical Lesion

    DTIC Science & Technology

    2013-01-01

    bacteria in clinically asymptomatic periapical pathosis. J Endod 1990;16:534–8. 5. Nair PNR. On the causes of persistent apical periodontitis : a review ...deter- mined by direct genome sequencing with the transposon-end primers . Results: Five mutants without the meshwork-like structures were identified...The biofilm infection is thought to be one of the most crucial factors for chronic orrecurrent diseases . More than half of the infectious diseases

  4. Gene identification by 3' terminal exon trapping.

    PubMed

    Krizman, D B

    1996-01-01

    3' terminal exon trapping offers a powerful and efficient technology for rendering fragments of transcribed genes from large stretches of unsequenced, vertebrate, genomic DNA. The products from this methodology are the starting point for further studies of gene discovery and analysis. Future considerations for this technology include answering questions about the degree of efficiency from various trapping substrates and whether or not this approach can be scaled up for large-scale gene discovery such as individual chromosome or whole genomic approaches. With the onset of EST database searching, the final analysis becomes a computer assay that is consistent with the future of genetics as this field continues to move towards informational experimentation based on DNA sequence.

  5. Graben Structure Identification Using Gravity Method

    NASA Astrophysics Data System (ADS)

    Hasanah, Lilik; Aminudin, Ahmad; Ardi, Nanang D.; Utomo, Agus. S.; Yuwono, Heru; Kamtono; Wardhana, Dadan. D.; Gaol, Karit L.; Iryanti, Mimin

    2016-01-01

    Graben (trench) is a natural expanse that is lower in altitude compared to its surrounding which is caused by normal faults shift. Changes in rock density can be identified to obtain the subsurface rock structure. Gravity method is a basic method yet very effective in determining subsurface rock structure. Identification of graben structure is the main focus of this research in order to identify the natural resources which may be available under the ground. Research work was performed in various locations in Bogor and according to our analysis using 2D Talwani model, the average density at the surface is 2.5 gram/cm3. 2D modelling results show a fault structure at rocks with relative direction West-East. The fault is forming an extension block faulting which makes the area a graben. In general, the crosssection profile of the model indicates rock layer structure made from limestone rocks (2.75 gr/cm3), sands, flakes, limestone (2.5 gr/cm3), volcanic sediment layer sandstone (2.3 gr/cm3), and clay layer and similar (2.00 - 2.10 gr/cm3).

  6. TRIM25 Identification in the Chinese Goose: Gene Structure, Tissue Expression Profiles, and Antiviral Immune Responses In Vivo and In Vitro

    PubMed Central

    Zhou, Hao; Wang, Anqi; Sun, Lipei; Wang, Mingshu; Jia, Renyong; Zhu, Dekang; Liu, Mafeng; Yang, Qiao; Wu, Ying; Sun, Kunfeng; Chen, Xiaoyue

    2016-01-01

    The retinoic acid-inducible gene I (RIG-I) and the RIG-I-like receptor (RLR) protein play a critical role in the interferon (IFN) response during RNA virus infection. The tripartite motif containing 25 proteins (TRIM25) was reported to modify caspase activation and RIG-I recruitment domains (CARDs) via ubiquitin. These modifications allow TRIM25 to interact with mitochondrial antiviral signaling molecules (MAVs) and form CARD-CARD tetramers. Goose TRIM25 was cloned from gosling lungs, which possess a 1662 bp open reading flame (ORF). This ORF encodes a predicted 554 amino acid protein consisting of a B-box domain, a coiled-coil domain, and a PRY/SPRY domain. The protein sequence has 89.25% sequence identity with Anas platyrhynchos TRIM25, 78.57% with Gallus gallus TRIM25, and 46.92% with Homo sapiens TRIM25. TRIM25 is expressed in all gosling and adult goose tissues examined. QRT-PCR revealed that goose TRIM25 transcription could be induced by goose IFN-α, goose IFN-γ, and goose IFN-λ, as well as a35 s polyinosinic-polycytidylic acid (poly(I:C)), oligodeoxynucleotides 2006 (ODN 2006), and resiquimod (R848) in vitro; however, it is inhibited in H9N2 infected goslings for unknown reasons. These data suggest that goose TRIM25 might play a positive role in the regulation of the antiviral immune response. PMID:27995135

  7. TRIM25 Identification in the Chinese Goose: Gene Structure, Tissue Expression Profiles, and Antiviral Immune Responses In Vivo and In Vitro.

    PubMed

    Wei, Yunan; Zhou, Hao; Wang, Anqi; Sun, Lipei; Wang, Mingshu; Jia, Renyong; Zhu, Dekang; Liu, Mafeng; Yang, Qiao; Wu, Ying; Sun, Kunfeng; Chen, Xiaoyue; Cheng, Anchun; Chen, Shun

    2016-01-01

    The retinoic acid-inducible gene I (RIG-I) and the RIG-I-like receptor (RLR) protein play a critical role in the interferon (IFN) response during RNA virus infection. The tripartite motif containing 25 proteins (TRIM25) was reported to modify caspase activation and RIG-I recruitment domains (CARDs) via ubiquitin. These modifications allow TRIM25 to interact with mitochondrial antiviral signaling molecules (MAVs) and form CARD-CARD tetramers. Goose TRIM25 was cloned from gosling lungs, which possess a 1662 bp open reading flame (ORF). This ORF encodes a predicted 554 amino acid protein consisting of a B-box domain, a coiled-coil domain, and a PRY/SPRY domain. The protein sequence has 89.25% sequence identity with Anas platyrhynchos TRIM25, 78.57% with Gallus gallus TRIM25, and 46.92% with Homo sapiens TRIM25. TRIM25 is expressed in all gosling and adult goose tissues examined. QRT-PCR revealed that goose TRIM25 transcription could be induced by goose IFN-α, goose IFN-γ, and goose IFN-λ, as well as a35 s polyinosinic-polycytidylic acid (poly(I:C)), oligodeoxynucleotides 2006 (ODN 2006), and resiquimod (R848) in vitro; however, it is inhibited in H9N2 infected goslings for unknown reasons. These data suggest that goose TRIM25 might play a positive role in the regulation of the antiviral immune response.

  8. Identification of the thiamin pyrophosphokinase gene in rainbow trout: Characteristic structure and expression of seven splice variants in tissues and cell lines and during embryo development

    USGS Publications Warehouse

    Yuge, Shinya; Richter, Catherine A.; Wright-Osment, Maureen K.; Nicks, Diane; Saloka, Stephanie K.; Tillitt, Donald E.; Li, Weiming

    2012-01-01

    Thiamin pyrophosphokinase (TPK) converts thiamin to its active form, thiamin diphosphate. In humans, TPK expression is down-regulated in some thiamin deficiency related syndrome, and enhanced during pregnancy. Rainbow trout are also vulnerable to thiamin deficiency in wild life and are useful models for thiamin metabolism research. We identified the tpk gene transcript including seven splice variants in the rainbow trout. Almost all cell lines and tissues examined showed co-expression of several tpk splice variants including a potentially major one at both mRNA and protein levels. However, relative to other tissues, the longest variant mRNA expression was predominant in the ovary and abundant in embryos. During embryogenesis, total tpk transcripts increased abruptly in early development, and decreased to about half of the peak shortly after hatching. In rainbow trout, the tpk transcript complex is ubiquitously expressed for all tissues and cells examined, and its increase in expression could be important in the early-middle embryonic stages. Moreover, decimated tpk expression in a hepatoma cell line relative to hepatic and gonadal cell lines appears to be consistent with previously reported down-regulation of thiamin metabolism in cancer.

  9. Identification of the thiamin pyrophosphokinase gene in rainbow trout: characteristic structure and expression of seven splice variants in tissues and cell lines and during embryo development.

    PubMed

    Yuge, Shinya; Richter, Catherine A; Wright-Osment, Maureen K; Nicks, Diane; Saloka, Stephanie K; Tillitt, Donald E; Li, Weiming

    2012-10-01

    Thiamin pyrophosphokinase (TPK) converts thiamin to its active form, thiamin diphosphate. In humans, TPK expression is down-regulated in some thiamin deficiency related syndrome, and enhanced during pregnancy. Rainbow trout are also vulnerable to thiamin deficiency in wild life and are useful models for thiamin metabolism research. We identified the tpk gene transcript including seven splice variants in the rainbow trout. Almost all cell lines and tissues examined showed co-expression of several tpk splice variants including a potentially major one at both mRNA and protein levels. However, relative to other tissues, the longest variant mRNA expression was predominant in the ovary and abundant in embryos. During embryogenesis, total tpk transcripts increased abruptly in early development, and decreased to about half of the peak shortly after hatching. In rainbow trout, the tpk transcript complex is ubiquitously expressed for all tissues and cells examined, and its increase in expression could be important in the early-middle embryonic stages. Moreover, decimated tpk expression in a hepatoma cell line relative to hepatic and gonadal cell lines appears to be consistent with previously reported down-regulation of thiamin metabolism in cancer. Copyright © 2012 Elsevier Inc. All rights reserved.

  10. Positive-unlabeled learning for disease gene identification.

    PubMed

    Yang, Peng; Li, Xiao-Li; Mei, Jian-Ping; Kwoh, Chee-Keong; Ng, See-Kiong

    2012-10-15

    Identifying disease genes from human genome is an important but challenging task in biomedical research. Machine learning methods can be applied to discover new disease genes based on the known ones. Existing machine learning methods typically use the known disease genes as the positive training set P and the unknown genes as the negative training set N (non-disease gene set does not exist) to build classifiers to identify new disease genes from the unknown genes. However, such kind of classifiers is actually built from a noisy negative set N as there can be unknown disease genes in N itself. As a result, the classifiers do not perform as well as they could be. Instead of treating the unknown genes as negative examples in N, we treat them as an unlabeled set U. We design a novel positive-unlabeled (PU) learning algorithm PUDI (PU learning for disease gene identification) to build a classifier using P and U. We first partition U into four sets, namely, reliable negative set RN, likely positive set LP, likely negative set LN and weak negative set WN. The weighted support vector machines are then used to build a multi-level classifier based on the four training sets and positive training set P to identify disease genes. Our experimental results demonstrate that our proposed PUDI algorithm outperformed the existing methods significantly. The proposed PUDI algorithm is able to identify disease genes more accurately by treating the unknown data more appropriately as unlabeled set U instead of negative set N. Given that many machine learning problems in biomedical research do involve positive and unlabeled data instead of negative data, it is possible that the machine learning methods for these problems can be further improved by adopting PU learning methods, as we have done here for disease gene identification. The executable program and data are available at http://www1.i2r.a-star.edu.sg/~xlli/PUDI/PUDI.html.

  11. Identification of structural and morphogenesis genes of Pseudoalteromonas phage φRIO-1 and placement within the evolutionary history of Podoviridae.

    PubMed

    Hardies, Stephen C; Thomas, Julie A; Black, Lindsay; Weintraub, Susan T; Hwang, Chung Y; Cho, Byung C

    2016-02-01

    The virion proteins of Pseudoalteromonas phage φRIO-1 were identified and quantitated by mass spectrometry and gel densitometry. Bioinformatic methods customized to deal with extreme divergence defined a φRIO-1 tail structure homology group of phages, which was further related to T7 tail and internal virion proteins (IVPs). Similarly, homologs of tubular tail components and internal virion proteins were identified in essentially all completely sequenced podoviruses other than those in the subfamily Picovirinae. The podoviruses were subdivided into several tail structure homology groups, in addition to the RIO-1 and T7 groups. Molecular phylogeny indicated that these groups all arose about the same ancient time as the φRIO-1/T7 split. Hence, the T7-like infection mechanism involving the IVPs was an ancestral property of most podoviruses. The IVPs were found to variably host both tail lysozyme domains and domains destined for the cytoplasm, including the N4 virion RNA polymerase embedded within an IVP-D homolog.

  12. Identification of structural and morphogenesis genes of Pseudoalteromonas phage φRIO-1 and placement within the evolutionary history of Podoviridae

    PubMed Central

    Hardies, Stephen C.; Thomas, Julie A.; Black, Lindsay; Weintraub, Susan T.; Hwang, Chung Y.; Cho, Byung C.

    2016-01-01

    The virion proteins of Pseudoalteromonas phage φRIO-1 were identified and quantitated by mass spectrometry and gel densitometry. Bioinformatic methods customized to deal with extreme divergence defined a φRIO-1 tail structure homology group of phages, which was further related to T7 tail and internal virion proteins (IVPs). Similarly, homologs of tubular tail components and internal virion proteins were identified in essentially all completely sequenced podoviruses other than those in the subfamily Picovirinae. The podoviruses were subdivided into several tail structure homology groups, in addition to the RIO-1 and T7 groups. Molecular phylogeny indicated that these groups all arose about the same ancient time as the φRIO-1/T7 split. Hence, the T7-like infection mechanism involving the IVPs was an ancestral property of most podoviruses. The IVPs were found to variably host both tail lysozyme domains and domains destined for the cytoplasm, including the N4 virion RNA polymerase embedded within an IVP-D homolog. PMID:26748333

  13. Structural identification and damage assessment of large space structures

    NASA Technical Reports Server (NTRS)

    Nelson, Richard B.; Fourney, Michael E.

    1988-01-01

    Two different methods are proposed for identifying the structural properties of large orbiting space structures under ordinary service loads, and for assessing potential damage due to impact or other extreme loadings. It is shown that the behavior of a structure in a weightless environment is nonlinear due to unloaded or lightly loaded connections, an effect which not only complicates structural control, but makes the problem of system identification more difficult than for ground based systems. Both proposed methods assume that the structure is subjected to loads imposed by prescribed self stressing systems sufficient to produce repeatable internal force systems in the structure. The first method is based on statical response and requires a survey of structural displacements produced by the self stressing systems. The displacements do not have to be determined completely (i.e., in three directions at each connection), but more displacement information produces more accurate structural stiffness information. It is anticipated that displacement measurements will be taken using on-board laser measurement devices. The second technique employs dynamic stress wave measurement techniques using on-board loading devices and strain gages to track stress wave propagation through the space structure. This approach, which is in its early stages of development, relies on an analysis of transit times of impulsive stress waves and changes in transit times and wave forms due to changes in structural parameters.

  14. Structural identification and damage assessment of large space structures

    NASA Technical Reports Server (NTRS)

    Nelson, Richard B.; Fourney, Michael E.

    1988-01-01

    Two different methods are proposed for identifying the structural properties of large orbiting space structures under ordinary service loads, and for assessing potential damage due to impact or other extreme loadings. It is shown that the behavior of a structure in a weightless environment is nonlinear due to unloaded or lightly loaded connections, an effect which not only complicates structural control, but makes the problem of system identification more difficult than for ground based systems. Both proposed methods assume that the structure is subjected to loads imposed by prescribed self stressing systems sufficient to produce repeatable internal force systems in the structure. The first method is based on statical response and requires a survey of structural displacements produced by the self stressing systems. The displacements do not have to be determined completely (i.e., in three directions at each connection), but more displacement information produces more accurate structural stiffness information. It is anticipated that displacement measurements will be taken using on-board laser measurement devices. The second technique employs dynamic stress wave measurement techniques using on-board loading devices and strain gages to track stress wave propagation through the space structure. This approach, which is in its early stages of development, relies on an analysis of transit times of impulsive stress waves and changes in transit times and wave forms due to changes in structural parameters.

  15. Identification of key player genes in gene regulatory networks.

    PubMed

    Nazarieh, Maryam; Wiese, Andreas; Will, Thorsten; Hamed, Mohamed; Helms, Volkhard

    2016-09-06

    Identifying the gene regulatory networks governing the workings and identity of cells is one of the main challenges in understanding processes such as cellular differentiation, reprogramming or cancerogenesis. One particular challenge is to identify the main drivers and master regulatory genes that control such cell fate transitions. In this work, we reformulate this problem as the optimization problems of computing a Minimum Dominating Set and a Minimum Connected Dominating Set for directed graphs. Both MDS and MCDS are applied to the well-studied gene regulatory networks of the model organisms E. coli and S. cerevisiae and to a pluripotency network for mouse embryonic stem cells. The results show that MCDS can capture most of the known key player genes identified so far in the model organisms. Moreover, this method suggests an additional small set of transcription factors as novel key players for governing the cell-specific gene regulatory network which can also be investigated with regard to diseases. To this aim, we investigated the ability of MCDS to define key drivers in breast cancer. The method identified many known drug targets as members of the MDS and MCDS. This paper proposes a new method to identify key player genes in gene regulatory networks. The Java implementation of the heuristic algorithm explained in this paper is available as a Cytoscape plugin at http://apps.cytoscape.org/apps/mcds . The SageMath programs for solving integer linear programming formulations used in the paper are available at https://github.com/maryamNazarieh/KeyRegulatoryGenes and as supplementary material.

  16. Identification of a Colonial Chordate Histocompatibility Gene

    PubMed Central

    Voskoboynik, Ayelet; Newman, Aaron M.; Corey, Daniel M.; Sahoo, Debashis; Pushkarev, Dmitry; Neff, Norma F.; Passarelli, Benedetto; Koh, Winston; Ishizuka, Katherine J.; Palmeri, Karla J.; Dimov, Ivan K.; Keasar, Chen; Fan, H. Christina; Mantalas, Gary L.; Sinha, Rahul; Penland, Lolita; Quake, Stephen R.; Weissman, Irving L.

    2013-01-01

    Histocompatibility is the basis by which multicellular organisms of the same species distinguish self from non-self. Relatively little is known about the mechanisms underlying histocompatibility reactions in lower organisms. Botryllus schlosseri is a colonial urochordate, a sister group of vertebrates, that exhibits a genetically determined natural transplantation reaction, whereby self-recognition between colonies leads to formation of parabionts with a common vasculature, whereas rejection occurs between incompatible colonies. Using genetically defined lines, whole-transcriptome sequencing, and genomics, we identified a single gene that encodes self/non-self and determines “graft” outcomes in this organism. This gene is significantly upregulated in colonies poised to undergo fusion or rejection, is highly expressed in the vasculature, and is functionally linked to histocompatibility outcomes. These findings establish a platform for advancing the science of allorecognition. PMID:23888037

  17. Gene-based and semantic structure of the Gene Ontology as a complex network

    NASA Astrophysics Data System (ADS)

    Coronnello, Claudia; Tumminello, Michele; Miccichè, Salvatore

    2016-09-01

    The last decade has seen the advent and consolidation of ontology based tools for the identification and biological interpretation of classes of genes, such as the Gene Ontology. The Gene Ontology (GO) is constantly evolving over time. The information accumulated time-by-time and included in the GO is encoded in the definition of terms and in the setting up of semantic relations amongst terms. Here we investigate the Gene Ontology from a complex network perspective. We consider the semantic network of terms naturally associated with the semantic relationships provided by the Gene Ontology consortium. Moreover, the GO is a natural example of bipartite network of terms and genes. Here we are interested in studying the properties of the projected network of terms, i.e. a gene-based weighted network of GO terms, in which a link between any two terms is set if at least one gene is annotated in both terms. One aim of the present paper is to compare the structural properties of the semantic and the gene-based network. The relative importance of terms is very similar in the two networks, but the community structure changes. We show that in some cases GO terms that appear to be distinct from a semantic point of view are instead connected, and appear in the same community when considering their gene content. The identification of such gene-based communities of terms might therefore be the basis of a simple protocol aiming at improving the semantic structure of GO. Information about terms that share large gene content might also be important from a biomedical point of view, as it might reveal how genes over-expressed in a certain term also affect other biological processes, molecular functions and cellular components not directly linked according to GO semantics.

  18. Optimal matrix approximants in structural identification

    NASA Technical Reports Server (NTRS)

    Beattie, C. A.; Smith, S. W.

    1992-01-01

    Problems of model correlation and system identification are central in the design, analysis, and control of large space structures. Of the numerous methods that have been proposed, many are based on finding minimal adjustments to a model matrix sufficient to introduce some desirable quality into that matrix. In this work, several of these methods are reviewed, placed in a modern framework, and linked to other previously known ideas in computational linear algebra and optimization. This new framework provides a point of departure for a number of new methods which are introduced here. Significant among these is a method for stiffness matrix adjustment which preserves the sparsity pattern of an original matrix, requires comparatively modest computational resources, and allows robust handling of noisy modal data. Numerical examples are included to illustrate the methods presented herein.

  19. Streptococcus iniae, a Human and Animal Pathogen: Specific Identification by the Chaperonin 60 Gene Identification Method

    PubMed Central

    Goh, Swee Han; Driedger, David; Gillett, Sandra; Low, Donald E.; Hemmingsen, Sean M.; Amos, Mayben; Chan, David; Lovgren, Marguerite; Willey, Barbara M.; Shaw, Carol; Smith, John A.

    1998-01-01

    It was recently reported that Streptococcus iniae, a bacterial pathogen of aquatic animals, can cause serious disease in humans. Using the chaperonin 60 (Cpn60) gene identification method with reverse checkerboard hybridization and chemiluminescent detection, we identified correctly each of 12 S. iniae samples among 34 aerobic gram-positive isolates from animal and clinical human sources. PMID:9650992

  20. Computational Identification of Novel Genes: Current and Future Perspectives

    PubMed Central

    Klasberg, Steffen; Bitard-Feildel, Tristan; Mallet, Ludovic

    2016-01-01

    While it has long been thought that all genomic novelties are derived from the existing material, many genes lacking homology to known genes were found in recent genome projects. Some of these novel genes were proposed to have evolved de novo, ie, out of noncoding sequences, whereas some have been shown to follow a duplication and divergence process. Their discovery called for an extension of the historical hypotheses about gene origination. Besides the theoretical breakthrough, increasing evidence accumulated that novel genes play important roles in evolutionary processes, including adaptation and speciation events. Different techniques are available to identify genes and classify them as novel. Their classification as novel is usually based on their similarity to known genes, or lack thereof, detected by comparative genomics or against databases. Computational approaches are further prime methods that can be based on existing models or leveraging biological evidences from experiments. Identification of novel genes remains however a challenging task. With the constant software and technologies updates, no gold standard, and no available benchmark, evaluation and characterization of genomic novelty is a vibrant field. In this review, the classical and state-of-the-art tools for gene prediction are introduced. The current methods for novel gene detection are presented; the methodological strategies and their limits are discussed along with perspective approaches for further studies. PMID:27493475

  1. Identification of genes and gene clusters involved in mycotoxin synthesis

    USDA-ARS?s Scientific Manuscript database

    Research methods to identify and characterize genes involved in mycotoxin biosynthetic pathways have evolved considerably over the years. Before whole genome sequences were available (e.g. pre-genomics), work focused primarily on chemistry, biosynthetic mutant strains and molecular analysis of sing...

  2. Identification and manipulation of Rhizobium phytohormone genes

    SciTech Connect

    Ditta, G.S.

    1988-06-27

    The goal of this project was to determine whether phytohormone production by the gram-negative bacterium Rhizobium meliloti is required for successful modulation and symbiosis with alfalfa. specifically, we undertook the study of indoleacetic acid (IAA; auxin) production by R. meliloti and sought to create a mutant totally deficient in IAA biosynthesis. For many years it has been known that rhizobia are capable of synthesizing and excreting IAA, and it has often been suggested that this could be of importance for the initiation of root nodule development. Published work demonstrating the involvement of bacterial IAA genes in pathogenesis by Pseudomonas syringae and Agrobacterium tumefaciens further emphasized the need for this type of study in Rhizobium.

  3. Identification of brassinosteroid genes in Brachypodium distachyon.

    PubMed

    Corvalán, Claudia; Choe, Sunghwa

    2017-01-06

    Brassinosteroids (BRs) are steroidal phytohormones that are involved in diverse physiological processes and affect many important traits, such as plant stature, stress tolerance, leaf angle, fertility, and grain filling. BR signaling and biosynthetic pathways have been studied in various plants, such as the model dicot Arabidopsis thaliana; however, relatively little is known about these pathways in monocots. To characterize BR-related processes in the model grass Brachypodium distachyon, we studied the response of these plants to the specific BR biosynthesis inhibitor, propiconazole (Pcz). We found that treatments with Pcz produced a dwarf phenotype in B. distachyon seedlings, similar to that observed in Pcz-treated Arabidopsis plants and in characterized BR-deficient mutants. Through bioinformatics analysis, we identified a list of putative homologs of genes known to be involved in BR biosynthesis and signaling in Arabidopsis, such as DWF4, BR6OX2, CPD, BRI1, and BIN2. Evaluating the response of these genes to Pcz treatments revealed that candidates for BdDWF4, BR6OX2 and, CPD were under feedback regulation. In addition, Arabidopsis plants heterologously expressing BdDWF4 displayed tall statures and elongated petioles, as would be expected in plants with elevated levels of BRs. Moreover, heterologous expression of BdBIN2 in Arabidopsis resulted in dwarfism, suggesting that BdBIN2 functions as a negative regulator of BR signaling. However, the dwarf phenotypes of Arabidopsis bri1-5, a weak BRI1 mutant allele, were not complemented by overexpression of BdBRI1, indicating that BdBRI1 and BRI1 are not functionally equivalent. We identified components of the BR biosynthetic and signaling pathways in Brachypodium, and provided examples of both similarities and differences in the BR biology of these two plants. Our results suggest a framework for understanding BR biology in monocot crop plants such as Zea mays (maize) and Oryza sativa (rice).

  4. Gene probes versus classical methods in the identification of mycobacteria.

    PubMed

    Coelho, Andréa Gobetti Vieira; Zamarioli, Liliana Aparecida; Reis, Clemira Martins Pereira Vidal; Nascimento, Ana Carolina Chiou; Rodrigues, Juliana Dos Santos

    2008-11-01

    The emergence of tuberculosis/HIV co-infection and the increase in the number of cases of infection with nontuberculous mycobacteria (NTM) require rapid laboratory test results in the isolation and identification of mycobacteria. The objective of this study was to evaluate the identification of mycobacteria by means of gene probes in comparison with that obtained using classical biochemical methods. Between 2002 and 2004, 178 mycobacterial cultures, all testing positive for acid-fast bacilli, were analyzed. Samples were obtained from clinical specimens of patients with respiratory symptoms or with clinical suspicion of pulmonary tuberculosis/mycobacteriosis who were treated in the greater metropolitan area of Santos. The gene probe identified 137 samples (77%) as Mycobacterium tuberculosis complex and 41 (23%) as NTM. Discordant results between the methods (3%) were obtained only in the year of implementation (2002). When comparing the methods, the sensitivity, specificity, positive predictive value and negative predictive value of the gene probe method were 98%, 93%, 98% and 93%, respectively. Despite the cost, the identification of mycobacteria using the molecular technique is faster: maximum 3 h vs. 28-30 days for classical methods. The use of gene probes is a validated molecular technique. It is fast, easy to use and readily available on the market. It has high specificity and sensitivity, which justifies its implementation and routine use in referral laboratories, since it facilitates the diagnosis providing agile clinical interventions.

  5. SIBER: systematic identification of bimodally expressed genes using RNAseq data.

    PubMed

    Tong, Pan; Chen, Yong; Su, Xiao; Coombes, Kevin R

    2013-03-01

    Identification of bimodally expressed genes is an important task, as genes with bimodal expression play important roles in cell differentiation, signalling and disease progression. Several useful algorithms have been developed to identify bimodal genes from microarray data. Currently, no method can deal with data from next-generation sequencing, which is emerging as a replacement technology for microarrays. We present SIBER (systematic identification of bimodally expressed genes using RNAseq data) for effectively identifying bimodally expressed genes from next-generation RNAseq data. We evaluate several candidate methods for modelling RNAseq count data and compare their performance in identifying bimodal genes through both simulation and real data analysis. We show that the lognormal mixture model performs best in terms of power and robustness under various scenarios. We also compare our method with alternative approaches, including profile analysis using clustering and kurtosis (PACK) and cancer outlier profile analysis (COPA). Our method is robust, powerful, invariant to shifting and scaling, has no blind spots and has a sample-size-free interpretation. The R package SIBER is available at the website http://bioinformatics.mdanderson.org/main/OOMPA:Overview.

  6. SIBER: systematic identification of bimodally expressed genes using RNAseq data

    PubMed Central

    Tong, Pan; Chen, Yong; Su, Xiao; Coombes, Kevin R.

    2013-01-01

    Motivation: Identification of bimodally expressed genes is an important task, as genes with bimodal expression play important roles in cell differentiation, signalling and disease progression. Several useful algorithms have been developed to identify bimodal genes from microarray data. Currently, no method can deal with data from next-generation sequencing, which is emerging as a replacement technology for microarrays. Results: We present SIBER (systematic identification of bimodally expressed genes using RNAseq data) for effectively identifying bimodally expressed genes from next-generation RNAseq data. We evaluate several candidate methods for modelling RNAseq count data and compare their performance in identifying bimodal genes through both simulation and real data analysis. We show that the lognormal mixture model performs best in terms of power and robustness under various scenarios. We also compare our method with alternative approaches, including profile analysis using clustering and kurtosis (PACK) and cancer outlier profile analysis (COPA). Our method is robust, powerful, invariant to shifting and scaling, has no blind spots and has a sample-size-free interpretation. Availability: The R package SIBER is available at the website http://bioinformatics.mdanderson.org/main/OOMPA:Overview. Contact: kcoombes@mdanderson.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23303507

  7. Strategy for structural identification of highway bridges

    NASA Astrophysics Data System (ADS)

    Chalko, Tom J.; Haritos, Nicholas

    1996-11-01

    The University of Melbourne in collaboration with VicRoads, the road and bridge authority in the state of Victoria, has performed a series of static and dynamic tests to evaluate the in-service condition of a number of bridges of different design. From this experience, a strategy for a routine bridge testing procedure has emerged, the presentation of which is the main subject of this paper. The strategy presented involves the selective use of the following methods and techniques: 1) Measurements: vibration response to ambient/traffic excitation, Modal Testing using impact deices and/or shakers. 2) Modal parameter estimation from experimental measurements. 3) FEM modeling: development of generic parametric FEM models of standard/typical designs, and special models. 4) Correlating FEM models and experimental results: updating FEM model parameters, identification of bridge support conditions, estimation of effective stiffness of aged materials and structural elements. 5) Detection of structural faults: simple methods and advanced techniques if required. 6) Prediction of bridge load carrying capacity using verified FEM model: use in re- rating bridges and as a basis or a substitute for proof load testing. The outline of the strategy together with a brief description of the elements above is given. The motivation for the work presented in this paper was to select the state of the art engineering tools to assist relevant authorities in the decision processes necessary for implementing a cost- effective maintenance and replacement policy for the ageing bridge stock.

  8. Identification of a Candidate Gene for Astigmatism

    PubMed Central

    Lopes, Margarida C.; Hysi, Pirro G.; Verhoeven, Virginie J. M.; Macgregor, Stuart; Hewitt, Alex W.; Montgomery, Grant W.; Cumberland, Phillippa; Vingerling, Johannes R.; Young, Terri L.; van Duijn, Cornelia M.; Oostra, Ben; Uitterlinden, Andre G.; Rahi, Jugnoo S.; Mackey, David A.; Klaver, Caroline C. W.; Andrew, Toby; Hammond, Christopher J.

    2013-01-01

    Purpose. Astigmatism is a common refractive error that reduces vision, where the curvature and refractive power of the cornea in one meridian are less than those of the perpendicular axis. It is a complex trait likely to be influenced by both genetic and environmental factors. Twin studies of astigmatism have found approximately 60% of phenotypic variance is explained by genetic factors. This study aimed to identify susceptibility loci for astigmatism. Methods. We performed a meta-analysis of seven genome-wide association studies that included 22,100 individuals of European descent, where astigmatism was defined as the number of diopters of cylinder prescription, using fixed effect inverse variance-weighted methods. Results. A susceptibility locus was identified with lead single nucleotide polymorphism rs3771395 on chromosome 2p13.3 (meta-analysis, P = 1.97 × 10−7) in the VAX2 gene. VAX2 plays an important role in the development of the dorsoventral axis of the eye. Animal studies have shown a gradient in astigmatism along the vertical plane, with corresponding changes in refraction, particularly in the ventral field. Conclusions. This finding advances the understanding of refractive error, and provides new potential pathways to be evaluated with regard to the development of astigmatism. PMID:23322567

  9. Applications of graph theory in protein structure identification

    PubMed Central

    2011-01-01

    There is a growing interest in the identification of proteins on the proteome wide scale. Among different kinds of protein structure identification methods, graph-theoretic methods are very sharp ones. Due to their lower costs, higher effectiveness and many other advantages, they have drawn more and more researchers’ attention nowadays. Specifically, graph-theoretic methods have been widely used in homology identification, side-chain cluster identification, peptide sequencing and so on. This paper reviews several methods in solving protein structure identification problems using graph theory. We mainly introduce classical methods and mathematical models including homology modeling based on clique finding, identification of side-chain clusters in protein structures upon graph spectrum, and de novo peptide sequencing via tandem mass spectrometry using the spectrum graph model. In addition, concluding remarks and future priorities of each method are given. PMID:22165974

  10. Applications of graph theory in protein structure identification.

    PubMed

    Yan, Yan; Zhang, Shenggui; Wu, Fang-Xiang

    2011-10-14

    There is a growing interest in the identification of proteins on the proteome wide scale. Among different kinds of protein structure identification methods, graph-theoretic methods are very sharp ones. Due to their lower costs, higher effectiveness and many other advantages, they have drawn more and more researchers' attention nowadays. Specifically, graph-theoretic methods have been widely used in homology identification, side-chain cluster identification, peptide sequencing and so on. This paper reviews several methods in solving protein structure identification problems using graph theory. We mainly introduce classical methods and mathematical models including homology modeling based on clique finding, identification of side-chain clusters in protein structures upon graph spectrum, and de novo peptide sequencing via tandem mass spectrometry using the spectrum graph model. In addition, concluding remarks and future priorities of each method are given.

  11. Identification of feces by detection of Bacteroides genes.

    PubMed

    Nakanishi, Hiroaki; Shojo, Hideki; Ohmori, Takeshi; Hara, Masaaki; Takada, Aya; Adachi, Noboru; Saito, Kazuyuki

    2013-01-01

    In forensic science, the identification of feces is very important in a variety of crime investigations. However, no sensitive and simple fecal identification method using molecular biological techniques has been reported. Here, we focused on the fecal bacteria, Bacteroides uniformis, Bacteroides vulgatus and Bacteroides thetaiotaomicron, and developed a novel fecal identification method by detection of the gene sequences specific to these bacteria in various body (feces, blood, saliva, semen, urine, vaginal fluids and skin surfaces) and forensic (anal adhesions) specimens. Bacterial gene detection was performed by real-time PCR using a minor groove binding probe to amplify the RNA polymerase β-subunit gene of B. uniformis and B. vulgatus, and the α-1-6 mannanase gene of B. thetaiotaomicron. At least one of these bacteria was detected in the feces of 20 donors; the proportions of B. uniformis, B. vulgatus and B. thetaiotaomicron were 95, 85 and 60%, respectively. Bacteroides vulgatus was also detected in one of six vaginal fluid samples, but B. thetaiotaomicron and B. uniformis were not detected in body samples other than feces. Further, we applied this method to forensic specimens from 18 donors. Eighteen anal adhesions also contained at least one of three bacteria; B. uniformis, B. vulgatus and B. thetaiotaomicron were detected in 89, 78 and 56%, respectively, of the specimens. Thus, these bacteria were present at a high frequency in the fecal and forensic specimens, while either B. uniformis or B. vulgatus was detected in all samples. Therefore, B. uniformis and B. vulgatus represent more appropriate target species than B. thetaiotaomicron for the identification of fecal material. If B. vulgatus and/or B. uniformis are detected, it is likely that the sample contains feces. Taken together, our results suggest that the use of molecular biological techniques will aid the detection of feces in forensic practice, although it is possible that the samples contained

  12. Identification of candidate genes in the spinal muscular atrophy gene region

    SciTech Connect

    Carter, T.A.; Wang, C.H.; Vitale, E.

    1994-09-01

    The SMA disease gene region on chromosome 5q13 has been characterized by the presence of low copy repeat element DNA and concomitant genomic instability. The identification of candidate genes has been complicated by the low-copy repeat sequences which include coding and non-coding DNA. To circumvent this problem, we have focused on the identification and characterization of exonic DNA sequence isolated from YAC-derived bacteriophage subclones. Contrary to hybridization-based protocols which identify all closely homologous genes, exons isolated in this manner are known to map the disease gene region. Exon trapping was limited to an approximately 400 kb {open_quotes}minimum genetic region{close_quotes} defined by recombination mapping. Approximately six new genes have been identified by this method. One of the candidate genes is expressed predominantly in muscle and demonstrates sequence homology with known translational regulatory proteins. Physical mapping places the gene within the minimal genetic region and adjacent to a region characterized with genomic instability. We will report our progress in the identification of disease-specific mutations in this gene based upon comparison of normal and SMA cDNA sequence, amplification and sequencing of SMA DNA samples, and RT-PCR sequencing studies.

  13. Stochastic system identification in structural dynamics

    USGS Publications Warehouse

    Safak, Erdal

    1988-01-01

    Recently, new identification methods have been developed by using the concept of optimal-recursive filtering and stochastic approximation. These methods, known as stochastic identification, are based on the statistical properties of the signal and noise, and do not require the assumptions of current methods. The criterion for stochastic system identification is that the difference between the recorded output and the output from the identified system (i.e., the residual of the identification) should be equal to white noise. In this paper, first a brief review of the theory is given. Then, an application of the method is presented by using ambient vibration data from a nine-story building.

  14. Identification of genes responding to nematode infection in red grouse.

    PubMed

    Webster, L M I; Mello, L V; Mougeot, F; Martinez-Padilla, J; Paterson, S; Piertney, S B

    2011-03-01

    The identification of genes involved in a host's response to parasite infection provides both a means for understanding the pathways involved in immune defence and a target for examining host-parasite co-evolution. Most studies rely on a candidate gene approach derived from model systems to identify gene targets of interest, and there have been a dearth of studies geared towards providing a holistic overview of immune response from natural populations. We carried out an experiment in a natural population of red grouse (Lagopus lagopus scoticus) to manipulate levels of Trichostrongylus tenuis parasite infection. The transcriptomic response of individuals was examined from standard cDNA and suppressive subtractive hybridization (SSH) libraries produced from gut, liver and spleen, enriching for genes expressed in response to T. tenuis infection. A total of 2209 and 3716 unique transcript sequences were identified from the cDNA and SSH libraries, respectively. Forty-five of these had Gene Ontology annotation associated with immune response. Some of these genes have previously been reported from laboratory-based studies of model species as important in immune response to gastrointestinal parasite infection; however, multiple novel genes were also identified. These may reveal novel pathways involved in the host response of grouse to T. tenuis and provide a resource that can be utilized as candidate genes in other species. All sequences described have been deposited in GenBank (accession numbers GW698221-GW706922)

  15. Positive-unlabeled learning for disease gene identification

    PubMed Central

    Yang, Peng; Li, Xiao-Li; Mei, Jian-Ping; Kwoh, Chee-Keong; Ng, See-Kiong

    2012-01-01

    Background: Identifying disease genes from human genome is an important but challenging task in biomedical research. Machine learning methods can be applied to discover new disease genes based on the known ones. Existing machine learning methods typically use the known disease genes as the positive training set P and the unknown genes as the negative training set N (non-disease gene set does not exist) to build classifiers to identify new disease genes from the unknown genes. However, such kind of classifiers is actually built from a noisy negative set N as there can be unknown disease genes in N itself. As a result, the classifiers do not perform as well as they could be. Result: Instead of treating the unknown genes as negative examples in N, we treat them as an unlabeled set U. We design a novel positive-unlabeled (PU) learning algorithm PUDI (PU learning for disease gene identification) to build a classifier using P and U. We first partition U into four sets, namely, reliable negative set RN, likely positive set LP, likely negative set LN and weak negative set WN. The weighted support vector machines are then used to build a multi-level classifier based on the four training sets and positive training set P to identify disease genes. Our experimental results demonstrate that our proposed PUDI algorithm outperformed the existing methods significantly. Conclusion: The proposed PUDI algorithm is able to identify disease genes more accurately by treating the unknown data more appropriately as unlabeled set U instead of negative set N. Given that many machine learning problems in biomedical research do involve positive and unlabeled data instead of negative data, it is possible that the machine learning methods for these problems can be further improved by adopting PU learning methods, as we have done here for disease gene identification. Availability and implementation: The executable program and data are available at http://www1.i2r

  16. Identification of candidate genes in osteoporosis by integrated microarray analysis.

    PubMed

    Li, J J; Wang, B Q; Fei, Q; Yang, Y; Li, D

    2016-12-01

    . Li, B. Q. Wang, Q. Fei, Y. Yang, D. Li. Identification of candidate genes in osteoporosis by integrated microarray analysis. Bone Joint Res 2016;5:594-601. DOI: 10.1302/2046-3758.512.BJR-2016-0073.R1. © 2016 Fei et al.

  17. Identification of salt-induced genes of Zygosaccharomyces rouxii by using Saccharomyces cerevisiae GeneFilters.

    PubMed

    Schoondermark-Stolk, Sung Ah; ter Schure, Eelko G; Verrips, C Theo; Verkleij, Arie J; Boonstra, Johannes

    2002-12-01

    Yeast GeneFilters containing all Saccharomyces cerevisiae open reading frame (ORF) sequences were used to elucidate gene activity in the osmotolerant yeast Zygosaccharomyces rouxii. Labelled cDNA derived from Z. rouxii was targeted to spotted S. cerevisiae ORFs. Approximately 90-100% homology of Z. rouxii genes with those of S. cerevisiae was required for definitive identification of the cDNAs hybridised to GeneFilter. Hybridised labelled cDNAs were visualised as small spots on the microarray, providing simultaneous information on homologous genes present in Z. rouxii and on their level of gene activity. Cross-hybridisation of the GeneFilters displayed 155 as yet unidentified genes of Z. rouxii hybridising to S. cerevisiae ORFs. From those 155 genes, the activity of 86 genes was influenced as a result of NaCl stress. In comparison with S. cerevisiae 24% of Z. rouxii genes revealed a different transcription behaviour following NaCl stress. All of these genes had no previously defined function in osmotic-stress response in Z. rouxii. Therefore, cross-hybridisation of GeneFilters proves to be an appropriate and straightforward method for screening transcripts in Z. rouxii, which provides an extension of the knowledge of genes present in a yeast genus other than S. cerevisiae.

  18. Identification of p53-target genes in Danio rerio

    PubMed Central

    Mandriani, Barbara; Castellana, Stefano; Rinaldi, Carmela; Manzoni, Marta; Venuto, Santina; Rodriguez-Aznar, Eva; Galceran, Juan; Nieto, M. Angela; Borsani, Giuseppe; Monti, Eugenio; Mazza, Tommaso; Merla, Giuseppe; Micale, Lucia

    2016-01-01

    To orchestrate the genomic response to cellular stress signals, p53 recognizes and binds to DNA containing specific and well-characterized p53-responsive elements (REs). Differences in RE sequences can strongly affect the p53 transactivation capacity and occur even between closely related species. Therefore, the identification and characterization of a species-specific p53 Binding sistes (BS) consensus sequence and of the associated target genes may help to provide new insights into the evolution of the p53 regulatory networks across different species. Although p53 functions were studied in a wide range of species, little is known about the p53-mediated transcriptional signature in Danio rerio. Here, we designed and biochemically validated a computational approach to identify novel p53 target genes in Danio rerio genome. Screening all the Danio rerio genome by pattern-matching-based analysis, we found p53 RE-like patterns proximal to 979 annotated Danio rerio genes. Prioritization analysis identified a subset of 134 candidate pattern-related genes, 31 of which have been investigated in further biochemical assays. Our study identified runx1, axin1, traf4a, hspa8, col4a5, necab2, and dnajc9 genes as novel direct p53 targets and 12 additional p53-controlled genes in Danio rerio genome. The proposed combinatorial approach resulted to be highly sensitive and robust for identifying new p53 target genes also in additional animal species. PMID:27581768

  19. Identification of p53-target genes in Danio rerio.

    PubMed

    Mandriani, Barbara; Castellana, Stefano; Rinaldi, Carmela; Manzoni, Marta; Venuto, Santina; Rodriguez-Aznar, Eva; Galceran, Juan; Nieto, M Angela; Borsani, Giuseppe; Monti, Eugenio; Mazza, Tommaso; Merla, Giuseppe; Micale, Lucia

    2016-09-01

    To orchestrate the genomic response to cellular stress signals, p53 recognizes and binds to DNA containing specific and well-characterized p53-responsive elements (REs). Differences in RE sequences can strongly affect the p53 transactivation capacity and occur even between closely related species. Therefore, the identification and characterization of a species-specific p53 Binding sistes (BS) consensus sequence and of the associated target genes may help to provide new insights into the evolution of the p53 regulatory networks across different species. Although p53 functions were studied in a wide range of species, little is known about the p53-mediated transcriptional signature in Danio rerio. Here, we designed and biochemically validated a computational approach to identify novel p53 target genes in Danio rerio genome. Screening all the Danio rerio genome by pattern-matching-based analysis, we found p53 RE-like patterns proximal to 979 annotated Danio rerio genes. Prioritization analysis identified a subset of 134 candidate pattern-related genes, 31 of which have been investigated in further biochemical assays. Our study identified runx1, axin1, traf4a, hspa8, col4a5, necab2, and dnajc9 genes as novel direct p53 targets and 12 additional p53-controlled genes in Danio rerio genome. The proposed combinatorial approach resulted to be highly sensitive and robust for identifying new p53 target genes also in additional animal species.

  20. Bioinformatics-Based Identification of Candidate Genes from QTLs Associated with Cell Wall Traits in Populus

    SciTech Connect

    Ranjan, Priya; Yin, Tongming; Zhang, Xinye; Kalluri, Udaya C; Yang, Xiaohan; Jawdy, Sara; Tuskan, Gerald A

    2009-11-01

    Quantitative trait locus (QTL) studies are an integral part of plant research and are used to characterize the genetic basis of phenotypic variation observed in structured populations and inform marker-assisted breeding efforts. These QTL intervals can span large physical regions on a chromosome comprising hundreds of genes, thereby hampering candidate gene identification. Genome history, evolution, and expression evidence can be used to narrow the genes in the interval to a smaller list that is manageable for detailed downstream functional genomics characterization. Our primary motivation for the present study was to address the need for a research methodology that identifies candidate genes within a broad QTL interval. Here we present a bioinformatics-based approach for subdividing candidate genes within QTL intervals into alternate groups of high probability candidates. Application of this approach in the context of studying cell wall traits, specifically lignin content and S/G ratios of stem and root in Populus plants, resulted in manageable sets of genes of both known and putative cell wall biosynthetic function. These results provide a roadmap for future experimental work leading to identification of new genes controlling cell wall recalcitrance and, ultimately, in the utility of plant biomass as an energy feedstock.

  1. Ensemble positive unlabeled learning for disease gene identification.

    PubMed

    Yang, Peng; Li, Xiaoli; Chua, Hon-Nian; Kwoh, Chee-Keong; Ng, See-Kiong

    2014-01-01

    An increasing number of genes have been experimentally confirmed in recent years as causative genes to various human diseases. The newly available knowledge can be exploited by machine learning methods to discover additional unknown genes that are likely to be associated with diseases. In particular, positive unlabeled learning (PU learning) methods, which require only a positive training set P (confirmed disease genes) and an unlabeled set U (the unknown candidate genes) instead of a negative training set N, have been shown to be effective in uncovering new disease genes in the current scenario. Using only a single source of data for prediction can be susceptible to bias due to incompleteness and noise in the genomic data and a single machine learning predictor prone to bias caused by inherent limitations of individual methods. In this paper, we propose an effective PU learning framework that integrates multiple biological data sources and an ensemble of powerful machine learning classifiers for disease gene identification. Our proposed method integrates data from multiple biological sources for training PU learning classifiers. A novel ensemble-based PU learning method EPU is then used to integrate multiple PU learning classifiers to achieve accurate and robust disease gene predictions. Our evaluation experiments across six disease groups showed that EPU achieved significantly better results compared with various state-of-the-art prediction methods as well as ensemble learning classifiers. Through integrating multiple biological data sources for training and the outputs of an ensemble of PU learning classifiers for prediction, we are able to minimize the potential bias and errors in individual data sources and machine learning algorithms to achieve more accurate and robust disease gene predictions. In the future, our EPU method provides an effective framework to integrate the additional biological and computational resources for better disease gene predictions.

  2. Ensemble Positive Unlabeled Learning for Disease Gene Identification

    PubMed Central

    Yang, Peng; Li, Xiaoli; Chua, Hon-Nian; Kwoh, Chee-Keong; Ng, See-Kiong

    2014-01-01

    An increasing number of genes have been experimentally confirmed in recent years as causative genes to various human diseases. The newly available knowledge can be exploited by machine learning methods to discover additional unknown genes that are likely to be associated with diseases. In particular, positive unlabeled learning (PU learning) methods, which require only a positive training set P (confirmed disease genes) and an unlabeled set U (the unknown candidate genes) instead of a negative training set N, have been shown to be effective in uncovering new disease genes in the current scenario. Using only a single source of data for prediction can be susceptible to bias due to incompleteness and noise in the genomic data and a single machine learning predictor prone to bias caused by inherent limitations of individual methods. In this paper, we propose an effective PU learning framework that integrates multiple biological data sources and an ensemble of powerful machine learning classifiers for disease gene identification. Our proposed method integrates data from multiple biological sources for training PU learning classifiers. A novel ensemble-based PU learning method EPU is then used to integrate multiple PU learning classifiers to achieve accurate and robust disease gene predictions. Our evaluation experiments across six disease groups showed that EPU achieved significantly better results compared with various state-of-the-art prediction methods as well as ensemble learning classifiers. Through integrating multiple biological data sources for training and the outputs of an ensemble of PU learning classifiers for prediction, we are able to minimize the potential bias and errors in individual data sources and machine learning algorithms to achieve more accurate and robust disease gene predictions. In the future, our EPU method provides an effective framework to integrate the additional biological and computational resources for better disease gene predictions

  3. Dynamic Identification for Control of Large Space Structures

    NASA Technical Reports Server (NTRS)

    Ibrahim, S. R.

    1985-01-01

    This is a compilation of reports by the one author on one subject. It consists of the following five journal articles: (1) A Parametric Study of the Ibrahim Time Domain Modal Identification Algorithm; (2) Large Modal Survey Testing Using the Ibrahim Time Domain Identification Technique; (3) Computation of Normal Modes from Identified Complex Modes; (4) Dynamic Modeling of Structural from Measured Complex Modes; and (5) Time Domain Quasi-Linear Identification of Nonlinear Dynamic Systems.

  4. Model Structure Determination and Identifiability Problems in System Identification.

    DTIC Science & Technology

    System identification has become one of the most active areas in system theory and its applications. In many engineering applications where the...estimation. As the authors extend the concept of system identification to those classes of problems where prior knowledge on structure is limited, some...basic problems other than parameter estimation become important. System identification consists of three basic sub-problems: (1) pre-estimation

  5. Unraveling algal lipid metabolism: Recent advances in gene identification.

    PubMed

    Khozin-Goldberg, Inna; Cohen, Zvi

    2011-01-01

    Microalgae are now the focus of intensive research due to their potential as a renewable feedstock for biodiesel. This research requires a thorough understanding of the biochemistry and genetics of these organisms' lipid-biosynthesis pathways. Genes encoding lipid-biosynthesis enzymes can now be identified in the genomes of various eukaryotic microalgae. However, an examination of the predicted proteins at the biochemical and molecular levels is mandatory to verify their function. The essential molecular and genetic tools are now available for a comprehensive characterization of genes coding for enzymes of the lipid-biosynthesis pathways in some algal species. This review mainly summarizes the novel information emerging from recently obtained algal gene identification.

  6. Identification of large structures on orbit - A survey

    NASA Technical Reports Server (NTRS)

    Denman, Eugene E.; Juang, Jer-Nan; Junkins, John L.; Kamat, Manohar; Hasselman, T. K.

    1988-01-01

    This paper seeks to provide a brief overview of the somewhat unfamiliar concept underlying system identification especially as it applies to large flexible space structures. Having elaborated on the concept, the authors provide a detailed description of the identification process including model development, its experimental validation and final certification. This discussion is followed by a classification of the different identification methods and a brief evaluation of the potential of existing methodology to address special circumstances of large flexible space structures. The paper concludes by making a few recommendations that are deemed necessary to meet the enormous challenges posed by the deployment or erection of large space structures.

  7. Identification of Differentially Expressed Genes Between Osteoblasts and Osteocytes

    PubMed Central

    Paic, Frane; Igwe, John C.; Ravi, Nori; Kronenberg, Mark S.; Franceschetti, Tiziana; Harrington, Patrick; Kuo, Lynn; Shin, Don-Guk; Rowe, David W.; Harris, Stephen E.; Kalajzic, Ivo

    2009-01-01

    Osteocytes represent the most abundant cellular component of mammalian bones with important functions in bone mass maintenance and remodeling. To elucidate the differential gene expression between osteoblasts and osteocytes we completed a comprehensive analysis of their gene profiles. Selective identification of these two mature populations was achieved by utilization of visual markers of bone lineage cells. We have utilized dual GFP reporter mice in which osteocytes are expressing GFP (topaz) directed by the DMP1 promoter, while osteoblasts are identified by expression of GFP (cyan) driven by 2.3kb of the Col1a1 promoter. Histological analysis of 7-day-old neonatal calvaria confirmed the expression pattern of DMP1GFP in osteocytes and Col2.3 in osteoblasts and osteocytes. To isolate distinct populations of cells we utilized fluorescent activated cell sorting (FACS). Cells suspensions were subjected to RNA extraction, in vitro transcription and labeling of cDNA and gene expression was analyzed using the Illumina WG-6v1 BeadChip. Following normalization of raw data from four biological replicates, 3444 genes were called present in all three sorted cell populations: GFP negative, Col2.3cyan+ (osteoblasts), and DMP1topaz+(preosteocytes and osteocytes). We present the genes that showed in excess of a 2-fold change for gene expression between DMP1topaz+ and Col2.3cyan+ cells. The selected genes were classified and grouped according to their associated gene ontology terms. Genes clustered to osteogenesis and skeletal development such as Bmp4, Bmp8a, Dmp1, Enpp1, Phex and Ank were highly expressed in DMP1topaz+cells. Most of the genes encoding extracellular matrix components and secreted proteins had lower expression in DMP1topaz+ cells, while most of the genes encoding plasma membrane proteins were increased. Interestingly a large number of genes associated with muscle development and function and with neuronal phenotype were increased in DMP1topaz+ cells, indicating

  8. Search-based model identification of smart-structure damage

    NASA Technical Reports Server (NTRS)

    Glass, B. J.; Macalou, A.

    1991-01-01

    This paper describes the use of a combined model and parameter identification approach, based on modal analysis and artificial intelligence (AI) techniques, for identifying damage or flaws in a rotating truss structure incorporating embedded piezoceramic sensors. This smart structure example is representative of a class of structures commonly found in aerospace systems and next generation space structures. Artificial intelligence techniques of classification, heuristic search, and an object-oriented knowledge base are used in an AI-based model identification approach. A finite model space is classified into a search tree, over which a variant of best-first search is used to identify the model whose stored response most closely matches that of the input. Newly-encountered models can be incorporated into the model space. This adaptativeness demonstrates the potential for learning control. Following this output-error model identification, numerical parameter identification is used to further refine the identified model. Given the rotating truss example in this paper, noisy data corresponding to various damage configurations are input to both this approach and a conventional parameter identification method. The combination of the AI-based model identification with parameter identification is shown to lead to smaller parameter corrections than required by the use of parameter identification alone.

