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Sample records for conserved gene product

  1. Subtle variation within conserved effector operon gene products contributes to T6SS-mediated killing and immunity.

    Science.gov (United States)

    Alteri, Christopher J; Himpsl, Stephanie D; Zhu, Kevin; Hershey, Haley L; Musili, Ninette; Miller, Jessa E; Mobley, Harry L T

    2017-11-01

    Type VI secretion systems (T6SS) function to deliver lethal payloads into target cells. Many studies have shown that protection against a single, lethal T6SS effector protein requires a cognate antidote immunity protein, both of which are often encoded together in a two-gene operon. The T6SS and an effector-immunity pair is sufficient for both killing and immunity. HereIn this paper we describe a T6SS effector operon that differs from conventional effector-immunity pairs in that eight genes are necessary for lethal effector function, yet can be countered by a single immunity protein. In this study, we investigated the role that the PefE T6SS immunity protein plays in recognition between two strains harboring nearly identical effector operons. Interestingly, despite containing seven of eight identical effector proteins, the less conserved immunity proteins only provided protection against their native effectors, suggesting that specificity and recognition could be dependent on variation within an immunity protein and one effector gene product. The variable effector gene product, PefD, is encoded upstream from pefE, and displays toxic activity that can be countered by PefE independent of T6SS-activity. Interestingly, while the entire pef operon was necessary to exert toxic activity via the T6SS in P. mirabilis, production of PefD and PefE alone was unable to exert this effector activity. Chimeric PefE proteins constructed from two P. mirabilis strains were used to localize immunity function to three amino acids. A promiscuous immunity protein was created using site-directed mutagenesis to change these residues from one variant to another. These findings support the notion that subtle differences between conserved effectors are sufficient for T6SS-mediated kin discrimination and that PefD requires additional factors to function as a T6SS-dependent effector.

  2. Conservation and gene banking

    Science.gov (United States)

    Plant conservation has several objectives the main ones include safeguarding our food supply, preserving crop wild relatives for breeding and selection of new cultivars, providing material for industrial and pharmaceutical uses and preserving the beauty and diversity of our flora for generations to ...

  3. Gene pool conservation of teak in Myanmar

    International Nuclear Information System (INIS)

    Tin-Tun

    1995-01-01

    Myanmar with an area of 261, 228 Sq. miles is endowed with various types of forests which occupied nearly 50% of the country. Teak (Tectona grandis Linn. f.) is one of the most valuable timber species for its excellent wood quality and properties which are not observed with other timbers. Gene pool can be defined as a group of individual trees growing over a wide range of environmental conditions, and constituting different genetic complexes which can be transmitted to the offsprings. Topics such as: objectives of gene pool conservation, genetically improved seeds for large scale forest plantations, methodology of conservation, are discussed in the article. Myanmar teak dominates the world's teak market, and thus it is crucial to maintain the superiority in the conservation of gene complexes of teak. To some extent, the conservation of gene pools of teak and tree improvements are being undertaken by the Forest Research Institute of Myanmar. It is felt that the dissemination of the philosophy and concept of gene conservation to the personal involved in the forestry activities of the country are still inadequate

  4. Violation of an evolutionarily conserved immunoglobulin diversity gene sequence preference promotes production of dsDNA-specific IgG antibodies.

    Directory of Open Access Journals (Sweden)

    Aaron Silva-Sanchez

    Full Text Available Variability in the developing antibody repertoire is focused on the third complementarity determining region of the H chain (CDR-H3, which lies at the center of the antigen binding site where it often plays a decisive role in antigen binding. The power of VDJ recombination and N nucleotide addition has led to the common conception that the sequence of CDR-H3 is unrestricted in its variability and random in its composition. Under this view, the immune response is solely controlled by somatic positive and negative clonal selection mechanisms that act on individual B cells to promote production of protective antibodies and prevent the production of self-reactive antibodies. This concept of a repertoire of random antigen binding sites is inconsistent with the observation that diversity (DH gene segment sequence content by reading frame (RF is evolutionarily conserved, creating biases in the prevalence and distribution of individual amino acids in CDR-H3. For example, arginine, which is often found in the CDR-H3 of dsDNA binding autoantibodies, is under-represented in the commonly used DH RFs rearranged by deletion, but is a frequent component of rarely used inverted RF1 (iRF1, which is rearranged by inversion. To determine the effect of altering this germline bias in DH gene segment sequence on autoantibody production, we generated mice that by genetic manipulation are forced to utilize an iRF1 sequence encoding two arginines. Over a one year period we collected serial serum samples from these unimmunized, specific pathogen-free mice and found that more than one-fifth of them contained elevated levels of dsDNA-binding IgG, but not IgM; whereas mice with a wild type DH sequence did not. Thus, germline bias against the use of arginine enriched DH sequence helps to reduce the likelihood of producing self-reactive antibodies.

  5. Ubiquitin--conserved protein or selfish gene?

    Science.gov (United States)

    Catic, André; Ploegh, Hidde L

    2005-11-01

    The posttranslational modifier ubiquitin is encoded by a multigene family containing three primary members, which yield the precursor protein polyubiquitin and two ubiquitin moieties, Ub(L40) and Ub(S27), that are fused to the ribosomal proteins L40 and S27, respectively. The gene encoding polyubiquitin is highly conserved and, until now, those encoding Ub(L40) and Ub(S27) have been generally considered to be equally invariant. The evolution of the ribosomal ubiquitin moieties is, however, proving to be more dynamic. It seems that the genes encoding Ub(L40) and Ub(S27) are actively maintained by homologous recombination with the invariant polyubiquitin locus. Failure to recombine leads to deterioration of the sequence of the ribosomal ubiquitin moieties in several phyla, although this deterioration is evidently constrained by the structural requirements of the ubiquitin fold. Only a few amino acids in ubiquitin are vital for its function, and we propose that conservation of all three ubiquitin genes is driven not only by functional properties of the ubiquitin protein, but also by the propensity of the polyubiquitin locus to act as a 'selfish gene'.

  6. Food production and nature conservation

    NARCIS (Netherlands)

    Gordon, Iain J.; Squire, Geoff R.; Prins, Herbert H.T.