  9. Genome-wide identification and functional analyses of calmodulin genes in Solanaceous species

    PubMed Central

    2013-01-01

    Background Calmodulin (CaM) is a major calcium sensor in all eukaryotes. It binds calcium and modulates the activity of a wide range of downstream proteins in response to calcium signals. However, little is known about the CaM gene family in Solanaceous species, including the economically important species, tomato (Solanum lycopersicum), and the gene silencing model plant, Nicotiana benthamiana. Moreover, the potential function of CaM in plant disease resistance remains largely unclear. Results We performed genome-wide identification of CaM gene families in Solanaceous species. Employing bioinformatics approaches, multiple full-length CaM genes were identified from tomato, N. benthamiana and potato (S. tuberosum) genomes, with tomato having 6 CaM genes, N. benthamiana having 7 CaM genes, and potato having 4 CaM genes. Sequence comparison analyses showed that three tomato genes, SlCaM3/4/5, two potato genes StCaM2/3, and two sets of N. benthamiana genes, NbCaM1/2/3/4 and NbCaM5/6, encode identical CaM proteins, yet the genes contain different intron/exon organization and are located on different chromosomes. Further sequence comparisons and gene structural and phylogenetic analyses reveal that Solanaceous species gained a new group of CaM genes during evolution. These new CaM genes are unusual in that they contain three introns in contrast to only a single intron typical of known CaM genes in plants. The tomato CaM (SlCaM) genes were found to be expressed in all organs. Prediction of cis-acting elements in 5' upstream sequences and expression analyses demonstrated that SlCaM genes have potential to be highly responsive to a variety of biotic and abiotic stimuli. Additionally, silencing of SlCaM2 and SlCaM6 altered expression of a set of signaling and defense-related genes and resulted in significantly lower resistance to Tobacco rattle virus and the oomycete pathogen, Pythium aphanidermatum. Conclusions The CaM gene families in the Solanaceous species tomato, N

  10. [GSDS: a gene structure display server].

    PubMed

    Guo, An-Yuan; Zhu, Qi-Hui; Chen, Xin; Luo, Jing-Chu

    2007-08-01

    We developed a web server GSDS (Gene Structure Display Server) for drawing gene structure schematic diagrams. Users can submit three types of dataCDS and genomic sequences, NCBI GenBank accession numbers or GIs, exon positions on a gene. GSDS uses this information to obtain the gene structure and draw diagram for it. Users can also designate some special regions to mark on the gene structure diagram. The output result will be PNG or SVG format picture. The corresponding sequence will be shown in a new window by clicking the picture in PNG format. A Chinese version for the main page is also built. The GSDS is available on http://gsds.cbi.pku.edu.cn/.

  11. Identification of Sinorhizobium meliloti early symbiotic genes by use of a positive functional screen.

    PubMed

    Zhang, Xue-Song; Cheng, Hai-Ping

    2006-04-01

    The soil bacterium Sinorhizobium meliloti establishes nitrogen-fixing symbiosis with its leguminous host plant, alfalfa, following a series of continuous signal exchanges. The complexity of the changes of alfalfa root structures during symbiosis and the amount of S. meliloti genes with unknown functions raised the possibility that more S. meliloti genes may be required for early stages of the symbiosis. A positive functional screen of the entire S. meliloti genome for symbiotic genes was carried out using a modified in vivo expression technology. A group of genes and putative genes were found to be expressed in early stages of the symbiosis, and 23 of them were alfalfa root exudate inducible. These 23 genes were further separated into two groups based on their responses to apigenin, a known nodulation (nod) gene inducer. The group of six genes not inducible by apigenin included the lsrA gene, which is essential for the symbiosis, and the dgkA gene, which is involved in the synthesis of cyclic beta-1,2-glucan required for the S. meliloti-alfalfa symbiosis. In the group of 17 apigenin-inducible genes, most have not been previously characterized in S. meliloti, and none of them belongs to the nod gene family. The identification of this large group of alfalfa root exudate-inducible S. meliloti genes suggests that the interactions in the early stages of the S. meliloti and alfalfa symbiosis could be complex and that further characterization of these genes will lead to a better understanding of the symbiosis.

  12. Gene Identification Algorithms Using Exploratory Statistical Analysis of Periodicity

    NASA Astrophysics Data System (ADS)

    Mukherjee, Shashi Bajaj; Sen, Pradip Kumar

    2010-10-01

    Studying periodic pattern is expected as a standard line of attack for recognizing DNA sequence in identification of gene and similar problems. But peculiarly very little significant work is done in this direction. This paper studies statistical properties of DNA sequences of complete genome using a new technique. A DNA sequence is converted to a numeric sequence using various types of mappings and standard Fourier technique is applied to study the periodicity. Distinct statistical behaviour of periodicity parameters is found in coding and non-coding sequences, which can be used to distinguish between these parts. Here DNA sequences of Drosophila melanogaster were analyzed with significant accuracy.

  13. Structural damage identification using mathematical optimization techniques

    NASA Technical Reports Server (NTRS)

    Shen, Mo-How Herman

    1991-01-01

    An identification procedure is proposed to identify damage characteristics (location and size of the damage) from dynamic measurements. This procedure was based on minimization of the mean-square measure of difference between measurement data (natural frequencies and mode shapes) and the corresponding predictions obtained from the computational model. The procedure is tested for simulated damage in the form of stiffness changes in a simple fixed free spring mass system and symmetric cracks in a simply supported Bernoulli Euler beam. It is shown that when all the mode information is used in the identification procedure it is possible to uniquely determine the damage properties. Without knowing the complete set of modal information, a restricted region in the initial data space has been found for realistic and convergent solution from the identification process.

  14. Experimental Verification of Identification Algorithms for Control of Flexible Structures

    NASA Technical Reports Server (NTRS)

    Sridher, B.; Aubrun, J. N.; Lorell, K. R.

    1985-01-01

    An on going simple laboratory experiment, referred to as the Beam Control Experiment (BCE) is described which has the essential features of a large flexible structure. The experiment is used to develop and evaluate identification and control algorithms which lock promising in the active control of high performance large space structures. Some results on the maximum likelihood identification of the parameters of the beam actuator sensor assembly from experimental data is presented.

  15. Identification and study of Utah pseudo-isolate populations-prospects for gene identification.

    PubMed

    Cannon-Albright, L A; Farnham, J M; Thomas, A; Camp, N J

    2005-09-01

    Isolate populations of varied types have proven powerful for gene identification for rare Mendelian disorders, and continue to show such promise for more complex phenotypes. Existing isolate populations are limited in the phenotypes available for study, and new population isolates are unlikely to arise. We utilize genealogical data available for the state of Utah, dating back to its European founders, to retrospectively define and examine pseudo-isolate subpopulations. These pseudo-isolate populations are defined by selection of a set of "founders" from the genealogical data, and then limitation of "immigration" by censoring of matings and offspring that do not match the isolate population design. A wide variety of pseudo isolate and other study designs are possible by varying the number and type of founders and the extent of immigration allowed. We present several different example Birth-Country pseudo-isolate populations defined within the Utah Population Database (UPDB). We utilize linked cancer phenotype data available for the Utah population to show the utility of this pseudo-isolate approach for identification of more genetically homogeneous prostate cancer pedigrees for predisposition gene identification. In conclusion, we present a unique approach to retrospective "creation" of isolate populations using existing genealogical data. We use the UPDB to exhibit the utility of this approach for the highly heterogeneous Utah population, and suggest the approach is feasible for any population for which high quality genealogy and phenotype data are available. (c) 2005 Wiley-Liss, Inc.

  16. Optimal Sensor Locations for Structural Identification

    NASA Technical Reports Server (NTRS)

    Udwadia, F. E.; Garba, J.

    1985-01-01

    The optimum sensor location problem, OSLP, may be thought of in terms of the set of systems, S, the class of input time functions, I, and the identification algorithm (estimator) used, E. Thus, for a given time history of input, the technique of determining the OSL requires, in general, the solution of the optimization and the identification problems simultaneously. A technique which uncouples the two problems is introduced. This is done by means of the concept of an efficient estimator for which the covariance of the parameter estimates is inversely proportional to the Fisher Information Matrix.

  17. Gene function prediction based on the Gene Ontology hierarchical structure.

    PubMed

    Cheng, Liangxi; Lin, Hongfei; Hu, Yuncui; Wang, Jian; Yang, Zhihao

    2014-01-01

    The information of the Gene Ontology annotation is helpful in the explanation of life science phenomena, and can provide great support for the research of the biomedical field. The use of the Gene Ontology is gradually affecting the way people store and understand bioinformatic data. To facilitate the prediction of gene functions with the aid of text mining methods and existing resources, we transform it into a multi-label top-down classification problem and develop a method that uses the hierarchical relationships in the Gene Ontology structure to relieve the quantitative imbalance of positive and negative training samples. Meanwhile the method enhances the discriminating ability of classifiers by retaining and highlighting the key training samples. Additionally, the top-down classifier based on a tree structure takes the relationship of target classes into consideration and thus solves the incompatibility between the classification results and the Gene Ontology structure. Our experiment on the Gene Ontology annotation corpus achieves an F-value performance of 50.7% (precision: 52.7% recall: 48.9%). The experimental results demonstrate that when the size of training set is small, it can be expanded via topological propagation of associated documents between the parent and child nodes in the tree structure. The top-down classification model applies to the set of texts in an ontology structure or with a hierarchical relationship.

  18. Identification of wheat chromosomal regions containing expressed resistance genes.

    PubMed Central

    Dilbirligi, Muharrem; Erayman, Mustafa; Sandhu, Devinder; Sidhu, Deepak; Gill, Kulvinder S

    2004-01-01

    The objectives of this study were to isolate and physically localize expressed resistance (R) genes on wheat chromosomes. Irrespective of the host or pest type, most of the 46 cloned R genes from 12 plant species share a strong sequence similarity, especially for protein domains and motifs. By utilizing this structural similarity to perform modified RNA fingerprinting and data mining, we identified 184 putative expressed R genes of wheat. These include 87 NB/LRR types, 16 receptor-like kinases, and 13 Pto-like kinases. The remaining were seven Hm1 and two Hs1(pro-1) homologs, 17 pathogenicity related, and 42 unique NB/kinases. About 76% of the expressed R-gene candidates were rare transcripts, including 42 novel sequences. Physical mapping of 121 candidate R-gene sequences using 339 deletion lines localized 310 loci to 26 chromosomal regions encompassing approximately 16% of the wheat genome. Five major R-gene clusters that spanned only approximately 3% of the wheat genome but contained approximately 47% of the candidate R genes were observed. Comparative mapping localized 91% (82 of 90) of the phenotypically characterized R genes to 18 regions where 118 of the R-gene sequences mapped. PMID:15020436

  19. Identification of candidate genes in osteoporosis by integrated microarray analysis

    PubMed Central

    Li, J. J.; Wang, B. Q.; Yang, Y.; Li, D.

    2016-01-01

    bone formation. Cite this article: J. J. Li, B. Q. Wang, Q. Fei, Y. Yang, D. Li. Identification of candidate genes in osteoporosis by integrated microarray analysis. Bone Joint Res 2016;5:594–601. DOI: 10.1302/2046-3758.512.BJR-2016-0073.R1. PMID:27908864

  20. Identification of Nitrogen-Fixing Genes and Gene Clusters from Metagenomic Library of Acid Mine Drainage

    PubMed Central

    Yin, Huaqun; Liang, Yili; Cong, Jing; Liu, Xueduan

    2014-01-01

    Biological nitrogen fixation is an essential function of acid mine drainage (AMD) microbial communities. However, most acidophiles in AMD environments are uncultured microorganisms and little is known about the diversity of nitrogen-fixing genes and structure of nif gene cluster in AMD microbial communities. In this study, we used metagenomic sequencing to isolate nif genes in the AMD microbial community from Dexing Copper Mine, China. Meanwhile, a metagenome microarray containing 7,776 large-insertion fosmids was constructed to screen novel nif gene clusters. Metagenomic analyses revealed that 742 sequences were identified as nif genes including structural subunit genes nifH, nifD, nifK and various additional genes. The AMD community is massively dominated by the genus Acidithiobacillus. However, the phylogenetic diversity of nitrogen-fixing microorganisms is much higher than previously thought in the AMD community. Furthermore, a 32.5-kb genomic sequence harboring nif, fix and associated genes was screened by metagenome microarray. Comparative genome analysis indicated that most nif genes in this cluster are most similar to those of Herbaspirillum seropedicae, but the organization of the nif gene cluster had significant differences from H. seropedicae. Sequence analysis and reverse transcription PCR also suggested that distinct transcription units of nif genes exist in this gene cluster. nifQ gene falls into the same transcription unit with fixABCX genes, which have not been reported in other diazotrophs before. All of these results indicated that more novel diazotrophs survive in the AMD community. PMID:24498417

  1. Identification of nitrogen-fixing genes and gene clusters from metagenomic library of acid mine drainage.

    PubMed

    Dai, Zhimin; Guo, Xue; Yin, Huaqun; Liang, Yili; Cong, Jing; Liu, Xueduan

    2014-01-01

    Biological nitrogen fixation is an essential function of acid mine drainage (AMD) microbial communities. However, most acidophiles in AMD environments are uncultured microorganisms and little is known about the diversity of nitrogen-fixing genes and structure of nif gene cluster in AMD microbial communities. In this study, we used metagenomic sequencing to isolate nif genes in the AMD microbial community from Dexing Copper Mine, China. Meanwhile, a metagenome microarray containing 7,776 large-insertion fosmids was constructed to screen novel nif gene clusters. Metagenomic analyses revealed that 742 sequences were identified as nif genes including structural subunit genes nifH, nifD, nifK and various additional genes. The AMD community is massively dominated by the genus Acidithiobacillus. However, the phylogenetic diversity of nitrogen-fixing microorganisms is much higher than previously thought in the AMD community. Furthermore, a 32.5-kb genomic sequence harboring nif, fix and associated genes was screened by metagenome microarray. Comparative genome analysis indicated that most nif genes in this cluster are most similar to those of Herbaspirillum seropedicae, but the organization of the nif gene cluster had significant differences from H. seropedicae. Sequence analysis and reverse transcription PCR also suggested that distinct transcription units of nif genes exist in this gene cluster. nifQ gene falls into the same transcription unit with fixABCX genes, which have not been reported in other diazotrophs before. All of these results indicated that more novel diazotrophs survive in the AMD community.

  2. Identification of Epigenetically Altered Genes in Sporadic Amyotrophic Lateral Sclerosis

    PubMed Central

    Bender, Diane E.; Delaney, Colin E.; Cataldo, Michael D.; Smith, Andrea L.; Yung, Raymond; Ruden, Douglas M.; Callaghan, Brian C.; Feldman, Eva L.

    2012-01-01

    Amyotrophic lateral sclerosis (ALS) is a terminal disease involving the progressive degeneration of motor neurons within the motor cortex, brainstem and spinal cord. Most cases are sporadic (sALS) with unknown causes suggesting that the etiology of sALS may not be limited to the genotype of patients, but may be influenced by exposure to environmental factors. Alterations in epigenetic modifications are likely to play a role in disease onset and progression in ALS, as aberrant epigenetic patterns may be acquired throughout life. The aim of this study was to identify epigenetic marks associated with sALS. We hypothesize that epigenetic modifications may alter the expression of pathogenesis-related genes leading to the onset and progression of sALS. Using ELISA assays, we observed alterations in global methylation (5 mC) and hydroxymethylation (5 HmC) in postmortem sALS spinal cord but not in whole blood. Loci-specific differentially methylated and expressed genes in sALS spinal cord were identified by genome-wide 5mC and expression profiling using high-throughput microarrays. Concordant direction, hyper- or hypo-5mC with parallel changes in gene expression (under- or over-expression), was observed in 112 genes highly associated with biological functions related to immune and inflammation response. Furthermore, literature-based analysis identified potential associations among the epigenes. Integration of methylomics and transcriptomics data successfully revealed methylation changes in sALS spinal cord. This study represents an initial identification of epigenetic regulatory mechanisms in sALS which may improve our understanding of sALS pathogenesis for the identification of biomarkers and new therapeutic targets. PMID:23300739

  3. Genome-wide analysis of homeobox gene family in legumes: identification, gene duplication and expression profiling.

    PubMed

    Bhattacharjee, Annapurna; Ghangal, Rajesh; Garg, Rohini; Jain, Mukesh

    2015-01-01

    Homeobox genes encode transcription factors that are known to play a major role in different aspects of plant growth and development. In the present study, we identified homeobox genes belonging to 14 different classes in five legume species, including chickpea, soybean, Medicago, Lotus and pigeonpea. The characteristic differences within homeodomain sequences among various classes of homeobox gene family were quite evident. Genome-wide expression analysis using publicly available datasets (RNA-seq and microarray) indicated that homeobox genes are differentially expressed in various tissues/developmental stages and under stress conditions in different legumes. We validated the differential expression of selected chickpea homeobox genes via quantitative reverse transcription polymerase chain reaction. Genome duplication analysis in soybean indicated that segmental duplication has significantly contributed in the expansion of homeobox gene family. The Ka/Ks ratio of duplicated homeobox genes in soybean showed that several members of this family have undergone purifying selection. Moreover, expression profiling indicated that duplicated genes might have been retained due to sub-functionalization. The genome-wide identification and comprehensive gene expression profiling of homeobox gene family members in legumes will provide opportunities for functional analysis to unravel their exact role in plant growth and development.

  4. Genome-Wide Analysis of Homeobox Gene Family in Legumes: Identification, Gene Duplication and Expression Profiling

    PubMed Central

    Garg, Rohini; Jain, Mukesh

    2015-01-01

    Homeobox genes encode transcription factors that are known to play a major role in different aspects of plant growth and development. In the present study, we identified homeobox genes belonging to 14 different classes in five legume species, including chickpea, soybean, Medicago, Lotus and pigeonpea. The characteristic differences within homeodomain sequences among various classes of homeobox gene family were quite evident. Genome-wide expression analysis using publicly available datasets (RNA-seq and microarray) indicated that homeobox genes are differentially expressed in various tissues/developmental stages and under stress conditions in different legumes. We validated the differential expression of selected chickpea homeobox genes via quantitative reverse transcription polymerase chain reaction. Genome duplication analysis in soybean indicated that segmental duplication has significantly contributed in the expansion of homeobox gene family. The Ka/Ks ratio of duplicated homeobox genes in soybean showed that several members of this family have undergone purifying selection. Moreover, expression profiling indicated that duplicated genes might have been retained due to sub-functionalization. The genome-wide identification and comprehensive gene expression profiling of homeobox gene family members in legumes will provide opportunities for functional analysis to unravel their exact role in plant growth and development. PMID:25745864

  5. Identification of Drosophila Mitotic Genes by Combining Co-Expression Analysis and RNA Interference

    PubMed Central

    Somma, Maria Patrizia; Ceprani, Francesca; Bucciarelli, Elisabetta; Naim, Valeria; De Arcangelis, Valeria; Piergentili, Roberto; Palena, Antonella; Ciapponi, Laura; Giansanti, Maria Grazia; Pellacani, Claudia; Petrucci, Romano; Cenci, Giovanni; Vernì, Fiammetta; Fasulo, Barbara; Goldberg, Michael L.; Di Cunto, Ferdinando; Gatti, Maurizio

    2008-01-01

    RNAi screens have, to date, identified many genes required for mitotic divisions of Drosophila tissue culture cells. However, the inventory of such genes remains incomplete. We have combined the powers of bioinformatics and RNAi technology to detect novel mitotic genes. We found that Drosophila genes involved in mitosis tend to be transcriptionally co-expressed. We thus constructed a co-expression–based list of 1,000 genes that are highly enriched in mitotic functions, and we performed RNAi for each of these genes. By limiting the number of genes to be examined, we were able to perform a very detailed phenotypic analysis of RNAi cells. We examined dsRNA-treated cells for possible abnormalities in both chromosome structure and spindle organization. This analysis allowed the identification of 142 mitotic genes, which were subdivided into 18 phenoclusters. Seventy of these genes have not previously been associated with mitotic defects; 30 of them are required for spindle assembly and/or chromosome segregation, and 40 are required to prevent spontaneous chromosome breakage. We note that the latter type of genes has never been detected in previous RNAi screens in any system. Finally, we found that RNAi against genes encoding kinetochore components or highly conserved splicing factors results in identical defects in chromosome segregation, highlighting an unanticipated role of splicing factors in centromere function. These findings indicate that our co-expression–based method for the detection of mitotic functions works remarkably well. We can foresee that elaboration of co-expression lists using genes in the same phenocluster will provide many candidate genes for small-scale RNAi screens aimed at completing the inventory of mitotic proteins. PMID:18797514

  6. Ivory identification by DNA profiling of cytochrome b gene.

    PubMed

    Lee, James Chun-I; Hsieh, Hsing-Mei; Huang, Li-Hung; Kuo, Yi-Chen; Wu, Jane-Hong; Chin, Shih-Chien; Lee, An-Hsing; Linacre, Adrian; Tsai, Li-Chin

    2009-03-01

    Ivory can be visually identified in its native form as coming from an elephant species; however, determining from which of the three extant elephant species a section of ivory originates is more problematic. We report on a method that will identify and distinguish the protected and endangered elephant species, Elephas maximus or Loxodonta sp. To identify the species of elephant from ivory products, we developed three groups of nested PCR amplifications within the cytochrome b gene that generate amplification products using highly degraded DNA isolated from confiscated ivory samples dating from 1995. DNA from a total of 382 out of 453 ivory samples were successfully isolated and amplified leading to species identification. All sequences were searched against GenBank and found to match with E. maximus and Loxodonta sp. with at least 99% similarity. The samples that were tested came from eight Asian elephants, 14 African forest elephants (Loxodonta cyclotis), and 360 African savannah elephants (Loxodonta africana). This study demonstrates a high success rate in species identification of ivory by a nested PCR approach within the cytochrome b gene which provides the necessary information for the protection of endangered species conservation.

  7. Engineering of glucosinolate biosynthesis: candidate gene identification and validation.

    PubMed

    Møldrup, Morten E; Salomonsen, Bo; Halkier, Barbara A

    2012-01-01

    The diverse biological roles of glucosinolates as plant defense metabolites and anticancer compounds have spurred a strong interest in their biosynthetic pathways. Since the completion of the Arabidopsis genome, functional genomics approaches have enabled significant progress on the elucidation of glucosinolate biosynthesis, although in planta validation of candidate gene function often is hampered by time-consuming generation of knockout and overexpression lines in Arabidopsis. To better exploit the increasing amount of data available from genomic sequencing, microarray database and RNAseq, time-efficient methods for identification and validation of candidate genes are needed. This chapter covers the methodology we are using for gene discovery in glucosinolate engineering, namely, guilt-by-association-based in silico methods and fast proof-of-function screens by transient expression in Nicotiana benthamiana. Moreover, the lessons learned in the rapid, transient tobacco system are readily translated to our robust, versatile yeast expression platform, where additional genes critical for large-scale microbial production of glucosinolates can be identified. We anticipate that the methodology presented here will be beneficial to elucidate and engineer other plant biosynthetic pathways.

  8. Identification and characterization of essential genes in the human genome

    PubMed Central

    Wang, Tim; Birsoy, Kıvanç; Hughes, Nicholas W.; Krupczak, Kevin M.; Post, Yorick; Wei, Jenny J.; Lander, Eric S.; Sabatini, David M.

    2015-01-01

    Large-scale genetic analysis of lethal phenotypes has elucidated the molecular underpinnings of many biological processes. Using the bacterial clustered regularly interspaced short palindromic repeats (CRISPR) system, we constructed a genome-wide single-guide RNA (sgRNA) library to screen for genes required for proliferation and survival in a human cancer cell line. Our screen revealed the set of cell-essential genes, which was validated by an orthogonal gene-trap-based screen and comparison with yeast gene knockouts. This set is enriched for genes that encode components of fundamental pathways, are expressed at high levels, and contain few inactivating polymorphisms in the human population. We also uncovered a large group of uncharacterized genes involved in RNA processing, a number of whose products localize to the nucleolus. Lastly, screens in additional cell lines showed a high degree of overlap in gene essentiality, but also revealed differences specific to each cell line and cancer type that reflect the developmental origin, oncogenic drivers, paralogous gene expression pattern, and chromosomal structure of each line. These results demonstrate the power of CRISPR-based screens and suggest a general strategy for identifying liabilities in cancer cells. PMID:26472758

  9. Identification of susceptibility genes and genetic modifiers of human diseases

    NASA Astrophysics Data System (ADS)

    Abel, Kenneth; Kammerer, Stefan; Hoyal, Carolyn; Reneland, Rikard; Marnellos, George; Nelson, Matthew R.; Braun, Andreas

    2005-03-01

    The completion of the human genome sequence enables the discovery of genes involved in common human disorders. The successful identification of these genes is dependent on the availability of informative sample sets, validated marker panels, a high-throughput scoring technology, and a strategy for combining these resources. We have developed a universal platform technology based on mass spectrometry (MassARRAY) for analyzing nucleic acids with high precision and accuracy. To fuel this technology, we generated more than 100,000 validated assays for single nucleotide polymorphisms (SNPs) covering virtually all known and predicted human genes. We also established a large DNA sample bank comprised of more than 50,000 consented healthy and diseased individuals. This combination of reagents and technology allows the execution of large-scale genome-wide association studies. Taking advantage of MassARRAY"s capability for quantitative analysis of nucleic acids, allele frequencies are estimated in sample pools containing large numbers of individual DNAs. To compare pools as a first-pass "filtering" step is a tremendous advantage in throughput and cost over individual genotyping. We employed this approach in numerous genome-wide, hypothesis-free searches to identify genes associated with common complex diseases, such as breast cancer, osteoporosis, and osteoarthritis, and genes involved in quantitative traits like high density lipoproteins cholesterol (HDL-c) levels and central fat. Access to additional well-characterized patient samples through collaborations allows us to conduct replication studies that validate true disease genes. These discoveries will expand our understanding of genetic disease predisposition, and our ability for early diagnosis and determination of specific disease subtype or progression stage.

  10. Exon structure of the human dystrophin gene

    SciTech Connect

    Roberts, R.G.; Coffey, A.J.; Bobrow, M.; Bentley, D.R.

    1993-05-01

    Application of a novel vectorette PCR approach to defining intron-exon boundaries has permitted completion of analysis of the exon structure of the largest and most complex known human gene. The authors present here a summary of the exon structure of the entire human dystrophin gene, together with the sizes of genomic HindIII fragments recognized by each exon, and (where available) GenBank accession numbers for adjacent intron sequences. 20 refs., 1 tab.

  11. An effective data mining approach for structure damage identification

    NASA Astrophysics Data System (ADS)

    Hong, Soonyoung

    An efficient, neural network based, online nondestructive structural damage identification procedure is developed for determining the damage characteristics (the damage locations and the corresponding severity) from dynamic measurements in near real-time. The procedure utilizes unique data processing techniques to track the most useful modal information based on modal strain energy and to calculate the associated data based on principal component analysis for further processing in a neural network based identification scheme. With two unique features, this approach is significantly different from currently available damage identification procedures for real-time structural integrity monitoring/diagnostics. First, the most sensitive mode for the specific damage is selected in an automatic process which increases the accuracy of damage identification and decreases time spent on neural network training. Second, the approach creates unique data that extracts core characteristics from modal information for a number of different damage cases; and consequently, the accuracy of the damage identification improves significantly. This approach can be operated online providing real time structural damage identification. The method is tested for simulated damage cases, including situations of single and multiple damage in the closely-spaced frequencies of Kabe's model. The philosophy behind the proposed research is to provide a means to online and nondestructively predict the degradation of a structure's integrity (i.e. damage location and the corresponding severity, strength loss).

  12. Identification of human HK genes and gene expression regulation study in cancer from transcriptomics data analysis.

    PubMed

    Chen, Meili; Xiao, Jingfa; Zhang, Zhang; Liu, Jingxing; Wu, Jiayan; Yu, Jun

    2013-01-01

    The regulation of gene expression is essential for eukaryotes, as it drives the processes of cellular differentiation and morphogenesis, leading to the creation of different cell types in multicellular organisms. RNA-Sequencing (RNA-Seq) provides researchers with a powerful toolbox for characterization and quantification of transcriptome. Many different human tissue/cell transcriptome datasets coming from RNA-Seq technology are available on public data resource. The fundamental issue here is how to develop an effective analysis method to estimate expression pattern similarities between different tumor tissues and their corresponding normal tissues. We define the gene expression pattern from three directions: 1) expression breadth, which reflects gene expression on/off status, and mainly concerns ubiquitously expressed genes; 2) low/high or constant/variable expression genes, based on gene expression level and variation; and 3) the regulation of gene expression at the gene structure level. The cluster analysis indicates that gene expression pattern is higher related to physiological condition rather than tissue spatial distance. Two sets of human housekeeping (HK) genes are defined according to cell/tissue types, respectively. To characterize the gene expression pattern in gene expression level and variation, we firstly apply improved K-means algorithm and a gene expression variance model. We find that cancer-associated HK genes (a HK gene is specific in cancer group, while not in normal group) are expressed higher and more variable in cancer condition than in normal condition. Cancer-associated HK genes prefer to AT-rich genes, and they are enriched in cell cycle regulation related functions and constitute some cancer signatures. The expression of large genes is also avoided in cancer group. These studies will help us understand which cell type-specific patterns of gene expression differ among different cell types, and particularly for cancer.

  13. Identification of Human HK Genes and Gene Expression Regulation Study in Cancer from Transcriptomics Data Analysis

    PubMed Central

    Zhang, Zhang; Liu, Jingxing; Wu, Jiayan; Yu, Jun

    2013-01-01

    The regulation of gene expression is essential for eukaryotes, as it drives the processes of cellular differentiation and morphogenesis, leading to the creation of different cell types in multicellular organisms. RNA-Sequencing (RNA-Seq) provides researchers with a powerful toolbox for characterization and quantification of transcriptome. Many different human tissue/cell transcriptome datasets coming from RNA-Seq technology are available on public data resource. The fundamental issue here is how to develop an effective analysis method to estimate expression pattern similarities between different tumor tissues and their corresponding normal tissues. We define the gene expression pattern from three directions: 1) expression breadth, which reflects gene expression on/off status, and mainly concerns ubiquitously expressed genes; 2) low/high or constant/variable expression genes, based on gene expression level and variation; and 3) the regulation of gene expression at the gene structure level. The cluster analysis indicates that gene expression pattern is higher related to physiological condition rather than tissue spatial distance. Two sets of human housekeeping (HK) genes are defined according to cell/tissue types, respectively. To characterize the gene expression pattern in gene expression level and variation, we firstly apply improved K-means algorithm and a gene expression variance model. We find that cancer-associated HK genes (a HK gene is specific in cancer group, while not in normal group) are expressed higher and more variable in cancer condition than in normal condition. Cancer-associated HK genes prefer to AT-rich genes, and they are enriched in cell cycle regulation related functions and constitute some cancer signatures. The expression of large genes is also avoided in cancer group. These studies will help us understand which cell type-specific patterns of gene expression differ among different cell types, and particularly for cancer. PMID:23382867

  14. Genomic platform for efficient identification of fungal secondary metabolism genes

    USDA-ARS?s Scientific Manuscript database

    Fungal secondary metabolites (SMs) are structurally diverse natural compounds, which are thought to have great potential not only for medical industry but also for chemical and environmental industries. Since expansion of sequencing microbial genomes in 1990’s, it has been known that SM genes are ex...

  15. Structure-Based Subspace Method for Multichannel Blind System Identification

    NASA Astrophysics Data System (ADS)

    Mayyala, Qadri; Abed-Meraim, Karim; Zerguine, Azzedine

    2017-08-01

    In this work, a novel subspace-based method for blind identification of multichannel finite impulse response (FIR) systems is presented. Here, we exploit directly the impeded Toeplitz channel structure in the signal linear model to build a quadratic form whose minimization leads to the desired channel estimation up to a scalar factor. This method can be extended to estimate any predefined linear structure, e.g. Hankel, that is usually encountered in linear systems. Simulation findings are provided to highlight the appealing advantages of the new structure-based subspace (SSS) method over the standard subspace (SS) method in certain adverse identification scenarii.

  16. Identification of Methylmercury Tolerance Gene Candidates in Drosophila

    PubMed Central

    Mahapatra, Cecon T.; Bond, Jeffrey; Rand, David M.; Rand, Matthew D.

    2010-01-01

    Methylmercury (MeHg) is a ubiquitous environmental contaminant that preferentially targets the developing nervous system. Variable outcomes of prenatal MeHg exposure within a population point to a genetic component that regulates MeHg toxicity. We therefore sought to identify fundamental MeHg tolerance genes using the Drosophila model for genetic and molecular dissection of a MeHg tolerance trait. We observe autosomal dominance in a MeHg tolerance trait (development on MeHg food) in both wild-derived and laboratory-selected MeHg-tolerant strains of flies. We performed whole-genome transcript profiling of larval brains of tolerant (laboratory selected) and nontolerant (control) strains in the presence and absence of MeHg stress. Pairwise transcriptome comparisons of four conditions (+/−selection and +/−MeHg) identified a “down-down-up” expression signature, whereby MeHg alone and selection alone resulted in a greater number of downregulated transcripts, and the combination of selection + MeHg resulted in a greater number of upregulated transcripts. Functional annotation cluster analyses showed enrichment for monooxygenases/oxidoreductases, which include cytochrome P450 (CYP) family members. Among the 10 CYPs upregulated with selection + MeHg in tolerant strains, CYP6g1, previously identified as the dichlorodiphenyl trichloroethane resistance allele in flies, was the most highly expressed and responsive to MeHg. Among all the genes, Turandot A (TotA), an immune pathway–regulated humoral response gene, showed the greatest upregulation with selection + MeHg. Neural-specific transgenic overexpression of TotA enhanced MeHg tolerance during pupal development. Identification of TotA and CYP genes as MeHg tolerance genes is an inroad to investigating the conserved function of immune signaling and phase I metabolism pathways in MeHg toxicity and tolerance in higher organisms. PMID:20375079

  17. Identification of methylmercury tolerance gene candidates in Drosophila.

    PubMed

    Mahapatra, Cecon T; Bond, Jeffrey; Rand, David M; Rand, Matthew D

    2010-07-01

    Methylmercury (MeHg) is a ubiquitous environmental contaminant that preferentially targets the developing nervous system. Variable outcomes of prenatal MeHg exposure within a population point to a genetic component that regulates MeHg toxicity. We therefore sought to identify fundamental MeHg tolerance genes using the Drosophila model for genetic and molecular dissection of a MeHg tolerance trait. We observe autosomal dominance in a MeHg tolerance trait (development on MeHg food) in both wild-derived and laboratory-selected MeHg-tolerant strains of flies. We performed whole-genome transcript profiling of larval brains of tolerant (laboratory selected) and nontolerant (control) strains in the presence and absence of MeHg stress. Pairwise transcriptome comparisons of four conditions (+/-selection and +/-MeHg) identified a "down-down-up" expression signature, whereby MeHg alone and selection alone resulted in a greater number of downregulated transcripts, and the combination of selection + MeHg resulted in a greater number of upregulated transcripts. Functional annotation cluster analyses showed enrichment for monooxygenases/oxidoreductases, which include cytochrome P450 (CYP) family members. Among the 10 CYPs upregulated with selection + MeHg in tolerant strains, CYP6g1, previously identified as the dichlorodiphenyl trichloroethane resistance allele in flies, was the most highly expressed and responsive to MeHg. Among all the genes, Turandot A (TotA), an immune pathway-regulated humoral response gene, showed the greatest upregulation with selection + MeHg. Neural-specific transgenic overexpression of TotA enhanced MeHg tolerance during pupal development. Identification of TotA and CYP genes as MeHg tolerance genes is an inroad to investigating the conserved function of immune signaling and phase I metabolism pathways in MeHg toxicity and tolerance in higher organisms.

  18. Human gene correlation analysis (HGCA): a tool for the identification of transcriptionally co-expressed genes.

    PubMed

    Michalopoulos, Ioannis; Pavlopoulos, Georgios A; Malatras, Apostolos; Karelas, Alexandros; Kostadima, Myrto-Areti; Schneider, Reinhard; Kossida, Sophia

    2012-06-06

    Bioinformatics and high-throughput technologies such as microarray studies allow the measure of the expression levels of large numbers of genes simultaneously, thus helping us to understand the molecular mechanisms of various biological processes in a cell. We calculate the Pearson Correlation Coefficient (r-value) between probe set signal values from Affymetrix Human Genome Microarray samples and cluster the human genes according to the r-value correlation matrix using the Neighbour Joining (NJ) clustering method. A hyper-geometric distribution is applied on the text annotations of the probe sets to quantify the term overrepresentations. The aim of the tool is the identification of closely correlated genes for a given gene of interest and/or the prediction of its biological function, which is based on the annotations of the respective gene cluster. Human Gene Correlation Analysis (HGCA) is a tool to classify human genes according to their coexpression levels and to identify overrepresented annotation terms in correlated gene groups. It is available at: http://biobank-informatics.bioacademy.gr/coexpression/.

  19. Gene structure prediction by linguistic methods

    SciTech Connect

    Dong, S.; Searls, D.B.

    1994-10-01

    The higher-order structure of genes and other features of biological sequences can be described by means of formal grammars. These grammars can then be used by general-purpose parsers to detect and to assemble such structures by means of syntactic pattern recognition. We describe a grammar and parser for eukaryotic protein-encoding genes, which by some measures is as effective as current connectionist and combinatorial algorithms in predicting gene structures for sequence database entries. Parameters of the grammar rules are optimized for several different species, and mixing experiments are performed to determine the degree of species specificity and the relative importance of compositional, signal-based, and syntactic components in gene prediction. 24 refs., 5 figs., 3 tabs.

  20. Built structure identification in wildland fire decision support

    Treesearch

    David E. Calkin; Jon D. Rieck; Kevin D. Hyde; Jeffrey D. Kaiden

    2011-01-01

    Recent ex-urban development within the wildland interface has significantly increased the complexity and associated cost of federal wildland fire management in the United States. Rapid identification of built structures relative to probable fire spread can help to reduce that complexity and improve the performance of incident management teams. Approximate structure...

  1. Novel gene complex structure determination

    SciTech Connect

    Gatewood, J.M.

    1997-08-01

    This is the final report of a one-year, Laboratory-Directed Research and Development (LORD) project at the Los Alamos National Laboratory. `Operative` chromatin containing exclusively the minor hasten variants was successfully isolated. Linker hasten H1 is quantitatively missing from operative chromatin. One of the aims of this proposal was to determine the proteins responsible for stabilizing operative chromatin. This chromatin is stabilized by microtubule proteins tar and tubulin. Another goal of this project was the structural characterization of operate chromatin nucleosomes. Using solution scattering, nucleosomes containing the minor variants were shown to be structurally distinct from major variant containing nucleosomes. The unusual structure and stabilization of operative chromatin by microtubule proteins provides a possible mechanism for direct interaction of transcription machinery with specific chromatin domains.

  2. Identification of novel hereditary cancer genes by whole exome sequencing.

    PubMed

    Sokolenko, Anna P; Suspitsin, Evgeny N; Kuligina, Ekatherina Sh; Bizin, Ilya V; Frishman, Dmitrij; Imyanitov, Evgeny N

    2015-12-28

    Whole exome sequencing (WES) provides a powerful tool for medical genetic research. Several dozens of WES studies involving patients with hereditary cancer syndromes have already been reported. WES led to breakthrough in understanding of the genetic basis of some exceptionally rare syndromes; for example, identification of germ-line SMARCA4 mutations in patients with ovarian hypercalcemic small cell carcinomas indeed explains a noticeable share of familial aggregation of this disease. However, studies on common cancer types turned out to be more difficult. In particular, there is almost a dozen of reports describing WES analysis of breast cancer patients, but none of them yet succeeded to reveal a gene responsible for the significant share of missing heritability. Virtually all components of WES studies require substantial improvement, e.g. technical performance of WES, interpretation of WES results, mode of patient selection, etc. Most of contemporary investigations focus on genes with autosomal dominant mechanism of inheritance; however, recessive and oligogenic models of transmission of cancer susceptibility also need to be considered. It is expected that the list of medically relevant tumor-predisposing genes will be rapidly expanding in the next few years.

  3. Identification of quorum sensing-controlled genes in Burkholderia ambifaria.

    PubMed

    Chapalain, Annelise; Vial, Ludovic; Laprade, Natacha; Dekimpe, Valérie; Perreault, Jonathan; Déziel, Eric

    2013-04-01

    The Burkholderia cepacia complex (Bcc) comprises strains with a virulence potential toward immunocompromised patients as well as plant growth-promoting rhizobacteria (PGPR). Owing to the link between quorum sensing (QS) and virulence, most studies among Bcc species have been directed toward QS of pathogenic bacteria. We have investigated the QS of B. ambifaria, a PGPR only infrequently recovered from patients. The cepI gene, responsible for the synthesis of the main signaling molecule N-octanoylhomoserine lactone (C8 -HSL), was inactivated. Phenotypes of the B. ambifaria cepI mutant we observed, such as increased production of siderophores and decreased proteolytic and antifungal activities, are in agreement with those of other Bcc cepI mutants. The cepI mutant was then used as background strain for a whole-genome transposon-insertion mutagenesis strategy, allowing the identification of 20 QS-controlled genes, corresponding to 17 loci. The main functions identified are linked to antifungal and antimicrobial properties, as we have identified QS-controlled genes implicated in the production of pyrrolnitrin, burkholdines (occidiofungin-like molecules), and enacyloxins. This study provides insights in the QS-regulated functions of a PGPR, which could lead to beneficial potential biotechnological applications. © 2013 The Authors. Published by Blackwell Publishing Ltd.

  4. Identification of quorum sensing-controlled genes in Burkholderia ambifaria

    PubMed Central

    Chapalain, Annelise; Vial, Ludovic; Laprade, Natacha; Dekimpe, Valérie; Perreault, Jonathan; Déziel, Eric

    2013-01-01

    The Burkholderia cepacia complex (Bcc) comprises strains with a virulence potential toward immunocompromised patients as well as plant growth–promoting rhizobacteria (PGPR). Owing to the link between quorum sensing (QS) and virulence, most studies among Bcc species have been directed toward QS of pathogenic bacteria. We have investigated the QS of B. ambifaria, a PGPR only infrequently recovered from patients. The cepI gene, responsible for the synthesis of the main signaling molecule N-octanoylhomoserine lactone (C8-HSL), was inactivated. Phenotypes of the B. ambifaria cepI mutant we observed, such as increased production of siderophores and decreased proteolytic and antifungal activities, are in agreement with those of other Bcc cepI mutants. The cepI mutant was then used as background strain for a whole-genome transposon-insertion mutagenesis strategy, allowing the identification of 20 QS-controlled genes, corresponding to 17 loci. The main functions identified are linked to antifungal and antimicrobial properties, as we have identified QS-controlled genes implicated in the production of pyrrolnitrin, burkholdines (occidiofungin-like molecules), and enacyloxins. This study provides insights in the QS-regulated functions of a PGPR, which could lead to beneficial potential biotechnological applications. PMID:23382083

  5. Improved Stochastic Subspace System Identification for Structural Health Monitoring

    NASA Astrophysics Data System (ADS)

    Chang, Chia-Ming; Loh, Chin-Hsiung

    2015-07-01

    Structural health monitoring acquires structural information through numerous sensor measurements. Vibrational measurement data render the dynamic characteristics of structures to be extracted, in particular of the modal properties such as natural frequencies, damping, and mode shapes. The stochastic subspace system identification has been recognized as a power tool which can present a structure in the modal coordinates. To obtain qualitative identified data, this tool needs to spend computational expense on a large set of measurements. In study, a stochastic system identification framework is proposed to improve the efficiency and quality of the conventional stochastic subspace system identification. This framework includes 1) measured signal processing, 2) efficient space projection, 3) system order selection, and 4) modal property derivation. The measured signal processing employs the singular spectrum analysis algorithm to lower the noise components as well as to present a data set in a reduced dimension. The subspace is subsequently derived from the data set presented in a delayed coordinate. With the proposed order selection criteria, the number of structural modes is determined, resulting in the modal properties. This system identification framework is applied to a real-world bridge for exploring the feasibility in real-time applications. The results show that this improved system identification method significantly decreases computational time, while qualitative modal parameters are still attained.

  6. Human glucose phosphate isomerase: Exon mapping and gene structure

    SciTech Connect

    Xu, Weiming; Lee, Pauline; Beutler, E.

    1995-10-10

    The structure of the gene for human glucose phosphate isomerase (GPI) has been determined. Three GPI clones were isolated from a human genomic library by using a full-length GPI cDNA probe and were characterized. Oligonucleotides based on the known cDNA sequence were used as primers in amplification and sequence analyses. This led to the identification of the exon-intron junctions. By this approach, 18 exons and 17 introns have been identified. The exons range in size from 44 to 431 nucleotides. The intronic sequences surrounding the exons provide useful information for the identification of mutations that give rise to human GPI deficiency associated with chronic hemolytic anemia. 13 refs., 4 figs., 1 tab.

  7. Phylogeny and identification of Pantoea species and typing of Pantoea agglomerans strains by multilocus gene sequencing.

    PubMed

    Delétoile, Alexis; Decré, Dominique; Courant, Stéphanie; Passet, Virginie; Audo, Jennifer; Grimont, Patrick; Arlet, Guillaume; Brisse, Sylvain

    2009-02-01

    Pantoea agglomerans and other Pantoea species cause infections in humans and are also pathogenic to plants, but the diversity of Pantoea strains and their possible association with hosts and disease remain poorly known, and identification of Pantoea species is difficult. We characterized 36 Pantoea strains, including 28 strains of diverse origins initially identified as P. agglomerans, by multilocus gene sequencing based on six protein-coding genes, by biochemical tests, and by antimicrobial susceptibility testing. Phylogenetic analysis and comparison with other species of Enterobacteriaceae revealed that the genus Pantoea is highly diverse. Most strains initially identified as P. agglomerans by use of API 20E strips belonged to a compact sequence cluster together with the type strain, but other strains belonged to diverse phylogenetic branches corresponding to other species of Pantoea or Enterobacteriaceae and to probable novel species. Biochemical characteristics such as fosfomycin resistance and utilization of d-tartrate could differentiate P. agglomerans from other Pantoea species. All 20 strains of P. agglomerans could be distinguished by multilocus sequence typing, revealing the very high discrimination power of this method for strain typing and population structure in this species, which is subdivided into two phylogenetic groups. PCR detection of the repA gene, associated with pathogenicity in plants, was positive in all clinical strains of P. agglomerans, suggesting that clinical and plant-associated strains do not form distinct populations. We provide a multilocus gene sequencing method that is a powerful tool for Pantoea species delineation and identification and for strain tracking.

  8. Identification of flowering genes in strawberry, a perennial SD plant

    PubMed Central

    Mouhu, Katriina; Hytönen, Timo; Folta, Kevin; Rantanen, Marja; Paulin, Lars; Auvinen, Petri; Elomaa, Paula

    2009-01-01

    strawberry. However, novel regulatory mechanisms exist, like SFL that functions as a switch between short-day/low temperature and long-day/high temperature flowering responses between the short-day genotype and the everbearing 'Baron Solemacher'. The identification of putative flowering gene homologs and AP1 as potential marker gene for floral initiation will strongly facilitate the exploration of strawberry flowering pathways. PMID:19785732

  9. The use of gene interaction networks to improve the identification of cancer driver genes.

    PubMed

    Ramsahai, Emilie; Walkins, Kheston; Tripathi, Vrijesh; John, Melford

    2017-01-01

    Bioinformaticians have implemented different strategies to distinguish cancer driver genes from passenger genes. One of the more recent advances uses a pathway-oriented approach. Methods that employ this strategy are highly dependent on the quality and size of the pathway interaction network employed, and require a powerful statistical environment for analyses. A number of genomic libraries are available in R. DriverNet and DawnRank employ pathway-based methods that use gene interaction graphs in matrix form. We investigated the benefit of combining data from 3 different sources on the prediction outcome of cancer driver genes by DriverNet and DawnRank. An enriched dataset was derived comprising 13,862 genes with 372,250 interactions, which increased its accuracy by 17% and 28%, respectively, compared to their original networks. The study identified 33 new candidate driver genes. Our study highlights the potential of combining networks and weighting edges to provide greater accuracy in the identification of cancer driver genes.

  10. The use of gene interaction networks to improve the identification of cancer driver genes

    PubMed Central

    Walkins, Kheston; Tripathi, Vrijesh; John, Melford

    2017-01-01

    Bioinformaticians have implemented different strategies to distinguish cancer driver genes from passenger genes. One of the more recent advances uses a pathway-oriented approach. Methods that employ this strategy are highly dependent on the quality and size of the pathway interaction network employed, and require a powerful statistical environment for analyses. A number of genomic libraries are available in R. DriverNet and DawnRank employ pathway-based methods that use gene interaction graphs in matrix form. We investigated the benefit of combining data from 3 different sources on the prediction outcome of cancer driver genes by DriverNet and DawnRank. An enriched dataset was derived comprising 13,862 genes with 372,250 interactions, which increased its accuracy by 17% and 28%, respectively, compared to their original networks. The study identified 33 new candidate driver genes. Our study highlights the potential of combining networks and weighting edges to provide greater accuracy in the identification of cancer driver genes. PMID:28149674

  11. Loop substructure identification for shear structures of unknown structural mass using synthesized references

    NASA Astrophysics Data System (ADS)

    Zhang, Dongyu; Li, Hui

    2017-08-01

    Shear structure is widely adopted to model the dynamics for building structures. Thus, developing accurate and efficient parameter identification methods for a shear structure plays a crucial role in structural health monitoring for building structures. In the authors’ previous studies, a loop substructure identification (LSI) method was proposed for shear structures, in which the dynamic equation of a two-story substructure is utilized to establish a loop identification sequence, directly estimating the substructure’s parameters. To ensure the convergence of the loop identification sequence, some structural control (SC) systems are needed to change the critical structural responses in a favorable way. However, the limited availability of SC systems in general buildings restrains the wide application of this controlled loop substructure identification (CLSI) method. In this paper, the original LSI method is first reformed, which can perform the LSI even if the structural mass is unknown. Then, a new reference selection method is proposed to make the LSI method converge without the help of SC systems. Different synthesized reference responses, formed by a weighted linear combination of measured structural responses, are used to formulate the LSI sequence. Next, an optimization strategy is proposed to determine the optimal weighting factors of the synthesized reference responses, which makes the LSI converged. Finally, the LSI is carried out for a 20-story shear structure, the identification results of which show that the proposed LSI method, combined with the proposed reference selection method, can very accurately estimate the substructure parameters of the shear structure.

  12. Gene3D: Structural Assignment for Whole Genes and Genomes Using the CATH Domain Structure Database

    PubMed Central

    Buchan, Daniel W.A.; Shepherd, Adrian J.; Lee, David; Pearl, Frances M.G.; Rison, Stuart C.G.; Thornton, Janet M.; Orengo, Christine A.

    2002-01-01

    We present a novel web-based resource, Gene3D, of precalculated structural assignments to gene sequences and whole genomes. This resource assigns structural domains from the CATH database to whole genes and links these to their curated functional and structural annotations within the CATH domain structure database, the functional Dictionary of Homologous Superfamilies (DHS) and PDBsum. Currently Gene3D provides annotation for 36 complete genomes (two eukaryotes, six archaea, and 28 bacteria). On average, between 30% and 40% of the genes of a given genome can be structurally annotated. Matches to structural domains are found using the profile-based method (PSI-BLAST). and a novel protocol, DRange, is used to resolve conflicts in matches involving different homologous superfamilies. PMID:11875040

  13. Chicken rRNA Gene Cluster Structure.

    PubMed

    Dyomin, Alexander G; Koshel, Elena I; Kiselev, Artem M; Saifitdinova, Alsu F; Galkina, Svetlana A; Fukagawa, Tatsuo; Kostareva, Anna A; Gaginskaya, Elena R

    2016-01-01

    Ribosomal RNA (rRNA) genes, whose activity results in nucleolus formation, constitute an extremely important part of genome. Despite the extensive exploration into avian genomes, no complete description of avian rRNA gene primary structure has been offered so far. We publish a complete chicken rRNA gene cluster sequence here, including 5'ETS (1836 bp), 18S rRNA gene (1823 bp), ITS1 (2530 bp), 5.8S rRNA gene (157 bp), ITS2 (733 bp), 28S rRNA gene (4441 bp) and 3'ETS (343 bp). The rRNA gene cluster sequence of 11863 bp was assembled from raw reads and deposited to GenBank under KT445934 accession number. The assembly was validated through in situ fluorescent hybridization analysis on chicken metaphase chromosomes using computed and synthesized specific probes, as well as through the reference assembly against de novo assembled rRNA gene cluster sequence using sequenced fragments of BAC-clone containing chicken NOR (nucleolus organizer region). The results have confirmed the chicken rRNA gene cluster validity.

  14. Chicken rRNA Gene Cluster Structure

    PubMed Central

    Dyomin, Alexander G.; Koshel, Elena I.; Kiselev, Artem M.; Saifitdinova, Alsu F.; Galkina, Svetlana A.; Fukagawa, Tatsuo; Kostareva, Anna A.

    2016-01-01

    Ribosomal RNA (rRNA) genes, whose activity results in nucleolus formation, constitute an extremely important part of genome. Despite the extensive exploration into avian genomes, no complete description of avian rRNA gene primary structure has been offered so far. We publish a complete chicken rRNA gene cluster sequence here, including 5’ETS (1836 bp), 18S rRNA gene (1823 bp), ITS1 (2530 bp), 5.8S rRNA gene (157 bp), ITS2 (733 bp), 28S rRNA gene (4441 bp) and 3’ETS (343 bp). The rRNA gene cluster sequence of 11863 bp was assembled from raw reads and deposited to GenBank under KT445934 accession number. The assembly was validated through in situ fluorescent hybridization analysis on chicken metaphase chromosomes using computed and synthesized specific probes, as well as through the reference assembly against de novo assembled rRNA gene cluster sequence using sequenced fragments of BAC-clone containing chicken NOR (nucleolus organizer region). The results have confirmed the chicken rRNA gene cluster validity. PMID:27299357

  15. A Model-Based Joint Identification of Differentially Expressed Genes and Phenotype-Associated Genes

    PubMed Central

    Seo, Minseok; Shin, Su-kyung; Kwon, Eun-Young; Kim, Sung-Eun; Bae, Yun-Jung; Lee, Seungyeoun; Sung, Mi-Kyung; Choi, Myung-Sook; Park, Taesung

    2016-01-01

    Over the last decade, many analytical methods and tools have been developed for microarray data. The detection of differentially expressed genes (DEGs) among different treatment groups is often a primary purpose of microarray data analysis. In addition, association studies investigating the relationship between genes and a phenotype of interest such as survival time are also popular in microarray data analysis. Phenotype association analysis provides a list of phenotype-associated genes (PAGs). However, it is sometimes necessary to identify genes that are both DEGs and PAGs. We consider the joint identification of DEGs and PAGs in microarray data analyses. The first approach we used was a naïve approach that detects DEGs and PAGs separately and then identifies the genes in an intersection of the list of PAGs and DEGs. The second approach we considered was a hierarchical approach that detects DEGs first and then chooses PAGs from among the DEGs or vice versa. In this study, we propose a new model-based approach for the joint identification of DEGs and PAGs. Unlike the previous two-step approaches, the proposed method identifies genes simultaneously that are DEGs and PAGs. This method uses standard regression models but adopts different null hypothesis from ordinary regression models, which allows us to perform joint identification in one-step. The proposed model-based methods were evaluated using experimental data and simulation studies. The proposed methods were used to analyze a microarray experiment in which the main interest lies in detecting genes that are both DEGs and PAGs, where DEGs are identified between two diet groups and PAGs are associated with four phenotypes reflecting the expression of leptin, adiponectin, insulin-like growth factor 1, and insulin. Model-based approaches provided a larger number of genes, which are both DEGs and PAGs, than other methods. Simulation studies showed that they have more power than other methods. Through analysis of

  16. Spacecraft structural system identification by modal test

    NASA Technical Reports Server (NTRS)

    Chen, J.-C.; Peretti, L. F.; Garba, J. A.

    1984-01-01

    A structural parameter estimation procedure using the measured natural frequencies and kinetic energy distribution as observers is proposed. The theoretical derivation of the estimation procedure is described and its constraints and limitations are explained. This procedure is applied to a large complex spacecraft structural system to identify the inertia matrix using modal test results. The inertia matrix is chosen after the stiffness matrix has been updated by the static test results.

  17. Cytochrome b gene for species identification of the conservation animals.

    PubMed

    Hsieh, H M; Chiang, H L; Tsai, L C; Lai, S Y; Huang, N E; Linacre, A; Lee, J C

    2001-10-15

    A partial DNA sequence of cytochrome b gene was used to identify the remains of endangered animals and species endemic to Taiwan. The conservation of animals species included in this study were: the formosan gem-faced civets, leopard cats, tigers, clouded leopards, lion, formosan muntjacs, formosan sika deers, formosan sambars, formosan serows, water buffalo, formosan pangolins and formosan macaques. The control species used included domestic cats, domestic dogs, domestic sheeps, domestic cattles, domestic pigs and humans. Heteroplasmy was detected in the formosan macaque, domestic pig and domestic cats. The frequencies of heteroplasmy in these animals were about 0.25% (1 in 402bp). Sequences were aligned by Pileup program of GCG computer package, and the phylogenetic tree was constructed by the neighbor-joining method. The results of sequence comparison showed that the percentage range of sequence diversity in the same species was from 0.25 to 2.74%, and that between the different species was from 5.97 to 34.83%. The results of phylogenetic analysis showed that the genetic distance between the different species was from 6.33 to 40.59. Animals of the same species, both the endangered animal species and domestic animals, were clustered together in the neighbor-joining tree. Three unknown samples of animal remains were identified by this system. The partial sequence of cytochrome b gene adopted in this study proved to be usable for animal identification.

  18. Recursive stochastic subspace identification for structural parameter estimation

    NASA Astrophysics Data System (ADS)

    Chang, C. C.; Li, Z.

    2009-03-01

    Identification of structural parameters under ambient condition is an important research topic for structural health monitoring and damage identification. This problem is especially challenging in practice as these structural parameters could vary with time under severe excitation. Among the techniques developed for this problem, the stochastic subspace identification (SSI) is a popular time-domain method. The SSI can perform parametric identification for systems with multiple outputs which cannot be easily done using other time-domain methods. The SSI uses the orthogonal-triangular decomposition (RQ) and the singular value decomposition (SVD) to process measured data, which makes the algorithm efficient and reliable. The SSI however processes data in one batch hence cannot be used in an on-line fashion. In this paper, a recursive SSI method is proposed for on-line tracking of time-varying modal parameters for a structure under ambient excitation. The Givens rotation technique, which can annihilate the designated matrix elements, is used to update the RQ decomposition. Instead of updating the SVD, the projection approximation subspace tracking technique which uses an unconstrained optimization technique to track the signal subspace is employed. The proposed technique is demonstrated on the Phase I ASCE benchmark structure. Results show that the technique can identify and track the time-varying modal properties of the building under ambient condition.

  19. Towards the identification of (a) gene(s) for autosomal dominant medullary cystic kidney disease.

    PubMed

    Scolari, Francesco; Viola, Battista Fabio; Ghiggeri, Gian Marco; Caridi, Gianluca; Amoroso, Antonio; Rampoldi, Luca; Casari, Giorgio

    2003-01-01

    Medullary cystic kidney disease (MCKD) belongs with nephronophthisis (NPH) in a group of inherited tubulo-interstitial nephritis, which has been referred to as the NPH-MCKD complex. Although MCKD and NPH share morphological features, they differ in several respects. The most common variant is recessive juvenile NPH, with onset in childhood and leading to end-stage renal disease (ESRD) within the 2nd decade of life; the most frequent extrarenal involvement is tapeto-retinal degeneration. MCKD is a dominant condition recognized in later life and leading to ESRD at the age of 50 years; hyperuricemia and gout can be associated features. The first sign of MCKD is polyuria; later, the clinical findings relate to renal insufficiency. Originally, NPH and MCKD were considered separate entities. Subsequently, it has been suggested that the two diseases were a single disorder due to the clinico-pathological identity. This unifying conception was later refuted due to the identification of MCKD dominant families. Recently, considerable insight has been gained into the genetics of the NPH-MCKD complex. The majority of juvenile NPH cases are due to deletion of the NPHP1 gene on chromosome 2q13. Genes for infantile and adolescent NPH have been localized respectively to chromosome 9q22-q31 and 3q22. A new locus, NPHP4, has been recently identified on chromosome 1p36. Two genes predisposing to dominant MCKD, MCKD1 and MCKD2, have been localized to chromosome 1q21 and 16p12. Independent confirmation of the locations of MCKD1 and MCKD2 in other MCKD families, with or without hyperuricemia and gout, has been reported. The gene for familial juvenile hyperuricemic nephropathy (FJHN), a phenotype that is very similar to MCKD, was recently mapped to 16p12, in a region overlapping with the MCKD2 locus, raising the question as to whether MCKD2 and FJHN are allelic variants of the same disease entity. The ultimate proof of the allelism between MCKD2 and FJHN will be provided by the

  20. Seismic characteristics and identification of negative flower structures, positive flower structures, and positive structural inversion

    SciTech Connect

    Harding, T.P.

    1985-04-01

    Negative and positive flower structures and positive inverted structures imply specific modes of formation, and their distinctive characteristics make them important criteria for the identification of certain structural styles. A negative flower structure from the Andaman Sea consists of a shallow synform bounded by upward-spreading strands of a wrench fault that have mostly normal separations. Paralleling monoclines and oblique, en echelon normal faults flank the divergent wrench fault. A positive flower structure from the Ardmore basin, Oklahoma, consists of a shallow antiform displaced by the upward diverging strands of a wrench fault that have mostly reverse separations. En echelon folds are present on either side of this convergent wrench fault. Positive structural inversion at the Rambutan oil field, South Sumatra basin, has formed a shallow anticlinorium and has partly uplifted the underlying graben. Deeper fault segments bounding the graben have retained their normal fault profiles, but at shallow levels some of these faults have reverse separations.

  1. Experimental identification of smart material coupling effects in composite structures

    NASA Astrophysics Data System (ADS)

    Chesne, S.; Jean-Mistral, C.; Gaudiller, L.

    2013-07-01

    Smart composite structures have an enormous potential for industrial applications, in terms of mass reduction, high material resistance and flexibility. The correct characterization of these complex structures is essential for active vibration control or structural health monitoring applications. The identification process generally calls for the determination of a generalized electromechanical coupling coefficient. As this process can in practice be difficult to implement, an original approach, presented in this paper, has been developed for the identification of the coupling effects of a smart material used in a composite curved beam. The accuracy of the proposed identification technique is tested by applying active modal control to the beam, using a reduced model based on this identification. The studied structure was as close to reality as possible, and made use of integrated transducers, low-cost sensors, clamped boundary conditions and substantial, complex excitation sources. PVDF (polyvinylidene fluoride) and MFC (macrofiber composite) transducers were integrated into the composite structure, to ensure their protection from environmental damage. The experimental identification described here was based on a curve fitting approach combined with the reduced model. It allowed a reliable, powerful modal control system to be built, controlling two modes of the structure. A linear quadratic Gaussian algorithm was used to determine the modal controller-observer gains. The selected modes were found to have an attenuation as strong as -13 dB in experiments, revealing the effectiveness of this method. In this study a generalized approach is proposed, which can be extended to most complex or composite industrial structures when they are subjected to vibration.

  2. Statistical Approaches for Gene Selection, Hub Gene Identification and Module Interaction in Gene Co-Expression Network Analysis: An Application to Aluminum Stress in Soybean (Glycine max L.)

    PubMed Central

    Das, Samarendra; Meher, Prabina Kumar; Bhar, Lal Mohan; Mandal, Baidya Nath

    2017-01-01

    Selection of informative genes is an important problem in gene expression studies. The small sample size and the large number of genes in gene expression data make the selection process complex. Further, the selected informative genes may act as a vital input for gene co-expression network analysis. Moreover, the identification of hub genes and module interactions in gene co-expression networks is yet to be fully explored. This paper presents a statistically sound gene selection technique based on support vector machine algorithm for selecting informative genes from high dimensional gene expression data. Also, an attempt has been made to develop a statistical approach for identification of hub genes in the gene co-expression network. Besides, a differential hub gene analysis approach has also been developed to group the identified hub genes into various groups based on their gene connectivity in a case vs. control study. Based on this proposed approach, an R package, i.e., dhga (https://cran.r-project.org/web/packages/dhga) has been developed. The comparative performance of the proposed gene selection technique as well as hub gene identification approach was evaluated on three different crop microarray datasets. The proposed gene selection technique outperformed most of the existing techniques for selecting robust set of informative genes. Based on the proposed hub gene identification approach, a few number of hub genes were identified as compared to the existing approach, which is in accordance with the principle of scale free property of real networks. In this study, some key genes along with their Arabidopsis orthologs has been reported, which can be used for Aluminum toxic stress response engineering in soybean. The functional analysis of various selected key genes revealed the underlying molecular mechanisms of Aluminum toxic stress response in soybean. PMID:28056073

  3. Statistical Approaches for Gene Selection, Hub Gene Identification and Module Interaction in Gene Co-Expression Network Analysis: An Application to Aluminum Stress in Soybean (Glycine max L.).

    PubMed

    Das, Samarendra; Meher, Prabina Kumar; Rai, Anil; Bhar, Lal Mohan; Mandal, Baidya Nath

    2017-01-01

    Selection of informative genes is an important problem in gene expression studies. The small sample size and the large number of genes in gene expression data make the selection process complex. Further, the selected informative genes may act as a vital input for gene co-expression network analysis. Moreover, the identification of hub genes and module interactions in gene co-expression networks is yet to be fully explored. This paper presents a statistically sound gene selection technique based on support vector machine algorithm for selecting informative genes from high dimensional gene expression data. Also, an attempt has been made to develop a statistical approach for identification of hub genes in the gene co-expression network. Besides, a differential hub gene analysis approach has also been developed to group the identified hub genes into various groups based on their gene connectivity in a case vs. control study. Based on this proposed approach, an R package, i.e., dhga (https://cran.r-project.org/web/packages/dhga) has been developed. The comparative performance of the proposed gene selection technique as well as hub gene identification approach was evaluated on three different crop microarray datasets. The proposed gene selection technique outperformed most of the existing techniques for selecting robust set of informative genes. Based on the proposed hub gene identification approach, a few number of hub genes were identified as compared to the existing approach, which is in accordance with the principle of scale free property of real networks. In this study, some key genes along with their Arabidopsis orthologs has been reported, which can be used for Aluminum toxic stress response engineering in soybean. The functional analysis of various selected key genes revealed the underlying molecular mechanisms of Aluminum toxic stress response in soybean.

  4. CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation.

    PubMed

    Nikulova, Anna A; Favorov, Alexander V; Sutormin, Roman A; Makeev, Vsevolod J; Mironov, Andrey A

    2012-07-01

    Identification of transcriptional regulatory regions and tracing their internal organization are important for understanding the eukaryotic cell machinery. Cis-regulatory modules (CRMs) of higher eukaryotes are believed to possess a regulatory 'grammar', or preferred arrangement of binding sites, that is crucial for proper regulation and thus tends to be evolutionarily conserved. Here, we present a method CORECLUST (COnservative REgulatory CLUster STructure) that predicts CRMs based on a set of positional weight matrices. Given regulatory regions of orthologous and/or co-regulated genes, CORECLUST constructs a CRM model by revealing the conserved rules that describe the relative location of binding sites. The constructed model may be consequently used for the genome-wide prediction of similar CRMs, and thus detection of co-regulated genes, and for the investigation of the regulatory grammar of the system. Compared with related methods, CORECLUST shows better performance at identification of CRMs conferring muscle-specific gene expression in vertebrates and early-developmental CRMs in Drosophila.

  5. Genome-wide identification and characterization of Glyceraldehyde-3-phosphate dehydrogenase genes family in wheat (Triticum aestivum).

    PubMed

    Zeng, Lingfeng; Deng, Rong; Guo, Ziping; Yang, Shushen; Deng, Xiping

    2016-03-16

    Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a central enzyme in glycolysi, we performed genome-wide identification of GAPDH genes in wheat and analyzed their structural characteristics and expression patterns under abiotic stress in wheat. A total of 22 GAPDH genes were identified in wheat cv. Chinese spring; the phylogenetic and structure analysis showed that these GAPDH genes could be divided into four distinct subfamilies. The expression profiles of GAPDH genes showed tissue specificity all over plant development stages. The qRT-PCR results revealed that wheat GAPDHs were involved in several abiotic stress response. Wheat carried 22 GAPDH genes, representing four types of plant GAPDHs (gapA/B, gapC, gapCp and gapN). Whole genome duplication and segmental duplication might account for the expansion of wheat GAPDHs. Expression analysis implied that GAPDHs play roles in plants abiotic stress tolerance.

  6. Structure, expression and functions of MTA genes.

    PubMed

    Kumar, Rakesh; Wang, Rui-An

    2016-05-15

    Metastatic associated proteins (MTA) are integrators of upstream regulatory signals with the ability to act as master coregulators for modifying gene transcriptional activity. The MTA family includes three genes and multiple alternatively spliced variants. The MTA proteins neither have their own enzymatic activity nor have been shown to directly interact with DNA. However, MTA proteins interact with a variety of chromatin remodeling factors and complexes with enzymatic activities for modulating the plasticity of nucleosomes, leading to the repression or derepression of target genes or other extra-nuclear and nucleosome remodeling and histone deacetylase (NuRD)-complex independent activities. The functions of MTA family members are driven by the steady state levels and subcellular localization of MTA proteins, the dynamic nature of modifying signals and enzymes, the structural features and post-translational modification of protein domains, interactions with binding proteins, and the nature of the engaged and resulting features of nucleosomes in the proximity of target genes. In general, MTA1 and MTA2 are the most upregulated genes in human cancer and correlate well with aggressive phenotypes, therapeutic resistance, poor prognosis and ultimately, unfavorable survival of cancer patients. Here we will discuss the structure, expression and functions of the MTA family of genes in the context of cancer cells.

  7. Identification and control of structures in space

    NASA Technical Reports Server (NTRS)

    Meirovitch, L.; Quinn, R. D.; Norris, M. A.

    1984-01-01

    The derivation of the equations of motion for the Spacecraft Control Laboratory Experiment (SCOLE) is reported and the equations of motion of a similar structure orbiting the earth are also derived. The structure is assumed to undergo large rigid-body maneuvers and small elastic deformations. A perturbation approach is proposed whereby the quantities defining the rigid-body maneuver are assumed to be relatively large, with the elastic deformations and deviations from the rigid-body maneuver being relatively small. The perturbation equations have the form of linear equations with time-dependent coefficients. An active control technique can then be formulated to permit maneuvering of the spacecraft and simultaneously suppressing the elastic vibration.

  8. Identification of large space structures on orbit : A survey

    NASA Technical Reports Server (NTRS)

    Denman, Eugene E.; Hasselman, T. K.; Juang, Jer-Nan; Junkins, John L.; Kamat, Manohar; Sun, C. T.; Udwadia, Firdaus; Venkayya, V. R.; Kippel, Edward; Dale, Eric

    1988-01-01

    The Task Committee on Methods for Identification of Large Structures in Space was founded in Jul. 1984. The charter of the committee was to prepare a state-of-the-art report on methods of system identification applicable to large space structures (LSS). Funding to support preparation of the report was received in Aug. 1985 from the Air Force Rocket Propulsion Laboratory (now the Air Force Astronautics Laboratory), in the form of a contract to the ASCE. The report was completed, and published by AFRPL in Sep. 1986. The Task Committee consisted of ten members, including ASCE and AFRPL representatives. The membership represented Government, Industry, and Universities, and consisted of electrical, mechanical, and civil engineers, with backgrounds in Structural Dynamics, Optimization, and Controls. An effort was made to use consistent terminology and notation throughout the report which would be compatible with the terminology used in both the structures and controls communities.

  9. Optimal Control and Identification of Space Structures.

    DTIC Science & Technology

    1987-12-21

    primary application to large flexible space structures. The research has developed both mathematical theory and numerical methods for design of control laws ...90089 ,J., ()This research was supported in part by the Air Force Office of Scientific Research under contract No. AFOSR-84-0309. (**)This research was...supported in part by the Air Force Office of Scientific Research under contract No. AFOSR-84-0393. (’[Part of this research was carried out while the

  10. Identification and control of structures in space

    NASA Technical Reports Server (NTRS)

    Meirovitch, L.

    1985-01-01

    Work during the period January 1 to June 30, 1985 has concentrated on the completion of the derivation of the equations of motion for the Spacecraft Control Laboratory Experiment (SCOLE) as well on the development of a control scheme for the maneuvering of the spacecraft. The report consists of a paper presented at the Fifth Symposium on Dynamics and Control of Large Structures, June 12 to 14, 1985 at Blacksburg, VA.

  11. Identification and analysis of the metacaspase gene family in tomato.

    PubMed

    Liu, Hui; Liu, Jian; Wei, Yongxuan

    2016-10-21

    Metacaspases play critical roles in developmentally regulated and environmentally induced programmed cell death in plants. In this study, we systematically identified and analyzed metacaspase gene family in tomato (Solanum lycopersicum). The results illustrated that tomato possesses eight metacaspase genes (SlMC1-8) located on chromosomes 1, 3, 5, 9, and 10. SlMC1-6 belonged to type I metacaspases and had 5 exon/4 intron structures. SlMC7 and 8 were type II metacaspases and had 2 and 3 exons, respectively. Expression analysis revealed distinct expression patterns of SlMCs in various tomato tissues. Cis-regulatory element prediction showed that there were many hormone- and stress-related cis-regulatory elements in SlMCs promoter regions. Quantitative real-time PCR analysis further demonstrated that most of the SlMCs were regulated by drought, cold, salt, methyl viologen, and ethephon treatments. This study provides insights into the characteristics of SlMC genes and laid the foundation for further functional analysis of these genes in tomato.

  12. [Structure and expression of thyroglobulin gene].

    PubMed

    Vassart, G; Brocas, H; Christophe, D; de Martynoff, G; Leriche, A; Mercken, L; Pohl, V; Van Heuverswyn, B

    1982-01-01

    Thyroglobulin is composed of two 300000 dalton polypeptide chains, translated from an 8000 base mRNA. Preparation of a full length cDNA and its cloning in E. coli have lead to the demonstration that the polypeptides of thyroglobulin protomers were identical. Used as molecular probes, the cloned cDNA allowed the isolation of a fragment of thyroglobulin gene. Electron microscopic studies have demonstrated that this gene contains more than 90% intronic material separating small size exons (less than 200 bp). Sequencing of bovine thyroglobulin structural gene is in progress. Preliminary results show evidence for the existence of repetitive segments. Availability of cloned DNA complementary to bovine and human thyroglobulin mRNA allows the study of genetic defects of thyroglobulin gene expression in the human and in various animal models.

  13. Recent literature on structural modeling, identification, and analysis

    NASA Technical Reports Server (NTRS)

    Craig, Roy R., Jr.

    1990-01-01

    The literature on the mathematical modeling of large space structures is first reviewed, with attention given to continuum models, model order reduction, substructuring, and computational techniques. System identification and mode verification are then discussed with reference to the verification of mathematical models of large space structures. In connection with analysis, the paper surveys recent research on eigensolvers and dynamic response solvers for large-order finite-element-based models.

  14. Structure and regulation of the envoplakin gene.

    PubMed

    Määttä, A; Ruhrberg, C; Watt, F M

    2000-06-30

    Envoplakin, a member of the plakin family of proteins, is a component of desmosomes and the epidermal cornified envelope. To understand how envoplakin expression is regulated, we have analyzed the structure of the mouse envoplakin gene and characterized the promoters of both the human and mouse genes. The mouse gene consists of 22 exons and maps to chromosome 11E1, syntenic to the location of the human gene on 17q25. The exon-intron structure of the mouse envoplakin gene is common to all members of the plakin family: the N-terminal protein domain is encoded by 21 small exons, and the central rod domain and the C-terminal globular domain are coded by a single large exon. The C terminus shows the highest sequence conservation between mouse and human envoplakins and between envoplakin and the other family members. The N terminus is also conserved, with sequence homology extending to Drosophila Kakapo. A region between nucleotides -101 and 288 was necessary for promoter activity in transiently transfected primary keratinocytes. This region is highly conserved between the human and mouse genes and contains at least two different positively acting elements identified by site-directed mutagenesis and electrophoretic mobility shift assays. Mutation of a GC box binding Sp1 and Sp3 proteins or a combined E box and Krüppel-like element interacting with unidentified nuclear proteins virtually abolished promoter activity. 600 base pairs of the mouse upstream sequence was sufficient to drive expression of a beta-galactosidase reporter gene in the suprabasal layers of epidermis, esophagus, and forestomach of transgenic mice. Thus, we have identified a regulatory region in the envoplakin gene that can account for the expression pattern of the endogenous protein in stratified squamous epithelia.

  15. Marfan syndrome gene search intensifies following identification of basic defect

    SciTech Connect

    Randall, T.

    1990-10-03

    Somewhere, quite possible along chromosomes 8 and/or 15, the gene(s) for Marfan syndrome will be found. The search is intensifying following a report that faulty scaffolding in the body's connective tissue appears to be the long sought after defect behind the syndrome, and inherited disorder that has caused the premature death of young, healthy-looking individuals. Finding that something in the living masonry of the human body has proven to be a 30-year inquisition of nearly two dozen molecules that has engaged investigators worldwide. Historically, researchers have searched for a structural flaw in one of the collagen molecules to explain the cause of Marfan Syndrome. Using monoclonal antibodies, researchers have implicated microfibrils, the extracellular filaments that provide a matrix for the deposit of elastin during embryonic development.

  16. Genome-Wide Identification and Expression Analysis of WRKY Gene Family in Capsicum annuum L.

    PubMed

    Diao, Wei-Ping; Snyder, John C; Wang, Shu-Bin; Liu, Jin-Bing; Pan, Bao-Gui; Guo, Guang-Jun; Wei, Ge

    2016-01-01

    The WRKY family of transcription factors is one of the most important families of plant transcriptional regulators with members regulating multiple biological processes, especially in regulating defense against biotic and abiotic stresses. However, little information is available about WRKYs in pepper (Capsicum annuum L.). The recent release of completely assembled genome sequences of pepper allowed us to perform a genome-wide investigation for pepper WRKY proteins. In the present study, a total of 71 WRKY genes were identified in the pepper genome. According to structural features of their encoded proteins, the pepper WRKY genes (CaWRKY) were classified into three main groups, with the second group further divided into five subgroups. Genome mapping analysis revealed that CaWRKY were enriched on four chromosomes, especially on chromosome 1, and 15.5% of the family members were tandemly duplicated genes. A phylogenetic tree was constructed depending on WRKY domain' sequences derived from pepper and Arabidopsis. The expression of 21 selected CaWRKY genes in response to seven different biotic and abiotic stresses (salt, heat shock, drought, Phytophtora capsici, SA, MeJA, and ABA) was evaluated by quantitative RT-PCR; Some CaWRKYs were highly expressed and up-regulated by stress treatment. Our results will provide a platform for functional identification and molecular breeding studies of WRKY genes in pepper.

  17. Genome-Wide Identification and Expression Analysis of WRKY Gene Family in Capsicum annuum L.

    PubMed Central

    Diao, Wei-Ping; Snyder, John C.; Wang, Shu-Bin; Liu, Jin-Bing; Pan, Bao-Gui; Guo, Guang-Jun; Wei, Ge

    2016-01-01

    The WRKY family of transcription factors is one of the most important families of plant transcriptional regulators with members regulating multiple biological processes, especially in regulating defense against biotic and abiotic stresses. However, little information is available about WRKYs in pepper (Capsicum annuum L.). The recent release of completely assembled genome sequences of pepper allowed us to perform a genome-wide investigation for pepper WRKY proteins. In the present study, a total of 71 WRKY genes were identified in the pepper genome. According to structural features of their encoded proteins, the pepper WRKY genes (CaWRKY) were classified into three main groups, with the second group further divided into five subgroups. Genome mapping analysis revealed that CaWRKY were enriched on four chromosomes, especially on chromosome 1, and 15.5% of the family members were tandemly duplicated genes. A phylogenetic tree was constructed depending on WRKY domain' sequences derived from pepper and Arabidopsis. The expression of 21 selected CaWRKY genes in response to seven different biotic and abiotic stresses (salt, heat shock, drought, Phytophtora capsici, SA, MeJA, and ABA) was evaluated by quantitative RT-PCR; Some CaWRKYs were highly expressed and up-regulated by stress treatment. Our results will provide a platform for functional identification and molecular breeding studies of WRKY genes in pepper. PMID:26941768

  18. Identification of the Pr1 Gene Product Completes the Anthocyanin Biosynthesis Pathway of Maize

    PubMed Central

    Sharma, Mandeep; Cortes-Cruz, Moises; Ahern, Kevin R.; McMullen, Michael; Brutnell, Thomas P.; Chopra, Surinder

    2011-01-01

    In maize, mutations in the pr1 locus lead to the accumulation of pelargonidin (red) rather than cyanidin (purple) pigments in aleurone cells where the anthocyanin biosynthetic pathway is active. We characterized pr1 mutation and isolated a putative F3′H encoding gene (Zmf3′h1) and showed by segregation analysis that the red kernel phenotype is linked to this gene. Genetic mapping using SNP markers confirms its position on chromosome 5L. Furthermore, genetic complementation experiments using a CaMV 35S::ZmF3′H1 promoter–gene construct established that the encoded protein product was sufficient to perform a 3′-hydroxylation reaction. The Zmf3′h1-specific transcripts were detected in floral and vegetative tissues of Pr1 plants and were absent in pr1. Four pr1 alleles were characterized: two carry a 24 TA dinucleotide repeat insertion in the 5′-upstream promoter region, a third has a 17-bp deletion near the TATA box, and a fourth contains a Ds insertion in exon1. Genetic and transcription assays demonstrated that the pr1 gene is under the regulatory control of anthocyanin transcription factors red1 and colorless1. The cloning and characterization of pr1 completes the molecular identification of all genes encoding structural enzymes of the anthocyanin pathway of maize. PMID:21385724

  19. Protein structure protection commits gene expression patterns.

    PubMed

    Chen, Jianping; Liang, Han; Fernández, Ariel

    2008-01-01

    Gene co-expressions often determine module-defining spatial and temporal concurrences of proteins. Yet, little effort has been devoted to tracing coordinating signals for expression correlations to the three-dimensional structures of gene products. We performed a global structure-based analysis of the yeast and human proteomes and contrasted this information against their respective transcriptome organizations obtained from comprehensive microarray data. We show that protein vulnerability quantifies dosage sensitivity for metabolic adaptation phases and tissue-specific patterns of mRNA expression, determining the extent of co-expression similarity of binding partners. The role of protein intrinsic disorder in transcriptome organization is also delineated by interrelating vulnerability, disorder propensity and co-expression patterns. Extremely vulnerable human proteins are shown to be subject to severe post-transcriptional regulation of their expression through significant micro-RNA targeting, making mRNA levels poor surrogates for protein-expression levels. By contrast, in yeast the expression of extremely under-wrapped proteins is likely regulated through protein aggregation. Thus, the 85 most vulnerable proteins in yeast include the five confirmed prions, while in human, the genes encoding extremely vulnerable proteins are predicted to be targeted by microRNAs. Hence, in both vastly different organisms protein vulnerability emerges as a structure-encoded signal for post-transcriptional regulation. Vulnerability of protein structure and the concurrent need to maintain structural integrity are shown to quantify dosage sensitivity, compelling gene expression patterns across tissue types and temporal adaptation phases in a quantifiable manner. Extremely vulnerable proteins impose additional constraints on gene expression: They are subject to high levels of regulation at the post-transcriptional level.

  20. Identification and Validation of Housekeeping Genes for Gene Expression Analysis of Cancer Stem Cells.

    PubMed

    Lemma, Silvia; Avnet, Sofia; Salerno, Manuela; Chano, Tokuhiro; Baldini, Nicola

    2016-01-01

    The characterization of cancer stem cell (CSC) subpopulation, through the comparison of the gene expression signature in respect to the native cancer cells, is particularly important for the identification of novel and more effective anticancer strategies. However, CSC have peculiar characteristics in terms of adhesion, growth, and metabolism that possibly implies a different modulation of the expression of the most commonly used housekeeping genes (HKG), like b-actin (ACTB). Although it is crucial to identify which are the most stable HKG genes to normalize the data derived from quantitative Real-Time PCR analysis to obtain robust and consistent results, an exhaustive validation of reference genes in CSC is still missing. Here, we isolated CSC spheres from different musculoskeletal sarcomas and carcinomas as a model to investigate on the stability of the mRNA expression of 15 commonly used HKG, in respect to the native cells. The selected genes were analysed for the variation coefficient and compared using the popular algorithms NormFinder and geNorm to evaluate stability ranking. As a result, we found that: 1) Tata Binding Protein (TBP), Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta polypeptide (YWHAZ), Peptidylprolyl isomerase A (PPIA), and Hydroxymethylbilane synthase (HMBS) are the most stable HKG for the comparison between CSC and native cells; 2) at least four reference genes should be considered for robust results; 3) the use of ACTB should not be recommended, 4) specific HKG should be considered for studies that are focused only on a specific tumor type, like sarcoma or carcinoma. Our results should be taken in consideration for all the studies of gene expression analysis of CSC, and will substantially contribute for future investigations aimed to identify novel anticancer therapy based on CSC targeting.

  1. Nonparametric identification of structural modifications in Laplace domain

    NASA Astrophysics Data System (ADS)

    Suwała, G.; Jankowski, Ł.

    2017-02-01

    This paper proposes and experimentally verifies a Laplace-domain method for identification of structural modifications, which (1) unlike time-domain formulations, allows the identification to be focused on these parts of the frequency spectrum that have a high signal-to-noise ratio, and (2) unlike frequency-domain formulations, decreases the influence of numerical artifacts related to the particular choice of the FFT exponential window decay. In comparison to the time-domain approach proposed earlier, advantages of the proposed method are smaller computational cost and higher accuracy, which leads to reliable performance in more difficult identification cases. Analytical formulas for the first- and second-order sensitivity analysis are derived. The approach is based on a reduced nonparametric model, which has the form of a set of selected structural impulse responses. Such a model can be collected purely experimentally, which obviates the need for design and laborious updating of a parametric model, such as a finite element model. The approach is verified experimentally using a 26-node lab 3D truss structure and 30 identification cases of a single mass modification or two concurrent mass modifications.

  2. Structure of the human annexin VI gene

    SciTech Connect

    Smith, P.D.; Moss, S.E.; Davies, A.; Crumpton, M.J.

    1994-03-29

    The authors report the structure of the human annexin VI gene and compare the intron-exon organization with the known structures of the human annexin I and II genes. The gene is {approximately}60 kbp long and contains 26 exons. Consistent with the published annexin VI cDNA sequence, the genomic sequence at the 3{prime} end does not contain a canonical polyadenylation signal. The genomic sequence upstream of the transcription start site contains TATAA and CAAT motifs. The spatial organization of the exons does not reveal any obvious similarities between the two halves of the annexin VI gene. Comparison of the intron-exon boundary positions of the annexin VI gene with those of annexins I and II reveals that within the repeated domains the break points are perfectly conserved except for exon 8, which is one codon smaller in annexin II. The corresponding point in the second half of annexin VI is represented by two exons, exons 20 and 21. The latter exon is alternatively spliced, giving rise to two annexin VI isoforms that differ with respect to a 6-amino acid insertion at the start of repeat 7. 32 refs., 6 figs.

  3. Identification, distribution and molecular evolution of the pacifastin gene family in Metazoa

    PubMed Central

    Breugelmans, Bert; Simonet, Gert; van Hoef, Vincent; Van Soest, Sofie; Broeck, Jozef Vanden

    2009-01-01

    Background Members of the pacifastin family are serine peptidase inhibitors, most of which are produced as multi domain precursor proteins. Structural and biochemical characteristics of insect pacifastin-like peptides have been studied intensively, but only one inhibitor has been functionally characterised. Recent sequencing projects of metazoan genomes have created an unprecedented opportunity to explore the distribution, evolution and functional diversification of pacifastin genes in the animal kingdom. Results A large scale in silico data mining search led to the identification of 83 pacifastin members with 284 inhibitor domains, distributed over 55 species from three metazoan phyla. In contrast to previous assumptions, members of this family were also found in other phyla than Arthropoda, including the sister phylum Onychophora and the 'primitive', non-bilaterian Placozoa. In Arthropoda, pacifastin members were found to be distributed among insect families of nearly all insect orders and for the first time also among crustacean species other than crayfish and the Chinese mitten crab. Contrary to precursors from Crustacea, the majority of insect pacifastin members contain dibasic cleavage sites, indicative for posttranslational processing into numerous inhibitor peptides. Whereas some insect species have lost the pacifastin gene, others were found to have several (often clustered) paralogous genes. Amino acids corresponding to the reactive site or involved in the folding of the inhibitor domain were analysed as a basis for the biochemical properties. Conclusion The absence of the pacifastin gene in some insect genomes and the extensive gene expansion in other insects are indicative for the rapid (adaptive) evolution of this gene family. In addition, differential processing mechanisms and a high variability in the reactive site residues and the inner core interactions contribute to a broad functional diversification of inhibitor peptides, indicating wide ranging

  4. Optimal experiment design for identification of large space structures

    NASA Technical Reports Server (NTRS)

    Bayard, D. S.; Hadaegh, F. Y.; Meldrum, D. R.

    1988-01-01

    The optimal experiment design for on-orbit identification of modal frequency and damping parameters in large flexible space structures is discussed. The main result is a separation principle for D-optimal design which states that under certain conditions the sensor placement problem is decoupled from the input design problem. This decoupling effect significantly simplifies the overall optimal experiment design determination for large MIMO structural systems with many unknown modal parameters. The error from using the uncoupled design is estimated in terms of the inherent damping of the structure. A numerical example is given, demonstrating the usefulness of the simplified criteria in determining optimal designs for on-orbit Space Station identification experiments.

  5. A Benchmark Problem for Development of Autonomous Structural Modal Identification

    NASA Technical Reports Server (NTRS)

    Pappa, Richard S.; Woodard, Stanley E.; Juang, Jer-Nan

    1996-01-01

    This paper summarizes modal identification results obtained using an autonomous version of the Eigensystem Realization Algorithm on a dynamically complex, laboratory structure. The benchmark problem uses 48 of 768 free-decay responses measured in a complete modal survey test. The true modal parameters of the structure are well known from two previous, independent investigations. Without user involvement, the autonomous data analysis identified 24 to 33 structural modes with good to excellent accuracy in 62 seconds of CPU time (on a DEC Alpha 4000 computer). The modal identification technique described in the paper is the baseline algorithm for NASA's Autonomous Dynamics Determination (ADD) experiment scheduled to fly on International Space Station assembly flights in 1997-1999.

  6. Identification of Androgen Receptor and Beta-Catenin Target Genes in Prostate and Prostate Cancer

    DTIC Science & Technology

    2013-10-01

    Transdisciplinary Research in Epigenetics and Cancer Journal Clubs and Transdisciplinary Science Meetings, biweekly and monthly 3. To gain expertise...Target Genes in Prostate and Prostate Cancer PRINCIPAL INVESTIGATOR: Laura Lamb CONTRACTING ORGANIZATION: Washington University...TITLE AND SUBTITLE Identification of Androgen Receptor and Beta-Catenin Target Genes in Prostate and Prostate Cancer 5a. CONTRACT NUMBER Genes in

  7. Identification, cloning, and expression analysis of three putative Lymantria dispar nuclear polyhedrosis virus immediate early genes

    Treesearch

    James M. Slavicek; Nancy Hayes-Plazolles

    1991-01-01

    Viral immediate early gene products are usually regulatory proteins that control expression of other viral genes at the transcriptional level or are proteins that are part of the viral DNA replication complex. The identification and functional characterization of the immediate early gene products of Lymantria dispar nuclear polyhedrosis virus (LdNPV...

  8. Frequency domain identification experiment on a large flexible structure

    NASA Technical Reports Server (NTRS)

    Bayard, D. S.; Hadaegh, F. Y.; Yam, Y.; Scheid, R. E.; Mettler, E.; Milman, M. H.

    1989-01-01

    Recent experiences in the field of flexible structure control in space have indicated a need for on-orbit system identification to support robust control redesign to avoid in-flight instabilities and maintain high spacecraft performance. The authors highlight an automated frequency domain system identification methodology recently developed to fill this need. The methodology supports (1) the estimation of system quantities useful for robust control analysis and design, (2) experiment design tailored to performing system identification in a typically constrained on-orbit environment, and (3) the automation of operations to reduce human-in-the-loop requirements. A basic overview of the methodology is presented first, followed by an experimental verification of the approach performed on the JPL/AFAL testbed facility.

  9. Rapid identification of Streptococcus intermedius by PCR with the ily gene as a species marker gene.

    PubMed

    Goto, Takatsugu; Nagamune, Hideaki; Miyazaki, Aiko; Kawamura, Yoshiaki; Ohnishi, Ooki; Hattori, Kanako; Ohkura, Kazuto; Miyamoto, Kazuaki; Akimoto, Shigeru; Ezaki, Takayuki; Hirota, Katsuhiko; Miyake, Yoichiro; Maeda, Takuya; Kourai, Hiroki

    2002-02-01

    Streptococcus intermedius belongs to the anginosus group of streptococci (AGS) and is associated with endogenous infections leading to abscesses in the oral cavity and at deepseated sites, such as the brain and liver. Two other species, S. anginosus and S. constellatus, and some presently unnamed taxa, are also classified as AGS. Recently, S. constellatus subsp. pharyngis, a new subspecies with biochemical characteristics similar to S. intermedius, was described with the potential for causing confusion when trying to identify isolates of these two species routinely with commercial identification kits, such as Rapid ID32 Strep and Fluo-Card Milleri. To correctly identify S. intermedius, this study attempted to develop an accurate PCR identification system with the ily gene as a species marker. This approach relies on amplification of an 819-bp fragment of the ily gene and its 3'-flanking region and is shown here to be specific for S. intermedius strains among all other streptococcal species. Moreover, this PCR system was applicable in direct rapid PCR with whole bacterial cells and TaKaRa Z-Taq (TaKaRa), a highly efficient DNA polymerase, as the template and DNA amplification enzyme, respectively.

  10. Amplification and characterization of eukaryotic structural genes.

    PubMed

    Maniatis, T; Efstratiadis, A; Sim, G K; Kafatos, F

    1978-05-01

    An approach to the study of eukaryotic structural genes which are differentially expressed during development is described. This approach involves the isolation and amplification of mRNA sequences by in vitro conversion of mRNA to double-stranded cDNA followed by molecular cloning in bacterial plasmids. This procedure provides highly specific hybridization probes that can be used to identify genes and their contiguous DNA sequences in genomic DNA, and to detect specific RNA transcripts during development. The nature of the method allows the isolation of individual mRNA sequences from a complex population of molecules at different stages of development.

  11. The rice B-box zinc finger gene family: genomic identification, characterization, expression profiling and diurnal analysis.

    PubMed

    Huang, Jianyan; Zhao, Xiaobo; Weng, Xiaoyu; Wang, Lei; Xie, Weibo

    2012-01-01

    The B-box (BBX) -containing proteins are a class of zinc finger proteins that contain one or two B-box domains and play important roles in plant growth and development. The Arabidopsis BBX gene family has recently been re-identified and renamed. However, there has not been a genome-wide survey of the rice BBX (OsBBX) gene family until now. In this study, we identified 30 rice BBX genes through a comprehensive bioinformatics analysis. Each gene was assigned a uniform nomenclature. We described the chromosome localizations, gene structures, protein domains, phylogenetic relationship, whole life-cycle expression profile and diurnal expression patterns of the OsBBX family members. Based on the phylogeny and domain constitution, the OsBBX gene family was classified into five subfamilies. The gene duplication analysis revealed that only chromosomal segmental duplication contributed to the expansion of the OsBBX gene family. The expression profile of the OsBBX genes was analyzed by Affymetrix GeneChip microarrays throughout the entire life-cycle of rice cultivar Zhenshan 97 (ZS97). In addition, microarray analysis was performed to obtain the expression patterns of these genes under light/dark conditions and after three phytohormone treatments. This analysis revealed that the expression patterns of the OsBBX genes could be classified into eight groups. Eight genes were regulated under the light/dark treatments, and eleven genes showed differential expression under at least one phytohormone treatment. Moreover, we verified the diurnal expression of the OsBBX genes using the data obtained from the Diurnal Project and qPCR analysis, and the results indicated that many of these genes had a diurnal expression pattern. The combination of the genome-wide identification and the expression and diurnal analysis of the OsBBX gene family should facilitate additional functional studies of the OsBBX genes.

  12. Identification and characterisation of synaptonemal complex genes in monotremes.

    PubMed

    Casey, Aaron E; Daish, Tasman J; Grutzner, Frank

    2015-08-10

    The platypus and echidna are the only extant species belonging to the clade of monotremata, the most basal mammalian lineage. The platypus is particularly well known for its mix of mammalian and reptilian characteristics and work in recent years has revealed this also extends to the genetic level. Amongst the monotreme specific features is the unique multiple sex chromosome system (5X4Y in the echidna and 5X5Y in the platypus), which forms a chain in meiosis. This raises questions about sex chromosome organisation at meiosis, including whether there has been changes in genes coding for synaptonemal complex proteins which are involved in homologous synapsis. Here we investigate the key structural components of the synaptonemal complex in platypus and echidna, synaptonemal complex proteins 1, 2 and 3 (SYCP1, SYCP2 and SYCP3). SYCP1 and SYCP2 orthologues are present, conserved and expressed in platypus testis. SYCP3 in contrast is highly diverged, but key residues required for self-association are conserved, while those required for tetramer stabilisation and DNA binding are missing. We also discovered a second SYCP3-like gene (SYCP3-like) in the same region. Comparison with the recently published Y-borne SYCP3 amino acid sequences revealed that SYCP3Y is more similar to SYCP3 in other mammals than the monotreme autosomal SYCP3. It is currently unclear if these changes in the SYCP3 gene repertoire are related to meiotic organisation of the extraordinary monotreme sex chromosome system.

  13. Structures of two molluscan hemocyanin genes: Significance for gene evolution

    PubMed Central

    Lieb, Bernhard; Altenhein, Benjamin; Markl, Jürgen; Vincent, Alexandra; van Olden, Erin; van Holde, Kensal E.; Miller, Karen I.

    2001-01-01

    We present here the description of genes coding for molluscan hemocyanins. Two distantly related mollusks, Haliotis tuberculata and Octopus dofleini, were studied. The typical architecture of a molluscan hemocyanin subunit, which is a string of seven or eight globular functional units (FUs, designated a to h, about 50 kDa each), is reflected by the gene organization: a series of eight structurally related coding regions in Haliotis, corresponding to FU-a to FU-h, with seven highly variable linker introns of 174 to 3,198 bp length (all in phase 1). In Octopus seven coding regions (FU-a to FU-g) are found, separated by phase 1 introns varying in length from 100 bp to 910 bp. Both genes exhibit typical signal (export) sequences, and in both cases these are interrupted by an additional intron. Each gene also contains an intron between signal peptide and FU-a and in the 3′ untranslated region. Of special relevance for evolutionary considerations are introns interrupting those regions that encode a discrete functional unit. We found that five of the eight FUs in Haliotis each are encoded by a single exon, whereas FU-f, FU-g, and FU-a are encoded by two, three and four exons, respectively. Similarly, in Octopus four of the FUs each correspond to an uninterrupted exon, whereas FU-b, FU-e, and FU-f each contain a single intron. Although the positioning of the introns between FUs is highly conserved in the two mollusks, the introns within FUs show no relationship either in location nor phase. It is proposed that the introns between FUs were generated as the eight-unit polypeptide evolved from a monomeric precursor, and that the internal introns have been added later. A hypothesis for evolution of the ring-like quaternary structure of molluscan hemocyanins is presented. PMID:11287637

  14. Automated output-only dynamic identification of civil engineering structures

    NASA Astrophysics Data System (ADS)

    Rainieri, C.; Fabbrocino, G.

    2010-04-01

    Modal-based damage detection algorithms are well-known techniques for structural health assessment, but they are not commonly used due to the lack of automated modal identification and tracking procedures. Development of such procedures is not a trivial task since traditional modal identification requires extensive interaction from an expert user. Nevertheless, computational efforts have to be carefully considered. If fast on-line data processing is crucial for quickly varying in time systems (such as a rocket burning fuel), a number of vibration-based condition monitoring applications are performed at very different time scales, resulting in satisfactory time steps for on-line data analysis. Moreover, promising results in the field of automated modal identification have been recently achieved. In the present paper, a literature review on this topic is presented and recent developments concerning fully automated output-only modal identification procedures are described. Some case studies are also reported in order to validate the approach. They are characterized by different levels of complexity, in terms of mode coupling, dynamic interaction effects and level of vibration. Advantages and drawbacks of the proposed approach will be pointed out with reference to available experimental results. The final objective is the implementation of a fully automated system for vibration-based structural health monitoring of civil engineering structures and identification of adequate requirements about sensor number and layout, record duration and hardware characteristics able to ensure a reliable low-cost health assessment of constructions. Results of application of the proposed methodology to modal parameter estimation in operational conditions and during ground motions induced by the recent L'Aquila earthquake will be finally presented and discussed.

  15. Network-Based Enriched Gene Subnetwork Identification: A Game-Theoretic Approach

    PubMed Central

    Razi, Abolfazl; Afghah, Fatemeh; Singh, Salendra; Varadan, Vinay

    2016-01-01

    Identifying subsets of genes that jointly mediate cancer etiology, progression, or therapy response remains a challenging problem due to the complexity and heterogeneity in cancer biology, a problem further exacerbated by the relatively small number of cancer samples profiled as compared with the sheer number of potential molecular factors involved. Pure data-driven methods that merely rely on multiomics data have been successful in discovering potentially functional genes but suffer from high false-positive rates and tend to report subsets of genes whose biological interrelationships are unclear. Recently, integrative data-driven models have been developed to integrate multiomics data with signaling pathway networks in order to identify pathways associated with clinical or biological phenotypes. However, these approaches suffer from an important drawback of being restricted to previously discovered pathway structures and miss novel genomic interactions as well as potential crosstalk among the pathways. In this article, we propose a novel coalition-based game-theoretic approach to overcome the challenge of identifying biologically relevant gene subnetworks associated with disease phenotypes. The algorithm starts from a set of seed genes and traverses a protein–protein interaction network to identify modulated subnetworks. The optimal set of modulated subnetworks is identified using Shapley value that accounts for both individual and collective utility of the subnetwork of genes. The algorithm is applied to two illustrative applications, including the identification of subnetworks associated with (i) disease progression risk in response to platinum-based therapy in ovarian cancer and (ii) immune infiltration in triple-negative breast cancer. The results demonstrate an improved predictive power of the proposed method when compared with state-of-the-art feature selection methods, with the added advantage of identifying novel potentially functional gene subnetworks

  16. Network-Based Enriched Gene Subnetwork Identification: A Game-Theoretic Approach.

    PubMed

    Razi, Abolfazl; Afghah, Fatemeh; Singh, Salendra; Varadan, Vinay

    2016-01-01

    Identifying subsets of genes that jointly mediate cancer etiology, progression, or therapy response remains a challenging problem due to the complexity and heterogeneity in cancer biology, a problem further exacerbated by the relatively small number of cancer samples profiled as compared with the sheer number of potential molecular factors involved. Pure data-driven methods that merely rely on multiomics data have been successful in discovering potentially functional genes but suffer from high false-positive rates and tend to report subsets of genes whose biological interrelationships are unclear. Recently, integrative data-driven models have been developed to integrate multiomics data with signaling pathway networks in order to identify pathways associated with clinical or biological phenotypes. However, these approaches suffer from an important drawback of being restricted to previously discovered pathway structures and miss novel genomic interactions as well as potential crosstalk among the pathways. In this article, we propose a novel coalition-based game-theoretic approach to overcome the challenge of identifying biologically relevant gene subnetworks associated with disease phenotypes. The algorithm starts from a set of seed genes and traverses a protein-protein interaction network to identify modulated subnetworks. The optimal set of modulated subnetworks is identified using Shapley value that accounts for both individual and collective utility of the subnetwork of genes. The algorithm is applied to two illustrative applications, including the identification of subnetworks associated with (i) disease progression risk in response to platinum-based therapy in ovarian cancer and (ii) immune infiltration in triple-negative breast cancer. The results demonstrate an improved predictive power of the proposed method when compared with state-of-the-art feature selection methods, with the added advantage of identifying novel potentially functional gene subnetworks

  17. Identification and characterization of the carbapenem MM 4550 and its gene cluster in Streptomyces argenteolus ATCC 11009

    PubMed Central

    Li, Rongfeng; Lloyd, Evan P.; Moshos, Kristos A.

    2014-01-01

    Nearly 50 naturally-occurring carbapenem β-lactam antibiotics, most produced by Streptomyces, have been identified. The structural diversity of these compounds is limited to variance of the C-2 and C-6 side chains as well as the stereochemistry at C-5/C-6. These structural motifs are of interest both for their antibiotic effects and their biosynthesis. While the thienamycin gene cluster is the only active gene cluster publically available in this group, more comparative information is needed to understand the genetic basis of these structural differences. We report here the identification of MM 4550, a member of the olivanic acids, as the major carbapenem produced by S. argenteolus ATCC 11009. Its gene cluster was also identified by degenerate PCR and targeted gene inactivation. Sequence analysis revealed that genes encoding the biosynthesis of the bicyclic core and the C-6 and C-2 side chains are well conserved in the MM 4550 and thienamycin gene clusters. Three new genes, cmmSu, cmm17 and cmmPah were found in the new cluster and their putative functions in the sulfonation and epimerization of MM 4550 are proposed. Gene inactivation showed that, in addition to cmmI, two new genes, cmm22/23, encode a two-component response system thought to regulate the production of MM 4550. Overexpression of cmmI, cmm22 and cmm23 promoted MM 4550 production in an engineered strain. Finally, the involvement and putative roles of all genes in the MM 4550 cluster are proposed based on the results of bioinformatics analysis, gene inactivation, and analysis of disruption mutants. Overall, the differences between the thienamycin and MM 4550 gene clusters are reflected in characteristic structural elements and provide new insights into the biosynthesis of the complex carbapenems. PMID:24420617

  18. Identification and characterization of the carbapenem MM 4550 and its gene cluster in Streptomyces argenteolus ATCC 11009.

    PubMed

    Li, Rongfeng; Lloyd, Evan P; Moshos, Kristos A; Townsend, Craig A

    2014-01-24

    Nearly 50 naturally occurring carbapenem β-lactam antibiotics, most produced by Streptomyces, have been identified. The structural diversity of these compounds is limited to variance of the C-2 and C-6 side chains as well as the stereochemistry at C-5/C-6. These structural motifs are of interest both for their antibiotic effects and their biosynthesis. Although the thienamycin gene cluster is the only active gene cluster publically available in this group, more comparative information is needed to understand the genetic basis of these structural differences. We report here the identification of MM 4550, a member of the olivanic acids, as the major carbapenem produced by Streptomyces argenteolus ATCC 11009. Its gene cluster was also identified by degenerate PCR and targeted gene inactivation. Sequence analysis revealed that the genes encoding the biosynthesis of the bicyclic core and the C-6 and C-2 side chains are well conserved in the MM 4550 and thienamycin gene clusters. Three new genes, cmmSu, cmm17 and cmmPah were found in the new cluster, and their putative functions in the sulfonation and epimerization of MM 4550 are proposed. Gene inactivation showed that, in addition to cmmI, two new genes, cmm22 and -23, encode a two-component response system thought to regulate the production of MM 4550. Overexpression of cmmI, cmm22 and cmm23 promoted MM 4550 production in an engineered strain. Finally, the involvement and putative roles of all genes in the MM 4550 cluster are proposed based on the results of bioinformatics analysis, gene inactivation, and analysis of disruption mutants. Overall, the differences between the thienamycin and MM 4550 gene clusters are reflected in characteristic structural elements and provide new insights into the biosynthesis of the complex carbapenems. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Identification and characterization of Arabidopsis thaliana genes involved in xylem secondary cell walls.

    PubMed

    Yokoyama, Ryusuke; Nishitani, Kazuhiko

    2006-05-01

    The xylem of higher plants offers support to aerial portions of the plant body and serves as conduit for the translocation of water and nutrients. Terminal differentiation of xylem cells typically involves deposition of thick secondary cell walls. This is a dynamic cellular process accompanied by enhanced rates of cellulose deposition and the induction of synthesis of specific secondary-wall matrix polysaccharides and lignin. The secondary cell wall is essential for the function of conductive and supportive xylem tissues. Recently, significant progress has been made in identifying the genes responsible for xylem secondary cell wall formation. However, our present knowledge is still insufficient to account for the molecular processes by which this complex system operates. To acquire further information about xylem secondary cell walls, we initially focused our research effort on a set of genes specifically implicated in secondary cell wall formation, as well as on loss-of-function mutants. Results from two microarray screens identified several key candidate genes responsible for secondary cell wall formation. Reverse genetic analyses led to the identification of a glycine-rich protein involved in maintaining the stable structure of protoxylem, which is essential for the transport of water and nutrients. A combination of expression analyses and reverse genetics allows us to systematically identify new genes required for the development of physical properties of the xylem secondary wall.

  20. Large scale in silico identification of MYB family genes from wheat expressed sequence tags.

    PubMed

    Cai, Hongsheng; Tian, Shan; Dong, Hansong

    2012-10-01

    The MYB proteins constitute one of the largest transcription factor families in plants. Much research has been performed to determine their structures, functions, and evolution, especially in the model plants, Arabidopsis, and rice. However, this transcription factor family has been much less studied in wheat (Triticum aestivum), for which no genome sequence is yet available. Despite this, expressed sequence tags are an important resource that permits opportunities for large scale gene identification. In this study, a total of 218 sequences from wheat were identified and confirmed to be putative MYB proteins, including 1RMYB, R2R3-type MYB, 3RMYB, and 4RMYB types. A total of 36 R2R3-type MYB genes with complete open reading frames were obtained. The putative orthologs were assigned in rice and Arabidopsis based on the phylogenetic tree. Tissue-specific expression pattern analyses confirmed the predicted orthologs, and this meant that gene information could be inferred from the Arabidopsis genes. Moreover, the motifs flanking the MYB domain were analyzed using the MEME web server. The distribution of motifs among wheat MYB proteins was investigated and this facilitated subfamily classification.

  1. Identification and characterization of two phospholipid hydroperoxide glutathione peroxidase genes from Apis cerana cerana.

    PubMed

    Wang, Mian; Kang, Mingjiang; Guo, Xingqi; Xu, Baohua

    2010-06-01

    Phospholipid hydroperoxide glutathione peroxidase (PHGPX) plays a crucial role in maintaining the integrity of membrane by reducing hydroperoxides of phospholipids. Here, we report the identification and characterization of two genes, designated AccGtpx-1 and AccGtpx-2, encoding PHGPX proteins from the Chinese honeybees, Apis cerana cerana. Alignment analysis showed that AccGtpx-1 and AccGtpx-2 shared high similarity with other known PHGPXs, which show similar structure to thioredoxin. These single copy genes showed complex exon-intron structures. The mRNA of AccGtpx-1 was detected in larvae, pupae and adults and that AccGtpx-2 was only found in adult worker bees. Furthermore, the expression of AccGtpx-1 could be induced by H(2)O(2), ultraviolet (UV) light, heat shock (37 degrees C), HgCl(2), imidacloprid, cyhalothrin, pyriproxyfen and methomyl. In contrast, AccGtpx-2 expression could only be induced by UV. These results indicated for the first time that the AccGtpx-1 and AccGtpx-2 genes encoding A. cerana cerana PHGPXs are regulated differently in response to environmental stressors.

  2. Identification of a Maize Locus that Modulates the Hypersensitive Defense Response, Using Mutant-Assisted Gene Identification and Characterization (MAGIC)

    USDA-ARS?s Scientific Manuscript database

    The hypersensitive response (HR) is the most visible and arguably the most important defense response in plants, although the details of how it is controlled and executed remain patchy. In this paper a novel genetic technique called MAGIC (Mutant-Assisted Gene Identification and Characterization) i...

  3. Precise Identification of Graphene's Crystal Structures by Removable Nanowire Epitaxy.

    PubMed

    Kim, Jonghyeok; Lim, Kitaek; Lee, Yangjin; Kim, Jongin; Kim, Kihwan; Park, Jungwon; Kim, Kwanpyo; Lee, Won Chul

    2017-03-16

    Monitoring crystallographic orientations of graphene is important for the reliable generation of graphene-based nanostructures such as van der Waals heterostructures and graphene nanoribbons because their physical properties are dependent on crystal structures. However, facile and precise identification of graphene's crystallographic orientations is still challenging because the majority of current tools rely on complex atomic-scale imaging. Here, we present an identification method for the crystal orientations and grain boundaries of graphene using the directional alignment between epitaxially grown AuCN nanowires and the underlying graphene. Because the nanowires are visible in scanning electron microscopy, crystal orientations of graphene can be inspected with simple procedures. Kernel density estimation that we used in analyzing the nanowire directions enables precise measurement of graphene's crystal orientations. We also confirm that the imaged nanowires can be simply removed without degrading graphene's quality, thus showing that the present method can be practically used for measuring graphene's crystal structures.