    2016-01-01

    Feeding the world's growing human population is increasingly challenging, especially as more people adopt a western diet and lifestyle. Doing so without causing damage to nature poses an even greater challenge. This book argues that in order to create a sustainable food supply whilst conserving

  7. The constancy of gene conservation across divergent bacterial orders

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    Ackermann Martin

    2009-01-01

    Full Text Available Abstract Background Orthologous genes are frequently presumed to perform similar functions. However, outside of model organisms, this is rarely tested. One means of inferring changes in function is if there are changes in the level of gene conservation and selective constraint. Here we compare levels of gene conservation across three bacterial groups to test for changes in gene functionality. Findings The level of gene conservation for different orthologous genes is highly correlated across clades, even for highly divergent groups of bacteria. These correlations do not arise from broad differences in gene functionality (e.g. informational genes vs. metabolic genes, but instead seem to result from very specific differences in gene function. Furthermore, these functional differences appear to be maintained over very long periods of time. Conclusion These results suggest that even over broad time scales, most bacterial genes are under a nearly constant level of purifying selection, and that bacterial evolution is thus dominated by selective and functional stasis.

  8. Gene pool conservation and tree improvement in Serbia

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    Isajev Vasilije

    2009-01-01

    Full Text Available This paper presents the concepts applied in the gene pool conservation and tree improvement in Serbia. Gene pool conservation of tree species in Serbia includes a series of activities aiming at the sustainability and protection of genetic and species variability. This implies the investigation of genetic resources and their identification through the research of the genetic structure and the breeding system of individual species. Paper also includes the study of intra- and inter-population variability in experiments - provenance tests, progeny tests, half- and full-sib lines, etc. The increased use of the genetic potential in tree improvement in Serbia should be intensified by the following activities: improvement of production of normal forest seed, application of the concept of new selections directed primarily to the improvement of only one character, because in that case the result would be certain, establishment and management of seed orchards as specialized plantations for long-term production of genetically good-quality forest seeds, and the shortening of the improvement process by introducing new techniques and methods (molecular markers, somaclonal variation, genetic engineering, protoplast fusion, micropropagation, etc..

  9. Visualizing conserved gene location across microbe genomes

    Science.gov (United States)

    Shaw, Chris D.

    2009-01-01

    This paper introduces an analysis-based zoomable visualization technique for displaying the location of genes across many related species of microbes. The purpose of this visualizatiuon is to enable a biologist to examine the layout of genes in the organism of interest with respect to the gene organization of related organisms. During the genomic annotation process, the ability to observe gene organization in common with previously annotated genomes can help a biologist better confirm the structure and function of newly analyzed microbe DNA sequences. We have developed a visualization and analysis tool that enables the biologist to observe and examine gene organization among genomes, in the context of the primary sequence of interest. This paper describes the visualization and analysis steps, and presents a case study using a number of Rickettsia genomes.

  10. Evolutionary conservation of regulatory elements in vertebrate HOX gene clusters

    Energy Technology Data Exchange (ETDEWEB)

    Santini, Simona; Boore, Jeffrey L.; Meyer, Axel

    2003-12-31

    Due to their high degree of conservation, comparisons of DNA sequences among evolutionarily distantly-related genomes permit to identify functional regions in noncoding DNA. Hox genes are optimal candidate sequences for comparative genome analyses, because they are extremely conserved in vertebrates and occur in clusters. We aligned (Pipmaker) the nucleotide sequences of HoxA clusters of tilapia, pufferfish, striped bass, zebrafish, horn shark, human and mouse (over 500 million years of evolutionary distance). We identified several highly conserved intergenic sequences, likely to be important in gene regulation. Only a few of these putative regulatory elements have been previously described as being involved in the regulation of Hox genes, while several others are new elements that might have regulatory functions. The majority of these newly identified putative regulatory elements contain short fragments that are almost completely conserved and are identical to known binding sites for regulatory proteins (Transfac). The conserved intergenic regions located between the most rostrally expressed genes in the developing embryo are longer and better retained through evolution. We document that presumed regulatory sequences are retained differentially in either A or A clusters resulting from a genome duplication in the fish lineage. This observation supports both the hypothesis that the conserved elements are involved in gene regulation and the Duplication-Deletion-Complementation model.

  11. Conserved genomic organisation of Group B Sox genes in insects.

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    Woerfel Gertrud

    2005-05-01

    Full Text Available Abstract Background Sox domain containing genes are important metazoan transcriptional regulators implicated in a wide rage of developmental processes. The vertebrate B subgroup contains the Sox1, Sox2 and Sox3 genes that have early functions in neural development. Previous studies show that Drosophila Group B genes have been functionally conserved since they play essential roles in early neural specification and mutations in the Drosophila Dichaete and SoxN genes can be rescued with mammalian Sox genes. Despite their importance, the extent and organisation of the Group B family in Drosophila has not been fully characterised, an important step in using Drosophila to examine conserved aspects of Group B Sox gene function. Results We have used the directed cDNA sequencing along with the output from the publicly-available genome sequencing projects to examine the structure of Group B Sox domain genes in Drosophila melanogaster, Drosophila pseudoobscura, Anopheles gambiae and Apis mellifora. All of the insect genomes contain four genes encoding Group B proteins, two of which are intronless, as is the case with vertebrate group B genes. As has been previously reported and unusually for Group B genes, two of the insect group B genes, Sox21a and Sox21b, contain introns within their DNA-binding domains. We find that the highly unusual multi-exon structure of the Sox21b gene is common to the insects. In addition, we find that three of the group B Sox genes are organised in a linked cluster in the insect genomes. By in situ hybridisation we show that the pattern of expression of each of the four group B genes during embryogenesis is conserved between D. melanogaster and D. pseudoobscura. Conclusion The DNA-binding domain sequences and genomic organisation of the group B genes have been conserved over 300 My of evolution since the last common ancestor of the Hymenoptera and the Diptera. Our analysis suggests insects have two Group B1 genes, SoxN and

  12. Isospin conservation in many-particle production

    International Nuclear Information System (INIS)

    Reinders, L.J.