  4. Identification of microRNA Genes in Three Opisthorchiids

    PubMed Central

    Ovchinnikov, Vladimir Y.; Afonnikov, Dmitry A.; Vasiliev, Gennady V.; Kashina, Elena V.; Sripa, Banchob; Mordvinov, Viacheslav A.; Katokhin, Alexey V.

    2015-01-01

    Background Opisthorchis felineus, O. viverrini, and Clonorchis sinensis (family Opisthorchiidae) are parasitic flatworms that pose a serious threat to humans in some countries and cause opisthorchiasis/clonorchiasis. Chronic disease may lead to a risk of carcinogenesis in the biliary ducts. MicroRNAs (miRNAs) are small noncoding RNAs that control gene expression at post-transcriptional level and are implicated in the regulation of various cellular processes during the parasite- host interplay. However, to date, the miRNAs of opisthorchiid flukes, in particular those essential for maintaining their complex biology and parasitic mode of existence, have not been satisfactorily described. Methodology/Principal Findings Using a SOLiD deep sequencing-bioinformatic approach, we identified 43 novel and 18 conserved miRNAs for O. felineus (miracidia, metacercariae and adult worms), 20 novel and 16 conserved miRNAs for O. viverrini (adult worms), and 33 novel and 18 conserved miRNAs for C. sinensis (adult worms). The analysis of the data revealed differences in the expression level of conserved miRNAs among the three species and among three the developmental stages of O. felineus. Analysis of miRNA genes revealed two gene clusters, one cluster-like region and one intronic miRNA in the genome. The presence and structure of the two gene clusters were validated using a PCR-based approach in the three flukes. Conclusions This study represents a comprehensive description of miRNAs in three members of the family Opistorchiidae, significantly expands our knowledge of miRNAs in multicellular parasites and provides a basis for understanding the structural and functional evolution of miRNAs in these metazoan parasites. Results of this study also provides novel resources for deeper understanding the complex parasite biology, for further research on the pathogenesis and molecular events of disease induced by the liver flukes. The present data may also facilitate the development of novel

  5. Structure of the human retinoblastoma gene

    SciTech Connect

    Hong, F.D.; Huang, Hueijen S.; To, Hoang; Young, Lihjiuan S.; Oro, A.; Bookstein, R.; Lee, E.Y.H.P.; Lee, Wenhwa )

    1989-07-01

    Complete inactivation of the human retinoblastoma gene (RB) is believed to be an essential step in tumorigenesis of several different cancers. To provide a framework for understanding inactivation mechanisms, the structure of RB was delineated. The RB transcript is encoded in 27 exons dispersed over about 200 kilobases (kb) of genomic DNA. The length of individual exons ranges from 31 to 1,889 base pairs (bp). The largest intron spans >60 kb and the smallest one has only 80 bp. Deletion of exons 13-17 is frequently observed in various types of tumors, including retinoblastoma, breast cancer, and osteosarcoma, and the presence of a potential hot spot for recombination in the region is predicted. A putative leucine-zipper motif is exclusively encoded by exon 20. The detailed RB structure presented should prove useful in defining potential functional domains of its encoded protein. Transcription of RB is initiated at multiple positions and the sequences surrounding the initiation sites have a high G+C content. A typical upstream TATA box is not present. Localization of the RB promoter region was accomplished by utilizing a heterologous expression system containing a bacterial chloramphenicol acetyltransferase gene. Deletion analysis revealed that a region as small as 70 bp is sufficient for RB promoter activity, similar to other previously characterized G+C-rich gene promoters. Several direct repeats and possible stem-and-loop structures are found in the promoter region.

  6. Computational identification of genes modulating stem height-diameter allometry.

    PubMed

    Jiang, Libo; Ye, Meixia; Zhu, Sheng; Zhai, Yi; Xu, Meng; Huang, Minren; Wu, Rongling

    2016-12-01

    The developmental variation in stem height with respect to stem diameter is related to a broad range of ecological and evolutionary phenomena in trees, but the underlying genetic basis of this variation remains elusive. We implement a dynamic statistical model, functional mapping, to formulate a general procedure for the computational identification of quantitative trait loci (QTLs) that control stem height-diameter allometry during development. Functional mapping integrates the biological principles underlying trait formation and development into the association analysis of DNA genotype and endpoint phenotype, thus providing an incentive for understanding the mechanistic interplay between genes and development. Built on the basic tenet of functional mapping, we explore two core ecological scenarios of how stem height and stem diameter covary in response to environmental stimuli: (i) trees pioneer sunlit space by allocating more growth to stem height than diameter and (ii) trees maintain their competitive advantage through an inverse pattern. The model is equipped to characterize 'pioneering' QTLs (piQTLs) and 'maintaining' QTLs (miQTLs) which modulate these two ecological scenarios, respectively. In a practical application to a mapping population of full-sib hybrids derived from two Populus species, the model has well proven its versatility by identifying several piQTLs that promote height growth at a cost of diameter growth and several miQTLs that benefit radial growth at a cost of height growth. Judicious application of functional mapping may lead to improved strategies for studying the genetic control of the formation mechanisms underlying trade-offs among quantities of assimilates allocated to different growth parts. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

  7. The Phaseolus vulgaris ZIP gene family: identification, characterization, mapping, and gene expression

    PubMed Central

    Astudillo, Carolina; Fernandez, Andrea C.; Blair, Matthew W.; Cichy, Karen A.

    2013-01-01

    Zinc is an essential mineral for humans and plants and is involved in many physiological and biochemical processes. In humans, Zn deficiency has been associated with retarded growth and reduction of immune response. In plants, Zn is an essential component of more than 300 enzymes including RNA polymerase, alkaline phosphatase, alcohol dehydrogenase, Cu/Zn superoxidase dismutase, and carbonic anhydrase. The accumulation of Zn in plants involves many genes and characterization of the role of these genes will be useful in biofortification. Here we report the identification and phlyogenetic and sequence characterization of the 23 members of the ZIP (ZRT, IRT like protein) family of metal transporters and three transcription factors of the bZIP family in Phaseolus vulgaris L. Expression patterns of seven of these genes were characterized in two bean genotypes (G19833 and DOR364) under two Zn treatments. Tissue analyzed included roots and leaves at vegetative and flowering stages, and pods at 20 days after flowering. Four of the genes, PvZIP12, PvZIP13, PvZIP16, and Pv bZIP1, showed differential expression based on tissue, Zn treatment, and/or genotype. PvZIP12 and PvZIP13 were both more highly expressed in G19833 than DOR364. PvZIP12 was most highly expressed in vegetative leaves under the Zn (−) treatment. PvZIP16 was highly expressed in leaf tissue, especially leaf tissue at flowering stage grown in the Zn (−) treatment. Pv bZIP1 was most highly expressed in leaf and pod tissue. The 23 PvZIP genes and three bZIP genes were mapped on the DOR364 × G19833 linkage map. PvZIP12, PvZIP13, and PvZIP18, Pv bZIP2, and Pv bZIP3 were located near QTLs for Zn accumulation in the seed. Based on the expression and mapping results, PvZIP12 is a good candidate gene for increasing seed Zn concentration and increase understanding of the role of ZIP genes in metal uptake, distribution, and accumulation of zinc in P. vulgaris. PMID:23908661

  8. Identification of crucial genes related to postmenopausal osteoporosis using gene expression profiling.

    PubMed

    Ma, Min; Chen, Xiaofei; Lu, Liangyu; Yuan, Feng; Zeng, Wen; Luo, Shulin; Yin, Feng; Cai, Junfeng

    2016-12-01

    Postmenopausal osteoporosis is a common bone disease and characterized by low bone mineral density. This study aimed to reveal key genes associated with postmenopausal osteoporosis (PMO), and provide a theoretical basis for subsequent experiments. The dataset GSE7429 was obtained from Gene Expression Omnibus. A total of 20 B cell samples (ten ones, respectively from postmenopausal women with low or high bone mineral density (BMD) were included in this dataset. Following screening of differentially expressed genes (DEGs), coexpression analysis of all genes was performed, and key genes in the coexpression network were screened using the random walk algorithm. Afterwards, functional and pathway analyses were conducted. Additionally, protein-protein interactions (PPIs) between DEGs and key genes were analyzed. A set of 308 DEGs (170 up-regulated ones and 138 down-regulated ones) between low BMD and high BMD samples were identified, and 101 key genes in the coexpression network were screened out. In the coexpression network, some genes had a higher score and degree, such as CSTA. The key genes in the coexpression network were mainly enriched in GO terms of the defense response (e.g., SERPINA1 and CST3), immune response (e.g., IL32 and CLEC7A); while, the DEGs were mainly enriched in structural constituent of cytoskeleton (e.g., CYLC2 and TUBA1B) and membrane-enclosed lumen (e.g., CCNE1 and INTS5). In the PPI network, CCNE1 interacted with REL; and TUBA1B interacted with ESR1. A series of interactions, such as CSTA/TYROBP, CCNE1/REL and TUBA1B/ESR1 might play pivotal roles in the occurrence and development of PMO.

  9. Identification of local variations within secondary structures of proteins.

    PubMed

    Kumar, Prasun; Bansal, Manju

    2015-05-01

    Secondary-structure elements (SSEs) play an important role in the folding of proteins. Identification of SSEs in proteins is a common problem in structural biology. A new method, ASSP (Assignment of Secondary Structure in Proteins), using only the path traversed by the C(α) atoms has been developed. The algorithm is based on the premise that the protein structure can be divided into continuous or uniform stretches, which can be defined in terms of helical parameters, and depending on their values the stretches can be classified into different SSEs, namely α-helices, 310-helices, π-helices, extended β-strands and polyproline II (PPII) and other left-handed helices. The methodology was validated using an unbiased clustering of these parameters for a protein data set consisting of 1008 protein chains, which suggested that there are seven well defined clusters associated with different SSEs. Apart from α-helices and extended β-strands, 310-helices and π-helices were also found to occur in substantial numbers. ASSP was able to discriminate non-α-helical segments from flanking α-helices, which were often identified as part of α-helices by other algorithms. ASSP can also lead to the identification of novel SSEs. It is believed that ASSP could provide a better understanding of the finer nuances of protein secondary structure and could make an important contribution to the better understanding of comparatively less frequently occurring structural motifs. At the same time, it can contribute to the identification of novel SSEs. A standalone version of the program for the Linux as well as the Windows operating systems is freely downloadable and a web-server version is also available at http://nucleix.mbu.iisc.ernet.in/assp/index.php.

  10. Identification of the sex genes in an early diverged fungus.

    PubMed

    Idnurm, Alexander; Walton, Felicia J; Floyd, Anna; Heitman, Joseph

    2008-01-10

    Sex determination in fungi is controlled by a small, specialized region of the genome in contrast to the large sex-specific chromosomes of animals and some plants. Different gene combinations reside at these mating-type (MAT) loci and confer sexual identity; invariably they encode homeodomain, alpha-box, or high mobility group (HMG)-domain transcription factors. So far, MAT loci have been characterized from a single monophyletic clade of fungi, the Dikarya (the ascomycetes and basidiomycetes), and the ancestral state and evolutionary history of these loci have remained a mystery. Mating in the basal members of the kingdom has been less well studied, and even their precise taxonomic inter-relationships are still obscure. Here we apply bioinformatic and genetic mapping to identify the sex-determining (sex) region in Phycomyces blakesleeanus (Zygomycota), which represents an early branch within the fungi. Each sex allele contains a single gene that encodes an HMG-domain protein, implicating the HMG-domain proteins as an earlier form of fungal MAT loci. Additionally, one allele also contains a copy of a unique, chromosome-specific repetitive element, suggesting a generalized mechanism for the earliest steps in the evolution of sex determination and sex chromosome structure in eukaryotes.

  11. Identification, Phylogeny, and Transcript of Chitinase Family Genes in Sugarcane

    PubMed Central

    Su, Yachun; Xu, Liping; Wang, Shanshan; Wang, Zhuqing; Yang, Yuting; Chen, Yun; Que, Youxiong

    2015-01-01

    Chitinases are pathogensis-related proteins, which play an important role in plant defense mechanisms. The role of the sugarcane chitinase family genes remains unclear due to the highly heterozygous and aneuploidy chromosome genetic background of sugarcane. Ten differentially expressed chitinase genes (belonging to class I~VII) were obtained from RNA-seq analysis of both incompatible and compatible sugarcane genotypes during Sporisorium scitamineum challenge. Their structural properties and expression patterns were analyzed. Seven chitinases (ScChiI1, ScChiI2, ScChiI3, ScChiIII1, ScChiIII2, ScChiIV1 and ScChiVI1) showed more positive with early response and maintained increased transcripts in the incompatible interaction than those in the compatible one. Three (ScChiII1, ScChiV1 and ScChiVII1) seemed to have no significant difference in expression patterns between incompatible and compatible interactions. The ten chitinases were expressed differentially in response to hormone treatment as well as having distinct tissue specificity. ScChiI1, ScChiIV1 and ScChiVII1 were induced by various abiotic stresses (NaCl, CuCl2, PEG and 4 °C) and their involvement in plant immunity was demonstrated by over-expression in Nicotiana benthamiana. The results suggest that sugarcane chitinase family exhibit differential responses to biotic and abiotic stress, providing new insights into their function. PMID:26035173

  12. Parameter identification of material constants in a composite shell structure

    SciTech Connect

    Martinez, D.R.; Carne, T.G.

    1988-01-01

    One of the basic requirements in engineering analysis is the development of a mathematical model describing the system. Frequently, comparisons with test data are used as a measurement of the adequacy of the model. An attempt is typically made to update or improve the model to provide a test-verified analysis tool. System identification provides a systematic procedure for accomplishing this task. The terms system identification, parameter estimation, and model correlation all refer to techniques that use test information to update or verify mathematical models. The goal of system identification is to improve the correlation of model predictions with measured test data, and produce accurate, predictive models. For nonmetallic structures the modeling task is often difficult due to uncertainties in the elastic constants. In this work a parameter identification procedure was used to determine the elastic constants of a cylindrical, graphite epoxy composite shell. A finite element model of the shell was created, which included uncertain orthotropic elastic constants. A modal survey test was then performed on the shell. The resulting modal data, along with the finite element model of the shell, were used in a Bayes estimation algorithm. This permitted the use of covariance matrices to weight the confidence in the initial parameter values as well as confidence in the measured test data. The estimation procedure also employed the concept of successive linearization to obtain an approximate solution to the original nonlinear estimation problem. 17 refs., 7 figs.

  13. Identification, isolation, and analysis of a gene cluster involved in iron acquisition by Pseudomonas mendocina ymp.

    PubMed

    Awaya, Jonathan D; Dubois, Jennifer L

    2008-06-01

    Microbial acquisition of iron from natural sources in aerobic environments is a little-studied process that may lead to mineral instability and trace metal mobilization. Pseudomonas mendocina ymp was isolated from the Yucca Mountain Site for long-term nuclear waste storage. Its ability to solubilize a variety of Fe-containing minerals under aerobic conditions has been previously investigated but its molecular and genetic potential remained uncharacterized. Here, we have shown that the organism produces a hydroxamate and not a catecholate-based siderophore that is synthesized via non-ribosomal peptide synthetases. Gene clustering patterns observed in other Pseudomonads suggested that hybridizing multiple probes to the same library could allow for the identification of one or more clusters of syntenic siderophore-associated genes. Using this approach, two independent clusters were identified. An unfinished draft genome sequence of P. mendocina ymp indicated that these mapped to two independent contigs. The sequenced clusters were investigated informatically and shown to contain respectively a potentially complete set of genes responsible for siderophore biosynthesis, uptake, and regulation, and an incomplete set of genes with low individual homology to siderophore-associated genes. A mutation in the cluster's pvdA homolog (pmhA) resulted in a siderophore-null phenotype, which could be reversed by complementation. The organism likely produces one siderophore with possibly different isoforms and a peptide backbone structure containing seven residues (predicted sequence: Acyl-Asp-Dab-Ser-fOHOrn-Ser-fOHorn). A similar approach could be applied for discovery of Fe- and siderophore-associated genes in unsequenced or poorly annotated organisms.

  14. Identification, isolation, and analysis of a gene cluster involved in iron acquisition by Pseudomonas mendocina ymp

    PubMed Central

    Awaya, Jonathan D.

    2013-01-01

    Microbial acquisition of iron from natural sources in aerobic environments is a little-studied process that may lead to mineral instability and trace metal mobilization. Pseudomonas mendocina ymp was isolated from the Yucca Mountain Site for long-term nuclear waste storage. Its ability to solubilize a variety of Fe-containing minerals under aerobic conditions has been previously investigated but its molecular and genetic potential remained uncharacterized. Here, we have shown that the organism produces a hydroxamate and not a catecholate-based siderophore that is synthesized via non-ribosomal peptide synthetases. Gene clustering patterns observed in other Pseudomonads suggested that hybridizing multiple probes to the same library could allow for the identification of one or more clusters of syntenic siderophore-associated genes. Using this approach, two independent clusters were identified. An unfinished draft genome sequence of P. mendocina ymp indicated that these mapped to two independent contigs. The sequenced clusters were investigated informatically and shown to contain respectively a potentially complete set of genes responsible for siderophore biosynthesis, uptake, and regulation, and an incomplete set of genes with low individual homology to siderophore-associated genes. A mutation in the cluster’s pvdA homolog (pmhA) resulted in a siderophore-null phenotype, which could be reversed by complementation. The organism likely produces one siderophore with possibly different isoforms and a peptide backbone structure containing seven residues (predicted sequence: Acyl-Asp-Dab-Ser-fOHOrn-Ser-fOHorn). A similar approach could be applied for discovery of Fe− and siderophore-associated genes in unsequenced or poorly annotated organisms. PMID:18058194

  15. Gene Expression Analysis for the Identification of Genes Involved in Early Tumour Development

    NASA Astrophysics Data System (ADS)

    Forte, Stefano; Scarpulla, Salvatore; Lagana, Alessandro; Memeo, Lorenzo; Gulisano, Massimo

    Prostatic tissues can undergo to cancer insurgence and prostate cancer is one of the most common types of malignancies affecting adult men in the United States. Primary adenocarcinoma of the seminal vesi-cles (SVCA) is a very rare neoplasm with only 48 histologically confirmed cases reported in the European and United States literature. Prostatic tissues, seminal vesicles and epididymis belongs all to the same microenvironment, shows a very close morphology and share the same embryological origin. Despite these common features the rate of cancer occurrence is very different. The understanding of molecular differences between non neoplastic prostatic tissues and non neoplastic epididymis or seminal vesicles may suggest potential mechanisms of resistance to tumour occurrence. The comparison of expression patterns of non neoplastic prostatic and seminal vesicles tissues to identify differentially expressed genes can help researchers in the identification of biological actors involved in the early stages of the tumour development.

  16. Structure identification methods for atomistic simulations of crystalline materials

    DOE PAGES

    Stukowski, Alexander

    2012-05-28

    Here, we discuss existing and new computational analysis techniques to classify local atomic arrangements in large-scale atomistic computer simulations of crystalline solids. This article includes a performance comparison of typical analysis algorithms such as common neighbor analysis (CNA), centrosymmetry analysis, bond angle analysis, bond order analysis and Voronoi analysis. In addition we propose a simple extension to the CNA method that makes it suitable for multi-phase systems. Finally, we introduce a new structure identification algorithm, the neighbor distance analysis, which is designed to identify atomic structure units in grain boundaries.

  17. Structure identification methods for atomistic simulations of crystalline materials

    NASA Astrophysics Data System (ADS)

    Stukowski, Alexander

    2012-06-01

    We discuss existing and new computational analysis techniques to classify local atomic arrangements in large-scale atomistic computer simulations of crystalline solids. This article includes a performance comparison of typical analysis algorithms such as common neighbor analysis (CNA), centrosymmetry analysis, bond angle analysis, bond order analysis and Voronoi analysis. In addition we propose a simple extension to the CNA method that makes it suitable for multi-phase systems. Finally, we introduce a new structure identification algorithm, the neighbor distance analysis, which is designed to identify atomic structure units in grain boundaries.

  18. An adaptive identification and control scheme for large space structures

    NASA Technical Reports Server (NTRS)

    Carroll, J. V.

    1988-01-01

    A unified identification and control scheme capable of achieving space at form performance objectives under nominal or failure conditions is described. Preliminary results are also presented, showing that the methodology offers much promise for effective robust control of large space structures. The control method is a multivariable, adaptive, output predictive controller called Model Predictive Control (MPC). MPC uses a state space model and input reference trajectories of set or tracking points to adaptively generate optimum commands. For a fixed model, MPC processes commands with great efficiency, and is also highly robust. A key feature of MPC is its ability to control either nonminimum phase or open loop unstable systems. As an output controller, MPC does not explicitly require full state feedback, as do most multivariable (e.g., Linear Quadratic) methods. Its features are very useful in LSS operations, as they allow non-collocated actuators and sensors. The identification scheme is based on canonical variate analysis (CVA) of input and output data. The CVA technique is particularly suited for the measurement and identification of structural dynamic processes - that is, unsteady transient or dynamically interacting processes such as between aerodynamics and structural deformation - from short, noisy data. CVA is structured so that the identification can be done in real or near real time, using computationally stable algorithms. Modeling LSS dynamics in 1-g laboratories has always been a major impediment not only to understanding their behavior in orbit, but also to controlling it. In cases where the theoretical model is not confirmed, current methods provide few clues concerning additional dynamical relationships that are not included in the theoretical models. CVA needs no a priori model data, or structure; all statistically significant dynamical states are determined using natural, entropy-based methods. Heretofore, a major limitation in applying adaptive

  19. An adaptive identification and control scheme for large space structures

    NASA Technical Reports Server (NTRS)

    Carroll, J. V.

    1988-01-01

    A unified identification and control scheme capable of achieving space at form performance objectives under nominal or failure conditions is described. Preliminary results are also presented, showing that the methodology offers much promise for effective robust control of large space structures. The control method is a multivariable, adaptive, output predictive controller called Model Predictive Control (MPC). MPC uses a state space model and input reference trajectories of set or tracking points to adaptively generate optimum commands. For a fixed model, MPC processes commands with great efficiency, and is also highly robust. A key feature of MPC is its ability to control either nonminimum phase or open loop unstable systems. As an output controller, MPC does not explicitly require full state feedback, as do most multivariable (e.g., Linear Quadratic) methods. Its features are very useful in LSS operations, as they allow non-collocated actuators and sensors. The identification scheme is based on canonical variate analysis (CVA) of input and output data. The CVA technique is particularly suited for the measurement and identification of structural dynamic processes - that is, unsteady transient or dynamically interacting processes such as between aerodynamics and structural deformation - from short, noisy data. CVA is structured so that the identification can be done in real or near real time, using computationally stable algorithms. Modeling LSS dynamics in 1-g laboratories has always been a major impediment not only to understanding their behavior in orbit, but also to controlling it. In cases where the theoretical model is not confirmed, current methods provide few clues concerning additional dynamical relationships that are not included in the theoretical models. CVA needs no a priori model data, or structure; all statistically significant dynamical states are determined using natural, entropy-based methods. Heretofore, a major limitation in applying adaptive

  20. Identification of genes that mediate protection against soybean pathogens

    USDA-ARS?s Scientific Manuscript database

    In the last twenty years, over 40 resistance genes (R-genes) have been cloned and characterized from plants. Of these, only three have been cloned in soybean. Cloning of resistance genes in soybean has been hampered by a complex, duplicated genome, clustering of R-genes, and lack of tools to charac...

  1. Cyclic nucleotide gated channel gene family in tomato: genome-wide identification and functional analyses in disease resistance

    PubMed Central

    Saand, Mumtaz A.; Xu, You-Ping; Li, Wen; Wang, Ji-Peng; Cai, Xin-Zhong

    2015-01-01

    The cyclic nucleotide gated channel (CNGC) is suggested to be one of the important calcium conducting channels. Nevertheless, genome-wide identification and systemic functional analysis of CNGC gene family in crop plant species have not yet been conducted. In this study, we performed genome-wide identification of CNGC gene family in the economically important crop tomato (Solanum lycopersicum L.) and analyzed function of the group IVb SlCNGC genes in disease resistance. Eighteen CNGC genes were identified in tomato genome, and four CNGC loci that were misannotated at database were corrected by cloning and sequencing. Detailed bioinformatics analyses on gene structure, domain composition and phylogenetic relationship of the SlCNGC gene family were conducted and the group-specific feature was revealed. Comprehensive expression analyses demonstrated that SlCNGC genes were highly, widely but differently responsive to diverse stimuli. Pharmacological assays showed that the putative CNGC activators cGMP and cAMP enhanced resistance against Sclerotinia sclerotiorum. Silencing of group IVb SlCNGC genes significantly enhanced resistance to fungal pathogens Pythium aphanidermatum and S. sclerotiorum, strongly reduced resistance to viral pathogen Tobacco rattle virus, while attenuated PAMP- and DAMP-triggered immunity as shown by obvious decrease of the flg22- and AtPep1-elicited hydrogen peroxide accumulation in SlCNGC-silenced plants. Additionally, silencing of these SlCNGC genes significantly altered expression of a set of Ca2+ signaling genes including SlCaMs, SlCDPKs, and SlCAMTA3. Collectively, our results reveal that group IV SlCNGC genes regulate a wide range of resistance in tomato probably by affecting Ca2+ signaling. PMID:25999969

  2. Genome-wide identification, classification, and expression analysis of sHSP genes in Chinese cabbage (Brassica rapa ssp pekinensis).

    PubMed

    Tao, P; Guo, W L; Li, B Y; Wang, W H; Yue, Z C; Lei, J L; Zhong, X M

    2015-10-05

    Small heat shock proteins (sHSPs) are essential for the plant's normal development and stress responses, especially the heat stress response. The information regarding sHSP genes in Chinese cabbage (Brassica rapa ssp pekinensis) is sparse, hence we performed a genome-wide analysis to identify sHSP genes in this species. We identified 26 non-redundant sHSP genes distributed on all chromosomes, except chromosome A7, with one additional sHSP gene identified from an expressed sequence tag library. Chinese cabbage was found to contain more sHSP genes than Arabidopsis. The 27 sHSP genes were classified into 11 subfamilies. We identified 22 groups of sHSP syntenic orthologous genes between Chinese cabbage and Arabidopsis. In addition, eight groups of paralogous genes were uncovered in Chinese cabbage. Protein structures of the 27 Chinese cabbage sHSPs were modeled using Phyre2, which revealed that all of them contain several conserved β strands across different subfamilies. In general, gene structure was conserved within each subfamily between Chinese cabbage and Arabidopsis, except for peroxisome sHSP. Analysis of promoter motifs showed that most sHSP genes contain heat shock elements or variants. We also found that biased gene loss has occurred during the evolution of the sHSP subfamily in Chinese cabbage. Expression analysis indicated that the greatest transcript abundance of most Chinese cabbage sHSP genes was found in siliques and early cotyledon embryos. Thus, genome-wide identification and characterization of sHSP genes is a first and important step in the investigation of sHSPs in Chinese cabbage.

  3. Applications of nonlinear system identification to structural health monitoring.

    SciTech Connect

    Farrar, C. R.; Sohn, H.; Robertson, A. N.

    2004-01-01

    The process of implementing a damage detection strategy for aerospace, civil and mechanical engineering infrastructure is referred to as structural health monitoring (SHM). In many cases damage causes a structure that initially behaves in a predominantly linear manner to exhibit nonlinear response when subject to its operating environment. The formation of cracks that subsequently open and close under operating loads is an example of such damage. The damage detection process can be significantly enhanced if one takes advantage of these nonlinear effects when extracting damage-sensitive features from measured data. This paper will provide an overview of nonlinear system identification techniques that are used for the feature extraction process. Specifically, three general approaches that apply nonlinear system identification techniques to the damage detection process are discussed. The first two approaches attempt to quantify the deviation of the system from its initial linear characteristics that is a direct result of damage. The third approach is to extract features from the data that are directly related to the specific nonlinearity associated with the damaged condition. To conclude this discussion, a summary of outstanding issues associated with the application of nonlinear system identification techniques to the SHM problem is presented.

  4. Modal identification experiment design for large space structures

    NASA Technical Reports Server (NTRS)

    Kim, Hyoung M.; Doiron, Harold H.

    1991-01-01

    This paper describes an on-orbit modal identification experiment design for large space structures. Space Station Freedom (SSF) systems design definition and structural dynamic models were used as representative large space structures for optimizing experiment design. Important structural modes of study models were selected to provide a guide for experiment design and used to assess the design performance. A pulsed random excitation technique using propulsion jets was developed to identify closely-spaced modes. A measuremenat location selection approach was developed to estimate accurate mode shapes as well as frequencies and damping factors. The data acquisition system and operational scenarios were designed to have minimal impacts on the SSF. A comprehensive simulation was conducted to assess the overall performance of the experiment design.

  5. Simultaneous expansion and orthogonalization of measured modes for structure identification

    NASA Technical Reports Server (NTRS)

    Smith, Suzanne Weaver; Beattie, Christopher A.

    1990-01-01

    Tests of large structures on-orbit will be performed with measurements at a relatively few structure points. Values for the unmeasured degrees of freedom (dofs) can be estimated based on measured dofs and analytical model dynamic information. These 'expanded' mode shapes are useful for optimal-update identification and damage location as well as test/analysis correlation. A new method of expansion for test mode shape vectors is developed from the orthogonal Procrustes problem from computational linear algebra. A subspace defined by the set of measured dofs is compared to a subspace defined by mode shapes from an analytical model of the structure. The method simultaneously expands and orthogonalizes the mode shape vectors. Two demonstration problems are used to compare the new method to current expansion techniques. One demonstration uses test data from a laboratory scale-model truss structure. Performance of the new method is comparable or superior to that of the previous expansion methods which require separate orthogonalization.

  6. Partial rpoB gene sequencing for identification of Leptospira species.

    PubMed

    La Scola, Bernard; Bui, Lan T M; Baranton, Guy; Khamis, Atieh; Raoult, Didier

    2006-10-01

    The usual target for sequence-based identification of Leptospira species is the 16S rRNA gene. However, because the 16S rRNA gene is not polymorphic enough, it is necessary to sequence a 1500 bp segment of this gene for accurate identification. Based on the alignment of previously determined rpoB of three Leptospira strains, we designed and tested a primer pair that enabled us to amplify and sequence a 600 bp segment of Leptospira rpoB. This segment was species-specific for the 16 species tested, but was unable to separate Leptospira interrogans serovars accurately. For the 11 L. interrogans serovars tested, only seven genotypes could be determined. We thus think that analysis of partial rpoB may be useful as an initial screening test for the identification of a new isolate of Leptospira and detection or identification of Leptospira in clinical or environmental samples, but not for serovar determination.

  7. Rapid detection and identification of Clostridium chauvoei by PCR based on flagellin gene sequence.

    PubMed

    Kojima, A; Uchida, I; Sekizaki, T; Sasaki, Y; Ogikubo, Y; Tamura, Y

    2001-02-26

    We developed a one-step polymerase chain reaction (PCR) system that specifically detects Clostridium chauvoei. Oligonucleotide primers were designed to amplify a 516-bp fragment of the structural flagellin gene. The specificity of the PCR was investigated by analyzing 59 strains of clostridia, and seven strain of other genera. A 516-bp fragment could be amplified from all the C. chauvoei strains tested, and no amplification was observed by using DNAs from the other strains tested, including Clostridium septicum. Similarly, this PCR-based method specifically detected C. chauvoei DNA sequences in samples of muscle and exudate of obtained from mice within 12h of inoculation. In tests using samples of muscle or liver, the limit of detection was about 200 organisms per reaction. These results suggest that the one-step PCR system may be useful for direct detection and identification of C. chauvoei in clinical specimens.

  8. Altered gene expression correlates with DNA structure.

    PubMed

    Kohwi, Y; Kohwi-Shigematsu, T

    1991-12-01

    We examined the participation of triplex DNA structure in gene regulation using a poly(dG)-poly(dC) sequence as a model. We show that a poly(dG)-poly(dC) sequence, which can adopt an intramolecular dG.dG.dC triplex under superhelical strain, strongly augments gene expression when placed 5' to a promoter. The activity of this sequence exhibits a striking length dependency: dG tracts of 27-30 bp augment the expression of a reporter gene to a level comparable to that observed with the polyoma enhancer in mouse LTK- cells, whereas tracts of 35 bp and longer have virtually no effect. A supercoiled plasmid containing a dG tract of 30 bp competes in vivo for a trans-acting factor as revealed by reduction in the reporter gene transcription driven by the (dG)29/promoter of the test plasmid, while dGs of 35 bp and longer in the competition plasmid failed to compete. In purified supercoiled plasmid DNA at a superhelical density of -0.05, dG tracts of 32 bp and longer form a triplex, whereas those of 30 bp and shorter remain double-stranded under a PBS solution. These results suggest that a localized superhelical strain can exist, at least transiently, in mouse LTK- cells, and before being relaxed by topoisomerases this rapidly induces dG tracts of 35 bp and longer to adopt a triplex preventing the factor from binding. Thus, these data suggest that a poly(dG)-poly(dC) sequence can function as a negative regulator by adopting an intramolecular triple helix structure in vivo.

  9. Mode shape identification using residues of measured offshore structure data

    NASA Astrophysics Data System (ADS)

    Wang, Chao; Liu, Fushun; Lu, Hongchao

    2017-04-01

    Compared to traditional mode shape identification methods such as eigensystem realization algorithm (ERA), this article proposes a mode shape identification method based on estimated residues of measured data and the theoretical relationship between the estimated residues and the mode shapes from the state space model is obtained by defining a coefficient matrix. A mass-spring model with five degrees of freedom (DOFs) is utilized to demonstrate the approach. The numerical results indicate that the estimated residues are the mode shapes of structures, but with a coefficient matrix to maintain consistency with the mode shapes from the ERA. Using MATLAB a complicated numerical jacket platform is built to further study the proposed method. The results show that mode shapes consistent with those from the ERA could be obtained by taking the defined coefficient matrix into account, which is also demonstrated by a physical beam model that was built at Ocean University of China.

  10. Chromosomal Anomalies in Individuals with Autism: A Strategy Towards the Identification of Genes Involved in Autism

    ERIC Educational Resources Information Center

    Castermans, Dries; Wilquet, Valerie; Steyaert, Jean; van de Ven, Wim; Fryns, Jean-Pierre; Devriendt, Koen

    2004-01-01

    We review the different strategies currently used to try to identify susceptibility genes for idiopathic autism. Although identification of genes is usually straightforward in Mendelian disorders, it has proved to be much more difficult to establish in polygenic disorders like autism. Neither genome screens of affected siblings nor the large…

  11. Chromosomal Anomalies in Individuals with Autism: A Strategy Towards the Identification of Genes Involved in Autism

    ERIC Educational Resources Information Center

    Castermans, Dries; Wilquet, Valerie; Steyaert, Jean; van de Ven, Wim; Fryns, Jean-Pierre; Devriendt, Koen

    2004-01-01

    We review the different strategies currently used to try to identify susceptibility genes for idiopathic autism. Although identification of genes is usually straightforward in Mendelian disorders, it has proved to be much more difficult to establish in polygenic disorders like autism. Neither genome screens of affected siblings nor the large…

  12. Diagnostic test for prenatal identification of Down's syndrome and mental retardation and gene therapy therefor

    DOEpatents

    Smith, Desmond J.; Rubin, Edward M.

    2000-01-01

    A a diagnostic test useful for prenatal identification of Down syndrome and mental retardation. A method for gene therapy for correction and treatment of Down syndrome. DYRK gene involved in the ability to learn. A method for diagnosing Down's syndrome and mental retardation and an assay therefor. A pharmaceutical composition for treatment of Down's syndrome mental retardation.

  13. The Trametes hirsuta 072 laccase multigene family: Genes identification and transcriptional analysis under copper ions induction.

    PubMed

    Vasina, Daria V; Mustafaev, Orkhan N; Moiseenko, Konstantin V; Sadovskaya, Natalia S; Glazunova, Olga A; Tyurin, Аlexander А; Fedorova, Tatiana V; Pavlov, Andrey R; Tyazhelova, Tatiana V; Goldenkova-Pavlova, Irina V; Koroleva, Olga V

    2015-09-01

    Laccases, blue copper-containing oxidases, ≿ an play an important role in a variety of natural processes. The majority of fungal laccases are encoded by multigene families that express closely related proteins with distinct functions. Currently, only the properties of major gene products of the fungal laccase families have been described. Our study is focused on identification and characterization of laccase genes, which are transcribed in basidiomycete Trametes hirsuta 072, an efficient lignin degrader, in a liquid medium, both without and with induction of laccase transcription by copper ions. We carried out production of cDNA libraries from total fungal RNA, followed by suppression subtractive hybridization and mirror orientation selection procedures, and then used Next Generation Sequencing to identify low abundance and differentially expressed laccase transcripts. This approach resulted in description of five laccase genes of the fungal family, which, according to the phylogenetic analysis, belong to distinct clusters within the Trametes genus. Further analysis established similarity of physical, chemical, and catalytic properties between laccases inside each cluster. Structural modeling suggested importance of the sequence differences in the clusters for laccase substrate specificity and catalytic efficiency. The implications of the laccase variations for the fungal physiology are discussed. Copyright © 2015 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

  14. Genome-wide identification and expression analysis of WNK kinase gene family in rice.

    PubMed

    Manuka, Rakesh; Saddhe, Ankush Ashok; Kumar, Kundan

    2015-12-01

    Eukaryotic protein kinases represent one of the largest gene families involved in diverse regulatory functions. WNK (With No Lysine) kinases are members of ser/thr protein kinase family, which lack conserved catalytic lysine (K) residue at protein kinase subdomain II and is replaced by either asparagine, serine or glycine residues. They are involved in regulation of flowering time, circadian rhythms and abiotic stresses in Arabidopsis thaliana. In the present study, we have identified 9 members of WNK in rice, showed resemblance to Arabidopsis and human WNK and clustered into five main clades phylogenetically. The predicted genes structure, bonafide conserved signature motif and domains strongly support their identity, as members of WNK kinase family. We have analyzed their chromosomal distribution, physio-chemical properties, subcellular localizations and cis-elements in the promoter regions in silico. Further, transcript analysis of OsWNK by qRT-PCR revealed their differential regulation in tissue specific and abiotic stresses libraries. In conclusion, the identification of nine OsWNK and transcript level expression pattern under abiotic stress using qRT-PCR in rice will significantly contribute towards the understanding of WNK genes in monocots and thus provide a set up for functional genomics studies of WNK protein kinases.

  15. Genome-wide identification and characterization of aquaporin gene family in Beta vulgaris

    PubMed Central

    Kong, Weilong; Yang, Shaozong; Wang, Yulu; Bendahmane, Mohammed

    2017-01-01

    Aquaporins (AQPs) are essential channel proteins that execute multi-functions throughout plant growth and development, including water transport, uncharged solutes uptake, stress response, and so on. Here, we report the first genome-wide identification and characterization AQP (BvAQP) genes in sugar beet (Beta vulgaris), an important crop widely cultivated for feed, for sugar production and for bioethanol production. Twenty-eight sugar beet AQPs (BvAQPs) were identified and assigned into five subfamilies based on phylogenetic analyses: seven of plasma membrane (PIPs), eight of tonoplast (TIPs), nine of NOD26-like (NIPs), three of small basic (SIPs), and one of x-intrinsic proteins (XIPs). BvAQP genes unevenly mapped on all chromosomes, except on chromosome 4. Gene structure and motifs analyses revealed that BvAQP have conserved exon-intron organization and that they exhibit conserved motifs within each subfamily. Prediction of BvAQPs functions, based on key protein domains conservation, showed a remarkable difference in substrate specificity among the five subfamilies. Analyses of BvAQPs expression, by mean of RNA-seq, in different plant organs and in response to various abiotic stresses revealed that they were ubiquitously expressed and that their expression was induced by heat and salt stresses. These results provide a reference base to address further the function of sugar beet aquaporins and to explore future applications for plants growth and development improvements as well as in response to environmental stresses. PMID:28948097

  16. Inferring gene structures in genomic sequences using pattern recognition and expressed sequence tags

    SciTech Connect

    Xu, Y.; Mural, R.; Uberbacher, E.

    1997-02-01

    Computational methods for gene identification in genomic sequences typically have two phases: coding region prediction and gene parsing. While there are many effective methods for predicting coding regions (exons), parsing the predicted exons into proper gene structures, to a large extent, remains an unsolved problem. This paper presents an algorithm for inferring gene structures from predicted exon candidates, based on Expressed Sequence Tags (ESTs) and biological intuition/rules. The algorithm first finds all the related ESTs in the EST database (dbEST) for each predicted exon, and infers the boundaries of one or a series of genes based on the available EST information and biological rules. Then it constructs gene models within each pair of gene boundaries, that are most consistent with the EST information. By exploiting EST information and biological rules, the algorithm can (1) model complicated multiple gene structures, including embedded genes, (2) identify falsely-predicted exons and locate missed exons, and (3) make more accurate exon boundary predictions. The algorithm has been implemented and tested on long genomic sequences with a number of genes. Test results show that very accurate (predicted) gene models can be expected when related ESTs exist for the predicted exons.

  17. Inferring gene structures in genomic sequences using pattern recognition and expressed sequence tags.

    PubMed

    Xu, Y; Mural, R J; Uberbacher, E C

    1997-01-01

    Computational methods for gene identification in genomic sequences typically have two phases: coding region prediction and gene parsing. While there are many effective methods for predicting coding regions (exons), parsing the predicted exons into proper gene structures, to a large extent, remains an unsolved problem. This paper presents an algorithm for inferring gene structures from predicted exon candidates, based on Expressed Sequence Tags (ESTs) and biological intuition/rules. The algorithm first finds all the related ESTs in the EST database (dbEST) for each predicted exon, and infers the boundaries of one or a series of genes based on the available EST information and biological rules. Then it constructs gene models within each pair of gene boundaries, that are most consistent with the EST information. By exploiting EST information and biological rules, the algorithm can (1) model complicated multiple gene structures, including embedded genes, (2) identify falsely-predicted exons and locate missed exons, and (3) make more accurate exon boundary predictions. The algorithm has been implemented and tested on long genomic sequences with a number of genes. Test results show that very accurate (predicted) gene models can be expected when related ESTs exist for the predicted exons.

  18. Identification of oral cancer related candidate genes by integrating protein-protein interactions, gene ontology, pathway analysis and immunohistochemistry.

    PubMed

    Kumar, Ravindra; Samal, Sabindra K; Routray, Samapika; Dash, Rupesh; Dixit, Anshuman

    2017-05-30

    In the recent years, bioinformatics methods have been reported with a high degree of success for candidate gene identification. In this milieu, we have used an integrated bioinformatics approach assimilating information from gene ontologies (GO), protein-protein interaction (PPI) and network analysis to predict candidate genes related to oral squamous cell carcinoma (OSCC). A total of 40973 PPIs were considered for 4704 cancer-related genes to construct human cancer gene network (HCGN). The importance of each node was measured in HCGN by ten different centrality measures. We have shown that the top ranking genes are related to a significantly higher number of diseases as compared to other genes in HCGN. A total of 39 candidate oral cancer target genes were predicted by combining top ranked genes and the genes corresponding to significantly enriched oral cancer related GO terms. Initial verification using literature and available experimental data indicated that 29 genes were related with OSCC. A detailed pathway analysis led us to propose a role for the selected candidate genes in the invasion and metastasis in OSCC. We further validated our predictions using immunohistochemistry (IHC) and found that the gene FLNA was upregulated while the genes ARRB1 and HTT were downregulated in the OSCC tissue samples.

  19. Identification of Constrained Cancer Driver Genes Based on Mutation Timing

    PubMed Central

    Sakoparnig, Thomas; Fried, Patrick; Beerenwinkel, Niko

    2015-01-01

    Cancer drivers are genomic alterations that provide cells containing them with a selective advantage over their local competitors, whereas neutral passengers do not change the somatic fitness of cells. Cancer-driving mutations are usually discriminated from passenger mutations by their higher degree of recurrence in tumor samples. However, there is increasing evidence that many additional driver mutations may exist that occur at very low frequencies among tumors. This observation has prompted alternative methods for driver detection, including finding groups of mutually exclusive mutations and incorporating prior biological knowledge about gene function or network structure. Dependencies among drivers due to epistatic interactions can also result in low mutation frequencies, but this effect has been ignored in driver detection so far. Here, we present a new computational approach for identifying genomic alterations that occur at low frequencies because they depend on other events. Unlike passengers, these constrained mutations display punctuated patterns of occurrence in time. We test this driver–passenger discrimination approach based on mutation timing in extensive simulation studies, and we apply it to cross-sectional copy number alteration (CNA) data from ovarian cancer, CNA and single-nucleotide variant (SNV) data from breast tumors and SNV data from colorectal cancer. Among the top ranked predicted drivers, we find low-frequency genes that have already been shown to be involved in carcinogenesis, as well as many new candidate drivers. The mutation timing approach is orthogonal and complementary to existing driver prediction methods. It will help identifying from cancer genome data the alterations that drive tumor progression. PMID:25569148

  20. Identification and characterization of mouse otic sensory lineage genes

    PubMed Central

    Hartman, Byron H.; Durruthy-Durruthy, Robert; Laske, Roman D.; Losorelli, Steven; Heller, Stefan

    2015-01-01

    Vertebrate embryogenesis gives rise to all cell types of an organism through the development of many unique lineages derived from the three primordial germ layers. The otic sensory lineage arises from the otic vesicle, a structure formed through invagination of placodal non-neural ectoderm. This developmental lineage possesses unique differentiation potential, giving rise to otic sensory cell populations including hair cells, supporting cells, and ganglion neurons of the auditory and vestibular organs. Here we present a systematic approach to identify transcriptional features that distinguish the otic sensory lineage (from early otic progenitors to otic sensory populations) from other major lineages of vertebrate development. We used a microarray approach to analyze otic sensory lineage populations including microdissected otic vesicles (embryonic day 10.5) as well as isolated neonatal cochlear hair cells and supporting cells at postnatal day 3. Non-otic tissue samples including periotic tissues and whole embryos with otic regions removed were used as reference populations to evaluate otic specificity. Otic populations shared transcriptome-wide correlations in expression profiles that distinguish members of this lineage from non-otic populations. We further analyzed the microarray data using comparative and dimension reduction methods to identify individual genes that are specifically expressed in the otic sensory lineage. This analysis identified and ranked top otic sensory lineage-specific transcripts including Fbxo2, Col9a2, and Oc90, and additional novel otic lineage markers. To validate these results we performed expression analysis on select genes using immunohistochemistry and in situ hybridization. Fbxo2 showed the most striking pattern of specificity to the otic sensory lineage, including robust expression in the early otic vesicle and sustained expression in prosensory progenitors and auditory and vestibular hair cells and supporting cells. PMID:25852475

  1. Identification and characterization of mouse otic sensory lineage genes.

    PubMed

    Hartman, Byron H; Durruthy-Durruthy, Robert; Laske, Roman D; Losorelli, Steven; Heller, Stefan

    2015-01-01

    Vertebrate embryogenesis gives rise to all cell types of an organism through the development of many unique lineages derived from the three primordial germ layers. The otic sensory lineage arises from the otic vesicle, a structure formed through invagination of placodal non-neural ectoderm. This developmental lineage possesses unique differentiation potential, giving rise to otic sensory cell populations including hair cells, supporting cells, and ganglion neurons of the auditory and vestibular organs. Here we present a systematic approach to identify transcriptional features that distinguish the otic sensory lineage (from early otic progenitors to otic sensory populations) from other major lineages of vertebrate development. We used a microarray approach to analyze otic sensory lineage populations including microdissected otic vesicles (embryonic day 10.5) as well as isolated neonatal cochlear hair cells and supporting cells at postnatal day 3. Non-otic tissue samples including periotic tissues and whole embryos with otic regions removed were used as reference populations to evaluate otic specificity. Otic populations shared transcriptome-wide correlations in expression profiles that distinguish members of this lineage from non-otic populations. We further analyzed the microarray data using comparative and dimension reduction methods to identify individual genes that are specifically expressed in the otic sensory lineage. This analysis identified and ranked top otic sensory lineage-specific transcripts including Fbxo2, Col9a2, and Oc90, and additional novel otic lineage markers. To validate these results we performed expression analysis on select genes using immunohistochemistry and in situ hybridization. Fbxo2 showed the most striking pattern of specificity to the otic sensory lineage, including robust expression in the early otic vesicle and sustained expression in prosensory progenitors and auditory and vestibular hair cells and supporting cells.

  2. Identification of genes associated with asexual reproduction in Phyllosticta citricarpa mutants obtained through Agrobacterium tumefaciens transformation.

    PubMed

    Goulin, Eduardo Henrique; Savi, Daiani Cristina; Petters, Desirrê Alexia Lourenço; Kava, Vanessa; Galli-Terasawa, Lygia; Silva, Geraldo José; Glienke, Chirlei

    2016-11-01

    Phyllosticta citricarpa is the epidemiological agent of Citrus Black Spot (CBS) disease, which is responsible for large economic losses worldwide. CBS is characterized by the presence of spores (pycnidiospores) in dark lesions of fruit, which are also responsible for short distance dispersal of the disease. The identification of genes involved in asexual reproduction of P. citricarpa can be an alternative for directional disease control. We analyzed a library of mutants obtained through Agrobacterium tumefaciens transformation system, looking for alterations in growth and reproductive structure formation. Two mutant strains were found to have lost the ability to form pycnidia. The flanking T-DNA insertion regions were identified on P. citricarpa genome by using blast analysis and further gene prediction. The predicted genes containing the T-DNA insertions were identified as Spindle Poison Sensitivity Scp3, Ion Transport protein, and Cullin Binding proteins. The Ion Transport and Cullin Binding proteins are known to be correlated with sexual and asexual reproduction in fungi; however, the exact mechanism by which these proteins act on spore formation in P. citricarpa needs to be better characterized. The Scp3 proteins are suggested here for the first time as being associated with asexual reproduction in fungus. This protein is associated with microtubule formation, and as microtubules play an essential role as spindle machinery for chromosome segregation and cytokinesis, insertions in this gene can lead to abnormal formations, such as that observed here in P. citricarpa. We suggest these genes as new targets for fungicide development and CBS disease control, by iRNA. Copyright © 2016 Elsevier GmbH. All rights reserved.

  3. Genome-wide identification and expression profile of homeodomain-leucine zipper Class I gene family in Cucumis sativus.

    PubMed

    Liu, Wei; Fu, Rao; Li, Qiang; Li, Jing; Wang, Lina; Ren, Zhonghai

    2013-12-01

    The HD-Zip proteins comprise one of the largest families of transcription factors in plants. HD-Zip genes have been grouped into four different classes: HD-Zip I to IV. In this study, we described the identification and structural characterization of Class I HD-Zip genes in cucumber. A complete set of 13 HD-Zip I genes were identified in the cucumber genome using Blast search tools and phylogeny. The cucumber HD-Zip I family contained a smaller number of identified genes compared to other higher plants such as Arabidopsis and maize due to the absence of recent gene duplication events. Chromosomal location of these genes revealed that they are distributed unevenly across 5 of 7 chromosomes. Tissue-specific expression profiles showed that 13 cucumber HD-Zip I genes were expressed in at least one of the tissues, which suggested that cucumber HD-Zip I genes took part in many cellular processes. The transcript abundance level analysis during abiotic stress conditions (NaCl, ABA and low temperature treatments) identified a group of HD-Zip I genes that responded to one or more treatments.

  4. S-score: a scoring system for the identification and prioritization of predicted cancer genes.

    PubMed

    de Souza, Jorge E S; Fonseca, André F; Valieris, Renan; Carraro, Dirce M; Wang, Jean Y J; Kolodner, Richard D; de Souza, Sandro J

    2014-01-01

    A new method, which allows for the identification and prioritization of predicted cancer genes for future analysis, is presented. This method generates a gene-specific score called the "S-Score" by incorporating data from different types of analysis including mutation screening, methylation status, copy-number variation and expression profiling. The method was applied to the data from The Cancer Genome Atlas and allowed the identification of known and potentially new oncogenes and tumor suppressors associated with different clinical features including shortest term of survival in ovarian cancer patients and hormonal subtypes in breast cancer patients. Furthermore, for the first time a genome-wide search for genes that behave as oncogenes and tumor suppressors in different tumor types was performed. We envisage that the S-score can be used as a standard method for the identification and prioritization of cancer genes for follow-up studies.

  5. Density based pruning for identification of differentially expressed genes from microarray data

    PubMed Central

    2010-01-01

    Motivation Identification of differentially expressed genes from microarray datasets is one of the most important analyses for microarray data mining. Popular algorithms such as statistical t-test rank genes based on a single statistics. The false positive rate of these methods can be improved by considering other features of differentially expressed genes. Results We proposed a pattern recognition strategy for identifying differentially expressed genes. Genes are mapped to a two dimension feature space composed of average difference of gene expression and average expression levels. A density based pruning algorithm (DB Pruning) is developed to screen out potential differentially expressed genes usually located in the sparse boundary region. Biases of popular algorithms for identifying differentially expressed genes are visually characterized. Experiments on 17 datasets from Gene Omnibus Database (GEO) with experimentally verified differentially expressed genes showed that DB pruning can significantly improve the prediction accuracy of popular identification algorithms such as t-test, rank product, and fold change. Conclusions Density based pruning of non-differentially expressed genes is an effective method for enhancing statistical testing based algorithms for identifying differentially expressed genes. It improves t-test, rank product, and fold change by 11% to 50% in the numbers of identified true differentially expressed genes. The source code of DB pruning is freely available on our website http://mleg.cse.sc.edu/degprune PMID:21047384

  6. An approach for the identification of targets specific to bone metastasis using cancer genes interactome and gene ontology analysis.

    PubMed

    Vashisht, Shikha; Bagler, Ganesh

    2012-01-01

    Metastasis is one of the most enigmatic aspects of cancer pathogenesis and is a major cause of cancer-associated mortality. Secondary bone cancer (SBC) is a complex disease caused by metastasis of tumor cells from their primary site and is characterized by intricate interplay of molecular interactions. Identification of targets for multifactorial diseases such as SBC, the most frequent complication of breast and prostate cancers, is a challenge. Towards achieving our aim of identification of targets specific to SBC, we constructed a 'Cancer Genes Network', a representative protein interactome of cancer genes. Using graph theoretical methods, we obtained a set of key genes that are relevant for generic mechanisms of cancers and have a role in biological essentiality. We also compiled a curated dataset of 391 SBC genes from published literature which serves as a basis of ontological correlates of secondary bone cancer. Building on these results, we implement a strategy based on generic cancer genes, SBC genes and gene ontology enrichment method, to obtain a set of targets that are specific to bone metastasis. Through this study, we present an approach for probing one of the major complications in cancers, namely, metastasis. The results on genes that play generic roles in cancer phenotype, obtained by network analysis of 'Cancer Genes Network', have broader implications in understanding the role of molecular regulators in mechanisms of cancers. Specifically, our study provides a set of potential targets that are of ontological and regulatory relevance to secondary bone cancer.

  7. An Approach for the Identification of Targets Specific to Bone Metastasis Using Cancer Genes Interactome and Gene Ontology Analysis

    PubMed Central

    Vashisht, Shikha; Bagler, Ganesh

    2012-01-01

    Metastasis is one of the most enigmatic aspects of cancer pathogenesis and is a major cause of cancer-associated mortality. Secondary bone cancer (SBC) is a complex disease caused by metastasis of tumor cells from their primary site and is characterized by intricate interplay of molecular interactions. Identification of targets for multifactorial diseases such as SBC, the most frequent complication of breast and prostate cancers, is a challenge. Towards achieving our aim of identification of targets specific to SBC, we constructed a ‘Cancer Genes Network’, a representative protein interactome of cancer genes. Using graph theoretical methods, we obtained a set of key genes that are relevant for generic mechanisms of cancers and have a role in biological essentiality. We also compiled a curated dataset of 391 SBC genes from published literature which serves as a basis of ontological correlates of secondary bone cancer. Building on these results, we implement a strategy based on generic cancer genes, SBC genes and gene ontology enrichment method, to obtain a set of targets that are specific to bone metastasis. Through this study, we present an approach for probing one of the major complications in cancers, namely, metastasis. The results on genes that play generic roles in cancer phenotype, obtained by network analysis of ‘Cancer Genes Network’, have broader implications in understanding the role of molecular regulators in mechanisms of cancers. Specifically, our study provides a set of potential targets that are of ontological and regulatory relevance to secondary bone cancer. PMID:23166660

  8. Identification of candidates for human disease genes using large-scale PCR mapping of gene-based STSs

    SciTech Connect

    Berry, R.; Stevens, T.J.; Wilcox, A.S.

    1994-09-01

    We have developed a strategy for the rapid identification of possible human disease/syndrome genes. Using this procedure we found candidates for 45 human disease/syndrome genes from the first 200 genes mapped. New human genes are identified through automated single-pass sequencing into the 3{prime} untranslated (3{prime}UT) regions of human cDNAs. Primers derived from the 3{prime}UT region sequences, representing gene-based STSs, are used for PCR analyses of the CEPH megabase YAC DNA pools. With this approach {approximately}18,000 megabase YACs can be screened and a single YAC identified using only 52 PCR reactions. The YAC localization in conjunction with other mapping approaches, such as PCR mapping to chromosomes by means of somatic hybrids, allows mapping to chromosomal band locations. In this manner, each gene can be associated with its own STS which in turn specifies both a corresponding genomic clone and a specific location in the genome. These locations can be compared to purported locations of disease genes listed in Online Mendelian Inheritance in Man. Using our current collection of >3,000 human brain cDNA sequences as a resource, we have carried out a proof of principle study in which {approximately}200 cDNAs were mapped to YACs within a few months. Appropriate scale up of this strategy could permit mapping of most human genes and identification of many candidate disease genes over the next few years.

  9. Identification of breast cancer candidate genes using gene co-expression and protein-protein interaction information.

    PubMed

    Yue, Zhenyu; Li, Hai-Tao; Yang, Yabing; Hussain, Sajid; Zheng, Chun-Hou; Xia, Junfeng; Chen, Yan

    2016-06-14

    Breast cancer (BC) is one of the most common malignancies that could threaten female health. As the molecular mechanism of BC has not yet been completely discovered, identification of related genes of this disease is an important area of research that could provide new insights into gene function as well as potential treatment targets. Here we used subnetwork extraction algorithms to identify novel BC related genes based on the known BC genes (seed genes), gene co-expression profiles and protein-protein interaction network. We computationally predicted seven key genes (EPHX2, GHRH, PPYR1, ALPP, KNG1, GSK3A and TRIT1) as putative genes of BC. Further analysis shows that six of these have been reported as breast cancer associated genes, and one (PPYR1) as cancer associated gene. Lastly, we developed an expression signature using these seven key genes which significantly stratified 1660 BC patients according to relapse free survival (hazard ratio [HR], 0.55; 95% confidence interval [CI], 0.46-0.65; Logrank p = 5.5e-13). The 7-genes signature could be established as a useful predictor of disease prognosis in BC patients. Overall, the identified seven genes might be useful prognostic and predictive molecular markers to predict the clinical outcome of BC patients.

  10. Identification of Krit1B: a novel alternative splicing isoform of cerebral cavernous malformation gene-1.

    PubMed

    Retta, Saverio Francesco; Avolio, Maria; Francalanci, Floriana; Procida, Simone; Balzac, Fiorella; Degani, Simona; Tarone, Guido; Silengo, Lorenzo

    2004-01-21

    Cerebral cavernous malformations (CCM) are vascular malformations, mostly located in the central nervous system, which occur in 0.1-0.5% of the population. They are characterized by abnormally enlarged and often leaking capillary cavities without intervening neural parenchyma. Some are clinically silent, whereas others cause seizures, intracerebral haemorrhage or focal neurological deficits. These vascular malformations can arise sporadically or may be inherited as an autosomal dominant condition with incomplete penetrance. At least 45% of families affected with cerebral cavernous malformations harbour a mutation in Krev interaction trapped-1 (Krit1) gene (cerebral cavernous malformation gene-1, CCM1). This gene contains 16 coding exons which encode a 736-amino acid protein containing three ankyrin repeats and a FERM domain. Neither the CCM1 pathogenetic mechanisms nor the function of the Krit1 protein are understood so far, although several hypotheses have been inferred from the predicted consequences of Krit1 mutations as well as from the identification of Krit1 as a binding partner of Rap1A, ICAP1A and microtubules. Here, we report the identification of Krit1B, a novel Krit1 isoform characterized by the alternative splicing of the 15th coding exon. We show that the Krit1B splice isoform is widely expressed in mouse cell lines and tissues, whereas its expression is highly restricted in human. In addition, we developed a real-time PCR strategy to accurately quantify the relative ratio of the two Krit1 alternative transcripts in different tissues, demonstrating a Krit1B/Krit1A ratio up to 20% in mouse thymus, but significantly lower ratios in other tissues. Bioinformatic analysis using exon/gene-prediction, comparative alignment and structure analysis programs supported the existence of Krit1 alternative transcripts lacking the 15th coding exon and showed that the splicing out of this exon occurs outside of potentially important Krit1 structural domains but in a

  11. Compressive-Sensing-Based Structure Identification for Multilayer Networks.

    PubMed

    Mei, Guofeng; Wu, Xiaoqun; Wang, Yingfei; Hu, Mi; Lu, Jun-An; Chen, Guanrong

    2017-02-13

    The coexistence of multiple types of interactions within social, technological, and biological networks has motivated the study of the multilayer nature of real-world networks. Meanwhile, identifying network structures from dynamical observations is an essential issue pervading over the current research on complex networks. This paper addresses the problem of structure identification for multilayer networks, which is an important topic but involves a challenging inverse problem. To clearly reveal the formalism, the simplest two-layer network model is considered and a new approach to identifying the structure of one layer is proposed. Specifically, if the interested layer is sparsely connected and the node behaviors of the other layer are observable at a few time points, then a theoretical framework is established based on compressive sensing and regularization. Some numerical examples illustrate the effectiveness of the identification scheme, its requirement of a relatively small number of observations, as well as its robustness against small noise. It is noteworthy that the framework can be straightforwardly extended to multilayer networks, thus applicable to a variety of real-world complex systems.

  12. Identification of Prostate Cancer-Related Genes Using Inhibition of NMD in Prostate Cancer Cell Lines

    DTIC Science & Technology

    2005-01-01

    TITLE AND SUBTITLE 5. FUNDING NUMBERS Identification of Prostate Cancer -Related Genes Using W81XWH-04- 1 -0045 Inhibition of NMD in Prostate Cancer Cell...analytical filter to the prostate cancer cell lines 22RV- 1 and DU-145. Ten genes for each cell line have been selected for sequencing analysis.(Table...list of candidate genes for sequencing analysis from the LNCaP, PC3, 22RV- 1 and DU- 145 prostate cancer cell lines has been produced REPORTABLE

  13. Parameter identification of material constants in a composite shell structure

    NASA Technical Reports Server (NTRS)

    Martinez, David R.; Carne, Thomas G.

    1988-01-01

    One of the basic requirements in engineering analysis is the development of a mathematical model describing the system. Frequently comparisons with test data are used as a measurement of the adequacy of the model. An attempt is typically made to update or improve the model to provide a test verified analysis tool. System identification provides a systematic procedure for accomplishing this task. The terms system identification, parameter estimation, and model correlation all refer to techniques that use test information to update or verify mathematical models. The goal of system identification is to improve the correlation of model predictions with measured test data, and produce accurate, predictive models. For nonmetallic structures the modeling task is often difficult due to uncertainties in the elastic constants. A finite element model of the shell was created, which included uncertain orthotropic elastic constants. A modal survey test was then performed on the shell. The resulting modal data, along with the finite element model of the shell, were used in a Bayes estimation algorithm. This permitted the use of covariance matrices to weight the confidence in the initial parameter values as well as confidence in the measured test data. The estimation procedure also employed the concept of successive linearization to obtain an approximate solution to the original nonlinear estimation problem.

  14. A hybrid method for identification of structural domains

    NASA Astrophysics Data System (ADS)

    Hua, Yongpan; Zhu, Min; Wang, Yuelong; Xie, Zhaoyang; Li, Menglong

    2014-12-01

    Structural domains in proteins are the basic units to form various proteins. In the protein's evolution and functioning, domains play important roles. But the definition of domain is not yet precisely given, and the update cycle of structural domain databases is long. The automatic algorithms identify domains slowly, while protein entities with great structural complexity are on the rise. Here, we present a method which recognizes the compact and modular segments of polypeptide chains to identify structural domains, and contrast some data sets to illuminate their effect. The method combines support vector machine (SVM) with K-means algorithm. It is faster and more stable than most current algorithms and performs better. It also indicates that when proteins are presented as some Alpha-carbon atoms in 3D space, it is feasible to identify structural domains by the spatially structural properties. We have developed a web-server, which would be helpful in identification of structural domains (http://vis.sculab.org/~huayongpan/cgi-bin/domainAssignment.cgi).

  15. Identification of ovarian cancer associated genes using an integrated approach in a Boolean framework

    PubMed Central

    2013-01-01

    Background Cancer is a complex disease where molecular mechanism remains elusive. A systems approach is needed to integrate diverse biological information for the prognosis and therapy risk assessment using mechanistic approach to understand gene interactions in pathways and networks and functional attributes to unravel the biological behaviour of tumors. Results We weighted the functional attributes based on various functional properties observed between cancerous and non-cancerous genes reported from literature. This weighing schema was then encoded in a Boolean logic framework to rank differentially expressed genes. We have identified 17 genes to be differentially expressed from a total of 11,173 genes, where ten genes are reported to be down-regulated via epigenetic inactivation and seven genes are up-regulated. Here, we report that the overexpressed genes IRAK1, CHEK1 and BUB1 may play an important role in ovarian cancer. We also show that these 17 genes can be used to form an ovarian cancer signature, to distinguish normal from ovarian cancer subjects and that the set of three genes, CHEK1, AR, and LYN, can be used to classify good and poor prognostic tumors. Conclusion We provided a workflow using a Boolean logic schema for the identification of differentially expressed genes by integrating diverse biological information. This integrated approach resulted in the identification of genes as potential biomarkers in ovarian cancer. PMID:23383610

  16. Identification of suitable reference genes in the mouse placenta.

    PubMed

    Solano, María Emilia; Thiele, Kristin; Kowal, Mirka Katharina; Arck, Petra Clara

    2016-03-01

    Quantitative real-time reverse transcription polymerase chain reaction (RT-qPCR) is a reliable tool to analyse gene expression profiles. The expression of housekeeping genes generally serves as a reference for mRNA amount, assuming that it remains stable under pathophysiological and experimental conditions. To date, an empirical validation of reference genes suitable for RT-qPCR-based studies in the mouse placenta is missing. We used NormFinder and BestKeeper statistical software to analyse the expression stability of candidate housekeeping genes quantified by RT-qPCR in mouse placentas. Fifteen of 32 potential candidate housekeeping genes analysed on gestation day (gd) 16.5 in mouse placentas exhibited an optimal cycle threshold (Ct). Among them B2m, Polr2a, Ubc, and Ywhaz genes showed the highest expression stability in placentas from control, but also experimentally-challenged mice. These genes as well as the currently widely used housekeeping genes Hprt1, Actb, and Gapdh were selected for further quality assessments. We quantified the Ct values of these selected genes in placental samples obtained from wild-type or genetically engineered dams at different gds, or upon selected experimental interventions known to affect placental phenotype. Among all housekeeping genes analysed, Polr2a was the most stably expressed and its expression stability excelled in combination with Ubc. Polr2a, especially in combination with Ubc, can be proposed as highly suitable endogenous reference for gene expression analysis in mouse-derived placental tissue. Moreover, the validation of both genes as a stable reference gene in human placenta-derived tissue strengthens the translational relevance of RT-qPCR findings using mouse placenta. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. Gene structure, phylogeny and expression profile of the sucrose synthase gene family in cacao (Theobroma cacao L.).

    PubMed

    Li, Fupeng; Hao, Chaoyun; Yan, Lin; Wu, Baoduo; Qin, Xiaowei; Lai, Jianxiong; Song, Yinghui

    2015-09-01

    In higher plants, sucrose synthase (Sus, EC 2.4.1.13) is widely considered as a key enzyme involved in sucrose metabolism. Although, several paralogous genes encoding different isozymes of Sus have been identified and characterized in multiple plant genomes, to date detailed information about the Sus genes is lacking for cacao. This study reports the identification of six novel Sus genes from economically important cacao tree. Analyses of the gene structure and phylogeny of the Sus genes demonstrated evolutionary conservation in the Sus family across cacao and other plant species. The expression of cacao Sus genes was investigated via real-time PCR in various tissues, different developmental phases of leaf, flower bud and pod. The Sus genes exhibited distinct but partially redundant expression profiles in cacao, with TcSus1, TcSus5 and TcSus6, being the predominant genes in the bark with phloem, TcSus2 predominantly expressing in the seed during the stereotype stage. TcSus3 and TcSus4 were significantly detected more in the pod husk and seed coat along the pod development, and showed development dependent expression profiles in the cacao pod. These results provide new insights into the evolution, and basic information that will assist in elucidating the functions of cacao Sus gene family.

  18. A Kalman-Filter Based Approach to Identification of Time-Varying Gene Regulatory Networks

    PubMed Central

    Xiong, Jie; Zhou, Tong

    2013-01-01

    Motivation Conventional identification methods for gene regulatory networks (GRNs) have overwhelmingly adopted static topology models, which remains unchanged over time to represent the underlying molecular interactions of a biological system. However, GRNs are dynamic in response to physiological and environmental changes. Although there is a rich literature in modeling static or temporally invariant networks, how to systematically recover these temporally changing networks remains a major and significant pressing challenge. The purpose of this study is to suggest a two-step strategy that recovers time-varying GRNs. Results It is suggested in this paper to utilize a switching auto-regressive model to describe the dynamics of time-varying GRNs, and a two-step strategy is proposed to recover the structure of time-varying GRNs. In the first step, the change points are detected by a Kalman-filter based method. The observed time series are divided into several segments using these detection results; and each time series segment belonging to two successive demarcating change points is associated with an individual static regulatory network. In the second step, conditional network structure identification methods are used to reconstruct the topology for each time interval. This two-step strategy efficiently decouples the change point detection problem and the topology inference problem. Simulation results show that the proposed strategy can detect the change points precisely and recover each individual topology structure effectively. Moreover, computation results with the developmental data of Drosophila Melanogaster show that the proposed change point detection procedure is also able to work effectively in real world applications and the change point estimation accuracy exceeds other existing approaches, which means the suggested strategy may also be helpful in solving actual GRN reconstruction problem. PMID:24116005

  19. Identification of an Efficient Gene Expression Panel for Glioblastoma Classification

    PubMed Central

    Zelaya, Ivette; Laks, Dan R.; Zhao, Yining; Kawaguchi, Riki; Gao, Fuying; Kornblum, Harley I.; Coppola, Giovanni

    2016-01-01

    We present here a novel genetic algorithm-based random forest (GARF) modeling technique that enables a reduction in the complexity of large gene disease signatures to highly accurate, greatly simplified gene panels. When applied to 803 glioblastoma multiforme samples, this method allowed the 840-gene Verhaak et al. gene panel (the standard in the field) to be reduced to a 48-gene classifier, while retaining 90.91% classification accuracy, and outperforming the best available alternative methods. Additionally, using this approach we produced a 32-gene panel which allows for better consistency between RNA-seq and microarray-based classifications, improving cross-platform classification retention from 69.67% to 86.07%. A webpage producing these classifications is available at http://simplegbm.semel.ucla.edu. PMID:27855170

  20. Identification of a family of muscarinic acetylcholine receptor genes

    SciTech Connect

    Bonner, T.I.; Buckley, N.J.; Young, A.C.; Brann, M.R.

    1987-07-31

    Complementary DNAs for three different muscarinic acetylcholine receptors were isolated from a rat cerebral cortex library, and the cloned receptors were expressed in mammalian cells. Analysis of human and rat genomic clones indicates that there are at least four functional muscarinic receptor genes and that these genes lack introns in the coding sequence. This gene family provides a new basis for evaluating the diversity of muscarinic mechanisms in the nervous system.

  1. Identification of Haemophilus ducreyi genes expressed during human infection.

    PubMed

    Bauer, Margaret E; Fortney, Kate R; Harrison, Alistair; Janowicz, Diane M; Munson, Robert S; Spinola, Stanley M

    2008-04-01

    To identify Haemophilus ducreyi transcripts that are expressed during human infection, we used selective capture of transcribed sequences (SCOTS) with RNA isolated from pustules obtained from three volunteers infected with H. ducreyi, and with RNA isolated from broth-grown bacteria used to infect volunteers. With SCOTS, competitive hybridization of tissue-derived and broth-derived sequences identifies genes that may be preferentially expressed in vivo. Among the three tissue specimens, we identified 531 genes expressed in vivo. Southern blot analysis of 60 genes from each tissue showed that 87 % of the identified genes hybridized better with cDNA derived from tissue specimens than with cDNA derived from broth-grown bacteria. RT-PCR on nine additional pustules confirmed in vivo expression of 10 of 11 selected genes in other volunteers. Of the 531 genes, 139 were identified in at least two volunteers. These 139 genes fell into several functional categories, including biosynthesis and metabolism, regulation, and cellular processes, such as transcription, translation, cell division, DNA replication and repair, and transport. Detection of genes involved in anaerobic and aerobic respiration indicated that H. ducreyi likely encounters both microenvironments within the pustule. Other genes detected suggest an increase in DNA damage and stress in vivo. Genes involved in virulence in other bacterial pathogens and 32 genes encoding hypothetical proteins were identified, and may represent novel virulence factors. We identified three genes, lspA1, lspA2 and tadA, known to be required for virulence in humans. This is the first study to broadly define transcripts expressed by H. ducreyi in humans.

  2. Identification of Microbial Gene Biomarkers for in situ RDX Biodegradation

    DTIC Science & Technology

    2012-12-01

    Cloning and characterization of the genes encoding a cytochrome P450 (PipA) involved in piperidine and pyrrolidine utilization and...Depot xplA Flavodoxin- cytochrome P450 gene XplA Flavodoxin- cytochrome P450 protein xplB Flavodoxin reductase gene XplB Flavodoxin reductase ...system composed of the fused flavodoxin- cytochrome P450 enzyme, XplA, and a flavodoxin reductase , XplB (Rylott et al. 2006; Seth-Smith et al.

  3. An Alzheimers disease related genes identification method based on multiple classifier integration.

    PubMed

    Miao, Yu; Jiang, Huiyan; Liu, Huiling; Yao, Yu-Dong

    2017-10-01

    Alzheimers disease (AD) is a fatal neurodegenerative disease and the onset of AD is insidious. Full understanding of the AD-related genes (ADGs) has not been completed. The National Center for Biotechnology Information (NCBI) provides an AD dataset of 22,283 genes. Among these genes, 71 genes have been identified as ADGs. But there may still be underlying ADGs that have not yet been identified in the remaining 22,212 genes. This paper aims to identify additional ADGs using machine learning techniques. To improve the accuracy of ADG identification, we propose a gene identification method through multiple classifier integration. First, a feature selection algorithm is applied to select the most relevant attributes. Second, a two-stage cascading classifier is developed to identify ADGs. The first stage classification task is based on the relevance vector machine and, in the second stage, the results of three classifiers, support vector machine, random forest and extreme learning machine, are combined through voting. According to our results, feature selection improves accuracy and reduces training time. Voting based classifier reduces the classification errors. The proposed ADG identification system provides accuracy, sensitivity and specificity at levels of 78.77%, 83.10% and 74.67%, respectively. Based on the proposed ADG identification method, potentially additional ADGs are identified and top 13 genes (predicted ADGs) are presented. In this paper, an ADG identification method for identifying ADGs is presented. The proposed method which combines feature selection, cascading classifier and majority voting leads to higher specificity and significantly increases the accuracy and sensitivity of ADG identification. Potentially new ADGs are identified. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Structure identification in fuzzy inference using reinforcement learning

    NASA Technical Reports Server (NTRS)

    Berenji, Hamid R.; Khedkar, Pratap

    1993-01-01

    In our previous work on the GARIC architecture, we have shown that the system can start with surface structure of the knowledge base (i.e., the linguistic expression of the rules) and learn the deep structure (i.e., the fuzzy membership functions of the labels used in the rules) by using reinforcement learning. Assuming the surface structure, GARIC refines the fuzzy membership functions used in the consequents of the rules using a gradient descent procedure. This hybrid fuzzy logic and reinforcement learning approach can learn to balance a cart-pole system and to backup a truck to its docking location after a few trials. In this paper, we discuss how to do structure identification using reinforcement learning in fuzzy inference systems. This involves identifying both surface as well as deep structure of the knowledge base. The term set of fuzzy linguistic labels used in describing the values of each control variable must be derived. In this process, splitting a label refers to creating new labels which are more granular than the original label and merging two labels creates a more general label. Splitting and merging of labels directly transform the structure of the action selection network used in GARIC by increasing or decreasing the number of hidden layer nodes.

  5. Seismic damage identification for steel structures using distributed fiber optics.

    PubMed

    Hou, Shuang; Cai, C S; Ou, Jinping

    2009-08-01

    A distributed fiber optic monitoring methodology based on optic time domain reflectometry technology is developed for seismic damage identification of steel structures. Epoxy with a strength closely associated to a specified structure damage state is used for bonding zigzagged configured optic fibers on the surfaces of the structure. Sensing the local deformation of the structure, the epoxy modulates the signal change within the optic fiber in response to the damage state of the structure. A monotonic loading test is conducted on a steel specimen installed with the proposed sensing system using selected epoxy that will crack at the designated strain level, which indicates the damage of the steel structure. Then, using the selected epoxy, a varying degree of cyclic loading amplitudes, which is associated with different damage states, is applied on a second specimen. The test results show that the specimen's damage can be identified by the optic sensors, and its maximum local deformation can be recorded by the sensing system; moreover, the damage evolution can also be identified.

  6. Identification of genes and proteins associated with anagen wool growth.

    PubMed

    Zhao, J; Liu, N; Liu, K; He, J; Yu, J; Bu, R; Cheng, M; De, W; Liu, J; Li, H

    2017-02-01

    Identifying genes of major effect for wool growth would offer strategies for improving the quality and increasing the yield of fine wool. In this study, we employed the Agilent Sheep Gene Expression Microarray and proteomic technology to investigate the gene expression patterns of body side skin (more wool growing) in Aohan fine wool sheep (a Chinese indigenous breed) in comparison with groin skin (no wool growing) at the anagen stage of the wool follicle. A microarray study revealed that 4772 probes were differentially expressed, including 2071 upregulated and 2701 downregulated probes, in the comparisons of body side skin vs. groin skin (S/G). The microarray results were verified by means of quantitative PCR. A total of 1099 probes were assigned to unique genes/transcripts. The number of distinct genes/transcripts (annotated) was 926, of which 352 were upregulated and 574 were downregulated. In S/G, 13 genes were upregulated by more than 10 fold, whereas 60 genes were downregulated by more than 10 fold. Further analysis revealed that the majority of the genes possibly related to the wool growth could be assigned to categories including regulation of cell division, intermediate filament, cytoskeletal part and growth factor activity. Several potential gene families may participate in hair growth regulation, including fibroblast growth factors, transforming growth factor-β, WNTs, insulin-like growth factor, vascular endothelial growth factors and so on. Proteomic analysis also revealed 196 differentially expressed protein points, of which 121 were identified as single protein points.

  7. Identification of druggable cancer driver genes amplified across TCGA datasets.

    PubMed

    Chen, Ying; McGee, Jeremy; Chen, Xianming; Doman, Thompson N; Gong, Xueqian; Zhang, Youyan; Hamm, Nicole; Ma, Xiwen; Higgs, Richard E; Bhagwat, Shripad V; Buchanan, Sean; Peng, Sheng-Bin; Staschke, Kirk A; Yadav, Vipin; Yue, Yong; Kouros-Mehr, Hosein

    2014-01-01

    The Cancer Genome Atlas (TCGA) projects have advanced our understanding of the driver mutations, genetic backgrounds, and key pathways activated across cancer types. Analysis of TCGA datasets have mostly focused on somatic mutations and translocations, with less emphasis placed on gene amplifications. Here we describe a bioinformatics screening strategy to identify putative cancer driver genes amplified across TCGA datasets. We carried out GISTIC2 analysis of TCGA datasets spanning 16 cancer subtypes and identified 486 genes that were amplified in two or more datasets. The list was narrowed to 75 cancer-associated genes with potential "druggable" properties. The majority of the genes were localized to 14 amplicons spread across the genome. To identify potential cancer driver genes, we analyzed gene copy number and mRNA expression data from individual patient samples and identified 42 putative cancer driver genes linked to diverse oncogenic processes. Oncogenic activity was further validated by siRNA/shRNA knockdown and by referencing the Project Achilles datasets. The amplified genes represented a number of gene families, including epigenetic regulators, cell cycle-associated genes, DNA damage response/repair genes, metabolic regulators, and genes linked to the Wnt, Notch, Hedgehog, JAK/STAT, NF-KB and MAPK signaling pathways. Among the 42 putative driver genes were known driver genes, such as EGFR, ERBB2 and PIK3CA. Wild-type KRAS was amplified in several cancer types, and KRAS-amplified cancer cell lines were most sensitive to KRAS shRNA, suggesting that KRAS amplification was an independent oncogenic event. A number of MAP kinase adapters were co-amplified with their receptor tyrosine kinases, such as the FGFR adapter FRS2 and the EGFR family adapters GRB2 and GRB7. The ubiquitin-like ligase DCUN1D1 and the histone methyltransferase NSD3 were also identified as novel putative cancer driver genes. We discuss the patient tailoring implications for existing cancer

  8. Identification and interpretation of longitudinal gene expression changes in trauma.

    PubMed

    Rajicic, Natasa; Cuschieri, Joseph; Finkelstein, Dianne M; Miller-Graziano, Carol L; Hayden, Douglas; Moldawer, Lyle L; Moore, Ernest; O'Keefe, Grant; Pelik, Kimberly; Warren, H Shaw; Schoenfeld, David A

    2010-12-20

    The relationship between leukocyte gene expression and recovery of respiratory function after injury may provide information on the etiology of multiple organ dysfunction. To find a list of genes for which expression after injury predicts respiratory recovery, and to identify which networks and pathways characterize these genes. Blood was sampled at 12 hours and at 1, 4, 7, 21 and 28 days from 147 patients who had been admitted to the hospital after blunt trauma. Leukocyte gene expression was measured using Affymetrix oligonucleotide arrays. A linear model, fit to each probe-set expression value, was used to impute the gene expression trajectory over the entire follow-up period. The proportional hazards model score test was used to calculate the statistical significance of each probe-set trajectory in predicting respiratory recovery. A list of genes was determined such that the expected proportion of false positive results was less than 10%. These genes were compared to the Gene Ontology for 'response to stimulus' and, using Ingenuity software, were mapped into networks and pathways. The median time to respiratory recovery was 6 days. There were 170 probe-sets representing 135 genes that were found to be related to respiratory recovery. These genes could be mapped to nine networks. Two known pathways that were activated were antigen processing and presentation and JAK-signaling. The examination of the relationship of gene expression over time with a patient's clinical course can provide information which may be useful in determining the mechanism of recovery or lack of recovery after severe injury.

  9. Identification of Genetic Elements Associated with EPSPS Gene Amplification

    PubMed Central

    Gaines, Todd A.; Wright, Alice A.; Molin, William T.; Lorentz, Lothar; Riggins, Chance W.; Tranel, Patrick J.; Beffa, Roland; Westra, Philip; Powles, Stephen B.

    2013-01-01

    Weed populations can have high genetic plasticity and rapid responses to environmental selection pressures. For example, 100-fold amplification of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene evolved in the weed species Amaranthus palmeri to confer resistance to glyphosate, the world’s most important herbicide. However, the gene amplification mechanism is unknown. We sequenced the EPSPS gene and genomic regions flanking EPSPS loci in A. palmeri, and searched for mobile genetic elements or repetitive sequences. The EPSPS gene was 10,229 bp, containing 8 exons and 7 introns. The gene amplification likely proceeded through a DNA-mediated mechanism, as introns exist in the amplified gene copies and the entire amplified sequence is at least 30 kb in length. Our data support the presence of two EPSPS loci in susceptible (S) A. palmeri, and that only one of these was amplified in glyphosate-resistant (R) A. palmeri. The EPSPS gene amplification event likely occurred recently, as no sequence polymorphisms were found within introns of amplified EPSPS copies from R individuals. Sequences with homology to miniature inverted-repeat transposable elements (MITEs) were identified next to EPSPS gene copies only in R individuals. Additionally, a putative Activator (Ac) transposase and a repetitive sequence region were associated with amplified EPSPS genes. The mechanism controlling this DNA-mediated amplification remains unknown. Further investigation is necessary to determine if the gene amplification may have proceeded via DNA transposon-mediated replication, and/or unequal recombination between different genomic regions resulting in replication of the EPSPS gene. PMID:23762434

  10. Identification and Interpretation of Longitudinal Gene Expression Changes in Trauma

    PubMed Central

    Rajicic, Natasa; Cuschieri, Joseph; Finkelstein, Dianne M.; Miller-Graziano, Carol L.; Hayden, Douglas; Moldawer, Lyle L.; Moore, Ernest; O'Keefe, Grant; Pelik, Kimberly; Warren, H. Shaw; Schoenfeld, David A.

    2010-01-01

    Rationale The relationship between leukocyte gene expression and recovery of respiratory function after injury may provide information on the etiology of multiple organ dysfunction. Objectives To find a list of genes for which expression after injury predicts respiratory recovery, and to identify which networks and pathways characterize these genes. Methods Blood was sampled at 12 hours and at 1, 4, 7, 21 and 28 days from 147 patients who had been admitted to the hospital after blunt trauma. Leukocyte gene expression was measured using Affymetrix oligonucleotide arrays. A linear model, fit to each probe-set expression value, was used to impute the gene expression trajectory over the entire follow-up period. The proportional hazards model score test was used to calculate the statistical significance of each probe-set trajectory in predicting respiratory recovery. A list of genes was determined such that the expected proportion of false positive results was less than 10%. These genes were compared to the Gene Ontology for ‘response to stimulus’ and, using Ingenuity software, were mapped into networks and pathways. Measurements and Main Results The median time to respiratory recovery was 6 days. There were 170 probe-sets representing 135 genes that were found to be related to respiratory recovery. These genes could be mapped to nine networks. Two known pathways that were activated were antigen processing and presentation and JAK- signaling. Conclusions The examination of the relationship of gene expression over time with a patient's clinical course can provide information which may be useful in determining the mechanism of recovery or lack of recovery after severe injury. PMID:21187951

  11. Identification of novel genes involved in the plasticity of pituitary melanotropes in amphibians.

    PubMed

    Malagón, M M; Cruz-García, D; Díaz-Ruiz, A; Peinado, J R; Pulido, M R; Araújo, J; Garcia-Navarro, S; Gracia-Navarro, F; Castaño, J P; Vázquez-Martínez, R

    2009-04-01

    Melanotrope cells from the amphibian intermediate lobe are composed of two subpopulations that exhibit opposite secretory behavior: hypersecretory and hormone-storage hyposecretory melanotropes. Isolation of these subpopulations allowed a comparison of their gene expression profiles by differential display, leading to the identification of a number of genes differentially expressed in hypersecretory or hyposecretory melanotropes. Among them, we chose two (preferentially expressed in hyposecretory cells) of unknown function but structurally related to proteins involved in the secretory process: Rab18 and KIAA0555. We demonstrate that, upon activation of the regulated secretory pathway, Rab18 associates with secretory granules, inhibits their mobilization, and, consequently, reduces the secretory capacity of neuroendocrine cells. The other gene, KIAA0555, was predicted by in silico analysis to encode a protein with a long coiled-coil domain, a structural feature also shared by different proteins related to intracellular membrane traffic (i.e., golgins), and a hydrophobic C-terminal domain that could function as a transmembrane domain. A database search unveiled the existence of a KIAA0555 paralogue, KIAA4091, displaying a long coiled-coil region highly similar to that of KIAA0555 and an identical C-terminal transmembrane domain. Both KIAA0555 and KIAA4091 were found to be predominantly expressed in tissues containing cells with regulated secretory pathway, that is, endocrine and neural tissues. Moreover, when exogenously expressed in HEK293 cells, both proteins showed a yuxtanuclear distribution, which partially overlaps with that of a Golgi complex marker, thus suggesting a possible role of these two proteins in the control of the secretory process.

  12. A DEEP LEARNING APPROACH FOR CANCER DETECTION AND RELEVANT GENE IDENTIFICATION

    PubMed Central

    Ghaeini, Reza; Hendrix, David A.

    2016-01-01

    Cancer detection from gene expression data continues to pose a challenge due to the high dimensionality and complexity of these data. After decades of research there is still uncertainty in the clinical diagnosis of cancer and the identification of tumor-specific markers. Here we present a deep learning approach to cancer detection, and to the identification of genes critical for the diagnosis of breast cancer. First, we used Stacked Denoising Autoencoder (SDAE) to deeply extract functional features from high dimensional gene expression profiles. Next, we evaluated the performance of the extracted representation through supervised classification models to verify the usefulness of the new features in cancer detection. Lastly, we identified a set of highly interactive genes by analyzing the SDAE connectivity matrices. Our results and analysis illustrate that these highly interactive genes could be useful cancer biomarkers for the detection of breast cancer that deserve further studies. PMID:27896977

  13. The IL-9 receptor gene (IL9R): Genomic structure, chromosomal localization in the pseudoautosomal region of the long arm of sex chromosomes, and identification of IL9R pseudogenes at 9qter, 10pter, 16pter, 18pter

    SciTech Connect

    Kermouni, A.; Godelaine, D.; Lurquin, C.; Szikora, J.P.

    1995-09-20

    Cosmids containing the human IL-9 receptor (R) gene (IL9R) have been isolated from a genomic library using the IL9R cDNA as a probe. We have shown that the human IL9R gene is composed of 11 exons and 10 introns, stretching over {approx} 17 kb, and is located within the pseudoautosomal region of the Xq and Yq chromosome, in the vicinity of the telomere. Analysis of the 5` flanking region revealed multiple transcription initiation sites as well as potential binding motifs for AP1, AP2, AP3, Sp1, and NF-kB, although this region lacks a TATA box. Using the human IL9R cosmid as a probe to perform fluorescence in situ hybridization, additional signals were identified in the subtelomeric regions of chromosomes 9q, 10p, 16p, and 18p. IL9R homologs located on chromosomes 9 and 18 were partially characterized, while those located on chromosomes 16 and 10 were completely sequenced. Although they are similiar to the IL9R gene ({approx} 90% identity), none of these copies encodes a functional receptor: none of them contains sequences homologous to the 5` flanking region or exon 1 of the IL9R gene, and the remaining ORFs have been inactivated by various point mutations and deletions. Taken together, our results indicate that the IL9R gene is located at Xq28 and Yq12, in the long arm pseudoautosomal region, and that four IL9R pseudogenes are located on 9q34, 10p15, 16p13.3 and 18p11.3, probably dispersed as the result of translocations during evolution. 42 refs., 6 figs., 3 tabs.

  14. Identification and Functional Analysis of the Nocardithiocin Gene Cluster in Nocardia pseudobrasiliensis

    PubMed Central

    Sakai, Kanae; Komaki, Hisayuki; Gonoi, Tohru

    2015-01-01

    Nocardithiocin is a thiopeptide compound isolated from the opportunistic pathogen Nocardia pseudobrasiliensis. It shows a strong activity against acid-fast bacteria and is also active against rifampicin-resistant Mycobacterium tuberculosis. Here, we report the identification of the nocardithiocin gene cluster in N. pseudobrasiliensis IFM 0761 based on conserved thiopeptide biosynthesis gene sequence and the whole genome sequence. The predicted gene cluster was confirmed by gene disruption and complementation. As expected, strains containing the disrupted gene did not produce nocardithiocin while gene complementation restored nocardithiocin production in these strains. The predicted cluster was further analyzed using RNA-seq which showed that the nocardithiocin gene cluster contains 12 genes within a 15.2-kb region. This finding will promote the improvement of nocardithiocin productivity and its derivatives production. PMID:26588225

  15. Identification and Functional Analysis of the Nocardithiocin Gene Cluster in Nocardia pseudobrasiliensis.

    PubMed

    Sakai, Kanae; Komaki, Hisayuki; Gonoi, Tohru

    2015-01-01

    Nocardithiocin is a thiopeptide compound isolated from the opportunistic pathogen Nocardia pseudobrasiliensis. It shows a strong activity against acid-fast bacteria and is also active against rifampicin-resistant Mycobacterium tuberculosis. Here, we report the identification of the nocardithiocin gene cluster in N. pseudobrasiliensis IFM 0761 based on conserved thiopeptide biosynthesis gene sequence and the whole genome sequence. The predicted gene cluster was confirmed by gene disruption and complementation. As expected, strains containing the disrupted gene did not produce nocardithiocin while gene complementation restored nocardithiocin production in these strains. The predicted cluster was further analyzed using RNA-seq which showed that the nocardithiocin gene cluster contains 12 genes within a 15.2-kb region. This finding will promote the improvement of nocardithiocin productivity and its derivatives production.

  16. Identification of genes associated with low furanocoumarin content in grapefruit.

    PubMed

    Chen, Chunxian; Yu, Qibin; Wei, Xu; Cancalon, Paul F; Gmitter, Fred G

    2014-10-01

    Some furanocoumarins in grapefruit (Citrus paradisi) are associated with the so-called grapefruit juice effect. Previous phytochemical quantification and genetic analysis suggested that the synthesis of these furanocoumarins may be controlled by a single gene in the pathway. In this study, cDNA-amplified fragment length polymorphism (cDNA-AFLP) analysis of fruit tissues was performed to identify the candidate gene(s) likely associated with low furanocoumarin content in grapefruit. Fifteen tentative differentially expressed fragments were cloned through the cDNA-AFLP analysis of the grapefruit variety Foster and its spontaneous low-furanocoumarin mutant Low Acid Foster. Sequence analysis revealed a cDNA-AFLP fragment, Contig 6, was homologous to a substrate-proved psoralen synthase gene, CYP71A22, and was part of citrus unigenes Cit.3003 and Csi.1332, and predicted genes Ciclev10004717m in mandarin and orange1.1g041507m in sweet orange. The two predicted genes contained the highly conserved motifs at one of the substrate recognition sites of CYP71A22. Digital gene expression profile showed the unigenes were expressed only in fruit and seed. Quantitative real-time PCR also proved Contig 6 was down-regulated in Low Acid Foster. These results showed the differentially expressed Contig 6 was related to the reduced furanocoumarin levels in the mutant. The identified fragment, homologs, unigenes, and genes may facilitate further furanocoumarin genetic study and grapefruit variety improvement.

  17. Identification of major blast resistance genes in the southern US

    USDA-ARS?s Scientific Manuscript database

    Resistance (R) genes in rice play important roles in preventing infections of rice blast fungus, Magnaporthe oryzae. In order to identify more R genes for different rice growing areas in the Southern US, an extensive field survey of the blast fungus was performed from 2012 to 2013. A total of 500 is...

  18. Comprehensive identification of conditionally essential genes in mycobacteria.

    PubMed

    Sassetti, C M; Boyd, D H; Rubin, E J

    2001-10-23

    An increasing number of microbial genomes have been completely sequenced, and the identified genes are categorized based on their homology to genes of known function. However, the function of a large number of genes cannot be determined on this basis alone. Here, we describe a technique, transposon site hybridization (TraSH), which allows rapid functional characterization by identifying the complete set of genes required for growth under different conditions. TraSH combines high-density insertional mutagenesis with microarray mapping of pools of mutants. We have made large pools of independent transposon mutants in mycobacteria by using a mariner-based transposon and efficient phage transduction. By using TraSH, we have defined the set of genes required for growth of Mycobacterium bovis bacillus Calmette-Guérin on minimal but not rich medium. Genes of both known and unknown functions were identified. Of the genes with known functions, nearly all were involved in amino acid biosynthesis. TraSH is a powerful method for categorizing gene function that should be applicable to a variety of microorganisms.

  19. Identification of possible structural error in hydrological models

    NASA Astrophysics Data System (ADS)

    Singh, S. K.; Bárdossy, A.; McMillan, H.

    2012-04-01

    Hydrological Models are simplifications and theoretical approximations of complex natural phenomena. Hence, they cannot predict perfectly what happen in natural systems. There are several reasons; some of the main reasons are error in the input data, imperfect model structure, insufficient information for parameter identification etc. The identification of structural error in a complex model is very difficult task. This is especially difficult as the final differences between observation and model results are a combined consequence of the above reasons. In this study we aimed to develop a tool to identify possible model structural error in hydrological model by using the concept of the data depth function. The model was calibrated using the ROPE (Bárdossy and Singh 2008) algorithm and the optimal parameter space was obtained. From N optimal parameter sets N discharge series were obtained and boundary of the convex hull from d-dimensional dataset corresponding N discharge series (DB) is taken for further analysis. A d-dimensional dataset corresponding to the observed discharge (DX) is taken and depth of the each elements of observed discharge is calculated with respect to the boundary of the convex hull from N model discharge series. If there are elements in DX whose depths are zero with respect to the convex hull (DB), then those corresponding to d-days trajectories of the observation for which there is no similarity in any of the model parameterization. These elements can give possible indication for model structure errors. The methodology was demonstrated on two models HYMOD and TopNet in Pelorous catchment of New Zealand. Bárdossy, A. and S. K. Singh (2008). "Robust estimation of hydrological model parameters." Hydrology and Earth System Sciences 12: 1273-1283.

  20. Gene name identification and normalization using a model organism database.

    PubMed

    Morgan, Alexander A; Hirschman, Lynette; Colosimo, Marc; Yeh, Alexander S; Colombe, Jeff B

    2004-12-01

    Biology has now become an information science, and researchers are increasingly dependent on expert-curated biological databases to organize the findings from the published literature. We report here on a series of experiments related to the application of natural language processing to aid in the curation process for FlyBase. We focused on listing the normalized form of genes and gene products discussed in an article. We broke this into two steps: gene mention tagging in text, followed by normalization of gene names. For gene mention tagging, we adopted a statistical approach. To provide training data, we were able to reverse engineer the gene lists from the associated articles and abstracts, to generate text labeled (imperfectly) with gene mentions. We then evaluated the quality of the noisy training data (precision of 78%, recall 88%) and the quality of the HMM tagger output trained on this noisy data (precision 78%, recall 71%). In order to generate normalized gene lists, we explored two approaches. First, we explored simple pattern matching based on synonym lists to obtain a high recall/low precision system (recall 95%, precision 2%). Using a series of filters, we were able to improve precision to 50% with a recall of 72% (balanced F-measure of 0.59). Our second approach combined the HMM gene mention tagger with various filters to remove ambiguous mentions; this approach achieved an F-measure of 0.72 (precision 88%, recall 61%). These experiments indicate that the lexical resources provided by FlyBase are complete enough to achieve high recall on the gene list task, and that normalization requires accurate disambiguation; different strategies for tagging and normalization trade off recall for precision.

  1. Identification of novel TCDD-regulated genes by microarray analysis

    SciTech Connect

    Hanlon, Paul R.; Zheng, Wenchao; Ko, Alex Y.; Jefcoate, Colin R. . E-mail: jefcoate@facstaff.wisc.edu

    2005-02-01

    TCDD exposure of multipotential C3H10T1/2 fibroblasts for 72 h altered the expression of over 1000 genes, including coordinated changes across large functionally similar gene clusters. TCDD coordinately induced 23 cell cycle-related genes similar to epidermal growth factor (EGF)-induced levels but without any affect on the major mitogenic signaling pathway (extracellular signal-regulated kinase, ERK). TCDD treatment also decreased glycolytic and ribosomal clusters. Most of these TCDD-induced changes were attenuated by the presence of EGF or an adipogenic stimulus, each added during the final 24 h. TCDD prevented 10% of EGF-induced gene responses and 40% of adipogenic responses. Over 100 other genes responded to TCDD during adipogenesis. This group of responses included complete suppression of three proliferins and stimulations of several cytokine receptors. Despite these varied secondary effects of TCDD, direct AhR activation measured by integrated AhR-responsive luciferase reporters was similar under quiescent, EGF-stimulated or adipogenic conditions. Only 23 genes were similarly induced by TCDD regardless of conditions and 10 were suppressed. These 23 genes include: 4 genes previously recognized to contain AhR response elements (cytochrome P450 (CYP) 1B1, CYP1A1, NAD(P)H quinone reductase 1 (NQO1), and aldehyde dehydrogenase 3A1); two novel oxidative genes (alcohol dehydrogenase 3 and superoxide dismutase 3); and glypican 1, a plasma membrane proteoglycan that affects cell signaling. Further experiments demonstrated that TCDD maximally induced NQO1, glypican 1 and alcohol dehydrogenase 3 by 6 h. Glypican 1 activates the actions of many growth factors and therefore may contribute to secondary effects on gene expression.

  2. Identification of genes containing expanded purine repeats in the human genome and their apparent protective role against cancer.

    PubMed

    Singh, Himanshu Narayan; Rajeswari, Moganty R

    2016-01-01

    Purine repeat sequences present in a gene are unique as they have high propensity to form unusual DNA-triple helix structures. Friedreich's ataxia is the only human disease that is well known to be associated with DNA-triplexes formed by purine repeats. The purpose of this study was to recognize the expanded purine repeats (EPRs) in human genome and find their correlation with cancer pathogenesis. We developed "PuRepeatFinder.pl" algorithm to identify non-overlapping EPRs without pyrimidine interruptions in the human genome and customized for searching repeat lengths, n ≥ 200. A total of 1158 EPRs were identified in the genome which followed Wakeby distribution. Two hundred and ninety-six EPRs were found in geneic regions of 282 genes (EPR-genes). Gene clustering of EPR-genes was done based on their cellular function and a large number of EPR-genes were found to be enzymes/enzyme modulators. Meta-analysis of 282 EPR-genes identified only 63 EPR-genes in association with cancer, mostly in breast, lung, and blood cancers. Protein-protein interaction network analysis of all 282 EPR-genes identified proteins including those in cadherins and VEGF. The two observations, that EPRs can induce mutations under malignant conditions and that identification of some EPR-gene products in vital cell signaling-mediated pathways, together suggest the crucial role of EPRs in carcinogenesis. The new link between EPR-genes and their functionally interacting proteins throws a new dimension in the present understanding of cancer pathogenesis and can help in planning therapeutic strategies. Validation of present results using techniques like NGS is required to establish the role of the EPR genes in cancer pathology.

  3. Identification of critical regulatory genes in cancer signaling network using controllability analysis

    NASA Astrophysics Data System (ADS)

    Ravindran, Vandana; Sunitha, V.; Bagler, Ganesh

    2017-05-01

    Cancer is characterized by a complex web of regulatory mechanisms which makes it difficult to identify features that are central to its control. Molecular integrative models of cancer, generated with the help of data from experimental assays, facilitate use of control theory to probe for ways of controlling the state of such a complex dynamic network. We modeled the human cancer signaling network as a directed graph and analyzed it for its controllability, identification of driver nodes and their characterization. We identified the driver nodes using the maximum matching algorithm and classified them as backbone, peripheral and ordinary based on their role in regulatory interactions and control of the network. We found that the backbone driver nodes were key to driving the regulatory network into cancer phenotype (via mutations) as well as for steering into healthy phenotype (as drug targets). This implies that while backbone genes could lead to cancer by virtue of mutations, they are also therapeutic targets of cancer. Further, based on their impact on the size of the set of driver nodes, genes were characterized as indispensable, dispensable and neutral. Indispensable nodes within backbone of the network emerged as central to regulatory mechanisms of control of cancer. In addition to probing the cancer signaling network from the perspective of control, our findings suggest that indispensable backbone driver nodes could be potentially leveraged as therapeutic targets. This study also illustrates the application of structural controllability for studying the mechanisms underlying the regulation of complex diseases.

  4. Identification of driving network of cellular differentiation from single sample time course gene expression data

    NASA Astrophysics Data System (ADS)

    Chen, Ye; Wolanyk, Nathaniel; Ilker, Tunc; Gao, Shouguo; Wang, Xujing

    Methods developed based on bifurcation theory have demonstrated their potential in driving network identification for complex human diseases, including the work by Chen, et al. Recently bifurcation theory has been successfully applied to model cellular differentiation. However, there one often faces a technical challenge in driving network prediction: time course cellular differentiation study often only contains one sample at each time point, while driving network prediction typically require multiple samples at each time point to infer the variation and interaction structures of candidate genes for the driving network. In this study, we investigate several methods to identify both the critical time point and the driving network through examination of how each time point affects the autocorrelation and phase locking. We apply these methods to a high-throughput sequencing (RNA-Seq) dataset of 42 subsets of thymocytes and mature peripheral T cells at multiple time points during their differentiation (GSE48138 from GEO). We compare the predicted driving genes with known transcription regulators of cellular differentiation. We will discuss the advantages and limitations of our proposed methods, as well as potential further improvements of our methods.

  5. [16S rRNA gene sequence analysis for bacterial identification in the clinical laboratory].

    PubMed

    Matsumoto, Takehisa; Sugano, Mitsutoshi

    2013-12-01

    The traditional identification of bacteria on the basis of phenotypic characteristics is generally not as accurate as identification based on genotypic methods. For many years, sequencing of the 16S ribosomal RNA (rRNA) gene has served as an important tool for determining phylogenetic relationships between bacteria. The features of this molecular target that make it a useful phylogenetic tool also make it useful for bacterial detection and identification in the clinical laboratory. 16S rRNA gene sequence analysis can better identify poorly described, rarely isolated, or phenotypically aberrant strains, and can lead to the recognition of novel pathogens and noncultured bacteria. In clinical microbiology, molecular identification based on 16S rDNA sequencing is applied fundamentally to bacteria whose identification by means of other types of techniques is impossible or difficult. However, there are some cases in which 16S rRNA gene sequence analysis can not differentiate closely related bacteria such as Shigella spp. and Escherichia coli at the species level. Thus, it is important to understand the advantages and disadvantages of 16S rRNA gene sequence analysis.

  6. Resistance gene identification from Larimichthys crocea with machine learning techniques.

    PubMed

    Cai, Yinyin; Liao, Zhijun; Ju, Ying; Liu, Juan; Mao, Yong; Liu, Xiangrong

    2016-12-06

    The research on resistance genes (R-gene) plays a vital role in bioinformatics as it has the capability of coping with adverse changes in the external environment, which can form the corresponding resistance protein by transcription and translation. It is meaningful to identify and predict R-gene of Larimichthys crocea (L.Crocea). It is friendly for breeding and the marine environment as well. Large amounts of L.Crocea's immune mechanisms have been explored by biological methods. However, much about them is still unclear. In order to break the limited understanding of the L.Crocea's immune mechanisms and to detect new R-gene and R-gene-like genes, this paper came up with a more useful combination prediction method, which is to extract and classify the feature of available genomic data by machine learning. The effectiveness of feature extraction and classification methods to identify potential novel R-gene was evaluated, and different statistical analyzes were utilized to explore the reliability of prediction method, which can help us further understand the immune mechanisms of L.Crocea against pathogens. In this paper, a webserver called LCRG-Pred is available at http://server.malab.cn/rg_lc/.

  7. Identification of drought-responsive genes from maize inbred lines.

    PubMed

    Li, Fu-Hua; Fu, Feng-Ling; Sha, Li-Na; Li, Wan-Chen

    2007-12-01

    To provide a useful piece of information for the choice of molecular markers to be used in selection of drought tolerance, mRNA differential display was used to isolate genes from a drought-tolerant maize inbred line '81565'. After drought stress, two down-regulated expression gene fragments (MD1 and MD2) and one up-regulated expression fragment (MD3) were obtained. Results of sequence and homology analysis show that MD1 has 97% similarity with matK in maize chloroplast genome, a gene encoding RNA maturase involved in group II intron splicing of RNA transcript; MD2 has 99% similarity with the gene serine/threonine phosphorylase 2C in Sporobolus stapfianus; and MD3 has 99% similarity with rice the gene encoding metacaspase, an arginine/lysine-specific cysteine protease. Based on the sequence of fragment MD2, a new member of maize PP2C gene family, ZmPP2Ca, was cloned by in silicon cloning and reverse transcription polymerase chain reaction (RT-PCR). Real-time fluorescence quantitative polymerase chain reaction (FQ-PCR) showed that expression of the gene was down-regulated in the three drought-tolerant lines ('81565', 'N87-1' and 'R09') and up-regulated in the two drought-sensitive lines ('200B' and 'ES40') under drought stress.

  8. Identification and Characterization of Renal Cell Carcinoma Gene Markers

    PubMed Central

    Dalgin, Gul S.; Holloway, Dustin T.; Liou, Louis S.; DeLisi, Charles

    2007-01-01

    Microarray gene expression profiling has been used to distinguish histological subtypes of renal cell carcinoma (RCC), and consequently to identify specific tumor markers. The analytical procedures currently in use find sets of genes whose average differential expression across the two categories differ significantly. In general each of the markers thus identified does not distinguish tumor from normal with 100% accuracy, although the group as a whole might be able to do so. For the purpose of developing a widely used economically viable diagnostic signature, however, large groups of genes are not likely to be useful. Here we use two different methods, one a support vector machine variant, and the other an exhaustive search, to reanalyze data previously generated in our Lab (Lenburg et al. 2003). We identify 158 genes, each having an expression level that is higher (lower) in every tumor sample than in any normal sample, and each having a minimum differential expression across the two categories at a significance of 0.01. The set is highly enriched in cancer related genes (p = 1.6 × 10−12), containing 43 genes previously associated with either RCC or other types of cancer. Many of the biomarkers appear to be associated with the central alterations known to be required for cancer transformation. These include the oncogenes JAZF1, AXL, ABL2; tumor suppressors RASD1, PTPRO, TFAP2A, CDKN1C; and genes involved in proteolysis or cell-adhesion such as WASF2, and PAPPA. PMID:19455236

  9. Genome-Wide Identification of KANADI1 Target Genes

    PubMed Central

    Ott, Felix; Weigel, Detlef; Bowman, John L.; Heisler, Marcus G.; Wenkel, Stephan

    2013-01-01

    Plant organ development and polarity establishment is mediated by the action of several transcription factors. Among these, the KANADI (KAN) subclade of the GARP protein family plays important roles in polarity-associated processes during embryo, shoot and root patterning. In this study, we have identified a set of potential direct target genes of KAN1 through a combination of chromatin immunoprecipitation/DNA sequencing (ChIP-Seq) and genome-wide transcriptional profiling using tiling arrays. Target genes are over-represented for genes involved in the regulation of organ development as well as in the response to auxin. KAN1 affects directly the expression of several genes previously shown to be important in the establishment of polarity during lateral organ and vascular tissue development. We also show that KAN1 controls through its target genes auxin effects on organ development at different levels: transport and its regulation, and signaling. In addition, KAN1 regulates genes involved in the response to abscisic acid, jasmonic acid, brassinosteroids, ethylene, cytokinins and gibberellins. The role of KAN1 in organ polarity is antagonized by HD-ZIPIII transcription factors, including REVOLUTA (REV). A comparison of their target genes reveals that the REV/KAN1 module acts in organ patterning through opposite regulation of shared targets. Evidence of mutual repression between closely related family members is also shown. PMID:24155946

  10. Global Identification of Genes Specific for Rice Meiosis.

    PubMed

    Zhang, Bingwei; Xu, Meng; Bian, Shiquan; Hou, Lili; Tang, Ding; Li, Yafei; Gu, Minghong; Cheng, Zhukuan; Yu, Hengxiu

    2015-01-01

    The leptotene-zygotene transition is a major step in meiotic progression during which pairing between homologous chromosomes is initiated and double strand breaks occur. OsAM1, a homologue of maize AM1 and Arabidopsis SWI1, encodes a protein with a coiled-coil domain in its central region that is required for the leptotene-zygotene transition during rice meiosis. To gain more insight into the role of OsAM1 in rice meiosis and identify additional meiosis-specific genes, we characterized the transcriptomes of young panicles of Osam1 mutant and wild-type rice plants using RNA-Seq combined with bioinformatic and statistical analyses. As a result, a total of 25,750 and 28,455 genes were expressed in young panicles of wild-type and Osam1 mutant plants, respectively, and 4,400 differentially expressed genes (DEGs; log2 Ratio ≥ 1, FDR ≤ 0.05) were identified. Of these DEGs, four known rice meiosis-specific genes were detected, and 22 new putative meiosis-related genes were found by mapping these DEGs to reference biological pathways in the KEGG database. We identified eight additional well-conserved OsAM1-responsive rice meiotic genes by comparing our RNA-Seq data with known meiotic genes in Arabidopsis and fission yeast.