    1976-01-01

    Exact isospin conservation is incorporated into independent pion emission models at high energies. A multipion wave function is constructed which is an eigen state of the isospin operators I 2 and I 3 , with the only restriction being that the wave function is completely symmetric in all momentum variables. In this way isospin conservation can account for the observed broadening of the changed particle distribution, but not the positive changed-neutral correlation for pp and π + p inelastic scattering. The author shows that these difficulties can be overcome by the introduction of clusters. Using the generating function technique a general formalism is given for the production of isospin-zero and isospin-one clusters. In the simplest case of the uncorrelated production of clusters and their subsequent isotropic decay, the topological cross-sections for proton-proton scattering could be fitted fairly well resulting also in a possitive changed-neutral correlation. The number of clusters is approximately constant in an energy range between 110 and 400 GeV

  13. Energy production, conversion, storage, conservation, and coupling

    CERN Document Server

    Demirel, Yaşar

    2012-01-01

    Understanding the sustainable use of energy in various processes is an integral part of engineering and scientific studies, which rely on a sound knowledge of energy systems. Whilst many institutions now offer degrees in energy-related programs, a comprehensive textbook, which introduces and explains sustainable energy systems and can be used across engineering and scientific fields, has been lacking. Energy: Production, Conversion, Storage, Conservation, and Coupling provides the reader with a practical understanding of these five main topic areas of energy including 130 examples and over 600 practice problems. Each chapter contains a range of supporting figures, tables, thermodynamic diagrams and charts, while the Appendix supplies the reader with all the necessary data including the steam tables. This new textbook presents a clear introduction of basic vocabulary, properties, forms, sources, and balances of energy before advancing to the main topic areas of: • Energy production and conversion in importa...

  14. The drug target genes show higher evolutionary conservation than non-target genes.

    Science.gov (United States)

    Lv, Wenhua; Xu, Yongdeng; Guo, Yiying; Yu, Ziqi; Feng, Guanglong; Liu, Panpan; Luan, Meiwei; Zhu, Hongjie; Liu, Guiyou; Zhang, Mingming; Lv, Hongchao; Duan, Lian; Shang, Zhenwei; Li, Jin; Jiang, Yongshuai; Zhang, Ruijie

    2016-01-26

    Although evidence indicates that drug target genes share some common evolutionary features, there have been few studies analyzing evolutionary features of drug targets from an overall level. Therefore, we conducted an analysis which aimed to investigate the evolutionary characteristics of drug target genes. We compared the evolutionary conservation between human drug target genes and non-target genes by combining both the evolutionary features and network topological properties in human protein-protein interaction network. The evolution rate, conservation score and the percentage of orthologous genes of 21 species were included in our study. Meanwhile, four topological features including the average shortest path length, betweenness centrality, clustering coefficient and degree were considered for comparison analysis. Then we got four results as following: compared with non-drug target genes, 1) drug target genes had lower evolutionary rates; 2) drug target genes had higher conservation scores; 3) drug target genes had higher percentages of orthologous genes and 4) drug target genes had a tighter network structure including higher degrees, betweenness centrality, clustering coefficients and lower average shortest path lengths. These results demonstrate that drug target genes are more evolutionarily conserved than non-drug target genes. We hope that our study will provide valuable information for other researchers who are interested in evolutionary conservation of drug targets.

  15. Divergence and Conservative Evolution of XTNX Genes in Land Plants

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    Yan-Mei Zhang

    2017-10-01

    Full Text Available The Toll-interleukin-1 receptor (TIR and Nucleotide-binding site (NBS domains are two major components of the TIR-NBS-leucine-rich repeat family plant disease resistance genes. Extensive functional and evolutionary studies have been performed on these genes; however, the characterization of a small group of genes that are composed of atypical TIR and NBS domains, namely XTNX genes, is limited. The present study investigated this specific gene family by conducting genome-wide analyses of 59 green plant genomes. A total of 143 XTNX genes were identified in 51 of the 52 land plant genomes, whereas no XTNX gene was detected in any green algae genomes, which indicated that XTNX genes originated upon emergence of land plants. Phylogenetic analysis revealed that the ancestral XTNX gene underwent two rounds of ancient duplications in land plants, which resulted in the formation of clades I/II and clades IIa/IIb successively. Although clades I and IIb have evolved conservatively in angiosperms, the motif composition difference and sequence divergence at the amino acid level suggest that functional divergence may have occurred since the separation of the two clades. In contrast, several features of the clade IIa genes, including the absence in the majority of dicots, the long branches in the tree, the frequent loss of ancestral motifs, and the loss of expression in all detected tissues of Zea mays, all suggest that the genes in this lineage might have undergone pseudogenization. This study highlights that XTNX genes are a gene family originated anciently in land plants and underwent specific conservative pattern in evolution.

  16. Electrorheology for energy production and conservation

    Science.gov (United States)

    Huang, Ke

    Recently, based on the physics of viscosity, we developed a new technology, which utilizes electric or magnetic fields to change the rheology of complex fluids to reduce the viscosity, while keeping the temperature unchanged. The method is universal and applicable to all complex fluids with suspended particles of nano-meter, submicrometer, or micrometer size. Completely different from the traditional viscosity reduction method, raising the temperature, this technology is energy-efficient, as it only requires small amount of energy to aggregate the suspended particles. In this thesis, we will first discuss this new technology in detail, both in theory and practice. Then, we will report applications of our technology to energy science research. Presently, 80% of all energy sources are liquid fuels. The viscosity of liquid fuels plays an important role in energy production and energy conservation. With an electric field, we can reduce the viscosity of asphalt-based crude oil. This is important and useful for heavy crude oil and off-shore crude oil production and transportation. Especially, since there is no practical way to raise the temperature of crude oil inside the deepwater pipelines, our technology may play a key role in future off-shore crude oil production. Electrorehology can also be used to reduce the viscosity of refinery fuels, such as diesel fuel and gasoline. When we apply this technology to fuel injection, the fuel droplets in the fuel atomization become smaller, leading to faster combustion in the engine chambers. As the fuel efficiency of internal combustion engines depends on the combustion speed and timing, the fast combustion produces much higher fuel efficiency. Therefore, adding our technology on existing engines improves the engine efficiency significantly. A theoretical model for the engine combustion, which explains how fast combustion improves the engine efficiency, is also presented in the thesis. As energy is the key to our national

  17. Seed collection success and failure in fraxinus gene conservation efforts

    Science.gov (United States)

    Joseph D. Zeleznik; Andrew J. David

    2017-01-01

    National seed collection and gene conservation programs have expanded in recent years, especially in response to pressure from non-native pests such as the emerald ash borer (Agrilus planipennis). Since 2008, we have been working with the U.S. Department of Agriculture Agricultural Research Service (USDA ARS) and USDA Forest Service (USDA FS) leading seed collection...

  18. Conservation of gene co-regulation in prokaryotes and eukaryotes.

    NARCIS (Netherlands)

    Snel, B.; Bork, P.; Huynen, M.A.

    2002-01-01

    We raise some issues in detecting the conservation (or absence thereof) of co-regulation using gene order; how we think the variations in the cellular network in various species can be studied; and how to determine and interpret the higher order structure in networks of functional relations.