  11. Resistance gene identification from Larimichthys crocea with machine learning techniques

    PubMed Central

    Cai, Yinyin; Liao, Zhijun; Ju, Ying; Liu, Juan; Mao, Yong; Liu, Xiangrong

    2016-01-01

    The research on resistance genes (R-gene) plays a vital role in bioinformatics as it has the capability of coping with adverse changes in the external environment, which can form the corresponding resistance protein by transcription and translation. It is meaningful to identify and predict R-gene of Larimichthys crocea (L.Crocea). It is friendly for breeding and the marine environment as well. Large amounts of L.Crocea’s immune mechanisms have been explored by biological methods. However, much about them is still unclear. In order to break the limited understanding of the L.Crocea’s immune mechanisms and to detect new R-gene and R-gene-like genes, this paper came up with a more useful combination prediction method, which is to extract and classify the feature of available genomic data by machine learning. The effectiveness of feature extraction and classification methods to identify potential novel R-gene was evaluated, and different statistical analyzes were utilized to explore the reliability of prediction method, which can help us further understand the immune mechanisms of L.Crocea against pathogens. In this paper, a webserver called LCRG-Pred is available at http://server.malab.cn/rg_lc/. PMID:27922074

  12. Identification of highly related references about gene-disease association.

    PubMed

    Liu, Rey-Long; Shih, Chia-Chun

    2014-08-25

    Curation of gene-disease associations published in literature should be based on careful and frequent survey of the references that are highly related to specific gene-disease associations. Retrieval of the references is thus essential for timely and complete curation. We present a technique CRFref (Conclusive, Rich, and Focused References) that, given a gene-disease pair < g, d>, ranks high those biomedical references that are likely to provide conclusive, rich, and focused results about g and d. Such references are expected to be highly related to the association between g and d. CRFref ranks candidate references based on their scores. To estimate the score of a reference r, CRFref estimates and integrates three measures: degree of conclusiveness, degree of richness, and degree of focus of r with respect to < g, d>. To evaluate CRFref, experiments are conducted on over one hundred thousand references for over one thousand gene-disease pairs. Experimental results show that CRFref performs significantly better than several typical types of baselines in ranking high those references that expert curators select to develop the summaries for specific gene-disease associations. CRFref is a good technique to rank high those references that are highly related to specific gene-disease associations. It can be incorporated into existing search engines to prioritize biomedical references for curators and researchers, as well as those text mining systems that aim at the study of gene-disease associations.

  13. Resistance gene identification from Larimichthys crocea with machine learning techniques

    NASA Astrophysics Data System (ADS)

    Cai, Yinyin; Liao, Zhijun; Ju, Ying; Liu, Juan; Mao, Yong; Liu, Xiangrong

    2016-12-01

    The research on resistance genes (R-gene) plays a vital role in bioinformatics as it has the capability of coping with adverse changes in the external environment, which can form the corresponding resistance protein by transcription and translation. It is meaningful to identify and predict R-gene of Larimichthys crocea (L.Crocea). It is friendly for breeding and the marine environment as well. Large amounts of L.Crocea’s immune mechanisms have been explored by biological methods. However, much about them is still unclear. In order to break the limited understanding of the L.Crocea’s immune mechanisms and to detect new R-gene and R-gene-like genes, this paper came up with a more useful combination prediction method, which is to extract and classify the feature of available genomic data by machine learning. The effectiveness of feature extraction and classification methods to identify potential novel R-gene was evaluated, and different statistical analyzes were utilized to explore the reliability of prediction method, which can help us further understand the immune mechanisms of L.Crocea against pathogens. In this paper, a webserver called LCRG-Pred is available at http://server.malab.cn/rg_lc/.

  14. Identification of cell cycle-regulated genes in fission yeast.

    PubMed

    Peng, Xu; Karuturi, R Krishna Murthy; Miller, Lance D; Lin, Kui; Jia, Yonghui; Kondu, Pinar; Wang, Long; Wong, Lim-Soon; Liu, Edison T; Balasubramanian, Mohan K; Liu, Jianhua

    2005-03-01

    Cell cycle progression is both regulated and accompanied by periodic changes in the expression levels of a large number of genes. To investigate cell cycle-regulated transcriptional programs in the fission yeast Schizosaccharomyces pombe, we developed a whole-genome oligonucleotide-based DNA microarray. Microarray analysis of both wild-type and cdc25 mutant cell cultures was performed to identify transcripts whose levels oscillated during the cell cycle. Using an unsupervised algorithm, we identified 747 genes that met the criteria for cell cycle-regulated expression. Peaks of gene expression were found to be distributed throughout the entire cell cycle. Furthermore, we found that four promoter motifs exhibited strong association with cell cycle phase-specific expression. Examination of the regulation of MCB motif-containing genes through the perturbation of DNA synthesis control/MCB-binding factor (DSC/MBF)-mediated transcription in arrested synchronous cdc10 mutant cell cultures revealed a subset of functional targets of the DSC/MBF transcription factor complex, as well as certain gene promoter requirements. Finally, we compared our data with those for the budding yeast Saccharomyces cerevisiae and found approximately 140 genes that are cell cycle regulated in both yeasts, suggesting that these genes may play an evolutionarily conserved role in regulation of cell cycle-specific processes. Our complete data sets are available at http://giscompute.gis.a-star.edu.sg/~gisljh/CDC.

  15. Global Identification of Genes Specific for Rice Meiosis

    PubMed Central

    Zhang, Bingwei; Xu, Meng; Bian, Shiquan; Hou, Lili; Tang, Ding; Li, Yafei; Gu, Minghong; Cheng, Zhukuan; Yu, Hengxiu

    2015-01-01

    The leptotene-zygotene transition is a major step in meiotic progression during which pairing between homologous chromosomes is initiated and double strand breaks occur. OsAM1, a homologue of maize AM1 and Arabidopsis SWI1, encodes a protein with a coiled-coil domain in its central region that is required for the leptotene-zygotene transition during rice meiosis. To gain more insight into the role of OsAM1 in rice meiosis and identify additional meiosis-specific genes, we characterized the transcriptomes of young panicles of Osam1 mutant and wild-type rice plants using RNA-Seq combined with bioinformatic and statistical analyses. As a result, a total of 25,750 and 28,455 genes were expressed in young panicles of wild-type and Osam1 mutant plants, respectively, and 4,400 differentially expressed genes (DEGs; log2 Ratio ≥ 1, FDR ≤ 0.05) were identified. Of these DEGs, four known rice meiosis-specific genes were detected, and 22 new putative meiosis-related genes were found by mapping these DEGs to reference biological pathways in the KEGG database. We identified eight additional well-conserved OsAM1-responsive rice meiotic genes by comparing our RNA-Seq data with known meiotic genes in Arabidopsis and fission yeast. PMID:26394329

  16. Primary structure and regulation of vegetative specific genes of Dictyostelium discoideum.

    PubMed Central

    Singleton, C K; Manning, S S; Ken, R

    1989-01-01

    We have examined the expression and structure of several genes belonging to two classes of vegetative specific genes of the simple eukaryote, Dictyostelium discoideum. In amebae grown on bacteria, deactivation of all vegetative specific genes occurred at the onset of development and very little mRNA exists by 8 to 10 hours. In contrast, when cells were grown in axenic broth, the mRNA levels remained constant until a dramatic drop occurred around 10 to 12 hours. Thus, regulation of both classes of genes during the first several hours of development is dependent upon the prior growth conditions. Analysis of genomic clones has resulted in the identification of two V genes, V1 and V18, as ribosomal protein genes. Several other V genes were not found to be ribosomal protein genes, suggesting that in Dictyostelium non-ribosomal protein genes may be coordinately regulated with the ribosomal protein genes. Finally, using deletion analysis we show that the promoters of two of the V genes are composed of a constitutive positive element(s) located upstream of sequences involved in the regulated expression of these genes and within the first 545 upstream bp for V18 and 850 bp for V14. The regions involved in regulated expression were localized between -7 and -222 for V18 and -70 and -368 for V14. The sequences conferring protein synthesis sensitivity were shown to reside between -502 and -61 of the H4 promoter. Images PMID:2602140

  17. Gene and pathway identification with Lp penalized Bayesian logistic regression

    PubMed Central

    Liu, Zhenqiu; Gartenhaus, Ronald B; Tan, Ming; Jiang, Feng; Jiao, Xiaoli

    2008-01-01

    Background Identifying genes and pathways associated with diseases such as cancer has been a subject of considerable research in recent years in the area of bioinformatics and computational biology. It has been demonstrated that the magnitude of differential expression does not necessarily indicate biological significance. Even a very small change in the expression of particular gene may have dramatic physiological consequences if the protein encoded by this gene plays a catalytic role in a specific cell function. Moreover, highly correlated genes may function together on the same pathway biologically. Finally, in sparse logistic regression with Lp (p < 1) penalty, the degree of the sparsity obtained is determined by the value of the regularization parameter. Usually this parameter must be carefully tuned through cross-validation, which is time consuming. Results In this paper, we proposed a simple Bayesian approach to integrate the regularization parameter out analytically using a new prior. Therefore, there is no longer a need for parameter selection, as it is eliminated entirely from the model. The proposed algorithm (BLpLog) is typically two or three orders of magnitude faster than the original algorithm and free from bias in performance estimation. We also define a novel similarity measure and develop an integrated algorithm to hunt the regulatory genes with low expression changes but having high correlation with the selected genes. Pathways of those correlated genes were identified with DAVID . Conclusion Experimental results with gene expression data demonstrate that the proposed methods can be utilized to identify important genes and pathways that are related to cancer and build a parsimonious model for future patient predictions. PMID:18834526

  18. Identification of key target genes and pathways in laryngeal carcinoma

    PubMed Central

    Liu, Feng; Du, Jintao; Liu, Jun; Wen, Bei

    2016-01-01

    The purpose of the present study was to screen the key genes associated with laryngeal carcinoma and to investigate the molecular mechanism of laryngeal carcinoma progression. The gene expression profile of GSE10935 [Gene Expression Omnibus (GEO) accession number], including 12 specimens from laryngeal papillomas and 12 specimens from normal laryngeal epithelia controls, was downloaded from the GEO database. Differentially expressed genes (DEGs) were screened in laryngeal papillomas compared with normal controls using Limma package in R language, followed by Gene Ontology (GO) enrichment analysis and pathway enrichment analysis. Furthermore, the protein-protein interaction (PPI) network of DEGs was constructed using Cytoscape software and modules were analyzed using MCODE plugin from the PPI network. Furthermore, significant biological pathway regions (sub-pathway) were identified by using iSubpathwayMiner analysis. A total of 67 DEGs were identified, including 27 up-regulated genes and 40 down-regulated genes and they were involved in different GO terms and pathways. PPI network analysis revealed that Ras association (RalGDS/AF-6) domain family member 1 (RASSF1) was a hub protein. The sub-pathway analysis identified 9 significantly enriched sub-pathways, including glycolysis/gluconeogenesis and nitrogen metabolism. Genes such as phosphoglycerate kinase 1 (PGK1), carbonic anhydrase II (CA2), and carbonic anhydrase XII (CA12) whose node degrees were >10 were identified in the disease risk sub-pathway. Genes in the sub-pathway, such as RASSF1, PGK1, CA2 and CA12 were presumed to serve critical roles in laryngeal carcinoma. The present study identified DEGs and their sub-pathways in the disease, which may serve as potential targets for treatment of laryngeal carcinoma. PMID:27446427

  19. Identification of β-haemolysin-encoding genes in Streptococcus anginosus.

    PubMed

    Asam, D; Mauerer, S; Walheim, E; Spellerberg, B

    2013-08-01

    Streptococcus anginosus is an emerging pathogen, but little is known about its virulence factors. To detect the genes responsible for β-haemolysis we performed genomic mutagenesis of the β-haemolytic S. anginosus type strain ATCC 12395 using the vector pGhost9:ISS1. Integration site analysis of 15 non-haemolytic mutants identified a gene cluster with high homology to the genes of the streptolysin S (SLS) encoding sag gene cluster of S. pyogenes. The gene cluster harbours 10 open reading frames displaying significant similarities to the S. pyogenes genes sagA-sagI, with the identities on protein level ranging from 38 to 87%. Complementation assays of S. anginosus sagB and sagD integration mutants with the respective genes confirmed their importance for β-haemolysin production and suggest the presence of post-translational modifications in S. anginosus SLS similar to SLS of S. pyogenes. Characterization of the S. anginosus haemolysin in comparison to the S. pyogenes SLS showed that the haemolysin is surface bound, but in contrast to S. pyogenes neither fetal calf serum nor RNA was able to stabilize the haemolysin of S. anginosus in culture supernatants. Inhibition of β-haemolysis by polyethylene glycol of different sizes was carried out, giving no evidence of a pore-forming haemolytic mechanism. Analysis of a whole genome shotgun sequence of Streptococcus constellatus, a closely related streptococcal species that belongs to the S. anginosus group, revealed a similar sag gene cluster. Employing a genomic mutagenesis strategy we were able to determine an SLS encoding gene cluster in S. anginosus and demonstrate its importance for β-haemolysin production in S. anginosus.

  20. Identification and use of genes encoding amatoxin and phallotoxin

    DOEpatents

    Hallen, Heather E.; Walton, Jonathan D.; Luo, Hong; Scott-Craig, John S.

    2016-12-13

    The present invention relates to compositions and methods comprising genes and peptides associated with cyclic peptide toxins and toxin production in mushrooms. In particular, the present invention relates to using genes and proteins from Amanita species encoding Amanita peptides, specifically relating to amatoxins and phallotoxins. In a preferred embodiment, the present invention also relates to methods for detecting Amanita peptide toxin genes for identifying Amanita peptide-producing mushrooms and for diagnosing suspected cases of mushroom poisoning. Further, the present inventions relate to providing kits for diagnosing and monitoring suspected cases of mushroom poisoning in patients.

  1. Identification of the two rotavirus genes determining neutralization specificities

    SciTech Connect

    Offit, P.A.; Blavat, G.

    1986-01-01

    Bovine rotavirus NCDV and simian rotavirus SA-11 represent two distinct rotavirus serotypes. A genetic approach was used to determine which viral gene segments segregated with serotype-specific viral neutralization. There were 16 reassortant rotarviruses derived by coinfection of MA-104 cells in vitro with the SA-11 and NCDV strains. The parental origin of reassortant rotavirus double-stranded RNA segments was determined by gene segment mobility in polyacrylamide gels and by hybridization with radioactively labeled parental viral transcripts. The authors found that two rotavirus gene segments found previously to code for outer capsid proteins vp3 and vp7 cosegreated with virus neutralization specificities.

  2. Identification of Single- and Multiple-Class Specific Signature Genes from Gene Expression Profiles by Group Marker Index

    PubMed Central

    Tsai, Yu-Shuen; Aguan, Kripamoy; Pal, Nikhil R.; Chung, I-Fang

    2011-01-01

    Informative genes from microarray data can be used to construct prediction model and investigate biological mechanisms. Differentially expressed genes, the main targets of most gene selection methods, can be classified as single- and multiple-class specific signature genes. Here, we present a novel gene selection algorithm based on a Group Marker Index (GMI), which is intuitive, of low-computational complexity, and efficient in identification of both types of genes. Most gene selection methods identify only single-class specific signature genes and cannot identify multiple-class specific signature genes easily. Our algorithm can detect de novo certain conditions of multiple-class specificity of a gene and makes use of a novel non-parametric indicator to assess the discrimination ability between classes. Our method is effective even when the sample size is small as well as when the class sizes are significantly different. To compare the effectiveness and robustness we formulate an intuitive template-based method and use four well-known datasets. We demonstrate that our algorithm outperforms the template-based method in difficult cases with unbalanced distribution. Moreover, the multiple-class specific genes are good biomarkers and play important roles in biological pathways. Our literature survey supports that the proposed method identifies unique multiple-class specific marker genes (not reported earlier to be related to cancer) in the Central Nervous System data. It also discovers unique biomarkers indicating the intrinsic difference between subtypes of lung cancer. We also associate the pathway information with the multiple-class specific signature genes and cross-reference to published studies. We find that the identified genes participate in the pathways directly involved in cancer development in leukemia data. Our method gives a promising way to find genes that can involve in pathways of multiple diseases and hence opens up the possibility of using an existing

  3. Identification of single- and multiple-class specific signature genes from gene expression profiles by group marker index.

    PubMed

    Tsai, Yu-Shuen; Aguan, Kripamoy; Pal, Nikhil R; Chung, I-Fang

    2011-01-01

    Informative genes from microarray data can be used to construct prediction model and investigate biological mechanisms. Differentially expressed genes, the main targets of most gene selection methods, can be classified as single- and multiple-class specific signature genes. Here, we present a novel gene selection algorithm based on a Group Marker Index (GMI), which is intuitive, of low-computational complexity, and efficient in identification of both types of genes. Most gene selection methods identify only single-class specific signature genes and cannot identify multiple-class specific signature genes easily. Our algorithm can detect de novo certain conditions of multiple-class specificity of a gene and makes use of a novel non-parametric indicator to assess the discrimination ability between classes. Our method is effective even when the sample size is small as well as when the class sizes are significantly different. To compare the effectiveness and robustness we formulate an intuitive template-based method and use four well-known datasets. We demonstrate that our algorithm outperforms the template-based method in difficult cases with unbalanced distribution. Moreover, the multiple-class specific genes are good biomarkers and play important roles in biological pathways. Our literature survey supports that the proposed method identifies unique multiple-class specific marker genes (not reported earlier to be related to cancer) in the Central Nervous System data. It also discovers unique biomarkers indicating the intrinsic difference between subtypes of lung cancer. We also associate the pathway information with the multiple-class specific signature genes and cross-reference to published studies. We find that the identified genes participate in the pathways directly involved in cancer development in leukemia data. Our method gives a promising way to find genes that can involve in pathways of multiple diseases and hence opens up the possibility of using an existing

  4. Parallel Identification of New Genes in Saccharomyces cerevisiae

    PubMed Central

    Oshiro, Guy; Wodicka, Lisa M.; Washburn, Michael P.; Yates, John R.; Lockhart, David J.; Winzeler, Elizabeth A.

    2002-01-01

    Short open reading frames (ORFs) occur frequently in primary genome sequence. Distinguishing bona fide small genes from the tens of thousands of short ORFs is one of the most challenging aspects of genome annotation. Direct experimental evidence is often required. Here we use a combination of expression profiling and mass spectrometry to verify the independent transcription of 138 and the translation of 50 previously nonannotated genes in the Saccharomyces cerevisiae genome. Through combined evidence, we propose the addition of 62 new genes to the genome and provide experimental support for the inclusion of 10 previously identified genes. [The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: V. Velculescu. Supplementary material is available online at http://www.genome.org.] PMID:12176929

  5. Identification of novel androgen receptor target genes in prostate cancer

    PubMed Central

    Jariwala, Unnati; Prescott, Jennifer; Jia, Li; Barski, Artem; Pregizer, Steve; Cogan, Jon P; Arasheben, Armin; Tilley, Wayne D; Scher, Howard I; Gerald, William L; Buchanan, Grant; Coetzee, Gerhard A; Frenkel, Baruch

    2007-01-01

    Background The androgen receptor (AR) plays critical roles in both androgen-dependent and castrate-resistant prostate cancer (PCa). However, little is known about AR target genes that mediate the receptor's roles in disease progression. Results Using Chromatin Immunoprecipitation (ChIP) Display, we discovered 19 novel loci occupied by the AR in castrate resistant C4-2B PCa cells. Only four of the 19 AR-occupied regions were within 10-kb 5'-flanking regulatory sequences. Three were located up to 4-kb 3' of the nearest gene, eight were intragenic and four were in gene deserts. Whereas the AR occupied the same loci in C4-2B (castrate resistant) and LNCaP (androgen-dependent) PCa cells, differences between the two cell lines were observed in the response of nearby genes to androgens. Among the genes strongly stimulated by DHT in C4-2B cells – D-dopachrome tautomerase (DDT), Protein kinase C delta (PRKCD), Glutathione S- transferase theta 2 (GSTT2), Transient receptor potential cation channel subfamily V member 3 (TRPV3), and Pyrroline-5-carboxylate reductase 1 (PYCR1) – most were less strongly or hardly stimulated in LNCaP cells. Another AR target gene, ornithine aminotransferase (OAT), was AR-stimulated in a ligand-independent manner, since it was repressed by AR siRNA knockdown, but not stimulated by DHT. We also present evidence for in vivo AR-mediated regulation of several genes identified by ChIP Display. For example, PRKCD and PYCR1, which may contribute to PCa cell growth and survival, are expressed in PCa biopsies from primary tumors before and after ablation and in metastatic lesions in a manner consistent with AR-mediated stimulation. Conclusion AR genomic occupancy is similar between LNCaP and C4-2B cells and is not biased towards 5' gene flanking sequences. The AR transcriptionally regulates less than half the genes nearby AR-occupied regions, usually but not always, in a ligand-dependent manner. Most are stimulated and a few are repressed. In general

  6. Identification of genes from the Treacher Collins candidate region

    SciTech Connect

    Dixon, M.; Dixon, J.; Edwards, S. |

    1994-09-01

    Treacher Collins syndrome (TCOF1) is an autosomal dominant disorder of craniofacial development. The TCOF1 locus has previously been mapped to chromosome 5q32-33. The candidate gene region has been defined as being between two flanking markers, ribosomal protein S14 (RPS14) and Annexin 6 (ANX6), by analyzing recombination events in affected individuals. It is estimated that the distance between these flanking markers is 500 kb by three separate analysis methods: (1) radiation hybrid mapping; (2) genetic linkage; and (3) YAC contig analysis. A cosmid contig which spans the candidate gene region for TCOF1 has been constructed by screening the Los Alamos National Laboratory flow-sorted chromosome 5 cosmid library. Cosmids were obtained by using a combination of probes generated from YAC end clones, Alu-PCR fragments from YACs, and asymmetric PCR fragments from both T7 and T3 cosmid ends. Exon amplifications, the selection of genomic coding sequences based upon the presence of functional splice acceptor and donor sites, was used to identify potential exon sequences. Sequences found to be conserved between species were then used to screen cDNA libraries in order to identify candidate genes. To date, four different cDNAs have been isolated from this region and are being analyzed as potential candidate genes for TCOF1. These include the genes encoding plasma glutathione peroxidase (GPX3), heparin sulfate sulfotransferase (HSST), a gene with homology to the ETS family of proteins and one which shows no homology to any known genes. Work is also in progress to identify and characterize additional cDNAs from the candidate gene region.

  7. EMDomics: a robust and powerful method for the identification of genes differentially expressed between heterogeneous classes.

    PubMed

    Nabavi, Sheida; Schmolze, Daniel; Maitituoheti, Mayinuer; Malladi, Sadhika; Beck, Andrew H

    2016-02-15

    A major goal of biomedical research is to identify molecular features associated with a biological or clinical class of interest. Differential expression analysis has long been used for this purpose; however, conventional methods perform poorly when applied to data with high within class heterogeneity. To address this challenge, we developed EMDomics, a new method that uses the Earth mover's distance to measure the overall difference between the distributions of a gene's expression in two classes of samples and uses permutations to obtain q-values for each gene. We applied EMDomics to the challenging problem of identifying genes associated with drug resistance in ovarian cancer. We also used simulated data to evaluate the performance of EMDomics, in terms of sensitivity and specificity for identifying differentially expressed gene in classes with high within class heterogeneity. In both the simulated and real biological data, EMDomics outperformed competing approaches for the identification of differentially expressed genes, and EMDomics was significantly more powerful than conventional methods for the identification of drug resistance-associated gene sets. EMDomics represents a new approach for the identification of genes differentially expressed between heterogeneous classes and has utility in a wide range of complex biomedical conditions in which sample classes show within class heterogeneity. The R package is available at http://www.bioconductor.org/packages/release/bioc/html/EMDomics.html. © The Author 2015. Published by Oxford University Press.

  8. Identification and Evaluation of Reference Genes for Quantitative Analysis of Brazilian Pine (Araucaria angustifolia Bertol. Kuntze) Gene Expression.

    PubMed

    Elbl, Paula; Navarro, Bruno V; de Oliveira, Leandro F; Almeida, Juliana; Mosini, Amanda C; Dos Santos, André L W; Rossi, Magdalena; Floh, Eny I S

    2015-01-01

    Quantitative analysis of gene expression is a fundamental experimental approach in many fields of plant biology, but it requires the use of internal controls representing constitutively expressed genes for reliable transcript quantification. In this study, we identified fifteen putative reference genes from an A. angustifolia transcriptome database. Variation in transcript levels was first evaluated in silico by comparing read counts and then by quantitative real-time PCR (qRT-PCR), resulting in the identification of six candidate genes. The consistency of transcript abundance was also calculated applying geNorm and NormFinder software packages followed by a validation approach using four target genes. The results presented here indicate that a diverse set of samples should ideally be used in order to identify constitutively expressed genes, and that the use of any two reference genes in combination, of the six tested genes, is sufficient for effective expression normalization. Finally, in agreement with the in silico prediction, a comprehensive analysis of the qRT-PCR data combined with validation analysis revealed that AaEIF4B-L and AaPP2A are the most suitable reference genes for comparative studies of A. angustifolia gene expression.

  9. Identification of genes associated with chlorophyll accumulation in flower petals.

    PubMed

    Ohmiya, Akemi; Hirashima, Masumi; Yagi, Masafumi; Tanase, Koji; Yamamizo, Chihiro

    2014-01-01

    Plants have an ability to prevent chlorophyll accumulation, which would mask the bright flower color, in their petals. In contrast, leaves contain substantial amounts of chlorophyll, as it is essential for photosynthesis. The mechanisms of organ-specific chlorophyll accumulation are unknown. To identify factors that determine the chlorophyll content in petals, we compared the expression of genes related to chlorophyll metabolism in different stages of non-green (red and white) petals (very low chlorophyll content), pale-green petals (low chlorophyll content), and leaves (high chlorophyll content) of carnation (Dianthus caryophyllus L.). The expression of many genes encoding chlorophyll biosynthesis enzymes, in particular Mg-chelatase, was lower in non-green petals than in leaves. Non-green petals also showed higher expression of genes involved in chlorophyll degradation, including STAY-GREEN gene and pheophytinase. These data suggest that the absence of chlorophylls in carnation petals may be caused by the low rate of chlorophyll biosynthesis and high rate of degradation. Similar results were obtained by the analysis of Arabidopsis microarray data. In carnation, most genes related to chlorophyll biosynthesis were expressed at similar levels in pale-green petals and leaves, whereas the expression of chlorophyll catabolic genes was higher in pale-green petals than in leaves. Therefore, we hypothesize that the difference in chlorophyll content between non-green and pale-green petals is due to different levels of chlorophyll biosynthesis. Our study provides a basis for future molecular and genetic studies on organ-specific chlorophyll accumulation.

  10. Identification of candidate genes for phenolics accumulation in tomato fruit.

    PubMed

    Di Matteo, Antonio; Ruggieri, Valentino; Sacco, Adriana; Rigano, Maria Manuela; Carriero, Filomena; Bolger, Anthony; Fernie, Alisdair R; Frusciante, Luigi; Barone, Amalia

    2013-05-01

    Phenolics are antioxidants present in tomato fruit that confer healthy benefits and exhibit crucial roles for plant metabolism and response to environmental stimuli. An approach based on two genomics platforms was undertaken to identify candidate genes associated to higher phenolics content in tomato fruit. A comparative transcriptomic analysis between the S. pennellii Introgression Line 7-3, which produced an average higher level of fruit phenolics, and the cultivated variety M82, revealed that their differences are attributed to genes involved in phenolics accumulation into the vacuole. The up-regulation of genes coding for one MATE-transporter, one vacuolar sorting protein and three GSTs supported this hypothesis. The observed balancing effect between two ethylene responsive factors (ERF1 and ERF4) was also hypothesized to drive the transcriptional regulation of these transport genes. In order to confirm such model a TILLING platform was explored. A mutant was isolated harbouring a point mutation in the ERF1 cds that affects the protein sequence and its expected function. Fruits of the mutant exhibited a significant reduced level of phenolics than the control variety. Changes in the expression of genes involved in sequestration of phenolics in vacuole also supported the hypothesized key-role of ERF1 in orchestrating these genes.

  11. A Genomic Signature and the Identification of New Sporulation Genes

    PubMed Central

    Abecasis, Ana B.; Serrano, Mónica; Alves, Renato; Quintais, Leonor

    2013-01-01

    Bacterial endospores are the most resistant cell type known to humans, as they are able to withstand extremes of temperature, pressure, chemical injury, and time. They are also of interest because the endospore is the infective particle in a variety of human and livestock diseases. Endosporulation is characterized by the morphogenesis of an endospore within a mother cell. Based on the genes known to be involved in endosporulation in the model organism Bacillus subtilis, a conserved core of about 100 genes was derived, representing the minimal machinery for endosporulation. The core was used to define a genomic signature of about 50 genes that are able to distinguish endospore-forming organisms, based on complete genome sequences, and we show this 50-gene signature is robust against phylogenetic proximity and other artifacts. This signature includes previously uncharacterized genes that we can now show are important for sporulation in B. subtilis and/or are under developmental control, thus further validating this genomic signature. We also predict that a series of polyextremophylic organisms, as well as several gut bacteria, are able to form endospores, and we identified 3 new loci essential for sporulation in B. subtilis: ytaF, ylmC, and ylzA. In all, the results support the view that endosporulation likely evolved once, at the base of the Firmicutes phylum, and is unrelated to other bacterial cell differentiation programs and that this involved the evolution of new genes and functions, as well as the cooption of ancestral, housekeeping functions. PMID:23396918

  12. Identification and characterization of TIFY family genes in Brachypodium distachyon.

    PubMed

    Zhang, Lihua; You, Jun; Chan, Zhulong

    2015-11-01

    The TIFY family is a plant-specific gene family encoding proteins characterized by a conserved TIFY domain. This family encodes four subfamilies of proteins, including ZIM-like (ZML), TIFY, PPD and JASMONATE ZIM-Domain (JAZ) proteins. TIFY proteins play important roles in plant development and stress responses. In this study, 21 BdTIFYs were identified in Brachypodium distachyon through genome-wide analysis, including 15 JAZ and 6 ZML genes. Analysis of the distribution of conserved domains showed that there are three additional domains (CCT domain, GATA domain and Jas domain) in the BdTIFY proteins besides the TIFY domain. Phylogenetic analysis indicated that these 21 proteins were classified into two major groups. Expression profile of BdTIFY genes in response to abiotic stresses and phytohormones was analyzed using quantitative real-time RT-PCR. Among 21 BdTIFY genes, 12 of them were induced by JA treatment, and 4 of them were induced by ABA treatment. Most of BdTIFY genes were responsive to one or more abiotic stresses including drought, salinity, low temperature and heat. Especially, BdTIFY5, 9a, 9b, 10c and 11a were significantly up-regulated by multiple abiotic stresses. These results provided important clues for functional analysis of TIFY family genes in B. distachyon.

  13. Identification and characterization of a Dictyostelium discoideum ribosomal protein gene.

    PubMed Central

    Szymkowski, D E; Deering, R A

    1990-01-01

    We have identified a developmentally repressed large-subunit ribosomal protein gene of Dictyostelium discoideum based on sequence similarity to other ribosomal proteins. Protein rpl7 is homologous to large subunit ribosomal proteins from the rat and possibly to Mycoplasma capricolum and Escherichia coli, but is not similar to three sequenced ribosomal proteins in Dictyostelium. The rpl7 gene is present at one copy per genome, as are six other cloned Dictyostelium ribosomal proteins. Restriction fragment length polymorphisms exist for ribosomal protein genes rpl7, rp1024, and rp110 in strain HU182; most Dictyostelium ribosomal protein genes examined are linked no closer than 30-100 kb to each other in the genome. Dictyostelium ribosomal proteins are known to be developmentally regulated, and levels of rpl7 transcript gradually decrease during the 24-hour development cycle. This drop correlates with that of rp1024, indicating these and other ribosomal protein genes may be coordinately regulated. To determine the cellular location of the protein, we raised antibodies to an rpl7-derived branched synthetic peptide. These antibodies cross-reacted with one protein of the expected size in a ribosomal protein fraction of Dictyostelium, indicating that the product of gene rpl7 is localized in the ribosome. Images PMID:1975664

  14. Identification of two distinct Bacillus subtilis citrate synthase genes.

    PubMed

    Jin, S; Sonenshein, A L

    1994-08-01

    Two distinct Bacillus subtilis genes (citA and citZ) were found to encode citrate synthase isozymes that catalyze the first step of the Krebs cycle. The citA gene was cloned by genetic complementation of an Escherichia coli citrate synthase mutant strain (W620) and was in a monocistronic transcriptional unit. A divergently transcribed gene, citR, could encode a protein with strong similarity to the bacterial LysR family of regulatory proteins. A null mutation in citA had little effect on citrate synthase enzyme activity or sporulation. The residual citrate synthase activity was purified from a citA null mutant strain, and the partial amino acid sequence for the purified protein (CitZ) was determined. The citZ gene was cloned from B. subtilis chromosomal DNA by using a PCR-generated probe synthesized with oligonucleotide primers derived from the partial amino acid sequence of purified CitZ. The citZ gene proved to be the first gene in a tricistronic cluster that also included citC (coding for isocitrate dehydrogenase) and citH (coding for malate dehydrogenase). A mutation in citZ caused a substantial loss of citrate synthase enzyme activity, glutamate auxotrophy, and a defect in sporulation.

  15. The fur Gene as a New Phylogenetic Marker for Vibrionaceae Species Identification

    PubMed Central

    Gram, Lone

    2015-01-01

    Microbial taxonomy is essential in all areas of microbial science. The 16S rRNA gene sequence is one of the main phylogenetic species markers; however, it does not provide discrimination in the family Vibrionaceae, where other molecular techniques allow better interspecies resolution. Although multilocus sequence analysis (MLSA) has been used successfully in the identification of Vibrio species, the technique has several limitations. They include the fact that several locus amplifications and sequencing have to be performed, which still sometimes lead to doubtful identifications. Using an in silico approach based on genomes from 103 Vibrionaceae strains, we demonstrate here the high resolution of the fur gene in the identification of Vibrionaceae species and its usefulness as a phylogenetic marker. The fur gene showed within-species similarity higher than 95%, and the relationships inferred from its use were in agreement with those observed for 16S rRNA analysis and MLSA. Furthermore, we developed a fur PCR sequencing-based method that allowed identification of Vibrio species. The discovery of the phylogenetic power of the fur gene and the development of a PCR method that can be used in amplification and sequencing of the gene are of general interest whether for use alone or together with the previously suggested loci in an MLSA. PMID:25662978

  16. Detection of bacterial 16S ribosomal RNA genes for forensic identification of vaginal fluid.

    PubMed

    Akutsu, Tomoko; Motani, Hisako; Watanabe, Ken; Iwase, Hirotaro; Sakurada, Koichi

    2012-05-01

    To preliminarily evaluate the applicability of bacterial DNA as a marker for the forensic identification of vaginal fluid, we developed and performed PCR-based detection of 16S ribosomal RNA genes of Lactobacillus spp. dominating the vagina and of bacterial vaginosis-related bacteria from DNA extracted from body fluids and stains. As a result, 16S ribosomal RNA genes of Lactobacillus crispatus, Lactobacillus jensenii and Atopobium vaginae were specifically detected in vaginal fluid and female urine samples. Bacterial genes detected in female urine might have originated from contaminated vaginal fluid. In addition, those of Lactobacillus iners, Lactobacillus gasseri and Gardnerella vaginalis were also detected in non-vaginal body fluids such as semen. Because bacterial genes were successfully amplified in DNA samples extracted by using the general procedure for animal tissues without any optional treatments, DNA samples prepared for the identification of vaginal fluid can also be used for personal identification. In conclusion, 16S ribosomal RNA genes of L. crispatus, L. jensenii and A. vaginae could be effective markers for forensic identification of vaginal fluid.

  17. Genome-Wide Identification, Phylogenetic and Co-Expression Analysis of OsSET Gene Family in Rice

    PubMed Central

    Lu, Zhanhua; Huang, Xiaolong; Ouyang, Yidan; Yao, Jialing

    2013-01-01

    Background SET domain is responsible for the catalytic activity of histone lysine methyltransferases (HKMTs) during developmental process. Histone lysine methylation plays a crucial and diverse regulatory function in chromatin organization and genome function. Although several SET genes have been identified and characterized in plants, the understanding of OsSET gene family in rice is still very limited. Methodology/Principal Findings In this study, a systematic analysis was performed and revealed the presence of at least 43 SET genes in rice genome. Phylogenetic and structural analysis grouped SET proteins into five classes, and supposed that the domains out of SET domain were significant for the specific of histone lysine methylation, as well as the recognition of methylated histone lysine. Based on the global microarray, gene expression profile revealed that the transcripts of OsSET genes were accumulated differentially during vegetative and reproductive developmental stages and preferentially up or down-regulated in different tissues. Cis-elements identification, co-expression analysis and GO analysis of expression correlation of 12 OsSET genes suggested that OsSET genes might be involved in cell cycle regulation and feedback. Conclusions/Significance This study will facilitate further studies on OsSET family and provide useful clues for functional validation of OsSETs. PMID:23762371

  18. Application of Euclidean distance measurement and principal component analysis for gene identification.

    PubMed

    Ghosh, Antara; Barman, Soma

    2016-06-01

    Gene systems are extremely complex, heterogeneous, and noisy in nature. Many statistical tools which are used to extract relevant feature from genes provide fuzzy and ambiguous information. High-dimensional gene expression database available in public domain usually contains thousands of genes. Efficient prediction method is demanding nowadays for accurate identification of such database. Euclidean distance measurement and principal component analysis methods are applied on such databases to identify the genes. In both methods, prediction algorithm is based on homology search approach. Digital Signal Processing technique along with statistical method is used for analysis of genes in both cases. A two-level decision logic is used for gene classification as healthy or cancerous. This binary logic minimizes the prediction error and improves prediction accuracy. Superiority of the method is judged by receiver operating characteristic curve.

  19. PIECE: a database for plant gene structure comparison and evolution

    PubMed Central

    Wang, Yi; You, Frank M.; Lazo, Gerard R.; Luo, Ming-Cheng; Thilmony, Roger; Gordon, Sean; Kianian, Shahryar F.; Gu, Yong Q.

    2013-01-01

    Gene families often show degrees of differences in terms of exon–intron structures depending on their distinct evolutionary histories. Comparative analysis of gene structures is important for understanding their evolutionary and functional relationships within plant species. Here, we present a comparative genomics database named PIECE (http://wheat.pw.usda.gov/piece) for Plant Intron and Exon Comparison and Evolution studies. The database contains all the annotated genes extracted from 25 sequenced plant genomes. These genes were classified based on Pfam motifs. Phylogenetic trees were pre-constructed for each gene category. PIECE provides a user-friendly interface for different types of searches and a graphical viewer for displaying a gene structure pattern diagram linked to the resulting bootstrapped dendrogram for each gene family. The gene structure evolution of orthologous gene groups was determined using the GLOOME, Exalign and GECA software programs that can be accessed within the database. PIECE also provides a web server version of the software, GSDraw, for drawing schematic diagrams of gene structures. PIECE is a powerful tool for comparing gene sequences and provides valuable insights into the evolution of gene structure in plant genomes. PMID:23180792

  20. Phylogeny and Identification of Pantoea Species and Typing of Pantoea agglomerans Strains by Multilocus Gene Sequencing ▿ †

    PubMed Central

    Delétoile, Alexis; Decré, Dominique; Courant, Stéphanie; Passet, Virginie; Audo, Jennifer; Grimont, Patrick; Arlet, Guillaume; Brisse, Sylvain

    2009-01-01

    Pantoea agglomerans and other Pantoea species cause infections in humans and are also pathogenic to plants, but the diversity of Pantoea strains and their possible association with hosts and disease remain poorly known, and identification of Pantoea species is difficult. We characterized 36 Pantoea strains, including 28 strains of diverse origins initially identified as P. agglomerans, by multilocus gene sequencing based on six protein-coding genes, by biochemical tests, and by antimicrobial susceptibility testing. Phylogenetic analysis and comparison with other species of Enterobacteriaceae revealed that the genus Pantoea is highly diverse. Most strains initially identified as P. agglomerans by use of API 20E strips belonged to a compact sequence cluster together with the type strain, but other strains belonged to diverse phylogenetic branches corresponding to other species of Pantoea or Enterobacteriaceae and to probable novel species. Biochemical characteristics such as fosfomycin resistance and utilization of d-tartrate could differentiate P. agglomerans from other Pantoea species. All 20 strains of P. agglomerans could be distinguished by multilocus sequence typing, revealing the very high discrimination power of this method for strain typing and population structure in this species, which is subdivided into two phylogenetic groups. PCR detection of the repA gene, associated with pathogenicity in plants, was positive in all clinical strains of P. agglomerans, suggesting that clinical and plant-associated strains do not form distinct populations. We provide a multilocus gene sequencing method that is a powerful tool for Pantoea species delineation and identification and for strain tracking. PMID:19052179

  1. Screening poly(dA/dT)- cDNAs for gene identification.

    PubMed

    Wang, S M; Fears, S C; Zhang, L; Chen, J J; Rowley, J D

    2000-04-11

    Many genes expressed in the human genome have not been identified despite intensive efforts. We observed that the presence of long poly(dA/dT) sequences in the 3' end of cDNA templates contributes significantly to this problem, because the hybrids formed randomly between poly(dA) and poly(dT) sequences of unrelated cDNA templates lead to loss of many templates in the normalization/subtraction reactions. The low abundant copies, which account for the majority of the expressed genes, are affected in particular by this phenomenon. We have developed a strategy called screening poly(dA/dT)(-) cDNAs for gene identification to overcome this obstacle. Applying this strategy can significantly enhance the efficiency of genome-wide gene identification and should have an impact on many functional genomic studies in the postgenome era.

  2. Structural identification and cardiovascular activities of oxidized phospholipids.

    PubMed

    Salomon, Robert G

    2012-09-14

    Free radical-induced oxidation of membrane phospholipids generates complex mixtures of oxidized phospholipids (oxPLs). The combinatorial operation of a few dozen reaction types on a few dozen phospholipid structures results in the production of a dauntingly vast diversity of oxPL molecular species. Structural identification of the individual oxPL in these mixtures is a redoubtable challenge that is absolutely essential to allow determination of the biological activities of individual species. With an emphasis on cardiovascular consequences, this Review focuses on biological activities of oxPLs whose molecular structures are known and highlights 2 diametrically opposite approaches that were used to determine those structures, that is, (1) the classic approach from bioactivity of a complex mixture to isolation and structural characterization of the active molecule followed by confirmation of the structure by unambiguous chemical synthesis and (2) hypothesis of products that are likely to be generated by lipid oxidation, followed by synthesis, and then detection in vivo guided by the availability of authentic standards, and last, characterization of biological activities. Especially important for the application of the second paradigm is the capability of LC-MS/MS and derivatizations to selectively detect and quantify specific oxPL in complex mixtures, without the need for their isolation or complete separation. This technology can provide strong evidence for identity by comparisons with pure, well-characterized samples available by chemical syntheses. Those pure samples are critical for determining the biological activities attributable to specific molecular species of oxPLs in the complex mixtures generated in vivo as a consequence of oxidative stress.

  3. Structural Identification and Cardiovascular Activities of Oxidized Phospholipids

    PubMed Central

    Salomon, Robert G.

    2012-01-01

    Free radical-induced oxidation of membrane phospholipids generates complex mixtures of oxidized phospholipids (oxPLs). The combinatorial operation of a few dozen reaction types upon a few dozen phospholipid structures results in the production of a dauntingly vast diversity of oxPL molecular species. Structural identification of the individual oxPL in these mixtures is a redoubtable challenge that is absolutely essential to allow determination of the biological activities of individual species. With an emphasis on cardiovascular consequences, this review focuses on biological activities of oxPLs whose molecular structures are known and highlights two diametric opposite approaches that were used to determine those structures, i.e. (1) the classical approach from bioactivity of a complex mixture to isolation and structural characterization of the active molecule followed by confirmation of the structure by unambiguous chemical synthesis, and (2) hypothesis of products likely to be generated by lipid oxidation, followed by synthesis, and then detection in vivo guided by the availability of authentic standards, and lastly, characterization of biological activities. Especially important for the application of the second paradigm is the capability of LC-MS/MS and derivatizations to selectively detect and quantify specific oxPL in complex mixtures, without the need for their isolation or complete separation. This technology can provide strong evidence for identity by comparisons with pure, well characterized samples available by chemical syntheses. Those pure samples are critical for determining the biological activities attributable to specific molecular species of oxPLs in the complex mixtures generated in vivo as a consequence of oxidative stress. PMID:22982874

  4. A Graphic Method for Identification of Novel Glioma Related Genes

    PubMed Central

    Gao, Yu-Fei; Yang, Lei; He, Yi-Chun; Li, Li-Peng; Huang, GuaHua; Li, Hai-Peng

    2014-01-01

    Glioma, as the most common and lethal intracranial tumor, is a serious disease that causes many deaths every year. Good comprehension of the mechanism underlying this disease is very helpful to design effective treatments. However, up to now, the knowledge of this disease is still limited. It is an important step to understand the mechanism underlying this disease by uncovering its related genes. In this study, a graphic method was proposed to identify novel glioma related genes based on known glioma related genes. A weighted graph was constructed according to the protein-protein interaction information retrieved from STRING and the well-known shortest path algorithm was employed to discover novel genes. The following analysis suggests that some of them are related to the biological process of glioma, proving that our method was effective in identifying novel glioma related genes. We hope that the proposed method would be applied to study other diseases and provide useful information to medical workers, thereby designing effective treatments of different diseases. PMID:25050377

  5. Identification of Candidate Genes for Dyslexia Susceptibility on Chromosome 18

    PubMed Central

    Scerri, Thomas S.; Paracchini, Silvia; Morris, Andrew; MacPhie, I. Laurence; Talcott, Joel; Stein, John; Smith, Shelley D.; Pennington, Bruce F.; Olson, Richard K.; DeFries, John C.; Monaco, Anthony P.

    2010-01-01

    Background Six independent studies have identified linkage to chromosome 18 for developmental dyslexia or general reading ability. Until now, no candidate genes have been identified to explain this linkage. Here, we set out to identify the gene(s) conferring susceptibility by a two stage strategy of linkage and association analysis. Methodology/Principal Findings Linkage analysis: 264 UK families and 155 US families each containing at least one child diagnosed with dyslexia were genotyped with a dense set of microsatellite markers on chromosome 18. Association analysis: Using a discovery sample of 187 UK families, nearly 3000 SNPs were genotyped across the chromosome 18 dyslexia susceptibility candidate region. Following association analysis, the top ranking SNPs were then genotyped in the remaining samples. The linkage analysis revealed a broad signal that spans approximately 40 Mb from 18p11.2 to 18q12.2. Following the association analysis and subsequent replication attempts, we observed consistent association with the same SNPs in three genes; melanocortin 5 receptor (MC5R), dymeclin (DYM) and neural precursor cell expressed, developmentally down-regulated 4-like (NEDD4L). Conclusions Along with already published biological evidence, MC5R, DYM and NEDD4L make attractive candidates for dyslexia susceptibility genes. However, further replication and functional studies are still required. PMID:21060895

  6. Identification of candidate genes for dyslexia susceptibility on chromosome 18.

    PubMed

    Scerri, Thomas S; Paracchini, Silvia; Morris, Andrew; MacPhie, I Laurence; Talcott, Joel; Stein, John; Smith, Shelley D; Pennington, Bruce F; Olson, Richard K; DeFries, John C; Monaco, Anthony P; Richardson, Alex J

    2010-10-28

    Six independent studies have identified linkage to chromosome 18 for developmental dyslexia or general reading ability. Until now, no candidate genes have been identified to explain this linkage. Here, we set out to identify the gene(s) conferring susceptibility by a two stage strategy of linkage and association analysis. Linkage analysis: 264 UK families and 155 US families each containing at least one child diagnosed with dyslexia were genotyped with a dense set of microsatellite markers on chromosome 18. Association analysis: Using a discovery sample of 187 UK families, nearly 3000 SNPs were genotyped across the chromosome 18 dyslexia susceptibility candidate region. Following association analysis, the top ranking SNPs were then genotyped in the remaining samples. The linkage analysis revealed a broad signal that spans approximately 40 Mb from 18p11.2 to 18q12.2. Following the association analysis and subsequent replication attempts, we observed consistent association with the same SNPs in three genes; melanocortin 5 receptor (MC5R), dymeclin (DYM) and neural precursor cell expressed, developmentally down-regulated 4-like (NEDD4L). Along with already published biological evidence, MC5R, DYM and NEDD4L make attractive candidates for dyslexia susceptibility genes. However, further replication and functional studies are still required.

  7. A graphic method for identification of novel glioma related genes.

    PubMed

    Gao, Yu-Fei; Shu, Yang; Yang, Lei; He, Yi-Chun; Li, Li-Peng; Huang, GuaHua; Li, Hai-Peng; Jiang, Yang

    2014-01-01

    Glioma, as the most common and lethal intracranial tumor, is a serious disease that causes many deaths every year. Good comprehension of the mechanism underlying this disease is very helpful to design effective treatments. However, up to now, the knowledge of this disease is still limited. It is an important step to understand the mechanism underlying this disease by uncovering its related genes. In this study, a graphic method was proposed to identify novel glioma related genes based on known glioma related genes. A weighted graph was constructed according to the protein-protein interaction information retrieved from STRING and the well-known shortest path algorithm was employed to discover novel genes. The following analysis suggests that some of them are related to the biological process of glioma, proving that our method was effective in identifying novel glioma related genes. We hope that the proposed method would be applied to study other diseases and provide useful information to medical workers, thereby designing effective treatments of different diseases.

  8. Identification of the Fanconi anemia complementation group I gene, FANCI.

    PubMed

    Dorsman, Josephine C; Levitus, Marieke; Rockx, Davy; Rooimans, Martin A; Oostra, Anneke B; Haitjema, Anneke; Bakker, Sietske T; Steltenpool, Jûrgen; Schuler, Dezsö; Mohan, Sheila; Schindler, Detlev; Arwert, Fré; Pals, Gerard; Mathew, Christopher G; Waisfisz, Quinten; de Winter, Johan P; Joenje, Hans

    2007-01-01

    To identify the gene underlying Fanconi anemia (FA) complementation group I we studied informative FA-I families by a genome-wide linkage analysis, which resulted in 4 candidate regions together encompassing 351 genes. Candidates were selected via bioinformatics and data mining on the basis of their resemblance to other FA genes/proteins acting in the FA pathway, such as: degree of evolutionary conservation, presence of nuclear localization signals and pattern of tissue-dependent expression. We found a candidate, KIAA1794 on chromosome 15q25-26, to be mutated in 8 affected individuals previously assigned to complementation group I. Western blots of endogenous FANCI indicated that functionally active KIAA1794 protein is lacking in FA-I individuals. Knock-down of KIAA1794 expression by siRNA in HeLa cells caused excessive chromosomal breakage induced by mitomycin C, a hallmark of FA cells. Furthermore, phenotypic reversion of a patient-derived cell line was associated with a secondary genetic alteration at the KIAA1794 locus. These data add up to two conclusions. First, KIAA1794 is a FA gene. Second, this gene is identical to FANCI, since the patient cell lines found mutated in this study included the reference cell line for group I, EUFA592.

  9. Identification of three related human GRO genes encoding cytokine functions

    SciTech Connect

    Haskill, S.; Peace, A.; Morris, J.; Sporn, S.A. ); Anisowicz, A.; Lee, S.W.; Sager, R. ); Smith, T. ); Martin, G.; Ralph, P. )

    1990-10-01

    The product of the human GRO gene is a cytokine with inflammatory and growth-regulatory properties; GRO is also called MGSA for melanoma growth-stimulatory activity. The authors have identified two additional genes, GRO{beta} and GRO{gamma}, that share 90{percent} and 86{percent} identity at the deduced amino acid level with the original GRO{alpha} isolate. One amino acid substitution of proline in GRO{alpha} by leucine in GRO{beta} and GRO{gamma} leads to a large predicted change in protein conformation. Significant differences also exist in the 3' untranslated region, including different numbers of ATTTA repeats associated with mRNA instability. A 122-base-pair region in the 3' region is conserved among the three GRO genes, and a part of it is also conserved in the Chinese hamster genome, suggesting a role in regulation. DNA hybridization with oligonucleotide probes and partial sequence analysis of the genomic clones confirm that the three forms are derived from related but different genes. Only one chromosomal locus has been identified, at 4q21, by using a GRO{alpha} cDNA clone that hybridized to all three genes. Expression studies reveal tissue-specific regulation as well as regulation by specific inducing agents, including interleukin 1, tumor necrosis factor, phorbol 12-myristate 13-acetate, and lipopolysaccharide.

  10. Identification of Helicobacter pylori genes that contribute to stomach colonization.

    PubMed

    Baldwin, David N; Shepherd, Benjamin; Kraemer, Petra; Hall, Michael K; Sycuro, Laura K; Pinto-Santini, Delia M; Salama, Nina R

    2007-02-01

    Chronic infection of the human stomach by Helicobacter pylori leads to a variety of pathological sequelae, including peptic ulcer and gastric cancer, resulting in significant human morbidity and mortality. Several genes have been implicated in disease related to H. pylori infection, including the vacuolating cytotoxin and the cag pathogenicity island. Other factors important for the establishment and maintenance of infection include urease enzyme production, motility, iron uptake, and stress response. We utilized a C57BL/6 mouse infection model to query a collection of 2,400 transposon mutants in two different bacterial strain backgrounds for H. pylori genetic loci contributing to colonization of the stomach. Microarray-based tracking of transposon mutants allowed us to monitor the behavior of transposon insertions in 758 different gene loci. Of the loci measured, 223 (29%) had a predicted colonization defect. These included previously described H. pylori virulence genes, genes implicated in virulence in other pathogenic bacteria, and 81 hypothetical proteins. We have retested 10 previously uncharacterized candidate colonization gene loci by making independent null alleles and have confirmed their colonization phenotypes by using competition experiments and by determining the dose required for 50% infection. Of the genetic loci retested, 60% have strain-specific colonization defects, while 40% have phenotypes in both strain backgrounds for infection, highlighting the profound effect of H. pylori strain variation on the pathogenic potential of this organism.

  11. Identification of candidate genes of QTLs for seed weight in Brassica napus through comparative mapping among Arabidopsis and Brassica species

    PubMed Central

    2012-01-01

    Background Map-based cloning of quantitative trait loci (QTLs) in polyploidy crop species remains a challenge due to the complexity of their genome structures. QTLs for seed weight in B. napus have been identified, but information on candidate genes for identified QTLs of this important trait is still rare. Results In this study, a whole genome genetic linkage map for B. napus was constructed using simple sequence repeat (SSR) markers that covered a genetic distance of 2,126.4 cM with an average distance of 5.36 cM between markers. A procedure was developed to establish colinearity of SSR loci on B. napus with its two progenitor diploid species B. rapa and B. oleracea through extensive bioinformatics analysis. With the aid of B. rapa and B. oleracea genome sequences, the 421 homologous colinear loci deduced from the SSR loci of B. napus were shown to correspond to 398 homologous loci in Arabidopsis thaliana. Through comparative mapping of Arabidopsis and the three Brassica species, 227 homologous genes for seed size/weight were mapped on the B. napus genetic map, establishing the genetic bases for the important agronomic trait in this amphidiploid species. Furthermore, 12 candidate genes underlying 8 QTLs for seed weight were identified, and a gene-specific marker for BnAP2 was developed through molecular cloning using the seed weight/size gene distribution map in B. napus. Conclusions Our study showed that it is feasible to identify candidate genes of QTLs using a SSR-based B. napus genetic map through comparative mapping among Arabidopsis and B. napus and its two progenitor species B. rapa and B. oleracea. Identification of candidate genes for seed weight in amphidiploid B. napus will accelerate the process of isolating the mapped QTLs for this important trait, and this approach may be useful for QTL identification of other traits of agronomic significance. PMID:23216693

  12. Frequency domain identification for robust large space structure control design

    NASA Technical Reports Server (NTRS)

    Yam, Y.; Bayard, D. S.; Scheid, R. E.

    1991-01-01

    A methodology is demonstrated for frequency domain identification of large space structures which systematically transforms experimental raw data into a form required for synthesizing H(infinity) controllers using modern robust control design software (e.g., Matlab Toolboxes). A unique feature of this approach is that the additive uncertainty is characterized to a specified statistic confidence rather than with hard bounds. In this study, the difference in robust performance is minimal between the two levels of confidence. In general cases, the present methodology provides a tool for performance/confidence level tradeoff studies. For simplicity, the additive uncertainty on a frequency grid is considered and the interpolation error in between grid points is neglected.

  13. Frequency domain identification for robust large space structure control design

    NASA Technical Reports Server (NTRS)

    Yam, Y.; Bayard, D. S.; Scheid, R. E.

    1991-01-01

    A methodology is demonstrated for frequency domain identification of large space structures which systematically transforms experimental raw data into a form required for synthesizing H(infinity) controllers using modern robust control design software (e.g., Matlab Toolboxes). A unique feature of this approach is that the additive uncertainty is characterized to a specified statistic confidence rather than with hard bounds. In this study, the difference in robust performance is minimal between the two levels of confidence. In general cases, the present methodology provides a tool for performance/confidence level tradeoff studies. For simplicity, the additive uncertainty on a frequency grid is considered and the interpolation error in between grid points is neglected.

  14. Utility of rpoB Gene Sequencing for Identification of Nontuberculous Mycobacteria in the Netherlands

    PubMed Central

    de Zwaan, Rina; van Ingen, Jakko

    2014-01-01

    In the Netherlands, clinical isolation of nontuberculous mycobacteria (NTM) has increased over the past decade. Proper identification of isolates is important, as NTM species differ strongly in clinical relevance. Most of the currently applied identification methods cannot distinguish between all different Mycobacterium species and complexes within species. rpoB gene sequencing exhibits a promising level of discrimination among rapidly and slowly growing mycobacteria, including the Mycobacterium avium complex. In this study, we prospectively compared rpoB gene sequencing with our routine algorithm of reverse line blot identification combined with partial 16S rRNA gene sequencing of 455 NTM isolates. rpoB gene sequencing identified 403 isolates to species level as 45 different known species and identified 44 isolates to complex level, and eight isolates remained unidentifiable to species level. In contrast, our reference reverse line blot assay with adjunctive 16S rRNA gene sequencing identified 390 isolates to species level (30 distinct species) and identified 56 isolates to complex level, and nine isolates remained unidentified. The higher discriminatory power of rpoB gene sequencing results largely from the distinction of separate species within complexes and subspecies. Also, Mycobacterium gordonae, Mycobacterium kansasii, and Mycobacterium interjectum were separated into multiple groupings with relatively low sequence similarity (98 to 94%), suggesting that these are complexes of closely related species. We conclude that rpoB gene sequencing is a more discriminative identification technique than the combination of reverse line blot and 16S rRNA gene sequencing and could introduce a major improvement in clinical care of NTM disease and the research on the epidemiology and clinical relevance of NTM. PMID:24808238

  15. Identification of genes associated with tumor development in CaSki cells in the cosmic space.

    PubMed

    Guo, Fengjie; Li, Yalin; Liu, Yan; Huang, Jian; Zhang, Zhijie; Wang, Jiajia; Li, Yuehui; Hu, Jinyue; Li, Guancheng

    2012-06-01

    It is important to understand the mechanisms of tumor development for curing cervical cancer. However, the molecular basis determining the different characteristics of tumor remains unclear. Space environment as a special study model can expand the study field of tumor development. To approach this, after human cervical carcinoma CaSki cells were flown on “Shen Zhou IV” space shuttle mission, the cell morphology and proliferation was investigated after flying to ground. We found that the growth of 48A9 CaSki cell (flight group) became slow compared with ground groups. Observation of cells by light microscopy revealed differences in cell morphology between ground controls and flight groups, and the flight group exhibited morphologic differences, characterized by rounder, smoother, decreased, smaller and low-adhension cells. Transmission electron microscope images showed the structure of the ultrastructural characteristics of 48A9 CaSki cells were clearly distinct from those of the ground CaSki cells in aspects of mitochondrion, cytoplasm, nucleus and ribosomes. MTT and soft agar assay showed that 48A9 CaSki cells grew slowly compared to ground control. Furthermore, suppression subtractive hybridization combining with reverse Northern blot was used to identify differently expression genes between flight and ground groups. These differentially expressed genes included cytoskeleton, cell differentiation, cell apoptosis, signal transduction, DNA repair, protein synthesis, substance metabolism, and antigen presentation. The identification of differently expressed genes which is likely to increase our understanding of the molecular processes underlying tumor development will provide new insight into tumor development mechanisms, and may facilitate the development of new anticancer strategies.

  16. Identification of Carboxylesterase Genes Implicated in Temephos Resistance in the Dengue Vector Aedes aegypti

    PubMed Central

    Poupardin, Rodolphe; Srisukontarat, Wannaporn; Yunta, Cristina; Ranson, Hilary

    2014-01-01

    Background Thailand is currently experiencing one of its worst dengue outbreaks in decades. As in most countries where this disease is endemic, dengue control in Thailand is largely reliant on the use of insecticides targeting both immature and adult stages of the Aedes mosquito, with the organophosphate insecticide, temephos, being the insecticide of choice for attacking the mosquito larvae. Resistance to temephos was first detected in Aedes aegypti larvae in Thailand approximately 25 years ago but the mechanism responsible for this resistance has not been determined. Principal Findings Bioassays on Ae. aegypti larvae from Thailand detected temephos resistance ratios ranging from 3.5 fold in Chiang Mai to nearly 10 fold in Nakhon Sawan (NS) province. Synergist and biochemical assays suggested a role for increased carboxylesterase (CCE) activities in conferring temephos resistance in the NS population and microarray analysis revealed that the CCE gene, CCEae3a, was upregulated more than 60 fold in the NS population compared to the susceptible population. Upregulation of CCEae3a was shown to be partially due to gene duplication. Another CCE gene, CCEae6a, was also highly regulated in both comparisons. Sequencing and in silico structure prediction of CCEae3a showed that several amino acid polymorphisms in the NS population may also play a role in the increased resistance phenotype. Significance Carboxylesterases have previously been implicated in conferring temephos resistance in Ae aegypti but the specific member(s) of this family responsible for this phenotype have not been identified. The identification of a strong candidate is an important step in the development of new molecular diagnostic tools for management of temephos resistant populations and thus improved control of dengue. PMID:24651719

  17. Identification of Targetable FGFR Gene Fusions in Diverse Cancers

    PubMed Central

    Wu, Yi-Mi; Su, Fengyun; Kalyana-Sundaram, Shanker; Khazanov, Nick; Ateeq, Bushra; Cao, Xuhong; Lonigro, Robert J.; Vats, Pankaj; Wang, Rui; Lin, Su-Fang; Cheng, Ann-Joy; Kunju, Lakshmi P.; Siddiqui, Javed; Tomlins, Scott A.; Wyngaard, Peter; Sadis, Seth; Roychowdhury, Sameek; Hussain, Maha H.; Feng, Felix Y.; Zalupski, Mark M.; Talpaz, Moshe; Pienta, Kenneth J.; Rhodes, Daniel R.; Robinson, Dan R.; Chinnaiyan, Arul M.

    2013-01-01

    Through a prospective clinical sequencing program for advanced cancers, four index cases were identified which harbor gene rearrangements of FGFR2 including patients with cholangiocarcinoma, breast cancer, and prostate cancer. After extending our assessment of FGFR rearrangements across multiple tumor cohorts, we identified additional FGFR gene fusions with intact kinase domains in lung squamous cell cancer, bladder cancer, thyroid cancer, oral cancer, glioblastoma, and head and neck squamous cell cancer. All FGFR fusion partners tested exhibit oligomerization capability, suggesting a shared mode of kinase activation. Overexpression of FGFR fusion proteins induced cell proliferation. Two bladder cancer cell lines that harbor FGFR3 fusion proteins exhibited enhanced susceptibility to pharmacologic inhibition in vitro and in vivo. Due to the combinatorial possibilities of FGFR family fusion to a variety of oligomerization partners, clinical sequencing efforts which incorporate transcriptome analysis for gene fusions are poised to identify rare, targetable FGFR fusions across diverse cancer types. PMID:23558953

  18. Identification of Mechanosensitive Genes during Embryonic Bone Formation

    PubMed Central

    Nowlan, Niamh C.; Prendergast, Patrick J.; Murphy, Paula

    2008-01-01

    Although it is known that mechanical forces are needed for normal bone development, the current understanding of how biophysical stimuli are interpreted by and integrated with genetic regulatory mechanisms is limited. Mechanical forces are thought to be mediated in cells by “mechanosensitive” genes, but it is a challenge to demonstrate that the genetic regulation of the biological system is dependant on particular mechanical forces in vivo. We propose a new means of selecting candidate mechanosensitive genes by comparing in vivo gene expression patterns with patterns of biophysical stimuli, computed using finite element analysis. In this study, finite element analyses of the avian embryonic limb were performed using anatomically realistic rudiment and muscle morphologies, and patterns of biophysical stimuli were compared with the expression patterns of four candidate mechanosensitive genes integral to bone development. The expression patterns of two genes, Collagen X (ColX) and Indian hedgehog (Ihh), were shown to colocalise with biophysical stimuli induced by embryonic muscle contractions, identifying them as potentially being involved in the mechanoregulation of bone formation. An altered mechanical environment was induced in the embryonic chick, where a neuromuscular blocking agent was administered in ovo to modify skeletal muscle contractions. Finite element analyses predicted dramatic changes in levels and patterns of biophysical stimuli, and a number of immobilised specimens exhibited differences in ColX and Ihh expression. The results obtained indicate that computationally derived patterns of biophysical stimuli can be used to inform a directed search for genes that may play a mechanoregulatory role in particular in vivo events or processes. Furthermore, the experimental data demonstrate that ColX and Ihh are involved in mechanoregulatory pathways and may be key mediators in translating information from the mechanical environment to the molecular

  19. Identification of Unique Type II Polyketide Synthase Genes in Soil

    PubMed Central

    Wawrik, Boris; Kerkhof, Lee; Zylstra, Gerben J.; Kukor, Jerome J.

    2005-01-01

    Many bacteria, particularly actinomycetes, are known to produce secondary metabolites synthesized by polyketide synthases (PKS). Bacterial polyketides are a particularly rich source of bioactive molecules, many of which are of potential pharmaceutical relevance. To directly access PKS gene diversity from soil, we developed degenerate PCR primers for actinomycete type II KSα (ketosynthase) genes. Twenty-one soil samples were collected from diverse sources in New Jersey, and their bacterial communities were compared by terminal restriction fragment length polymorphism (TRFLP) analysis of PCR products generated using bacterial 16S rRNA gene primers (27F and 1525R) as well as an actinomycete-specific forward primer. The distribution of actinomycetes was highly variable but correlated with the overall bacterial species composition as determined by TRFLP. Two samples were identified to contain a particularly rich and unique actinomycete community based on their TRFLP patterns. The same samples also contained the greatest diversity of KSα genes as determined by TRFLP analysis of KSα PCR products. KSα PCR products from these and three additional samples with interesting TRFLP pattern were cloned, and seven novel clades of KSα genes were identified. Greatest sequence diversity was observed in a sample containing a moderate number of peaks in its KSα TRFLP. The nucleotide sequences were between 74 and 81% identical to known sequences in GenBank. One cluster of sequences was most similar to the KSα involved in ardacin (glycopeptide antibiotic) production by Kibdelosporangium aridum. The remaining sequences showed greatest similarity to the KSα genes in pathways producing the angucycline-derived antibiotics simocyclinone, pradimicin, and jasomycin. PMID:15870305

  20. Identification of mechanosensitive genes during embryonic bone formation.

    PubMed

    Nowlan, Niamh C; Prendergast, Patrick J; Murphy, Paula

    2008-12-01

    Although it is known that mechanical forces are needed for normal bone development, the current understanding of how biophysical stimuli are interpreted by and integrated with genetic regulatory mechanisms is limited. Mechanical forces are thought to be mediated in cells by "mechanosensitive" genes, but it is a challenge to demonstrate that the genetic regulation of the biological system is dependant on particular mechanical forces in vivo. We propose a new means of selecting candidate mechanosensitive genes by comparing in vivo gene expression patterns with patterns of biophysical stimuli, computed using finite element analysis. In this study, finite element analyses of the avian embryonic limb were performed using anatomically realistic rudiment and muscle morphologies, and patterns of biophysical stimuli were compared with the expression patterns of four candidate mechanosensitive genes integral to bone development. The expression patterns of two genes, Collagen X (ColX) and Indian hedgehog (Ihh), were shown to colocalise with biophysical stimuli induced by embryonic muscle contractions, identifying them as potentially being involved in the mechanoregulation of bone formation. An altered mechanical environment was induced in the embryonic chick, where a neuromuscular blocking agent was administered in ovo to modify skeletal muscle contractions. Finite element analyses predicted dramatic changes in levels and patterns of biophysical stimuli, and a number of immobilised specimens exhibited differences in ColX and Ihh expression. The results obtained indicate that computationally derived patterns of biophysical stimuli can be used to inform a directed search for genes that may play a mechanoregulatory role in particular in vivo events or processes. Furthermore, the experimental data demonstrate that ColX and Ihh are involved in mechanoregulatory pathways and may be key mediators in translating information from the mechanical environment to the molecular regulation

  1. Identification of Genes Associated with Chlorophyll Accumulation in Flower Petals

    PubMed Central

    Ohmiya, Akemi; Hirashima, Masumi; Yagi, Masafumi; Tanase, Koji; Yamamizo, Chihiro

    2014-01-01

    Plants have an ability to prevent chlorophyll accumulation, which would mask the bright flower color, in their petals. In contrast, leaves contain substantial amounts of chlorophyll, as it is essential for photosynthesis. The mechanisms of organ-specific chlorophyll accumulation are unknown. To identify factors that determine the chlorophyll content in petals, we compared the expression of genes related to chlorophyll metabolism in different stages of non-green (red and white) petals (very low chlorophyll content), pale-green petals (low chlorophyll content), and leaves (high chlorophyll content) of carnation (Dianthus caryophyllus L.). The expression of many genes encoding chlorophyll biosynthesis enzymes, in particular Mg-chelatase, was lower in non-green petals than in leaves. Non-green petals also showed higher expression of genes involved in chlorophyll degradation, including STAY-GREEN gene and pheophytinase. These data suggest that the absence of chlorophylls in carnation petals may be caused by the low rate of chlorophyll biosynthesis and high rate of degradation. Similar results were obtained by the analysis of Arabidopsis microarray data. In carnation, most genes related to chlorophyll biosynthesis were expressed at similar levels in pale-green petals and leaves, whereas the expression of chlorophyll catabolic genes was higher in pale-green petals than in leaves. Therefore, we hypothesize that the difference in chlorophyll content between non-green and pale-green petals is due to different levels of chlorophyll biosynthesis. Our study provides a basis for future molecular and genetic studies on organ-specific chlorophyll accumulation. PMID:25470367

  2. Identification and Functional Analysis of Light-Responsive Unique Genes and Gene Family Members in Rice

    PubMed Central

    Jung, Ki-Hong; Lee, Jinwon; Dardick, Chris; Seo, Young-Su; Cao, Peijian; Canlas, Patrick; Phetsom, Jirapa; Xu, Xia; Ouyang, Shu; An, Kyungsook; Cho, Yun-Ja; Lee, Geun-Cheol; Lee, Yoosook; An, Gynheung; Ronald, Pamela C.

    2008-01-01

    Functional redundancy limits detailed analysis of genes in many organisms. Here, we report a method to efficiently overcome this obstacle by combining gene expression data with analysis of gene-indexed mutants. Using a rice NSF45K oligo-microarray to compare 2-week-old light- and dark-grown rice leaf tissue, we identified 365 genes that showed significant 8-fold or greater induction in the light relative to dark conditions. We then screened collections of rice T-DNA insertional mutants to identify rice lines with mutations in the strongly light-induced genes. From this analysis, we identified 74 different lines comprising two independent mutant lines for each of 37 light-induced genes. This list was further refined by mining gene expression data to exclude genes that had potential functional redundancy due to co-expressed family members (12 genes) and genes that had inconsistent light responses across other publicly available microarray datasets (five genes). We next characterized the phenotypes of rice lines carrying mutations in ten of the remaining candidate genes and then carried out co-expression analysis associated with these genes. This analysis effectively provided candidate functions for two genes of previously unknown function and for one gene not directly linked to the tested biochemical pathways. These data demonstrate the efficiency of combining gene family-based expression profiles with analyses of insertional mutants to identify novel genes and their functions, even among members of multi-gene families. PMID:18725934

  3. Constrained maximum likelihood modal parameter identification applied to structural dynamics

    NASA Astrophysics Data System (ADS)

    El-Kafafy, Mahmoud; Peeters, Bart; Guillaume, Patrick; De Troyer, Tim

    2016-05-01

    A new modal parameter estimation method to directly establish modal models of structural dynamic systems satisfying two physically motivated constraints will be presented. The constraints imposed in the identified modal model are the reciprocity of the frequency response functions (FRFs) and the estimation of normal (real) modes. The motivation behind the first constraint (i.e. reciprocity) comes from the fact that modal analysis theory shows that the FRF matrix and therefore the residue matrices are symmetric for non-gyroscopic, non-circulatory, and passive mechanical systems. In other words, such types of systems are expected to obey Maxwell-Betti's reciprocity principle. The second constraint (i.e. real mode shapes) is motivated by the fact that analytical models of structures are assumed to either be undamped or proportional damped. Therefore, normal (real) modes are needed for comparison with these analytical models. The work done in this paper is a further development of a recently introduced modal parameter identification method called ML-MM that enables us to establish modal model that satisfies such motivated constraints. The proposed constrained ML-MM method is applied to two real experimental datasets measured on fully trimmed cars. This type of data is still considered as a significant challenge in modal analysis. The results clearly demonstrate the applicability of the method to real structures with significant non-proportional damping and high modal densities.

  4. Identification of internal reference genes for gene expression normalization between the two sexes in dioecious white Campion.

    PubMed

    Zemp, Niklaus; Minder, Aria; Widmer, Alex

    2014-01-01

    Quantitative real time (qRT)-PCR is a precise and efficient method for studying gene expression changes between two states of interest, and is frequently used for validating interesting gene expression patterns in candidate genes initially identified in genome-wide expression analyses, such as RNA-seq experiments. For an adequate normalisation of qRT-PCR data, it is essential to have reference genes available whose expression intensities are constant among the different states of interest. In this study we present and validate a catalogue of traditional and newly identified reference genes that were selected from RNA-seq data from multiple individuals from the dioecious plant Silene latifolia with the aim of studying gene expression differences between the two sexes in both reproductive and vegetative tissues. The catalogue contains more than 15 reference genes with both stable expression intensities and a range of expression intensities in flower buds and leaf tissues. These reference genes were used to normalize expression differences between reproductive and vegetative tissues in eight candidate genes with sex-biased expression. Our results suggest a trend towards a reduced sex-bias in sex-linked gene expression in vegetative tissues. In this study, we report on the systematic identification and validation of internal reference genes for adequate normalization of qRT-PCR-based analyses of gene expression differences between the two sexes in S. latifolia. We also show how RNA-seq data can be used efficiently to identify suitable reference genes in a wide diversity of species.

  5. Identification of blast resistance genes for managing rice blast disease

    USDA-ARS?s Scientific Manuscript database

    Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is one of the most devastating diseases worldwide. In the present study, an international set of monogenic differentials carrying 24 major blast resistance (R) genes (Pia, Pib, Pii, Pik, Pik-h, Pik-m, Pik-p, Pik-s, Pish, Pit, Pita, Pita2,...

  6. Identification of a Phytase Gene in Barley (Hordeum vulgare L.)

    PubMed Central

    Dai, Fei; Qiu, Long; Ye, Lingzhen; Wu, Dezhi; Zhou, Meixue; Zhang, Guoping

    2011-01-01

    Background Endogenous phytase plays a crucial role in phytate degradation and is thus closely related to nutrient efficiency in barley products. The understanding of genetic information of phytase in barley can provide a useful tool for breeding new barley varieties with high phytase activity. Methodology/Principal Findings Quantitative trait loci (QTL) analysis for phytase activity was conducted using a doubled haploid population. Phytase protein was purified and identified by the LC-ESI MS/MS Shotgun method. Purple acid phosphatase (PAP) gene was sequenced and the position was compared with the QTL controlling phytase activity. A major QTL for phytase activity was mapped to chromosome 5 H in barley. The gene controlling phytase activity in the region was named as mqPhy. The gene HvPAP a was mapped to the same position as mqPhy, supporting the colinearity between HvPAP a and mqPhy. Conclusions/Significance It is the first report on QTLs for phytase activity and the results showed that HvPAP a, which shares a same position with the QTL, is a major phytase gene in barley grains. PMID:21533044

  7. Identification of a gene regulatory network associated with prion replication

    PubMed Central

    Marbiah, Masue M; Harvey, Anna; West, Billy T; Louzolo, Anais; Banerjee, Priya; Alden, Jack; Grigoriadis, Anita; Hummerich, Holger; Kan, Ho-Man; Cai, Ying; Bloom, George S; Jat, Parmjit; Collinge, John; Klöhn, Peter-Christian

    2014-01-01

    Prions consist of aggregates of abnormal conformers of the cellular prion protein (PrPC). They propagate by recruiting host-encoded PrPC although the critical interacting proteins and the reasons for the differences in susceptibility of distinct cell lines and populations are unknown. We derived a lineage of cell lines with markedly differing susceptibilities, unexplained by PrPC expression differences, to identify such factors. Transcriptome analysis of prion-resistant revertants, isolated from highly susceptible cells, revealed a gene expression signature associated with susceptibility and modulated by differentiation. Several of these genes encode proteins with a role in extracellular matrix (ECM) remodelling, a compartment in which disease-related PrP is deposited. Silencing nine of these genes significantly increased susceptibility. Silencing of Papss2 led to undersulphated heparan sulphate and increased PrPC deposition at the ECM, concomitantly with increased prion propagation. Moreover, inhibition of fibronectin 1 binding to integrin α8 by RGD peptide inhibited metalloproteinases (MMP)-2/9 whilst increasing prion propagation. In summary, we have identified a gene regulatory network associated with prion propagation at the ECM and governed by the cellular differentiation state. PMID:24843046

  8. Identification of candidate genes for devil facial tumour disease tumourigenesis.

    PubMed

    Taylor, Robyn L; Zhang, Yiru; Schöning, Jennifer P; Deakin, Janine E

    2017-08-18

    Devil facial tumour (DFT) disease, a transmissible cancer where the infectious agent is the tumour itself, has caused a dramatic decrease in Tasmanian devil numbers in the wild. The purpose of this study was to take a candidate gene/pathway approach to identify potentially perturbed genes or pathways in DFT. A fusion of chromosome 1 and X is posited as the initial event leading to the development of DFT, with the rearranged chromosome 1 material now stably maintained as the tumour spreads through the population. This hypothesis makes chromosome 1 a prime chromosome on which to search for mutations involved in tumourigenesis. As DFT1 has a Schwann cell origin, we selected genes commonly implicated in tumour pathways in human nerve cancers, or cancers more generally, to determine whether they were rearranged in DFT1, and mapped them using molecular cytogenetics. Many cancer-related genes were rearranged, such as the region containing the tumour suppressor NF2 and a copy gain for ERBB3, a member of the epidermal growth factor receptor family of receptor tyrosine kinases implicated in proliferation and invasion of tumours in humans. Our mapping results have provided strong candidates not previously detected by sequencing DFT1 genomes.

  9. Identification of Fur-regulated genes in Actinobacillus actinomycetemcomitans.

    PubMed

    Haraszthy, Violet I; Jordan, Shawn F; Zambon, Joseph J

    2006-03-01

    Actinobacillus actinomycetemcomitans is an oral pathogen that causes aggressive periodontitis as well as sometimes life-threatening, extra-oral infections. Iron regulation is thought to be important in the pathogenesis of A. actinomycetemcomitans infections and, consistent with this hypothesis, the fur gene has recently been identified and characterized in A. actinomycetemcomitans. In this study, 14 putatively Fur-regulated genes were identified by Fur titration assay (Furta) in A. actinomycetemcomitans, including afuA, dgt, eno, hemA, tbpA, recO and yfe - some of which are known to be Fur regulated in other species. A fur mutant A. actinomycetemcomitans strain was created by selecting for manganese resistance in order to study the Fur regulon. Comparisons between the fur gene sequences revealed that nucleotide 66 changed from C in the wild-type to T in the mutant strain, changing leucine to isoleucine. The fur mutant strain expressed a nonfunctional Fur protein as determined by Escherichia coli-based ferric uptake assays and Western blotting. It was also more sensitive to acid stress and expressed higher levels of minC than the wild-type strain. minC, which inhibits cell division in other bacterial species and whose regulation by iron has not been previously described, was found to be Fur regulated in A. actinomycetemcomitans by Furta, by gel shift assays, and by RT-qPCR assays for gene expression.

  10. Identification of genes regulated by UV/salicylic acid.

    SciTech Connect

    Paunesku, T.; Chang-Liu, C.-M.; Shearin-Jones, P.; Watson, C.; Milton, J.; Oryhon, J.; Salbego, D.; Milosavljevic, A.; Woloschak, G. E.; CuraGen Corp.

    2000-02-01

    Purpose : Previous work from the authors' group and others has demonstrated that some of the effects of UV irradiation on gene expression are modulated in response to the addition of salicylic acid to irradiated cells. The presumed effector molecule responsible for this modulation is NF-kappaB. In the experiments described here, differential-display RT-PCR was used to identify those cDNAs that are differentially modulated by UV radiation with and without the addition of salicylic acid. Materials and methods : Differential-display RT-PCR was used to identify differentially expressed genes. Results : Eight such cDNAs are presented: lactate dehydrogenase (LDH-beta), nuclear encoded mitochondrial NADH ubiquinone reductase 24kDa (NDUFV2), elongation initiation factor 4B (eIF4B), nuclear dots protein SP100, nuclear encoded mitochondrial ATPase inhibitor (IF1), a cDNA similar to a subunit of yeast CCAAT transcription factor HAP5, and two expressed sequence tags (AA187906 and AA513156). Conclusions : Sequences of four of these genes contained NF-kappaB DNA binding sites of the type that may attract transrepressor p55/p55 NF-kappaB homodimers. Down-regulation of these genes upon UV irradiation may contribute to increased cell survival via suppression of p53 independent apoptosis.

  11. Identification of formaldehyde-responsive genes by suppression subtractive hybridization.

    PubMed

    Lee, Min-Ho; Kim, Young-Ae; Na, Tae-Young; Kim, Sung-Hye; Shin, Young Kee; Lee, Byung-Hoon; Shin, Ho-Sang; Lee, Mi-Ock

    2008-01-14

    Formaldehyde is frequently used in indoor household and occupational environments. Inhalation of formaldehyde invokes an inflammatory response, including a variety of allergic signs and symptoms. Therefore, formaldehyde has been considered as the most prevalent cause of sick building syndrome, which has become a major social problem, especially in developing urban areas. Further formaldehyde is classified as a genotoxicant in the respiratory tract of rats and humans. To better understand the molecular mechanisms involved in formaldehyde intoxication, we sought differentially regulated genes by formaldehyde exposure to Hs 680.Tr human trachea cells, using polymerase chain reaction (PCR)-based suppression subtractive hybridization. We identified 27 different formaldehyde-inducible genes, including those coding for the major histocompatibility complex, class IA, calcyclin, glutathione S-transferase pi, mouse double minute 2 (MDM2), platelet-derived growth factor receptor alpha, and which are known to be associated with cell proliferation and differentiation, immunity and inflammation, and detoxification. Induction of these genes by formaldehyde treatment was confirmed by reverse transcription PCR and western blot analysis. Further, the expression of calcyclin, glutathione S-transferase pi, PDGFRA and MDM2 were significantly induced in the tracheal epithelium of Sprague Dawley rats after formaldehyde inhalation. Our results suggest that the elevated levels of these genes may be associated with the formaldehyde-induced toxicity, and that they deserve evaluation as potential biomarkers for formaldehyde intoxication.

  12. Identification of genetic elements associated with EPSPS gene amplification

    USDA-ARS?s Scientific Manuscript database

    Weed populations can have high genetic plasticity and rapid responses to environmental selection pressures. For example, 100-fold amplification of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene evolved to confer resistance to glyphosate, the world's most important herbicide, in the wee...

  13. Identification of genes associated with low furanocoumarin content in grapefruit

    USDA-ARS?s Scientific Manuscript database

    Some furanocoumarins in grapefruit (Citrus paradisi) are associated with the so-called grapefruit juice effect. Previous phytochemical quantification and genetic analysis suggested that the synthesis of these furanocoumarins may be controlled by a single gene in the pathway. In this study, cDNA-ampl...

  14. Identification and expression profiling analysis of goose melanoma differentiation associated gene 5 (MDA5) gene.

    PubMed

    Wei, L M; Jiao, P R; Song, Y F; Han, F; Cao, L; Yang, F; Ren, T; Liao, M

    2013-10-01

    Melanoma differentiation associated gene 5 (MDA5) is an important cytoplasmic receptor that recognizes long molecules of viral double-stranded RNA and single-stranded RNA with 5' triphosphate and mediates type I interferon secretion. In this study, the full-length MDA5 gene in the goose was identified and characterized. The cDNA of goose MDA5 was 3,306 bp in length with an open reading frame of 3,018 bp, which encoded a polypeptide of 1,005 amino acids. The deduced amino acid sequence contained 6 main structure domains including 2 caspase activation and recruitment domains, one DExD/H-box helicase domain, one type III restriction enzyme domain, one helicase conserved C-terminal domain, and one RIG-I C-terminal domain. Quantitative real-time PCR analysis indicated that goose MDA5 mRNA was constitutively expressed in all sampled tissues. It was highly expressed in the jejunum, trachea, ileum, colon, and kidney, and lowly expressed in the muscular stomach, glandular stomach, and muscle. A significant increase in the transcription of MDA5 was detected in the brain, spleen, and lungs of geese after infection with H5N1 highly pathogenic avian influenza virus compared with uninfected tissues. These findings indicated that goose MDA5 was an important receptor, involved in the antiviral innate immune defense to H5N1 highly pathogenic avian influenza virus in geese.

  15. Identification of genes differentially expressed in menstrual breakdown and repair.

    PubMed

    Paiva, Premila; Lockhart, Michelle G; Girling, Jane E; Olshansky, Moshe; Woodrow, Nicole; Marino, Jennifer L; Hickey, Martha; Rogers, Peter A W

    2016-12-01

    Does the changing molecular profile of the endometrium during menstruation correlate with the histological profile of menstruation. We identified several genes not previously associated with menstruation; on Day 2 of menstruation (early-menstruation), processes related to inflammation are predominantly up-regulated and on Day 4 (late-menstruation), the endometrium is predominantly repairing and regenerating. Menstruation is induced by progesterone withdrawal at the end of the menstrual cycle and involves endometrial tissue breakdown, regeneration and repair. Perturbations in the regulation of menstruation may result in menstrual disorders including abnormal uterine bleeding. Endometrial samples were collected by Pipelle biopsy on Days 2 (n = 9), 3 (n = 9) or 4 (n = 6) of menstruation. RNA was extracted from endometrial biopsies and analysed by genome wide expression Illumina Sentrix Human HT12 arrays. Data were analysed using 'Remove Unwanted Variation-inverse (RUV-inv)'. Ingenuity pathway analysis (IPA) and the Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7 were used to identify canonical pathways, upstream regulators and functional gene clusters enriched between Days 2, 3 and 4 of menstruation. Selected individual genes were validated by quantitative PCR. Overall, 1753 genes were differentially expressed in one or more comparisons. Significant canonical pathways, gene clusters and upstream regulators enriched during menstrual bleeding included those associated with immune cell trafficking, inflammation, cell cycle regulation, extracellular remodelling and the complement and coagulation cascade. We provide the first evidence for a role for glutathione-mediated detoxification (glutathione-S-transferase mu 1 and 2; GSTM1 and GSTM2) during menstruation. The largest number of differentially expressed genes was between Days 2 and 4 of menstruation (n = 1176). We identified several genes not previously associated with menstruation

  16. Genome-wide identification and characterisation of R2R3-MYB genes in sugar beet (Beta vulgaris).

    PubMed

    Stracke, Ralf; Holtgräwe, Daniela; Schneider, Jessica; Pucker, Boas; Sörensen, Thomas Rosleff; Weisshaar, Bernd

    2014-09-25

    The R2R3-MYB genes comprise one of the largest transcription factor gene families in plants, playing regulatory roles in plant-specific developmental processes, metabolite accumulation and defense responses. Although genome-wide analysis of this gene family has been carried out in some species, the R2R3-MYB genes in Beta vulgaris ssp. vulgaris (sugar beet) as the first sequenced member of the order Caryophyllales, have not been analysed heretofore. We present a comprehensive, genome-wide analysis of the MYB genes from Beta vulgaris ssp. vulgaris (sugar beet) which is the first species of the order Caryophyllales with a sequenced genome. A total of 70 R2R3-MYB genes as well as genes encoding three other classes of MYB proteins containing multiple MYB repeats were identified and characterised with respect to structure and chromosomal organisation. Also, organ specific expression patterns were determined from RNA-seq data. The R2R3-MYB genes were functionally categorised which led to the identification of a sugar beet-specific clade with an atypical amino acid composition in the R3 domain, putatively encoding betalain regulators. The functional classification was verified by experimental confirmation of the prediction that the R2R3-MYB gene Bv_iogq encodes a flavonol regulator. This study provides the first step towards cloning and functional dissection of the role of MYB transcription factor genes in the nutritionally and evolutionarily interesting species B. vulgaris. In addition, it describes the flavonol regulator BvMYB12, being the first sugar beet R2R3-MYB with an experimentally proven function.

  17. Identification of Swedish mosquitoes based on molecular barcoding of the COI gene and SNP analysis.

    PubMed

    Engdahl, Cecilia; Larsson, Pär; Näslund, Jonas; Bravo, Mayra; Evander, Magnus; Lundström, Jan O; Ahlm, Clas; Bucht, Göran

    2014-05-01

    Mosquito-borne infectious diseases are emerging in many regions of the world. Consequently, surveillance of mosquitoes and concomitant infectious agents is of great importance for prediction and prevention of mosquito-borne infectious diseases. Currently, morphological identification of mosquitoes is the traditional procedure. However, sequencing of specified genes or standard genomic regions, DNA barcoding, has recently been suggested as a global standard for identification and classification of many different species. Our aim was to develop a genetic method to identify mosquitoes and to study their relationship. Mosquitoes were captured at collection sites in northern Sweden and identified morphologically before the cytochrome c oxidase subunit I (COI) gene sequences of 14 of the most common mosquito species were determined. The sequences obtained were then used for phylogenetic placement, for validation and benchmarking of phenetic classifications and finally to develop a hierarchical PCR-based typing scheme based on single nucleotide polymorphism sites (SNPs) to enable rapid genetic identification, circumventing the need for morphological characterization. The results showed that exact phylogenetic relationships between mosquito taxa were preserved at shorter evolutionary distances, but at deeper levels, they could not be inferred with confidence using COI gene sequence data alone. Fourteen of the most common mosquito species in Sweden were identified by the SNP/PCR-based typing scheme, demonstrating that genetic typing using SNPs of the COI gene is a useful method for identification of mosquitoes with potential for worldwide application. © 2013 John Wiley & Sons Ltd.

  18. Identification of patients with defects in the globin genes

    PubMed Central

    Dell’Edera, Domenico; Epifania, Annunziata Anna; Milazzo, Giusi Natalia; Leo, Manuela; Santacesaria, Carmela; Allegretti, Arianna; Mazzone, Eleonora; Panetta, Paolo; Iammarino, Giovanna; Lupo, Maria Giovanna; Barbieri, Rocchina; Lioi, Maria Brigida

    2013-01-01

    Summary Introduction hemoglobinopathies constitute a major health problem worldwide. These disorders are characterized by a clinical and hematological phenotypic heterogeneity. The increase of HbA2 is an invaluable hematological marker of the beta-thalassemia heterozygosis and of double heterozygosis for the alleles of delta and alpha globin genes or for the alleles of delta and beta globin genes which can cause the increase of HbA2 up to normal or borderline values. Case Report we report the case of a 30-year-old woman (first pregnant) who was admitted to our Unit at 12 weeks for a screening for thalassemia. The outcomes of the biochemical and haematological exams (MCV, MCH, HbA2, HbF) highlighted that the patient was a carrier of a beta-thalassemic trait. Molecular analysis of the beta globin genes highlighted a β039C>T heterozygous mutation. Biochemical and hematological parameters of the husband (MCV, MCH, HbA2, HbF) were normal except for the level of HbA2 (3,6%). The molecular analysis of the beta globin genes highlighted a IVS2 nt844 C>G heterozygous mutation. Furthermore, the heterozygous mutation δ+cod.27G>T was detected in his δ globin gene. For this reason, he was diagnosed a δ+β Thal. Conclusions the aim of this paper is to highlight that biochemical diagnosis could not exhaustive and a molecular diagnostic widening is required to detect the genetic deficiency causing the thalassemic trait. PMID:24611095

  19. Identification of metastasis-associated genes in colorectal cancer through an integrated genomic and transcriptomic analysis

    PubMed Central

    Peng, Sihua

    2013-01-01

    Objective Identification of colorectal cancer (CRC) metastasis genes is one of the most important issues in CRC research. For the purpose of mining CRC metastasis-associated genes, an integrated analysis of microarray data was presented, by combined with evidence acquired from comparative genomic hybridization (CGH) data. Methods Gene expression profile data of CRC samples were obtained at Gene Expression Omnibus (GEO) website. The 15 important chromosomal aberration sites detected by using CGH technology were used for integrated genomic and transcriptomic analysis. Significant Analysis of Microarray (SAM) was used to detect significantly differentially expressed genes across the whole genome. The overlapping genes were selected in their corresponding chromosomal aberration regions, and analyzed by using the Database for Annotation, Visualization and Integrated Discovery (DAVID). Finally, SVM-T-RFE gene selection algorithm was applied to identify metastasis-associated genes in CRC. Results A minimum gene set was obtained with the minimum number [14] of genes, and the highest classification accuracy (100%) in both PRI and META datasets. A fraction of selected genes are associated with CRC or its metastasis. Conclusions Our results demonstrated that integration analysis is an effective strategy for mining cancer-associated genes. PMID:24385689

  20. Stochastic Subspace-Based Structural Identification and Damage Detection —APPLICATION to the Steel-Quake Benchmark

    NASA Astrophysics Data System (ADS)

    Mevel, L.; Basseville, M.; Goursat, M.

    2003-01-01

    Numerical results from the application of new stochastic subspace-based structural identification and damage detection methods to the steel-quake structure are discussed. Particular emphasis is put on structural model identification, for which we display some modeshapes.

  1. Comparison of the Biolog OmniLog Identification System and 16S ribosomal RNA gene sequencing for accuracy in identification of atypical bacteria of clinical origin.

    PubMed

    Morgan, Megan C; Boyette, Marilyn; Goforth, Chris; Sperry, Katharine Volpe; Greene, Shermalyn R

    2009-12-01

    The Biolog OmniLog Identification System (Biolog) and the 16S ribosomal RNA (rRNA) gene sequencing methods were compared to conventional microbiological methods and evaluated for accuracy of bacterial identification. These methods were evaluated using 159 clinical isolates. Each isolate was initially identified by conventional biochemical tests and morphological characteristics and subsequently placed into one of seven categories: aerobic Actinomycetes, Bacillus, Coryneforms, fastidious Gram-negative rods (GNR), non-fermenting GNR, miscellaneous Gram-positive rods (GPR), and Vibrio/Aeromonas. After comparison to the conventional identification, the Biolog system and 16S rRNA gene sequence identifications were classified as follows: a) correct to the genus and species levels; b) correct to the genus level only; or c) neither (unacceptable) identification. Overall, 16S rRNA gene sequencing had the highest percent accuracy with 90.6% correct identifications, while the Biolog system identified 68.3% of the isolates correctly. For each category, 16S rRNA gene sequencing had a substantially higher percent accuracy compared to the conventional methods. It was determined that the Biolog system is deficient when identifying organisms in the fastidious GNR category (20.0%). The observed data suggest that 16S rRNA gene sequencing provides a more accurate identification of atypical bacteria than the Biolog system.

  2. Identification and validation of genes involved in cervical tumourigenesis

    PubMed Central

    2011-01-01

    Background Cervical cancer is the most common cancer among Indian women. This cancer has well defined pre-cancerous stages and evolves over 10-15 years or more. This study was undertaken to identify differentially expressed genes between normal, dysplastic and invasive cervical cancer. Materials and methods A total of 28 invasive cervical cancers, 4 CIN3/CIS, 4 CIN1/CIN2 and 5 Normal cervix samples were studied. We have used microarray technique followed by validation of the significant genes by relative quantitation using Taqman Low Density Array Real Time PCR. Immunohistochemistry was used to study the protein expression of MMP3, UBE2C and p16 in normal, dysplasia and cancers of the cervix. The effect of a dominant negative UBE2C on the growth of the SiHa cells was assessed using a MTT assay. Results Our study, for the first time, has identified 20 genes to be up-regulated and 14 down-regulated in cervical cancers and 5 up-regulated in CIN3. In addition, 26 genes identified by other studies, as to playing a role in cervical cancer, were also confirmed in our study. UBE2C, CCNB1, CCNB2, PLOD2, NUP210, MELK, CDC20 genes were overexpressed in tumours and in CIN3/CIS relative to both Normal and CIN1/CIN2, suggesting that they could have a role to play in the early phase of tumorigenesis. IL8, INDO, ISG15, ISG20, AGRN, DTXL, MMP1, MMP3, CCL18, TOP2A AND STAT1 were found to be upregulated in tumours. Using Immunohistochemistry, we showed over-expression of MMP3, UBE2C and p16 in cancers compared to normal cervical epithelium and varying grades of dysplasia. A dominant negative UBE2C was found to produce growth inhibition in SiHa cells, which over-expresses UBE2C 4 fold more than HEK293 cells. Conclusions Several novel genes were found to be differentially expressed in cervical cancer. MMP3, UBE2C and p16 protein overexpression in cervical cancers was confirmed by immunohistochemistry. These will need to be validated further in a larger series of samples. UBE2C could be

  3. Identification and validation of genes involved in cervical tumourigenesis.

    PubMed

    Rajkumar, Thangarajan; Sabitha, Kesavan; Vijayalakshmi, Neelakantan; Shirley, Sundersingh; Bose, Mayil Vahanan; Gopal, Gopisetty; Selvaluxmy, Ganesharaja

    2011-02-22

    Cervical cancer is the most common cancer among Indian women. This cancer has well defined pre-cancerous stages and evolves over 10-15 years or more. This study was undertaken to identify differentially expressed genes between normal, dysplastic and invasive cervical cancer. A total of 28 invasive cervical cancers, 4 CIN3/CIS, 4 CIN1/CIN2 and 5 Normal cervix samples were studied. We have used microarray technique followed by validation of the significant genes by relative quantitation using Taqman Low Density Array Real Time PCR. Immunohistochemistry was used to study the protein expression of MMP3, UBE2C and p16 in normal, dysplasia and cancers of the cervix. The effect of a dominant negative UBE2C on the growth of the SiHa cells was assessed using a MTT assay. Our study, for the first time, has identified 20 genes to be up-regulated and 14 down-regulated in cervical cancers and 5 up-regulated in CIN3. In addition, 26 genes identified by other studies, as to playing a role in cervical cancer, were also confirmed in our study. UBE2C, CCNB1, CCNB2, PLOD2, NUP210, MELK, CDC20 genes were overexpressed in tumours and in CIN3/CIS relative to both Normal and CIN1/CIN2, suggesting that they could have a role to play in the early phase of tumorigenesis. IL8, INDO, ISG15, ISG20, AGRN, DTXL, MMP1, MMP3, CCL18, TOP2A AND STAT1 were found to be upregulated in tumours. Using Immunohistochemistry, we showed over-expression of MMP3, UBE2C and p16 in cancers compared to normal cervical epithelium and varying grades of dysplasia. A dominant negative UBE2C was found to produce growth inhibition in SiHa cells, which over-expresses UBE2C 4 fold more than HEK293 cells. Several novel genes were found to be differentially expressed in cervical cancer. MMP3, UBE2C and p16 protein overexpression in cervical cancers was confirmed by immunohistochemistry. These will need to be validated further in a larger series of samples. UBE2C could be evaluated further to assess its potential as a

  4. Identification of genes involved in radioresistance of nasopharyngeal carcinoma by integrating gene ontology and protein-protein interaction networks.

    PubMed

    Guo, Ya; Zhu, Xiao-Dong; Qu, Song; Li, Ling; Su, Fang; Li, Ye; Huang, Shi-Ting; Li, Dan-Rong

    2012-01-01

    Radioresistance remains one of the important factors in relapse and metastasis of nasopharyngeal carcinoma. Thus, it is imperative to identify genes involved in radioresistance and explore the underlying biological processes in the development of radioresistance. In this study, we used cDNA microarrays to select differential genes between radioresistant CNE-2R and parental CNE-2 cell lines. One hundred and eighty-three significantly differentially expressed genes (p<0.05) were identified, of which 138 genes were upregulated and 45 genes were downregulated in CNE-2R. We further employed publicly available bioinformatics related software, such as GOEAST and STRING to examine the relationship among differentially expressed genes. The results show that these genes were involved in type I interferon-mediated signaling pathway biological processes; the nodes tended to have high connectivity with the EGFR pathway, IFN-related pathways, NF-κB. The node STAT1 has high connectivity with other nodes in the protein-protein interaction (PPI) networks. Finally, the reliability of microarray data was validated for selected genes by semi-quantitative RT-PCR and Western blotting. The results were consistent with the microarray data. Our study suggests that microarrays combined with gene ontology and protein interaction networks have great value in the identification of genes of radioresistance in nasopharyngeal carcinoma; genes involved in several biological processes and protein interaction networks may be relevant to NPC radioresistance; in particular, the verified genes CCL5, STAT1-α, STAT2 and GSTP1 may become potential biomarkers for predicting NPC response to radiotherapy.

  5. Identification of tapetum-specific genes by comparing global gene expression of four different male sterile lines in Brassica oleracea.

    PubMed

    Ma, Yuan; Kang, Jungen; Wu, Jian; Zhu, Yingguo; Wang, Xiaowu

    2015-04-01

    The tapetum plays an important role in anther development by providing necessary enzymes and nutrients for pollen development. However, it is difficult to identify tapetum-specific genes on a large-scale because of the difficulty of separating tapetum cells from other anther tissues. Here, we reported the identification of tapetum-specific genes by comparing the gene expression patterns of four male sterile (MS) lines of Brassica oleracea. The abortive phenotypes of the four MS lines revealed different defects in tapetum and pollen development but normal anther wall development when observed by transmission electron microscopy. These tapetum displayed continuous defective characteristics throughout the anther developmental stages. The transcriptome from flower buds, covering all anther developmental stages, was analyzed and bioinformatics analyses exploring tapetum development-related genes were performed. We identified 1,005 genes differentially expressed in at least one of the MS lines and 104 were non-pollen expressed genes (NPGs). Most of the identified NPGs were tapetum-specific genes considering that anther walls were normally developed in all four MS lines. Among the 104 NPGs, 22 genes were previously reported as being involved in tapetum development. We further separated the expressed NPGs into different developmental stages based on the MS defects. The data obtained in this study are not only informative for research on tapetum development in B. oleracea, but are also useful for genetic pathway research in other related species.

  6. Covariance Structure Models for Gene Expression Microarray Data

    ERIC Educational Resources Information Center

    Xie, Jun; Bentler, Peter M.

    2003-01-01

    Covariance structure models are applied to gene expression data using a factor model, a path model, and their combination. The factor model is based on a few factors that capture most of the expression information. A common factor of a group of genes may represent a common protein factor for the transcript of the co-expressed genes, and hence, it…

  7. Covariance Structure Models for Gene Expression Microarray Data

    ERIC Educational Resources Information Center

    Xie, Jun; Bentler, Peter M.

    2003-01-01

    Covariance structure models are applied to gene expression data using a factor model, a path model, and their combination. The factor model is based on a few factors that capture most of the expression information. A common factor of a group of genes may represent a common protein factor for the transcript of the co-expressed genes, and hence, it…

  8. Identification of a gene cluster associated with triclosan catabolism.

    PubMed

    Kagle, Jeanne M; Paxson, Clayton; Johnstone, Precious; Hay, Anthony G

    2015-06-01

    Aerobic degradation of bis-aryl ethers like the antimicrobial triclosan typically proceeds through oxygenase-dependent catabolic pathways. Although several studies have reported on bacteria capable of degrading triclosan aerobically, there are no reports describing the genes responsible for this process. In this study, a gene encoding the large subunit of a putative triclosan oxygenase, designated tcsA was identified in a triclosan-degrading fosmid clone from a DNA library of Sphingomonas sp. RD1. Consistent with tcsA's similarity to two-part dioxygenases, a putative FMN-dependent ferredoxin reductase, designated tcsB was found immediately downstream of tcsA. Both tcsAB were found in the midst of a putative chlorocatechol degradation operon. We show that RD1 produces hydroxytriclosan and chlorocatechols during triclosan degradation and that tcsA is induced by triclosan. This is the first study to report on the genetics of triclosan degradation.

  9. Identification of genes expressed by Cryptococcus gattii during iron deprivation.

    PubMed

    de Paula, Daphine Ariadne Jesus; Rosa e Silva, Lívia Kmetzsch; Staats, Charley Christian; Vainstein, Marilene H; Joanoni, Ana Lúcia Pinto; Nakazato, Luciano; Dutra, Valéria

    2014-01-01

    Cryptococcus neoformans and C. gattii are pathogenic yeasts that cause life-threatening diseases in humans and animals. Iron is an essential nutrient for virtually every organism as it functions as a cofactor in numerous essential enzymatic reactions. In the literature, the competition for iron between microbes and mammalian hosts during infection is well documented. In this study, we used representational difference analysis (RDA) in order to gain a better understanding of how C. gattii responds to iron starvation. A total of 15 and 29 genes were identified as having altered expression levels due to iron depletion after 3 h and 12 h, respectively. Of these, eight genes were identified in both libraries. The transcripts were related to many biological processes, such as cell cycle, ergosterol metabolism, cell wall organization, transportation, translation, cell respiration and the stress response. These data suggest a remodeling of C. gattii metabolism during conditions of iron deprivation.

  10. Identification of targetable FGFR gene fusions in diverse cancers.

    PubMed

    Wu, Yi-Mi; Su, Fengyun; Kalyana-Sundaram, Shanker; Khazanov, Nickolay; Ateeq, Bushra; Cao, Xuhong; Lonigro, Robert J; Vats, Pankaj; Wang, Rui; Lin, Su-Fang; Cheng, Ann-Joy; Kunju, Lakshmi P; Siddiqui, Javed; Tomlins, Scott A; Wyngaard, Peter; Sadis, Seth; Roychowdhury, Sameek; Hussain, Maha H; Feng, Felix Y; Zalupski, Mark M; Talpaz, Moshe; Pienta, Kenneth J; Rhodes, Daniel R; Robinson, Dan R; Chinnaiyan, Arul M

    2013-06-01

    Through a prospective clinical sequencing program for advanced cancers, four index cases were identified which harbor gene rearrangements of FGFR2, including patients with cholangiocarcinoma, breast cancer, and prostate cancer. After extending our assessment of FGFR rearrangements across multiple tumor cohorts, we identified additional FGFR fusions with intact kinase domains in lung squamous cell cancer, bladder cancer, thyroid cancer, oral cancer, glioblastoma, and head and neck squamous cell cancer. All FGFR fusion partners tested exhibit oligomerization capability, suggesting a shared mode of kinase activation. Overexpression of FGFR fusion proteins induced cell proliferation. Two bladder cancer cell lines that harbor FGFR3 fusion proteins exhibited enhanced susceptibility to pharmacologic inhibition in vitro and in vivo. Because of the combinatorial possibilities of FGFR family fusion to a variety of oligomerization partners, clinical sequencing efforts, which incorporate transcriptome analysis for gene fusions, are poised to identify rare, targetable FGFR fusions across diverse cancer types.

  11. Identification of three SNPs in the porcine myostatin gene (MSTN).

    PubMed

    Jiang, Y L; Li, N; Plastow, G; Liu, Z L; Hu, X X; Wu, C X

    2002-05-01

    Thirteen pairs of primers were designed for the entire porcine MSTN gene to enable PCR amplification for the detection of single nucleotide polymorphisms (SNPs) by a PCR-SSCP approach. Altogether 96.5% (1089/1128) of the encoding regions and 971 bp of the non-coding regions were screened. A total of three polymorphisms were identified with PCR-SSCP. They were located in the promoter, intron one and exon three regions of the gene. These polymorphisms were then confirmed to be point mutations (T --> A transversion, G --> A transition and C --> T transition respectively) by sequencing. Allele frequencies were determined for all three SNPs in several different pig breed populations. The polymorphisms were found to be rare in Western breeds, but much more common in Chinese breeds. Whether they have any relationship with the marked difference in lean meat mass between Western and Chinese breeds requires further study.

  12. Identification of Novel Mitotic Checkpoint Genes in Breast Cancer

    DTIC Science & Technology

    2002-05-01

    chromosomal instability to alterations in genes and proteins that regulate the mitotic spindle checkpoint. We first characterized the degree of chromosomal...chromosome attachment to mitotic spindle microtubules . Genetic events disrupting the mitotic spindle checkpoint may allow cells to proliferate with... Regulates onset of anaphase via monitoring S. cerevisiae, spans 1382 bp MAD2A 25 kDa kinetochore/ spindle attachments at metaphase homolog-like 1 693

  13. Identification of gravitropic response indicator genes in Arabidopsis inflorescence stems.

    PubMed

    Taniguchi, Masatoshi; Nakamura, Moritaka; Tasaka, Masao; Morita, Miyo Terao

    2014-01-01

    Differential organ growth during gravitropic response is caused by differential accumulation of auxin, that is, relative higher auxin concentration in lower flanks than in upper flanks of responding organs. Auxin responsive reporter systems such as DR5::GUS and DR5::GFP have usually been used as indicators of gravitropic response in roots and hypocotyls of Arabidopsis. However, in the inflorescence stems, the reporter systems don't work well to monitor gravitropic response. Here, we aim to certify appropriate gravitropic response indicators (GRIs) in inflorescence stems. We performed microarray analysis comparing gene expression profiles between upper and lower flanks of Arabidopsis inflorescence stems after gravistimulation. Thirty genes showed > 2-fold differentially increased expression in lower flanks at 30 min, of which 19 were auxin response genes. We focused on IAA5 and IAA2 and verified whether they are appropriate GRIs by real-time qRT-PCR analyses. Transcript levels of IAA5 and IAA2 were remarkably higher in lower flanks than in upper flanks after gravistimulation. The biased IAA5 or IAA2 expression is disappeared in sgr2-1 mutant which is defective in gravity perception, indicating that gravity perception process is essential for formation of the biased gene expression during gravitropism. IAA5 expression was remarkably increased in lower flanks at 30 min after gravistimulation, whereas IAA2 expression was gradually decreased in upper flanks in a time-dependent manner. Therefore, we conclude that IAA5 is a sensitive GRI to monitor asymmetric auxin signaling caused by gravistimulation in Arabidopsis inflorescence stems.