  19. Doublesex: a conserved downstream gene controlled by diverse ...

    Indian Academy of Sciences (India)

    The Drosophila doublesex (dsx) gene at the bottom of the sex-determination cascade is the best characterized candidate so far, and is conserved from worms (mab3 of Caenorhabditis elegans) to mammals (Dmrt-1). Studies of dsx homologues from insect species belonging to different orders position them at the bottom of ...

  20. Patterns of evolutionary conservation of essential genes correlate with their compensability.

    Directory of Open Access Journals (Sweden)

    Tobias Bergmiller

    2012-06-01

    Full Text Available Essential genes code for fundamental cellular functions required for the viability of an organism. For this reason, essential genes are often highly conserved across organisms. However, this is not always the case: orthologues of genes that are essential in one organism are sometimes not essential in other organisms or are absent from their genomes. This suggests that, in the course of evolution, essential genes can be rendered nonessential. How can a gene become non-essential? Here we used genetic manipulation to deplete the products of 26 different essential genes in Escherichia coli. This depletion results in a lethal phenotype, which could often be rescued by the overexpression of a non-homologous, non-essential gene, most likely through replacement of the essential function. We also show that, in a smaller number of cases, the essential genes can be fully deleted from the genome, suggesting that complete functional replacement is possible. Finally, we show that essential genes whose function can be replaced in the laboratory are more likely to be non-essential or not present in other taxa. These results are consistent with the notion that patterns of evolutionary conservation of essential genes are influenced by their compensability-that is, by how easily they can be functionally replaced, for example through increased expression of other genes.

  1. Economics, Ethics, Ecology: Roots of Productive Conservation.

    Science.gov (United States)

    Jeske, Walter E., Ed.

    Forty-seven articles represent most of the papers presented at the annual meeting of the Soil Conservation Society of America. The conference addressed the facts and values from economics, ethics, and ecology as they pertain to critical issues in land and water conservation in North America. Part I includes discussions of economic realities,…

  2. Human Intellectual Disability Genes Form Conserved Functional Modules in Drosophila

    Science.gov (United States)

    Oortveld, Merel A. W.; Keerthikumar, Shivakumar; Oti, Martin; Nijhof, Bonnie; Fernandes, Ana Clara; Kochinke, Korinna; Castells-Nobau, Anna; van Engelen, Eva; Ellenkamp, Thijs; Eshuis, Lilian; Galy, Anne; van Bokhoven, Hans; Habermann, Bianca; Brunner, Han G.; Zweier, Christiane; Verstreken, Patrik; Huynen, Martijn A.; Schenck, Annette

    2013-01-01

    Intellectual Disability (ID) disorders, defined by an IQ below 70, are genetically and phenotypically highly heterogeneous. Identification of common molecular pathways underlying these disorders is crucial for understanding the molecular basis of cognition and for the development of therapeutic intervention strategies. To systematically establish their functional connectivity, we used transgenic RNAi to target 270 ID gene orthologs in the Drosophila eye. Assessment of neuronal function in behavioral and electrophysiological assays and multiparametric morphological analysis identified phenotypes associated with knockdown of 180 ID gene orthologs. Most of these genotype-phenotype associations were novel. For example, we uncovered 16 genes that are required for basal neurotransmission and have not previously been implicated in this process in any system or organism. ID gene orthologs with morphological eye phenotypes, in contrast to genes without phenotypes, are relatively highly expressed in the human nervous system and are enriched for neuronal functions, suggesting that eye phenotyping can distinguish different classes of ID genes. Indeed, grouping genes by Drosophila phenotype uncovered 26 connected functional modules. Novel links between ID genes successfully predicted that MYCN, PIGV and UPF3B regulate synapse development. Drosophila phenotype groups show, in addition to ID, significant phenotypic similarity also in humans, indicating that functional modules are conserved. The combined data indicate that ID disorders, despite their extreme genetic diversity, are caused by disruption of a limited number of highly connected functional modules. PMID:24204314

  3. Gene family size conservation is a good indicator of evolutionary rates.

    Science.gov (United States)

    Chen, Feng-Chi; Chen, Chiuan-Jung; Li, Wen-Hsiung; Chuang, Trees-Juen

    2010-08-01

    The evolution of duplicate genes has been a topic of broad interest. Here, we propose that the conservation of gene family size is a good indicator of the rate of sequence evolution and some other biological properties. By comparing the human-chimpanzee-macaque orthologous gene families with and without family size conservation, we demonstrate that genes with family size conservation evolve more slowly than those without family size conservation. Our results further demonstrate that both family expansion and contraction events may accelerate gene evolution, resulting in elevated evolutionary rates in the genes without family size conservation. In addition, we show that the duplicate genes with family size conservation evolve significantly more slowly than those without family size conservation. Interestingly, the median evolutionary rate of singletons falls in between those of the above two types of duplicate gene families. Our results thus suggest that the controversy on whether duplicate genes evolve more slowly than singletons can be resolved when family size conservation is taken into consideration. Furthermore, we also observe that duplicate genes with family size conservation have the highest level of gene expression/expression breadth, the highest proportion of essential genes, and the lowest gene compactness, followed by singletons and then by duplicate genes without family size conservation. Such a trend accords well with our observations of evolutionary rates. Our results thus point to the importance of family size conservation in the evolution of duplicate genes.

  4. 78 FR 25626 - Energy Conservation Program for Consumer Products: Energy Conservation Standards for Ceiling Fans...

    Science.gov (United States)

    2013-05-02

    ... Conservation Program for Consumer Products: Energy Conservation Standards for Ceiling Fans and Ceiling Fan... for residential ceiling fans and ceiling fan light kits in the Federal Register. This document... other aspect of the rulemaking for ceiling fans and ceiling fan light kits. The comment period is...