  14. Identification of gravitropic response indicator genes in Arabidopsis inflorescence stems

    PubMed Central

    Taniguchi, Masatoshi; Nakamura, Moritaka; Tasaka, Masao; Morita, Miyo Terao

    2014-01-01

    Differential organ growth during gravitropic response is caused by differential accumulation of auxin, that is, relative higher auxin concentration in lower flanks than in upper flanks of responding organs. Auxin responsive reporter systems such as DR5::GUS and DR5::GFP have usually been used as indicators of gravitropic response in roots and hypocotyls of Arabidopsis. However, in the inflorescence stems, the reporter systems don’t work well to monitor gravitropic response. Here, we aim to certify appropriate gravitropic response indicators (GRIs) in inflorescence stems. We performed microarray analysis comparing gene expression profiles between upper and lower flanks of Arabidopsis inflorescence stems after gravistimulation. Thirty genes showed > 2-fold differentially increased expression in lower flanks at 30 min, of which 19 were auxin response genes. We focused on IAA5 and IAA2 and verified whether they are appropriate GRIs by real-time qRT-PCR analyses. Transcript levels of IAA5 and IAA2 were remarkably higher in lower flanks than in upper flanks after gravistimulation. The biased IAA5 or IAA2 expression is disappeared in sgr2–1 mutant which is defective in gravity perception, indicating that gravity perception process is essential for formation of the biased gene expression during gravitropism. IAA5 expression was remarkably increased in lower flanks at 30 min after gravistimulation, whereas IAA2 expression was gradually decreased in upper flanks in a time-dependent manner. Therefore, we conclude that IAA5 is a sensitive GRI to monitor asymmetric auxin signaling caused by gravistimulation in Arabidopsis inflorescence stems. PMID:25763694

  15. Identification of Susceptibility Loci and Genes for Colorectal Cancer Risk

    PubMed Central

    Zeng, Chenjie; Matsuda, Koichi; Jia, Wei-Hua; Chang, Jiang; Kweon, Sun-Seog; Xiang, Yong-Bing; Shin, Aesun; Jee, Sun Ha; Kim, Dong-Hyun; Zhang, Ben; Cai, Qiuyin; Guo, Xingyi; Long, Jirong; Wang, Nan; Courtney, Regina; Pan, Zhi-Zhong; Wu, Chen; Takahashi, Atsushi; Shin, Min-Ho; Matsuo, Keitaro; Matsuda, Fumihiko; Gao, Yu-Tang; Oh, Jae Hwan; Kim, Soriul; Jung, Keum Ji; Ahn, Yoon-Ok; Ren, Zefang; Li, Hong-Lan; Wu, Jie; Shi, Jiajun; Wen, Wanqing; Yang, Gong; Li, Bingshan; Ji, Bu-Tian; Brenner, Hermann; Schoen, Robert E.; Küry, Sébastien; Gruber, Stephen B.; Schumacher, Fredrick R.; Stenzel, Stephanie L.; Casey, Graham; Hopper, John L.; Jenkins, Mark A.; Kim, Hyeong-Rok; Jeong, Jin-Young; Park, Ji Won; Tajima, Kazuo; Cho, Sang-Hee; Kubo, Michiaki; Shu, Xiao-Ou; Lin, Dongxin; Zeng, Yi-Xin; Zheng, Wei

    2016-01-01

    Background & Aims Known Genetic factors explain only a small fraction of genetic variation in colorectal cancer (CRC). We conducted a genome-wide association study (GWAS) to identify risk loci for CRC. Methods This discovery stage included 8027 cases and 22577 controls of East-Asian ancestry. Promising variants were evaluated in studies including as many as 11044 cases and 12047 controls. Tumor-adjacent normal tissues from 188 patients were analyzed to evaluate correlations of risk variants with expression levels of nearby genes. Potential functionality of risk variants were evaluated using public genomic and epigenomic databases. Results We identified 4 loci associated with CRC risk; P values for the most significant variant in each locus ranged from 3.92×10−8 to 1.24×10−12: 6p21.1 (rs4711689), 8q23.3 (rs2450115, rs6469656), 10q24.3 (rs4919687), and 12p13.3 (rs11064437). We also identified 2 risk variants at loci previously associated with CRC: 10q25.2 (rs10506868) and 20q13.3 (rs6061231). These risk variants, conferring an approximate 10%–18% increase in risk per allele, are located either inside or near protein-coding genes that include TFEB (lysosome biogenesis and autophagy), EIF3H (initiation of translation), CYP17A1 (steroidogenesis), SPSB2 (proteasome degradation), and RPS21 (ribosome biogenesis). Gene expression analyses showed a significant association (P <.05) for rs4711689 with TFEB, rs6469656 with EIF3H, rs11064437 with SPSB2, and rs6061231 with RPS21. Conclusions We identified susceptibility loci and genes associated with CRC risk, linking CRC predisposition to steroid hormone, protein synthesis and degradation, and autophagy pathways and providing added insight into the mechanism of CRC pathogenesis. PMID:26965516

  16. Identification of GALNT14 as a novel neuroblastoma predisposition gene

    PubMed Central

    Chierici, Marco; Furlanello, Cesare; Conte, Massimo; Garaventa, Alberto; Croce, Michela; Ferrini, Silvano; Tonini, Gian Paolo; Longo, Luca

    2015-01-01

    Although several genes have been associated to neuroblastoma (NB) predisposition and aggressiveness, further genes are likely involved in the overall risk of developing this pediatric cancer. We thus carried out whole-exome sequencing on germline DNA from two affected second cousins and two unlinked healthy relatives from a large family with hereditary NB. Bioinformatics analysis revealed 6999 variations that were exclusively shared by the two familial NB cases. We then considered for further analysis all unknown or rare missense mutations, which involved 30 genes. Validation and analysis of these variants led to identify a GALNT14 mutation (c.802C > T) that properly segregated in the family and was predicted as functionally damaging by PolyPhen2 and SIFT. Screening of 8 additional NB families and 167 sporadic cases revealed this GALNT14 mutation in the tumors of two twins and in the germline of one sporadic NB patient. Moreover, a significant association between MYCN amplification and GALNT14 expression was observed in both NB patients and cell lines. Also, GALNT14 higher expression is associated with a worse OS in a public dataset of 88 NB samples (http://r2.amc.nl). GALNT14 is a member of the polypeptide N-acetylgalactosaminyl-transferase family and maps closely to ALK on 2p23.1, a region we previously discovered in linkage with NB in the family here considered. The aberrant function of GALNTs can result in altered glycoproteins that have been associated to the promotion of tumor aggressiveness in various cancers. Although rare, the recurrence of this mutation suggests GALNT14 as a novel gene potentially involved in NB predisposition. PMID:26309160

  17. Identification and validation of reference genes for quantitative RT-PCR normalization in wheat

    PubMed Central

    Paolacci, Anna R; Tanzarella, Oronzo A; Porceddu, Enrico; Ciaffi, Mario

    2009-01-01

    Background Usually the reference genes used in gene expression analysis have been chosen for their known or suspected housekeeping roles, however the variation observed in most of them hinders their effective use. The assessed lack of validated reference genes emphasizes the importance of a systematic study for their identification. For selecting candidate reference genes we have developed a simple in silico method based on the data publicly available in the wheat databases Unigene and TIGR. Results The expression stability of 32 genes was assessed by qRT-PCR using a set of cDNAs from 24 different plant samples, which included different tissues, developmental stages and temperature stresses. The selected sequences included 12 well-known HKGs representing different functional classes and 20 genes novel with reference to the normalization issue. The expression stability of the 32 candidate genes was tested by the computer programs geNorm and NormFinder using five different data-sets. Some discrepancies were detected in the ranking of the candidate reference genes, but there was substantial agreement between the groups of genes with the most and least stable expression. Three new identified reference genes appear more effective than the well-known and frequently used HKGs to normalize gene expression in wheat. Finally, the expression study of a gene encoding a PDI-like protein showed that its correct evaluation relies on the adoption of suitable normalization genes and can be negatively affected by the use of traditional HKGs with unstable expression, such as actin and α-tubulin. Conclusion The present research represents the first wide screening aimed to the identification of reference genes and of the corresponding primer pairs specifically designed for gene expression studies in wheat, in particular for qRT-PCR analyses. Several of the new identified reference genes outperformed the traditional HKGs in terms of expression stability under all the tested conditions

  18. Local identification of scalar hybrid models with tree structure

    NASA Astrophysics Data System (ADS)

    Fiedler, Bernold; Schuppert, Andreas

    2008-06-01

    Standard modelling approaches, e.g. in chemical engineering, suffer from two principal difficulties: the curse of dimension and a lack of extrapolability. We propose an approach via structured hybrid models (SHMs) to resolve both issues. For simplicity, we consider reactor models which can be written as a tree-like composition of scalar input-output (i/o) functions uj. The vertices j of the finite tree structure represent known or unknown subprocesses of the overall process. Known processes are modelled by white-box functions uj; unknown processes are represented by black boxes uj. Oriented edges of the tree indicate composition of the i/o relations uj in a feedforward structure. The tree structure of a mixture of black and white boxes constitutes what we call an SHM. Under certain assumptions on differentiability, genericity and monotonicity, we provide an inductive algorithm which uniquely identifies all black boxes in the SHM up to a trivial scaling calibration between adjacent black boxes. Our result does not require any extra measurements interior to the SHM. Instead, we only require global, overall i/o data clustered along a d-dimensional database of inputs. More precisely, information on partial derivatives of order up to 5 is required, in all directions, but only at base points within the d-dimensional database. The dimension d need not exceed the maximal input dimension of any individual black box in the SHM. Compared to the total input dimension n of the reactor, which may be much larger than d, this dimension reduction effectively avoids the curse of dimension: the complexity of our approach is polynomial in n and exponential in d, only, rather than exponential in n. Moreover, our unique identification of all black boxes accommodates a reliable global extrapolation, far beyond the original database, to input regions of full dimension. We illustrate our results with a model of an industrial continuous polymerization plant.

  19. Identification and Characterization of Clostridium sordellii Toxin Gene Regulator

    PubMed Central

    Sirigi Reddy, Apoorva Reddy; Girinathan, Brintha Parasumanna; Zapotocny, Ryan

    2013-01-01

    Toxigenic Clostridium sordellii causes uncommon but highly lethal infections in humans and animals. Recently, an increased incidence of C. sordellii infections has been reported in women undergoing obstetric interventions. Pathogenic strains of C. sordellii produce numerous virulence factors, including sordellilysin, phospholipase, neuraminidase, and two large clostridial glucosylating toxins, TcsL and TcsH. Recent studies have demonstrated that TcsL toxin is an essential virulence factor for the pathogenicity of C. sordellii. In this study, we identified and characterized TcsR as the toxin gene (tcsL) regulator in C. sordellii. High-throughput sequencing of two C. sordellii strains revealed that tcsR lies within a genomic region that encodes TcsL, TcsH, and TcsE, a putative holin. By using ClosTron technology, we inactivated the tcsR gene in strain ATCC 9714. Toxin production and tcsL transcription were decreased in the tcsR mutant strain. However, the complemented tcsR mutant produced large amounts of toxins, similar to the parental strain. Expression of the Clostridium difficile toxin gene regulator tcdR also restored toxin production to the C. sordellii tcsR mutant, showing that these sigma factors are functionally interchangeable. PMID:23873908

  20. Identification of a mouse synaptic glycoprotein gene in cultured neurons.

    PubMed

    Yu, Albert Cheung-Hoi; Sun, Chun Xiao; Li, Qiang; Liu, Hua Dong; Wang, Chen Ran; Zhao, Guo Ping; Jin, Meilei; Lau, Lok Ting; Fung, Yin-Wan Wendy; Liu, Shuang

    2005-10-01

    Neuronal differentiation and aging are known to involve many genes, which may also be differentially expressed during these developmental processes. From primary cultured cerebral cortical neurons, we have previously identified various differentially expressed gene transcripts from cultured cortical neurons using the technique of arbitrarily primed PCR (RAP-PCR). Among these transcripts, clone 0-2 was found to have high homology to rat and human synaptic glycoprotein. By in silico analysis using an EST database and the FACTURA software, the full-length sequence of 0-2 was assembled and the clone was named as mouse synaptic glycoprotein homolog 2 (mSC2). DNA sequencing revealed transcript size of mSC2 being smaller than the human and rat homologs. RT-PCR indicated that mSC2 was expressed differentially at various culture days. The mSC2 gene was located in various tissues with higher expression in brain, lung, and liver. Functions of mSC2 in neurons and other tissues remain elusive and will require more investigation.

  1. Identification and characterization of Clostridium sordellii toxin gene regulator.

    PubMed

    Sirigi Reddy, Apoorva Reddy; Girinathan, Brintha Parasumanna; Zapotocny, Ryan; Govind, Revathi

    2013-09-01

    Toxigenic Clostridium sordellii causes uncommon but highly lethal infections in humans and animals. Recently, an increased incidence of C. sordellii infections has been reported in women undergoing obstetric interventions. Pathogenic strains of C. sordellii produce numerous virulence factors, including sordellilysin, phospholipase, neuraminidase, and two large clostridial glucosylating toxins, TcsL and TcsH. Recent studies have demonstrated that TcsL toxin is an essential virulence factor for the pathogenicity of C. sordellii. In this study, we identified and characterized TcsR as the toxin gene (tcsL) regulator in C. sordellii. High-throughput sequencing of two C. sordellii strains revealed that tcsR lies within a genomic region that encodes TcsL, TcsH, and TcsE, a putative holin. By using ClosTron technology, we inactivated the tcsR gene in strain ATCC 9714. Toxin production and tcsL transcription were decreased in the tcsR mutant strain. However, the complemented tcsR mutant produced large amounts of toxins, similar to the parental strain. Expression of the Clostridium difficile toxin gene regulator tcdR also restored toxin production to the C. sordellii tcsR mutant, showing that these sigma factors are functionally interchangeable.

  2. Identification of genes and candidate agents associated with pancreatic cancer.

    PubMed

    Wang, Bao-sheng; Liu, Zhen; Sun, Shao-long; Zhao, Yi

    2014-01-01

    Pancreatic cancer is a malignant neoplasm originating from transformed cells arising in tissues forming the pancreas. A major challenge in current cancer research is biological interpretation of complexity of cancer somatic mutation profiles. It has been suggested that several molecular alterations may play important roles in pancreatic carcinogenesis. In this study, by using the GSE28735 affymetrix microarray data accessible from Gene Expression Omnibus (GEO) database, we identified differentially expressed genes (DEGs) between paired pancreatic cancer tissues and adjacent nontumor tissues, followed the protein-protein interaction of the DEGs. Our study identified thousands of DEGs involved in regulation of cell cycle and apoptosis in progression of pancreatic cancer. Sp1 was predicted to be the major regulator by transcription factors analysis. From the protein-protein interaction networks, we found that Tk1 might play an important role in the progression of pancreatic cancer. Finally, we predicted candidate agents, including tomatidine and nialamide, which may be used as drugs to treat pancreatic cancer. In conclusion, our data provide a comprehensive bioinformatics analysis of genes and pathways which may be involved in the progression of pancreatic cancer.

  3. Identification of new cell size control genes in S. cerevisiae

    PubMed Central

    2012-01-01

    Cell size homeostasis is a conserved attribute in many eukaryotic species involving a tight regulation between the processes of growth and proliferation. In budding yeast S. cerevisiae, growth to a “critical cell size” must be achieved before a cell can progress past START and commit to cell division. Numerous studies have shown that progression past START is actively regulated by cell size control genes, many of which have implications in cell cycle control and cancer. Two initial screens identified genes that strongly modulate cell size in yeast. Since a second generation yeast gene knockout collection has been generated, we screened an additional 779 yeast knockouts containing 435 new ORFs (~7% of the yeast genome) to supplement previous cell size screens. Upon completion, 10 new strong size mutants were identified: nine in log-phase cells and one in saturation-phase cells, and 97% of the yeast genome has now been screened for cell size mutations. The majority of the logarithmic phase size mutants have functions associated with translation further implicating the central role of growth control in the cell division process. Genetic analyses suggest ECM9 is directly associated with the START transition. Further, the small (whi) mutants mrpl49Δ and cbs1Δ are dependent on CLN3 for cell size effects. In depth analyses of new size mutants may facilitate a better understanding of the processes that govern cell size homeostasis. PMID:23234503

  4. Identification of the neurofibromatosis type 1 gene product

    SciTech Connect

    Gutmann, D.H.; Wood, D.L.; Collins, F.S. )

    1991-11-01

    The gene for neurofibromatosis type 1 (NF1) was recently identified by positional cloning. The complete cDNA encodes a polypeptide of 2818 amino acids. To study the NF1 gene product, antibodies were raised against both fusion proteins and synthetic peptides. Initial characterization of two anti-peptide antibodies and one fusion-protein antibody demonstrated a specific protein of {approx}250 kDa by both immunoprecipitation and immunoblotting. This protein was found in all tissues and cell lines examined and is detected in human, rat, and mouse tissues. To demonstrate that these antibodies specifically recognize the NF1 protein, additional fusion proteins containing the sequence specific to the synthetic peptide were generated. Both peptide antisera recognize the proper specific fusion proteins so generated. Immunoprecipitates using the peptide antisera were shown to recognize the same protein detected by immunoblotting with either the other peptide antiserum or the fusion-protein antiserum. Immunoblotting using antiserum specific to spatially distinct epitopes conducted on tissue homogenates demonstrated the NF1 protein in all adult tissues. Based on the homology between the NF1 gene product and members of the GTPase-activating protein (GAP) superfamily, the name NF1-GAP-related protein (NF1GRP) is suggested.

  5. Identification of novel stress-induced genes downstream of chop.

    PubMed Central

    Wang, X Z; Kuroda, M; Sok, J; Batchvarova, N; Kimmel, R; Chung, P; Zinszner, H; Ron, D

    1998-01-01

    CHOP (GADD153) is a small nuclear protein that dimerizes avidly with members of the C/EBP family of transcription factors. Normally undetectable, it is expressed at high levels in cells exposed to conditions that perturb protein folding in the endoplasmic reticulum and induce an endoplasmic reticulum stress response. CHOP expression in stressed cells is linked to the development of programmed cell death and, in some instances, cellular regeneration. In this study, representational difference analysis was used to compare the complement of genes expressed in stressed wild-type mouse embryonic fibroblasts with those expressed in cells nullizygous for chop. CHOP expression, in concert with a second signal, was found to be absolutely required for the activation by stress of a set of previously undescribed genes referred to as DOCs (for downstream of CHOP). DOC4 is a mammalian ortholog of a Drosophila gene, Tenm/Odz, implicated in patterning of the early fly embryo, whereas DOC6 encodes a newly recognized homolog of the actin-binding proteins villin and gelsolin. These results reveal the existence of a novel CHOP-dependent signaling pathway, distinct from the known endoplasmic reticulum unfolded protein response, which may mediate changes in cell phenotype in response to stress. PMID:9649432

  6. Identification of Dictyostelium G alpha genes expressed during multicellular development.

    PubMed Central

    Hadwiger, J A; Wilkie, T M; Strathmann, M; Firtel, R A

    1991-01-01

    Guanine nucleotide-binding protein (G protein)-mediated signal transduction constitutes a common mechanism by which cells receive and respond to a diverse set of environmental signals. Many of the signals involved in the developmental life cycle of the slime mold Dictyostelium have been postulated to be transduced by such pathways and, in some cases, these pathways have been demonstrated to be dependent on specific G proteins. Using the polymerase chain reaction, we have identified two additional Dictyostelium G alpha genes, G alpha 4 and G alpha 5, that are developmentally regulated. Transcripts from both of these genes are primarily expressed during the multicellular stages of development, suggesting possible roles in cell differentiation or morphogenesis. The entire G alpha 4 gene was sequenced and found to encode a protein consisting of 345 amino acids. The G alpha 4 subunit is homologous to other previously identified G alpha subunits, including the Dictyostelium G alpha 1 (43% identity) and G alpha 2 (41% identity) subunits. However, the G alpha 4 subunit contains some unusual sequence divergences in residues highly conserved among most eukaryotic G alpha subunits, suggesting that G alpha 4 may be a member of another class of G alpha subunits. Images PMID:1910174

  7. Sex identification using the ZFX and ZFY genes in common marmosets (Callithrix jacchus).

    PubMed

    Takabayashi, Shuji; Katoh, Hideki

    2011-01-01

    We investigated sex determination via the ZFX and ZFY genes using PCR-RFLP in the common marmoset. We designed a novel primer set to detect ZFX and ZFY. A 483-bp band from the ZFX gene and a 471-bp band from the ZFY gene were amplified. Sequencing data of the products amplified from ZFX and ZFY showed the recognition sites of two restriction enzymes, DdeI and MseI, respectively. After digestion of the products using each enzyme, we found that the band patterns between females and males were different. PCR-based sex identification might provide a tool for further breeding studies and experimental embryological studies using marmosets.

  8. Automated identification of elemental ions in macromolecular crystal structures

    SciTech Connect

    Echols, Nathaniel Morshed, Nader; Afonine, Pavel V.; McCoy, Airlie J.; Read, Randy J.; Terwilliger, Thomas C.; Adams, Paul D.

    2014-04-01

    The solvent-picking procedure in phenix.refine has been extended and combined with Phaser anomalous substructure completion and analysis of coordination geometry to identify and place elemental ions. Many macromolecular model-building and refinement programs can automatically place solvent atoms in electron density at moderate-to-high resolution. This process frequently builds water molecules in place of elemental ions, the identification of which must be performed manually. The solvent-picking algorithms in phenix.refine have been extended to build common ions based on an analysis of the chemical environment as well as physical properties such as occupancy, B factor and anomalous scattering. The method is most effective for heavier elements such as calcium and zinc, for which a majority of sites can be placed with few false positives in a diverse test set of structures. At atomic resolution, it is observed that it can also be possible to identify tightly bound sodium and magnesium ions. A number of challenges that contribute to the difficulty of completely automating the process of structure completion are discussed.

  9. Identification of disease genes: example-driven web-based tutorial.

    PubMed

    Bhagwat, Medha

    2007-01-01

    The National Center for Biotechnology Information (NCBI) has developed several web-based mini-courses (www.ncbi.nlm.nih.gov/Class/minicourses) illustrating the applications of NCBI resources. This chapter describes the problem-based minicourse called "Identification of Disease Genes." The mini-course guides us through one of the several ways to identify disease related genes, starting from the expressed sequence data such as that may have been obtained from patients. The chapter first provides an introduction to the human genome assembly and the resources such as the Basic Local Alignment Search Tool, Map Viewer, Single Nucleotide Polymorphism database, and Online Mendelian Inheritance in Man. The chapter then demonstrates the practical application of these resources to the identification of genes related to two diseases, hemochromatosis and sickle cell anemia. The chapter also provides links to the mini-course web pages and includes the screen images of the results of the applied steps.

  10. Identification, expression, and comparative genomic analysis of the IPT and CKX gene families in Chinese cabbage (Brassica rapa ssp. pekinensis)

    PubMed Central

    2013-01-01

    Background Cytokinins (CKs) have significant roles in various aspects of plant growth and development, and they are also involved in plant stress adaptations. The fine-tuning of the controlled CK levels in individual tissues, cells, and organelles is properly maintained by isopentenyl transferases (IPTs) and cytokinin oxidase/dehydrogenases (CKXs). Chinese cabbage is one of the most economically important vegetable crops worldwide. The whole genome sequencing of Brassica rapa enables us to perform the genome-wide identification and functional analysis of the IPT and CKX gene families. Results In this study, a total of 13 BrIPT genes and 12 BrCKX genes were identified. The gene structures, conserved domains and phylogenetic relationships were analyzed. The isoelectric point, subcellular localization and glycosylation sites of the proteins were predicted. Segmental duplicates were found in both BrIPT and BrCKX gene families. We also analyzed evolutionary patterns and divergence of the IPT and CKX genes in the Cruciferae family. The transcription levels of BrIPT and BrCKX genes were analyzed to obtain an initial picture of the functions of these genes. Abiotic stress elements related to adverse environmental stimuli were found in the promoter regions of BrIPT and BrCKX genes and they were confirmed to respond to drought and high salinity conditions. The effects of 6-BA and ABA on the expressions of BrIPT and BrCKX genes were also investigated. Conclusions The expansion of BrIPT and BrCKX genes after speciation from Arabidopsis thaliana is mainly attributed to segmental duplication events during the whole genome triplication (WGT) and substantial duplicated genes are lost during the long evolutionary history. Genes produced by segmental duplication events have changed their expression patterns or may adopted new functions and thus are obtained. BrIPT and BrCKX genes respond well to drought and high salinity stresses, and their transcripts are affected by exogenous

  11. PIECE: A database for plant gene structure comparison and evolution

    USDA-ARS?s Scientific Manuscript database

    Gene families often show degrees of differences in terms of exon-intron structures depending on their distinct evolutionary histories. Comparative analysis of gene structures is important for understanding their evolutionary and functional relationships within plant species. Here, we present a com...

  12. Genome-wide identification and analysis of the aldehyde dehydrogenase (ALDH) gene superfamily in apple (Malus × domestica Borkh.).

    PubMed

    Li, Xiaoqin; Guo, Rongrong; Li, Jun; Singer, Stacy D; Zhang, Yucheng; Yin, Xiangjing; Zheng, Yi; Fan, Chonghui; Wang, Xiping

    2013-10-01

    Aldehyde dehydrogenases (ALDHs) represent a protein superfamily encoding NAD(P)(+)-dependent enzymes that oxidize a wide range of endogenous and exogenous aliphatic and aromatic aldehydes. In plants, they are involved in many biological processes and play a role in the response to environmental stress. In this study, a total of 39 ALDH genes from ten families were identified in the apple (Malus × domestica Borkh.) genome. Synteny analysis of the apple ALDH (MdALDH) genes indicated that segmental and tandem duplications, as well as whole genome duplications, have likely contributed to the expansion and evolution of these gene families in apple. Moreover, synteny analysis between apple and Arabidopsis demonstrated that several MdALDH genes were found in the corresponding syntenic blocks of Arabidopsis, suggesting that these genes appeared before the divergence of lineages that led to apple and Arabidopsis. In addition, phylogenetic analysis, as well as comparisons of exon-intron and protein structures, provided further insight into both their evolutionary relationships and their putative functions. Tissue-specific expression analysis of the MdALDH genes demonstrated diverse spatiotemporal expression patterns, while their expression profiles under abiotic stress and various hormone treatments indicated that many MdALDH genes were responsive to high salinity and drought, as well as different plant hormones. This genome-wide identification, as well as characterization of evolutionary relationships and expression profiles, of the apple MdALDH genes will not only be useful for the further analysis of ALDH genes and their roles in stress response, but may also aid in the future improvement of apple stress tolerance. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

  13. Characterization and Functional Analysis of Five MADS-Box B Class Genes Related to Floral Organ Identification in Tagetes erecta.

    PubMed

    Ai, Ye; Zhang, Chunling; Sun, Yalin; Wang, Weining; He, Yanhong; Bao, Manzhu

    2017-01-01

    According to the floral organ development ABC model, B class genes specify petal and stamen identification. In order to study the function of B class genes in flower development of Tagetes erecta, five MADS-box B class genes were identified and their expression and putative functions were studied. Sequence comparisons and phylogenetic analyses indicated that there were one PI-like gene-TePI, two euAP3-like genes-TeAP3-1 and TeAP3-2, and two TM6-like genes-TeTM6-1 and TeTM6-2 in T. erecta. Strong expression levels of these genes were detected in stamens of the disk florets, but little or no expression was detected in bracts, receptacles or vegetative organs. Yeast hybrid experiments of the B class proteins showed that TePI protein could form a homodimer and heterodimers with all the other four B class proteins TeAP3-1, TeAP3-2, TeTM6-1 and TeTM6-2. No homodimer or interaction was observed between the euAP3 and TM6 clade members. Over-expression of five B class genes of T. erecta in Nicotiana rotundifolia showed that only the transgenic plants of 35S::TePI showed altered floral morphology compared with the non-transgenic line. This study could contribute to the understanding of the function of B class genes in flower development of T. erecta, and provide a theoretical basis for further research to change floral organ structures and create new materials for plant breeding.

  14. Commentary: When does understanding phenotypic evolution require identification of the underlying genes?

    PubMed

    Rausher, Mark D; Delph, Lynda F

    2015-07-01

    Adaptive evolution is fundamentally a genetic process. Over the past three decades, characterizing the genes underlying adaptive phenotypic change has revealed many important aspects of evolutionary change. At the same time, natural selection is often fundamentally an ecological process that can often be studied without identifying the genes underlying the variation on which it acts. This duality has given rise to disagreement about whether, and under what circumstances, it is necessary to identify specific genes associated with phenotypic change. This issue is of practical concern, especially for researchers who study nonmodel organisms, because of the often enormous cost and labor required to "go for the genes." We here consider a number of situations and questions commonly addressed by researchers. Our conclusion is that although gene identification can be crucial for answering some questions, there are others for which definitive answers can be obtained without finding underlying genes. It should thus not be assumed that considerations of "empirical completeness" dictate that gene identification is always desirable. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

  15. Evolutionary and Topological Properties of Genes and Community Structures in Human Gene Regulatory Networks.

    PubMed

    Szedlak, Anthony; Smith, Nicholas; Liu, Li; Paternostro, Giovanni; Piermarocchi, Carlo

    2016-06-01

    The diverse, specialized genes present in today's lifeforms evolved from a common core of ancient, elementary genes. However, these genes did not evolve individually: gene expression is controlled by a complex network of interactions, and alterations in one gene may drive reciprocal changes in its proteins' binding partners. Like many complex networks, these gene regulatory networks (GRNs) are composed of communities, or clusters of genes with relatively high connectivity. A deep understanding of the relationship between the evolutionary history of single genes and the topological properties of the underlying GRN is integral to evolutionary genetics. Here, we show that the topological properties of an acute myeloid leukemia GRN and a general human GRN are strongly coupled with its genes' evolutionary properties. Slowly evolving ("cold"), old genes tend to interact with each other, as do rapidly evolving ("hot"), young genes. This naturally causes genes to segregate into community structures with relatively homogeneous evolutionary histories. We argue that gene duplication placed old, cold genes and communities at the center of the networks, and young, hot genes and communities at the periphery. We demonstrate this with single-node centrality measures and two new measures of efficiency, the set efficiency and the interset efficiency. We conclude that these methods for studying the relationships between a GRN's community structures and its genes' evolutionary properties provide new perspectives for understanding evolutionary genetics.

  16. Identification and characterization of the lamprey IRF gene.

    PubMed

    Pang, Yue; Liu, Shuang; Zheng, Zhen; Liu, Xin; Li, Qingwei

    2015-04-01

    Interferon regulatory factors (IRFs) are named for their ability to bind to and regulate interferon genes when an organism becomes infected with a virus. Numerous studies have revealed the versatile and critical functions of IRFs. In this study, an IRF gene from Lampetra japonica was identified and analyzed using bioinformatic methods. The L. japonica IRF (Lj-IRF) shares high sequence homology with other vertebrate IRFs but low sequence homology with an ascidian IRF-like protein. We also used recombinant Lj-IRF protein (rLj-IRF) to immunize New Zealand rabbits to prepare specific anti-rLj-IRF polyclonal antibodies. Enzyme-linked immunosorbent assays (ELISAs) and Western blotting assays were performed to detect the valence and specificity of the antibody. FACS analysis revealed that the Lj-IRF protein was expressed in approximately 21.14% of leukocytes and 9.60% of supraneural body cells in L. japonica, with immunofluorescence staining indicating a cytoplasmic location. The immunohistochemistry results demonstrated that IRF is distributed in the epithelial cells of the heart, supraneural body, kidneys and gills but is not detectable in intestinals or oral gland tissues. However, the expression of IRF was upregulated in lamprey intestinal tissues upon stimulation with the rLj-HMGB1 protein. Lj-IRF gene expression levels were higher in the rLj-HMGB1-stimulated group than the control group, and the expression level of Lj-IRF was significantly increased in the intestines as determined by quantitative real-time PCR. These results provide a foundation for studying the origin and evolution of the innate immune system in lampreys.

  17. Identification of Susceptibility Loci and Genes for Colorectal Cancer Risk.

    PubMed

    Zeng, Chenjie; Matsuda, Koichi; Jia, Wei-Hua; Chang, Jiang; Kweon, Sun-Seog; Xiang, Yong-Bing; Shin, Aesun; Jee, Sun Ha; Kim, Dong-Hyun; Zhang, Ben; Cai, Qiuyin; Guo, Xingyi; Long, Jirong; Wang, Nan; Courtney, Regina; Pan, Zhi-Zhong; Wu, Chen; Takahashi, Atsushi; Shin, Min-Ho; Matsuo, Keitaro; Matsuda, Fumihiko; Gao, Yu-Tang; Oh, Jae Hwan; Kim, Soriul; Jung, Keum Ji; Ahn, Yoon-Ok; Ren, Zefang; Li, Hong-Lan; Wu, Jie; Shi, Jiajun; Wen, Wanqing; Yang, Gong; Li, Bingshan; Ji, Bu-Tian; Brenner, Hermann; Schoen, Robert E; Küry, Sébastien; Gruber, Stephen B; Schumacher, Fredrick R; Stenzel, Stephanie L; Casey, Graham; Hopper, John L; Jenkins, Mark A; Kim, Hyeong-Rok; Jeong, Jin-Young; Park, Ji Won; Tajima, Kazuo; Cho, Sang-Hee; Kubo, Michiaki; Shu, Xiao-Ou; Lin, Dongxin; Zeng, Yi-Xin; Zheng, Wei

    2016-06-01

    Known genetic factors explain only a small fraction of genetic variation in colorectal cancer (CRC). We conducted a genome-wide association study to identify risk loci for CRC. This discovery stage included 8027 cases and 22,577 controls of East-Asian ancestry. Promising variants were evaluated in studies including as many as 11,044 cases and 12,047 controls. Tumor-adjacent normal tissues from 188 patients were analyzed to evaluate correlations of risk variants with expression levels of nearby genes. Potential functionality of risk variants were evaluated using public genomic and epigenomic databases. We identified 4 loci associated with CRC risk; P values for the most significant variant in each locus ranged from 3.92 × 10(-8) to 1.24 × 10(-12): 6p21.1 (rs4711689), 8q23.3 (rs2450115, rs6469656), 10q24.3 (rs4919687), and 12p13.3 (rs11064437). We also identified 2 risk variants at loci previously associated with CRC: 10q25.2 (rs10506868) and 20q13.3 (rs6061231). These risk variants, conferring an approximate 10%-18% increase in risk per allele, are located either inside or near protein-coding genes that include transcription factor EB (lysosome biogenesis and autophagy), eukaryotic translation initiation factor 3, subunit H (initiation of translation), cytochrome P450, family 17, subfamily A, polypeptide 1 (steroidogenesis), splA/ryanodine receptor domain and SOCS box containing 2 (proteasome degradation), and ribosomal protein S2 (ribosome biogenesis). Gene expression analyses showed a significant association (P < .05) for rs4711689 with transcription factor EB, rs6469656 with eukaryotic translation initiation factor 3, subunit H, rs11064437 with splA/ryanodine receptor domain and SOCS box containing 2, and rs6061231 with ribosomal protein S2. We identified susceptibility loci and genes associated with CRC risk, linking CRC predisposition to steroid hormone, protein synthesis and degradation, and autophagy pathways and providing added insight into the

  18. Molecular identification of Leishmania spp. clinical isolates from Colombia based on hsp70 gene.

    PubMed

    Montalvo, Ana M; Fraga, Jorge; Montano, Ivón; Monzote, Lianet; Van der Auwera, Gert; Marín, Marcel; Muskus, Carlos

    2016-02-23

    Leishmaniasis is highly prevalent in Colombia, where at least six different species can cause disease of varying clinical presentations in humans. The identification of the infecting species is quite important for prognosis, therapeutics and epidemiology. Different techniques with variable discriminatory power have been used for the identification.  To carry out the molecular identification of Leishmania species through the amplification of a fragment of the hsp70 gene.  Molecular amplification of the hsp70 gene fragment (PCR-hsp70) followed by restriction fragment length polymorphism analysis (RFLP) was done for identification purposes using DNA from 81 clinical isolates of Leishmania.  A single amplicon was obtained for all samples analyzed. The enzymatic restrictions of the 81 PCR products identified 70 with a banding pattern corresponding to L. braziliensis with two different patterns (62 and eight isolates, respectively), nine isolates compatible with L. panamensis and two with L. guyanensis. The geographical origin of the isolates is consistent with previous reports about the distribution of the corresponding species in Colombia.  The PCR-hsp70/RFLP technique used is a valid tool for the identification of Leishmania species isolated from clinical samples of patients in Colombia, which may also be applicable to the study of strains obtained from vectors and reservoirs with epidemiological significance.

  19. Identification of Development and Pathogenicity Related Gene in Botrytis cinerea via Digital Gene Expression Profile

    PubMed Central

    Zhao, Bin; Si, He Long; Sun, Zhi Ying; Xu, Zheng; Chen, Zhan; Zhang, Jin lin; Xing, Ji Hong; Dong, Jin Gao

    2015-01-01

    Background: Botrytis cinerea, a haploid Euascomycete fungus that infects numerous crops, has been used as a model system for studying molecular phytopathology. Botrytis cinerea adopts various modes of infection, which are mediated by a number of pathogenicity and virulence-related genes. Many of these genes have not been reported previously. Objectives: This study aimed to investigate development and pathogenicity-related genes between a novel nonpathogenic mutant and the Wild Type (WT) in B. cinerea. Materials and Methods: Digital Gene Expression (DGE) tag profiling can reveal novel genes that may be involved in development and pathogenicity of plant pathogen. A large volume of B. cinerea tag-seq was generated to identify differential expressed genes by the Illumina DGE tag profiling technology. Results: A total of 4,182,944 and 4,182,021 clean tags were obtained from the WT and a nonpathogenic mutant stain (BCt89), respectively, and 10,410 differentially expressed genes were identified. In addition, 84 genes were expressed in the WT only while 34 genes were expressed in the mutant only. A total of 664 differentially expressed genes were involved in 91 Kyoto Encyclopedia of Genes and Genome pathways, including signaling and metabolic pathways. Conclusions: Expression levels of 1,426 genes were significantly up-regulated in the mutant compared to WT. Furthermore, 301 genes were down-regulated with False Discovery Rates (FDR) of < 0.001 and absolute value of log2 Ratio of ≥ 1. PMID:26034553

  20. Behavioral pattern identification for structural health monitoring in complex systems

    NASA Astrophysics Data System (ADS)

    Gupta, Shalabh

    Estimation of structural damage and quantification of structural integrity are critical for safe and reliable operation of human-engineered complex systems, such as electromechanical, thermofluid, and petrochemical systems. Damage due to fatigue crack is one of the most commonly encountered sources of structural degradation in mechanical systems. Early detection of fatigue damage is essential because the resulting structural degradation could potentially cause catastrophic failures, leading to loss of expensive equipment and human life. Therefore, for reliable operation and enhanced availability, it is necessary to develop capabilities for prognosis and estimation of impending failures, such as the onset of wide-spread fatigue crack damage in mechanical structures. This dissertation presents information-based online sensing of fatigue damage using the analytical tools of symbolic time series analysis ( STSA). Anomaly detection using STSA is a pattern recognition method that has been recently developed based upon a fixed-structure, fixed-order Markov chain. The analysis procedure is built upon the principles of Symbolic Dynamics, Information Theory and Statistical Pattern Recognition. The dissertation demonstrates real-time fatigue damage monitoring based on time series data of ultrasonic signals. Statistical pattern changes are measured using STSA to monitor the evolution of fatigue damage. Real-time anomaly detection is presented as a solution to the forward (analysis) problem and the inverse (synthesis) problem. (1) the forward problem - The primary objective of the forward problem is identification of the statistical changes in the time series data of ultrasonic signals due to gradual evolution of fatigue damage. (2) the inverse problem - The objective of the inverse problem is to infer the anomalies from the observed time series data in real time based on the statistical information generated during the forward problem. A computer-controlled special

  1. Identification of genes in anonymous DNA sequences. Final report: Report period, 15 April 1993--15 April 1994

    SciTech Connect

    Fields, C.A.

    1994-09-01

    This Report concludes the DOE Human Genome Program project, ``Identification of Genes in Anonymous DNA Sequence.`` The central goals of this project have been (1) understanding the problem of identifying genes in anonymous sequences, and (2) development of tools, primarily the automated identification system gm, for identifying genes. The activities supported under the previous award are summarized here to provide a single complete report on the activities supported as part of the project from its inception to its completion.

  2. Conserved gene structures and expression signals in methanogenic archaebacteria.

    PubMed

    Allmansberger, R; Bokranz, M; Kröckel, L; Schallenberg, J; Klein, A

    1989-01-01

    A comparative analysis of cotranscribed gene clusters comprising the structural genes mcrA, mcrB, mcrC, mcrD, and mcrG was carried out in three species of methanogens. mcrA, mcrB, and mcrG are the structural genes for the three subunits of methyl coenzyme M reductase, while the two other genes encode polypeptides of unknown functions. The degree of conservation of the mcr gene products among different species of methanogens varies. No correlation was found between the conservation of the G+C contents of the homologous genes and of the amino acid sequences of their products among the different bacteria. The comparison of RNA polymerase core subunit genes of Methanobacterium thermoautotrophicum as evolutionary markers with their equivalents in Escherichia coli, Saccharomyces cerevisiae, and Drosophila melanogaster showed that homologous polypeptide domains are encoded by different numbers of genes suggesting gene fusion of adjacent genes in the course of evolution. The archaebacterial subunits exhibit much stronger homology with their eukaryotic than with their eubacterial equivalents on the polypeptide sequence level. All the analyzed genes are preceded by ribosome binding sites of eubacterial type. In addition to known putative promoter sequences, conserved structural elements of the DNA were detected surrounding the transcription initiation sites of the mcr genes.

  3. Identification of Sphaeroma terebrans via morphology and the mitochondrial cytochrome c oxidase subunit I (COI) gene

    PubMed Central

    LI, Xiu-Feng; HAN, Chong; ZHONG, Cai-Rong; XU, Jun-Qiu; HUANG, Jian-Rong

    2016-01-01

    Sphaeroma terebrans, a wood-boring isopoda, is distributed worldwide in tropical and subtropical mangroves. The taxonomy of S. terebrans is usually based on morphological characteristics, with its molecular identification still poorly understood. The number of teeth on the uropodal exopod and the length of the propodus of the seventh pereopod are considered as the major morphological characteristics in S. terebrans, which can cause difficulty in regards to accurate identification. In this study, we identified S. terebrans via molecular and morphological data. Furthermore, the validity of the mitochondrial cytochrome c oxidase subunit I (COI) gene as a DNA barcode for the identification of genus Sphaeroma, including species S. terebrans, S. retrolaeve, and S. serratum, was examined. The mitochondrial COI gene sequences of all specimens were sequenced and analysed. The interspecific Kimura 2-parameter distances were higher than intraspecific distances and no intraspecific-interspecific distance overlaps were observed. In addition, genetic distance and nucleotide diversity (π) exhibited no differences within S. terebrans. Our results revealed that the mitochondrial COI gene can serve as a valid DNA barcode for the identification of S. terebrans. Furthermore, the number of teeth on the uropodal exopod and the length of the propodus of the seventh pereopod were found to be unreliable taxonomic characteristics for S. terebrans. PMID:27686791

  4. Identification of forensically important sarcophagid flies (Diptera: Sarcophagidae) in China based on COI and period gene.

    PubMed

    Guo, Yadong; Zha, Lagabaiyila; Yan, Weitao; Li, Pei; Cai, Jifeng; Wu, LiXiang

    2014-01-01

    Unequivocal identification of insect specimens is an essential requirement in forensic entomology. With the development of molecular identification, spate of discussions about the feature of the DNA fragments have been raised. Relying solely on single DNA fragment for delimiting closely related species is supposed to be dangerous. Aiming at obtaining more reliable markers that might be universally used, we explore the utility of 700-bp COI fragment and 678-bp period gene fragment in the identification of Sarcophagidae (Diptera). Thirty-six sarcophagid fly specimens were collected from 19 locations in 11 Chinese provinces. Phylogenetic analysis of the sequenced segments showed that all sarcophagid specimens were properly assigned into nine species with relatively strong supporting values, which indicated the possibility of separation congeneric species with COI and period gene fragments. The difference between intraspecific threshold and interspecific divergence confirmed that the combination of nuclear and mitochondrial genes for species identification is much more accurate. The results of this research will be instrumental for implementation of the Chinese Sarcophagidae database.

  5. Mitochondrial 16S ribosomal RNA gene for forensic identification of crocodile species.

    PubMed

    Naga Jogayya, K; Meganathan, P R; Dubey, Bhawna; Haque, I

    2013-05-01

    All crocodilians are under various threats due to over exploitation and these species have been listed in Appendix I or II of CITES. Lack of molecular techniques for the forensic identification of confiscated samples makes it difficult to enforce the law. Therefore, we herein present a molecular method developed on the basis on 16S rRNA gene of mitochondrial DNA for identification of crocodile species. We have developed a set of 16S rRNA primers for PCR based identification of crocodilian species. These novel primers amplify partial 16S rRNA sequences of six crocodile species which can be later combined to obtain a larger region (1290 bp) of 16S rRNA gene. This 16S rRNA gene could be used as an effective tool for forensic authentication of crocodiles. The described primers hold great promise in forensic identification of crocodile species, which can aid in the effective enforcement of law and conservation of these species.

  6. Expansion and orthogonalization of measured modes for structure identification

    NASA Technical Reports Server (NTRS)

    Smith, Suzanne Weaver

    1989-01-01

    The purpose was to investigate a new simultaneous expansion/orthogonalization method in comparison with two previously published expansion methods and a widely used orthogonalization technique. Each expansion method uses data from an analytical model of the structure to complete the estimate of the mode shape vectors. Berman and Nagy used Guyan expansion in their work with improving analytical models. In this method, modes are expanded one at a time, producing a set not orthogonal with respect to the mass matrix. Baruch and Bar Itzhack's optimal orthogonalization procedure was used to subsequently adjust the expanded modes. A second expansion technique was presented by O'Callahan, Avitabile, and Reimer and separately by Kammer. Again, modes are expanded individually and orthogonalized after expansion with the same optimal technique as above. Finally, a simultaneous expansion/orthogonalization method was developed from the orthogonal Procrustes problem of computational mathematics. In this method modes are optimally expanded as a set and orthogonal with respect to the mass matrix as a result. Two demonstation problems were selected for the comparison of the methods described. The first problem is an 8 degree of freedom spring-mass problem first presented by Kabe. Several conditions were examined for expansion method including the presence of errors in the measured data and in the analysis models. As a second demonstration problem, data from tests of laboratory scale model truss structures was expanded for system identification. Tests with a complete structure produced a correlated analysis model and the stiffness and mass matrices. Tests of various damaged configurations produced measured data for 6 modes at 14 dof locations.

  7. Gene dosage methods as diagnostic tools for the identification of chromosome abnormalities.

    PubMed

    Gouas, L; Goumy, C; Véronèse, L; Tchirkov, A; Vago, P

    2008-09-01

    Cytogenetics is the part of genetics that deals with chromosomes, particularly with numerical and structural chromosome abnormalities, and their implications in congenital or acquired genetic disorders. Standard karyotyping, successfully used for the last 50 years in investigating the chromosome etiology in patients with infertility, fetal abnormalities and congenital disorders, is constrained by the limits of microscopic resolution and is not suited for the detection of subtle chromosome abnormalities. The ability to detect submicroscopic chromosomal rearrangements that lead to copy-number changes has escalated progressively in recent years with the advent of molecular cytogenetic techniques. Here, we review various gene dosage methods such as FISH, PCR-based approaches (MLPA, QF-PCR, QMPSF and real time PCR), CGH and array-CGH, that can be used for the identification and delineation of copy-number changes for diagnostic purposes. Besides comparing their relative strength and weakness, we will discuss the impact that these detection methods have on our understanding of copy number variations in the human genome and their implications in genetic counseling.

  8. In silico identification and characterization of the WRKY gene superfamily in pepper (Capsicum annuum L.).

    PubMed

    Cheng, Y; Yao, Z P; Ruan, M Y; Ye, Q J; Wang, R Q; Zhou, G Z; Luo, J

    2016-09-23

    The WRKY family is one of the most important transcription factor families in plants, involved in the regulation of a broad range of biological roles. The recent releases of whole-genome sequences of pepper (Capsicum annuum L.) allow us to perform a genome-wide identification and characterization of the WRKY family. In this study, 61 CaWRKY proteins were identified in the pepper genome. Based on protein structural and phylogenetic analyses, these proteins were classified into four main groups (I, II, III, and NG), and Group II was further divided into five subgroups (IIa to IIe). Chromosome mapping analysis indicated that CaWRKY genes are distributed across all 12 chromosomes, although the location of four CaWRKYs (CaWRKY58-CaWRKY61) could not be identified. Two pairs of CaWRKYs located on chromosome 01 appear to be tandem duplications. Furthermore, the phylogenetic tree showed a close evolutionary relationship of WRKYs in three species from Solanaceae. In conclusion, this comprehensive analysis of CaWRKYs will provide rich resources for further functional studies in pepper.

  9. Genome-wide identification, characterization, and expression profile of aquaporin gene family in flax (Linum usitatissimum)

    PubMed Central

    Shivaraj, S. M.; Deshmukh, Rupesh K.; Rai, Rhitu; Bélanger, Richard; Agrawal, Pawan K.; Dash, Prasanta K.

    2017-01-01

    Membrane intrinsic proteins (MIPs) form transmembrane channels and facilitate transport of myriad substrates across the cell membrane in many organisms. Majority of plant MIPs have water transporting ability and are commonly referred as aquaporins (AQPs). In the present study, we identified aquaporin coding genes in flax by genome-wide analysis, their structure, function and expression pattern by pan-genome exploration. Cross-genera phylogenetic analysis with known aquaporins from rice, arabidopsis, and poplar showed five subgroups of flax aquaporins representing 16 plasma membrane intrinsic proteins (PIPs), 17 tonoplast intrinsic proteins (TIPs), 13 NOD26-like intrinsic proteins (NIPs), 2 small basic intrinsic proteins (SIPs), and 3 uncharacterized intrinsic proteins (XIPs). Amongst aquaporins, PIPs contained hydrophilic aromatic arginine (ar/R) selective filter but TIP, NIP, SIP and XIP subfamilies mostly contained hydrophobic ar/R selective filter. Analysis of RNA-seq and microarray data revealed high expression of PIPs in multiple tissues, low expression of NIPs, and seed specific expression of TIP3 in flax. Exploration of aquaporin homologs in three closely related Linum species bienne, grandiflorum and leonii revealed presence of 49, 39 and 19 AQPs, respectively. The genome-wide identification of aquaporins, first in flax, provides insight to elucidate their physiological and developmental roles in flax. PMID:28447607

  10. Identification, cloning, and expression of Pseudomonas aeruginosa phosphorylcholine phosphatase gene.

    PubMed

    Massimelli, María J; Beassoni, Paola R; Forrellad, Marina A; Barra, José L; Garrido, Mónica N; Domenech, Carlos E; Lisa, Angela T

    2005-05-01

    Pseudomonas aeruginosa phosphorylcholine phosphatase (PChP) is a periplasmic enzyme produced simultaneously with the hemolytic phospholipase C (PLc-H) when the bacteria are grown in the presence of choline, betaine, dimethylglycine or carnitine. Molecular analysis of the P. aeruginosa mutant JUF8-00, after Tn5-751 mutagenesis, revealed that the PA5292 gene in the P. aeruginosa PAO1 genome was responsible for the synthesis of PChP. The enzyme expressed in E. coli, rPChP-Ec, purified by a chitin-binding column (IMPACT-CN system, New England BioLabs) was homogeneous after SDS-PAGE analysis. PChP was also expressed in P. aeruginosa PAO1-LAC, rPChP-Pa. Both recombinant enzymes exhibited a molecular mass of approximately 40 kDa, as expected for the size of the PA5292 gene, and catalyzed the hydrolysis of phosphorylcholine, phosphorylethanolamine, and p-nitrophenylphosphate. The saturation curve of rPChP-Ec and rPChP-Pa by phosphorylcholine revealed that these recombinant enzymes, like the purified native PChP, also contained the high- and low-affinity sites for phosphorylcholine and that the enzyme activity was inhibited by high substrate concentration.

  11. IDENTIFICATION OF BIOLOGICALLY RELEVANT GENES USING A DATABASE OF RAT LIVER AND KIDNEY BASELINE GENE EXPRESSION

    EPA Science Inventory

    Microarray data from independent labs and studies can be compared to potentially identify toxicologically and biologically relevant genes. The Baseline Animal Database working group of HESI was formed to assess baseline gene expression from microarray data derived from control or...

  12. IDENTIFICATION OF BIOLOGICALLY RELEVANT GENES USING A DATABASE OF RAT LIVER AND KIDNEY BASELINE GENE EXPRESSION

    EPA Science Inventory

    Microarray data from independent labs and studies can be compared to potentially identify toxicologically and biologically relevant genes. The Baseline Animal Database working group of HESI was formed to assess baseline gene expression from microarray data derived from control or...

  13. Proceedings of the Workshop on Identification and Control of Flexible Space Structures, volume 1

    NASA Technical Reports Server (NTRS)

    Rodriguez, G. (Editor)

    1985-01-01

    Identification and control of flexible space structures were studied. Exploration of the most advanced modeling estimation, identification and control methodologies to flexible space structures was discussed. The following general areas were discussed: space platforms, antennas, and flight experiments; control/structure interactions - modeling, integrated design and optimization, control and stabilization, and shape control; control technology; control of space stations; large antenna control, dynamics and control experiments, and control/structure interaction experiments.

  14. Identification of mechanosensitive genes during skeletal development: alteration of genes associated with cytoskeletal rearrangement and cell signalling pathways

    PubMed Central

    2014-01-01

    Background Mechanical stimulation is necessary for regulating correct formation of the skeleton. Here we test the hypothesis that mechanical stimulation of the embryonic skeletal system impacts expression levels of genes implicated in developmentally important signalling pathways in a genome wide approach. We use a mutant mouse model with altered mechanical stimulation due to the absence of limb skeletal muscle (Splotch-delayed) where muscle-less embryos show specific defects in skeletal elements including delayed ossification, changes in the size and shape of cartilage rudiments and joint fusion. We used Microarray and RNA sequencing analysis tools to identify differentially expressed genes between muscle-less and control embryonic (TS23) humerus tissue. Results We found that 680 independent genes were down-regulated and 452 genes up-regulated in humeri from muscle-less Spd embryos compared to littermate controls (at least 2-fold; corrected p-value ≤0.05). We analysed the resulting differentially expressed gene sets using Gene Ontology annotations to identify significant enrichment of genes associated with particular biological processes, showing that removal of mechanical stimuli from muscle contractions affected genes associated with development and differentiation, cytoskeletal architecture and cell signalling. Among cell signalling pathways, the most strongly disturbed was Wnt signalling, with 34 genes including 19 pathway target genes affected. Spatial gene expression analysis showed that both a Wnt ligand encoding gene (Wnt4) and a pathway antagonist (Sfrp2) are up-regulated specifically in the developing joint line, while the expression of a Wnt target gene, Cd44, is no longer detectable in muscle-less embryos. The identification of 84 genes associated with the cytoskeleton that are down-regulated in the absence of muscle indicates a number of candidate genes that are both mechanoresponsive and potentially involved in mechanotransduction, converting a

  15. Identification of Staphylococcus species and subspecies by the chaperonin 60 gene identification method and reverse checkerboard hybridization.

    PubMed Central

    Goh, S H; Santucci, Z; Kloos, W E; Faltyn, M; George, C G; Driedger, D; Hemmingsen, S M

    1997-01-01

    A previous study (S. H. Goh et al., J. Clin. Microbiol. 34:818-823, 1996) demonstrated that a 600-bp region of the chaperonin 60 (Cpn60) genes from various bacterial isolates could be amplified by PCR with a pair of degenerate primers and that the products could be used as species-specific probes for Staphylococcus aureus, S. epidermidis, S. haemolyticus, S. lugdunensis, S. saprophyticus, and S. schleiferi. To further validate the utility of bacterial Cpn60 genes as universal targets for bacterial identification (ID), reverse checkerboar