  5. Conservation of gene linkage in dispersed vertebrate NK homeobox clusters.

    Science.gov (United States)

    Wotton, Karl R; Weierud, Frida K; Juárez-Morales, José L; Alvares, Lúcia E; Dietrich, Susanne; Lewis, Katharine E

    2009-10-01

    Nk homeobox genes are important regulators of many different developmental processes including muscle, heart, central nervous system and sensory organ development. They are thought to have arisen as part of the ANTP megacluster, which also gave rise to Hox and ParaHox genes, and at least some NK genes remain tightly linked in all animals examined so far. The protostome-deuterostome ancestor probably contained a cluster of nine Nk genes: (Msx)-(Nk4/tinman)-(Nk3/bagpipe)-(Lbx/ladybird)-(Tlx/c15)-(Nk7)-(Nk6/hgtx)-(Nk1/slouch)-(Nk5/Hmx). Of these genes, only NKX2.6-NKX3.1, LBX1-TLX1 and LBX2-TLX2 remain tightly linked in humans. However, it is currently unclear whether this is unique to the human genome as we do not know which of these Nk genes are clustered in other vertebrates. This makes it difficult to assess whether the remaining linkages are due to selective pressures or because chance rearrangements have "missed" certain genes. In this paper, we identify all of the paralogs of these ancestrally clustered NK genes in several distinct vertebrates. We demonstrate that tight linkages of Lbx1-Tlx1, Lbx2-Tlx2 and Nkx3.1-Nkx2.6 have been widely maintained in both the ray-finned and lobe-finned fish lineages. Moreover, the recently duplicated Hmx2-Hmx3 genes are also tightly linked. Finally, we show that Lbx1-Tlx1 and Hmx2-Hmx3 are flanked by highly conserved noncoding elements, suggesting that shared regulatory regions may have resulted in evolutionary pressure to maintain these linkages. Consistent with this, these pairs of genes have overlapping expression domains. In contrast, Lbx2-Tlx2 and Nkx3.1-Nkx2.6, which do not seem to be coexpressed, are also not associated with conserved noncoding sequences, suggesting that an alternative mechanism may be responsible for the continued clustering of these genes.

  6. The gsdf gene locus harbors evolutionary conserved and clustered genes preferentially expressed in fish previtellogenic oocytes.

    Science.gov (United States)

    Gautier, Aude; Le Gac, Florence; Lareyre, Jean-Jacques

    2011-02-01

    The gonadal soma-derived factor (GSDF) belongs to the transforming growth factor-β superfamily and is conserved in teleostean fish species. Gsdf is specifically expressed in the gonads, and gene expression is restricted to the granulosa and Sertoli cells in trout and medaka. The gsdf gene expression is correlated to early testis differentiation in medaka and was shown to stimulate primordial germ cell and spermatogonia proliferation in trout. In the present study, we show that the gsdf gene localizes to a syntenic chromosomal fragment conserved among vertebrates although no gsdf-related gene is detected on the corresponding genomic region in tetrapods. We demonstrate using quantitative RT-PCR that most of the genes localized in the synteny are specifically expressed in medaka gonads. Gsdf is the only gene of the synteny with a much higher expression in the testis compared to the ovary. In contrast, gene expression pattern analysis of the gsdf surrounding genes (nup54, aff1, klhl8, sdad1, and ptpn13) indicates that these genes are preferentially expressed in the female gonads. The tissue distribution of these genes is highly similar in medaka and zebrafish, two teleostean species that have diverged more than 110 million years ago. The cellular localization of these genes was determined in medaka gonads using the whole-mount in situ hybridization technique. We confirm that gsdf gene expression is restricted to Sertoli and granulosa cells in contact with the premeiotic and meiotic cells. The nup54 gene is expressed in spermatocytes and previtellogenic oocytes. Transcripts corresponding to the ovary-specific genes (aff1, klhl8, and sdad1) are detected only in previtellogenic oocytes. No expression was detected in the gonocytes in 10 dpf embryos. In conclusion, we show that the gsdf gene localizes to a syntenic chromosomal fragment harboring evolutionary conserved genes in vertebrates. These genes are preferentially expressed in previtelloogenic oocytes, and thus, they

  7. Patterns of intron gain and conservation in eukaryotic genes

    Directory of Open Access Journals (Sweden)

    Wolf Yuri I

    2007-10-01

    Full Text Available Abstract Background: The presence of introns in protein-coding genes is a universal feature of eukaryotic genome organization, and the genes of multicellular eukaryotes, typically, contain multiple introns, a substantial fraction of which share position in distant taxa, such as plants and animals. Depending on the methods and data sets used, researchers have reached opposite conclusions on the causes of the high fraction of shared introns in orthologous genes from distant eukaryotes. Some studies conclude that shared intron positions reflect, almost entirely, a remarkable evolutionary conservation, whereas others attribute it to parallel gain of introns. To resolve these contradictions, it is crucial to analyze the evolution of introns by using a model that minimally relies on arbitrary assumptions. Results: We developed a probabilistic model of evolution that allows for variability of intron gain and loss rates over branches of the phylogenetic tree, individual genes, and individual sites. Applying this model to an extended set of conserved eukaryotic genes, we find that parallel gain, on average, accounts for only ~8% of the shared intron positions. However, the distribution of parallel gains over the phylogenetic tree of eukaryotes is highly non-uniform. There are, practically, no parallel gains in closely related lineages, whereas for distant lineages, such as animals and plants, parallel gains appear to contribute up to 20% of the shared intron positions. In accord with these findings, we estimated that ancestral introns have a high probability to be retained in extant genomes, and conversely, that a substantial fraction of extant introns have retained their positions since the early stages of eukaryotic evolution. In addition, the density of sites that are available for intron insertion is estimated to be, approximately, one in seven basepairs. Conclusion: We obtained robust estimates of the contribution of parallel gain to the observed

  8. Production of tomato puree: an alternative to conservation of locally ...

    African Journals Online (AJOL)

    Mo

    suggest a mean of conservation of the surplus of production by processing tomato into puree. The most produced local ... processing into puree on industrial scale. The main .... functions contributing to the reaction of non-enzymatic browning ...

  9. Effects of using coding potential, sequence conservation and mRNA structure conservation for predicting pyrroly-sine containing genes

    DEFF Research Database (Denmark)

    Have, Christian Theil; Zambach, Sine; Christiansen, Henning

    2013-01-01

    for prediction of pyrrolysine incorporating genes in genomes of bacteria and archaea leading to insights about the factors driving pyrrolysine translation and identification of new gene candidates. The method predicts known conserved genes with high recall and predicts several other promising candidates...... for experimental verification. The method is implemented as a computational pipeline which is available on request....

  10. Energy conservation opportunities: audit vis-a-vis mine productivity

    Energy Technology Data Exchange (ETDEWEB)

    Iyer, G.H.

    2009-07-01

    Mining operation, whether opencast or underground, with modern equipment is highly energy intensive, needing energy conservation and management to ensure efficiency, cost effectiveness, and overall productivity. Exhaustible primary energy resources such as coal, lignite, oil, and nuclear fuels are being mined out to meet our energy needs. An attempt has been made in this paper to highlight the energy conservation opportunities, energy audit, the relevant Energy Conservation Act 2001 and certain energy saving measures leading to higher productivity followed by a few case study examples. 3 refs.

  11. Evolutionary conservation of vertebrate notochord genes in the ascidian Ciona intestinalis.

    Science.gov (United States)

    Kugler, Jamie E; Passamaneck, Yale J; Feldman, Taya G; Beh, Jeni; Regnier, Todd W; Di Gregorio, Anna

    2008-11-01

    To reconstruct a minimum complement of notochord genes evolutionarily conserved across chordates, we scanned the Ciona intestinalis genome using the sequences of 182 genes reported to be expressed in the notochord of different vertebrates and identified 139 candidate notochord genes. For 66 of these Ciona genes expression data were already available, hence we analyzed the expression of the remaining 73 genes and found notochord expression for 20. The predicted products of the newly identified notochord genes range from the transcription factors Ci-XBPa and Ci-miER1 to extracellular matrix proteins. We examined the expression of the newly identified notochord genes in embryos ectopically expressing Ciona Brachyury (Ci-Bra) and in embryos expressing a repressor form of this transcription factor in the notochord, and we found that while a subset of the genes examined are clearly responsive to Ci-Bra, other genes are not affected by alterations in its levels. We provide a first description of notochord genes that are not evidently influenced by the ectopic expression of Ci-Bra and we propose alternative regulatory mechanisms that might control their transcription. Copyright 2008 Wiley-Liss, Inc.

  12. Fermion production despite fermion number conservation

    International Nuclear Information System (INIS)

    Bock, W.; Hetrick, J.E.; Smit, J.

    1995-01-01

    Lattice proposals for a nonperturbative formulation of the Standard Model easily lead to a global U(1) symmetry corresponding to exactly conserved fermion number. The absence of an anomaly in the fermion current would then appear to inhibit anomalous processes, such as electroweak baryogenesis in the early universe. One way to circumvent this problem is to formulate the theory such that this U(1) symmetry is explicitly broken. However we argue that in the framework of spectral flow, fermion creation and annihilation still in fact occurs, despite the exact fermion number conservation. The crucial observation is that fermions are excitations relative to the vacuum, at the surface of the Dirac sea. The exact global U(1) symmetry prohibits a state from changing its fermion number during time evolution, however nothing prevents the fermionic ground state from doing so. We illustrate our reasoning with a model in two dimensions which has axial-vector couplings, first using a sharp momentum cutoff, then using the lattice regulator with staggered fermions. The difference in fermion number between the time evolved state and the ground state is indeed in agreement with the anomaly. Both the sharp momentum cutoff and the lattice regulator break gauge invariance. In the case of the lattice model a mass counterterm for the gauge field is sufficient to restore gauge invariance in the perturbative regime. A study of the vacuum energy shows however that the perturbative counterterm is insufficient in a nonperturbative setting and that further quartic counterterms are needed. For reference we also study a closely related model with vector couplings, the Schwinger model, and we examine the emergence of the θ-vacuum structure of both theories. ((orig.))

  13. 78 FR 79638 - Energy Conservation Program for Consumer Products: Proposed Determination of Hearth Products as a...

    Science.gov (United States)

    2013-12-31

    ... Conservation Program for Consumer Products: Proposed Determination of Hearth Products as a Covered Consumer... determined that hearth products qualify as a covered product under Part A of Title III of the Energy Policy and Conservation Act (EPCA), as amended. More specifically, DOE has tentatively determined that hearth...

  14. Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs

    Directory of Open Access Journals (Sweden)

    Hutchison Clyde A

    2006-01-01

    Full Text Available Abstract Background Experimental verification of gene products has not kept pace with the rapid growth of microbial sequence information. However, existing annotations of gene locations contain sufficient information to screen for probable errors. Furthermore, comparisons among genomes become more informative as more genomes are examined. We studied all open reading frames (ORFs of at least 30 codons from the genomes of 27 sequenced bacterial strains. We grouped the potential peptide sequences encoded from the ORFs by forming Clusters of Orthologous Groups (COGs. We used this grouping in order to find homologous relationships that would not be distinguishable from noise when using simple BLAST searches. Although COG analysis was initially developed to group annotated genes, we applied it to the task of grouping anonymous DNA sequences that may encode proteins. Results "Mixed COGs" of ORFs (clusters in which some sequences correspond to annotated genes and some do not are attractive targets when seeking errors of gene predicion. Examination of mixed COGs reveals some situations in which genes appear to have been missed in current annotations and a smaller number of regions that appear to have been annotated as gene loci erroneously. This technique can also be used to detect potential pseudogenes or sequencing errors. Our method uses an adjustable parameter for degree of conservation among the studied genomes (stringency. We detail results for one level of stringency at which we found 83 potential genes which had not previously been identified, 60 potential pseudogenes, and 7 sequences with existing gene annotations that are probably incorrect. Conclusion Systematic study of sequence conservation offers a way to improve existing annotations by identifying potentially homologous regions where the annotation of the presence or absence of a gene is inconsistent among genomes.

  15. Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs.

    Science.gov (United States)

    Powell, Bradford C; Hutchison, Clyde A

    2006-01-19

    Experimental verification of gene products has not kept pace with the rapid growth of microbial sequence information. However, existing annotations of gene locations contain sufficient information to screen for probable errors. Furthermore, comparisons among genomes become more informative as more genomes are examined. We studied all open reading frames (ORFs) of at least 30 codons from the genomes of 27 sequenced bacterial strains. We grouped the potential peptide sequences encoded from the ORFs by forming Clusters of Orthologous Groups (COGs). We used this grouping in order to find homologous relationships that would not be distinguishable from noise when using simple BLAST searches. Although COG analysis was initially developed to group annotated genes, we applied it to the task of grouping anonymous DNA sequences that may encode proteins. "Mixed COGs" of ORFs (clusters in which some sequences correspond to annotated genes and some do not) are attractive targets when seeking errors of gene prediction. Examination of mixed COGs reveals some situations in which genes appear to have been missed in current annotations and a smaller number of regions that appear to have been annotated as gene loci erroneously. This technique can also be used to detect potential pseudogenes or sequencing errors. Our method uses an adjustable parameter for degree of conservation among the studied genomes (stringency). We detail results for one level of stringency at which we found 83 potential genes which had not previously been identified, 60 potential pseudogenes, and 7 sequences with existing gene annotations that are probably incorrect. Systematic study of sequence conservation offers a way to improve existing annotations by identifying potentially homologous regions where the annotation of the presence or absence of a gene is inconsistent among genomes.

  16. Conserved gene regulatory module specifies lateral neural borders across bilaterians.

    Science.gov (United States)

    Li, Yongbin; Zhao, Di; Horie, Takeo; Chen, Geng; Bao, Hongcun; Chen, Siyu; Liu, Weihong; Horie, Ryoko; Liang, Tao; Dong, Biyu; Feng, Qianqian; Tao, Qinghua; Liu, Xiao

    2017-08-01

    The lateral neural plate border (NPB), the neural part of the vertebrate neural border, is composed of central nervous system (CNS) progenitors and peripheral nervous system (PNS) progenitors. In invertebrates, PNS progenitors are also juxtaposed to the lateral boundary of the CNS. Whether there are conserved molecular mechanisms determining vertebrate and invertebrate lateral neural borders remains unclear. Using single-cell-resolution gene-expression profiling and genetic analysis, we present evidence that orthologs of the NPB specification module specify the invertebrate lateral neural border, which is composed of CNS and PNS progenitors. First, like in vertebrates, the conserved neuroectoderm lateral border specifier Msx/vab-15 specifies lateral neuroblasts in Caenorhabditis elegans Second, orthologs of the vertebrate NPB specification module ( Msx/vab-15 , Pax3/7/pax-3 , and Zic/ref-2 ) are significantly enriched in worm lateral neuroblasts. In addition, like in other bilaterians, the expression domain of Msx/vab-15 is more lateral than those of Pax3/7/pax-3 and Zic/ref- 2 in C. elegans Third, we show that Msx/vab-15 regulates the development of mechanosensory neurons derived from lateral neural progenitors in multiple invertebrate species, including C. elegans , Drosophila melanogaster , and Ciona intestinalis We also identify a novel lateral neural border specifier, ZNF703/tlp-1 , which functions synergistically with Msx/vab- 15 in both C. elegans and Xenopus laevis These data suggest a common origin of the molecular mechanism specifying lateral neural borders across bilaterians.

  17. Identification of conserved drought-adaptive genes using a cross-species meta-analysis approach.

    Science.gov (United States)

    Shaar-Moshe, Lidor; Hübner, Sariel; Peleg, Zvi

    2015-05-03

    Drought is the major environmental stress threatening crop-plant productivity worldwide. Identification of new genes and metabolic pathways involved in plant adaptation to progressive drought stress at the reproductive stage is of great interest for agricultural research. We developed a novel Cross-Species meta-Analysis of progressive Drought stress at the reproductive stage (CSA:Drought) to identify key drought adaptive genes and mechanisms and to test their evolutionary conservation. Empirically defined filtering criteria were used to facilitate a robust integration of 17 deposited microarray experiments (148 arrays) of Arabidopsis, rice, wheat and barley. By prioritizing consistency over intensity, our approach was able to identify 225 differentially expressed genes shared across studies and taxa. Gene ontology enrichment and pathway analyses classified the shared genes into functional categories involved predominantly in metabolic processes (e.g. amino acid and carbohydrate metabolism), regulatory function (e.g. protein degradation and transcription) and response to stimulus. We further investigated drought related cis-acting elements in the shared gene promoters, and the evolutionary conservation of shared genes. The universal nature of the identified drought-adaptive genes was further validated in a fifth species, Brachypodium distachyon that was not included in the meta-analysis. qPCR analysis of 27, randomly selected, shared orthologs showed similar expression pattern as was found by the CSA:Drought.In accordance, morpho-physiological characterization of progressive drought stress, in B. distachyon, highlighted the key role of osmotic adjustment as evolutionary conserved drought-adaptive mechanism. Our CSA:Drought strategy highlights major drought-adaptive genes and metabolic pathways that were only partially, if at all, reported in the original studies included in the meta-analysis. These genes include a group of unclassified genes that could be involved

  18. Inferring the conservative causal core of gene regulatory networks

    Directory of Open Access Journals (Sweden)

    Emmert-Streib Frank

    2010-09-01

    Full Text Available Abstract Background Inferring gene regulatory networks from large-scale expression data is an important problem that received much attention in recent years. These networks have the potential to gain insights into causal molecular interactions of biological processes. Hence, from a methodological point of view, reliable estimation methods based on observational data are needed to approach this problem practically. Results In this paper, we introduce a novel gene regulatory network inference (GRNI algorithm, called C3NET. We compare C3NET with four well known methods, ARACNE, CLR, MRNET and RN, conducting in-depth numerical ensemble simulations and demonstrate also for biological expression data from E. coli that C3NET performs consistently better than the best known GRNI methods in the literature. In addition, it has also a low computational complexity. Since C3NET is based on estimates of mutual information values in conjunction with a maximization step, our numerical investigations demonstrate that our inference algorithm exploits causal structural information in the data efficiently. Conclusions For systems biology to succeed in the long run, it is of crucial importance to establish methods that extract large-scale gene networks from high-throughput data that reflect the underlying causal interactions among genes or gene products. Our method can contribute to this endeavor by demonstrating that an inference algorithm with a neat design permits not only a more intuitive and possibly biological interpretation of its working mechanism but can also result in superior results.

  19. Inferring the conservative causal core of gene regulatory networks.

    Science.gov (United States)

    Altay, Gökmen; Emmert-Streib, Frank

    2010-09-28

    Inferring gene regulatory networks from large-scale expression data is an important problem that received much attention in recent years. These networks have the potential to gain insights into causal molecular interactions of biological processes. Hence, from a methodological point of view, reliable estimation methods based on observational data are needed to approach this problem practically. In this paper, we introduce a novel gene regulatory network inference (GRNI) algorithm, called C3NET. We compare C3NET with four well known methods, ARACNE, CLR, MRNET and RN, conducting in-depth numerical ensemble simulations and demonstrate also for biological expression data from E. coli that C3NET performs consistently better than the best known GRNI methods in the literature. In addition, it has also a low computational complexity. Since C3NET is based on estimates of mutual information values in conjunction with a maximization step, our numerical investigations demonstrate that our inference algorithm exploits causal structural information in the data efficiently. For systems biology to succeed in the long run, it is of crucial importance to establish methods that extract large-scale gene networks from high-throughput data that reflect the underlying causal interactions among genes or gene products. Our method can contribute to this endeavor by demonstrating that an inference algorithm with a neat design permits not only a more intuitive and possibly biological interpretation of its working mechanism but can also result in superior results.

  20. Conceptualization about conservation, production and development

    International Nuclear Information System (INIS)

    Angel, Augusto

    1994-01-01

    The article tries the conceptualization, production and development, of the environmental sciences or environmentalism and ecology; they are made a series of reflections that it haven't just been defined still these sciences with clarity like a epistemological field in front of the other sciences, or in combination or in integration with them that doesn't have, unfortunately, for the way like it has been come developing the science western, many possibilities of theoretical approach, in fact for the sciences compartment. The author comments that this compartment was obligatory inside the development process begun by Europe and that it ends fundamentally in the capitalist development. That the positivism and the empiricism like expression forms have been indispensable to dominate the nature and to exploit it; so that there we needed specialized sciences that had the capacity the resources that it needed the development. The environmentalism and, before the environmentalism, the ecology is putting us in a quite complicated noise, and it is that more and more they are putting us before the pressure that in fact the natural resources are integrated to complex systems, and it is that the science is not organized to manage systems

  1. Reconciling biodiversity conservation and marine capture fisheries production

    DEFF Research Database (Denmark)

    Brander, Keith

    2010-01-01

    Pathways for moving towards the goals of biodiversity conservation and food security in terrestrial systems include the application of trait-based ecology to develop highly productive agroecosystems with less negative effects on biodiversity. Although marine ecosystems have been impacted by human...... activity over several centuries, the changes have been unintentional and undirected; we have not learned how to enhance food production from the sea and are reliant, as hunter-gatherers, on natural production. The goals of maximising fisheries production and maintaining biodiversity may be difficult...

  2. Forest gene conservation from the perspective of the international community

    Science.gov (United States)

    M. Hosny El-Lakany

    2017-01-01

    conservation of forest genetic resources (FGR). After presenting internationally adopted definitions of some terms related to FGR, the characteristics of the current state of FGR conservation from a global perspective are summarized. Many international and regional organizations and institutions are engaged in the conservation of FGR at degrees ranging from...

  3. Community Markets for Conservation (COMACO) links biodiversity conservation with sustainable improvements in livelihoods and food production.

    Science.gov (United States)

    Lewis, Dale; Bell, Samuel D; Fay, John; Bothi, Kim L; Gatere, Lydiah; Kabila, Makando; Mukamba, Mwangala; Matokwani, Edwin; Mushimbalume, Matthews; Moraru, Carmen I; Lehmann, Johannes; Lassoie, James; Wolfe, David; Lee, David R; Buck, Louise; Travis, Alexander J

    2011-08-23

    In the Luangwa Valley, Zambia, persistent poverty and hunger present linked challenges to rural development and biodiversity conservation. Both household coping strategies and larger-scale economic development efforts have caused severe natural resource degradation that limits future economic opportunities and endangers ecosystem services. A model based on a business infrastructure has been developed to promote and maintain sustainable agricultural and natural resource management practices, leading to direct and indirect conservation outcomes. The Community Markets for Conservation (COMACO) model operates primarily with communities surrounding national parks, strengthening conservation benefits produced by these protected areas. COMACO first identifies the least food-secure households and trains them in sustainable agricultural practices that minimize threats to natural resources while meeting household needs. In addition, COMACO identifies people responsible for severe natural resource depletion and trains them to generate alternative income sources. In an effort to maintain compliance with these practices, COMACO provides extension support and access to high-value markets that would otherwise be inaccessible to participants. Because the model is continually evolving via adaptive management, success or failure of the model as a whole is difficult to quantify at this early stage. We therefore test specific hypotheses and present data documenting the stabilization of previously declining wildlife populations; the meeting of thresholds of productivity that give COMACO access to stable, high-value markets and progress toward economic self-sufficiency; and the adoption of sustainable agricultural practices by participants and other community members. Together, these findings describe a unique, business-oriented model for poverty alleviation, food production, and biodiversity conservation.

  4. Zebrafish IGF genes: gene duplication, conservation and divergence, and novel roles in midline and notochord development.

    Directory of Open Access Journals (Sweden)

    Shuming Zou

    Full Text Available Insulin-like growth factors (IGFs are key regulators of development, growth, and longevity. In most vertebrate species including humans, there is one IGF-1 gene and one IGF-2 gene. Here we report the identification and functional characterization of 4 distinct IGF genes (termed as igf-1a, -1b, -2a, and -2b in zebrafish. These genes encode 4 structurally distinct and functional IGF peptides. IGF-1a and IGF-2a mRNAs were detected in multiple tissues in adult fish. IGF-1b mRNA was detected only in the gonad and IGF-2b mRNA only in the liver. Functional analysis showed that all 4 IGFs caused similar developmental defects but with different potencies. Many of these embryos had fully or partially duplicated notochords, suggesting that an excess of IGF signaling causes defects in the midline formation and an expansion of the notochord. IGF-2a, the most potent IGF, was analyzed in depth. IGF-2a expression caused defects in the midline formation and expansion of the notochord but it did not alter the anterior neural patterning. These results not only provide new insights into the functional conservation and divergence of the multiple igf genes but also reveal a novel role of IGF signaling in midline formation and notochord development in a vertebrate model.

  5. Genes with stable DNA methylation levels show higher evolutionary conservation than genes with fluctuant DNA methylation levels.

    Science.gov (United States)

    Zhang, Ruijie; Lv, Wenhua; Luan, Meiwei; Zheng, Jiajia; Shi, Miao; Zhu, Hongjie; Li, Jin; Lv, Hongchao; Zhang, Mingming; Shang, Zhenwei; Duan, Lian; Jiang, Yongshuai

    2015-11-24

    Different human genes often exhibit different degrees of stability in their DNA methylation levels between tissues, samples or cell types. This may be related to the evolution of human genome. Thus, we compared the evolutionary conservation between two types of genes: genes with stable DNA methylation levels (SM genes) and genes with fluctuant DNA methylation levels (FM genes). For long-term evolutionary characteristics between species, we compared the percentage of the orthologous genes, evolutionary rate dn/ds and protein sequence identity. We found that the SM genes had greater percentages of the orthologous genes, lower dn/ds, and higher protein sequence identities in all the 21 species. These results indicated that the SM genes were more evolutionarily conserved than the FM genes. For short-term evolutionary characteristics among human populations, we compared the single nucleotide polymorphism (SNP) density, and the linkage disequilibrium (LD) degree in HapMap populations and 1000 genomes project populations. We observed that the SM genes had lower SNP densities, and higher degrees of LD in all the 11 HapMap populations and 13 1000 genomes project populations. These results mean that the SM genes had more stable chromosome genetic structures, and were more conserved than the FM genes.

  6. Preferential transcription of conserved rif genes in two phenotypically distinct Plasmodium falciparum parasite lines

    DEFF Research Database (Denmark)

    Wang, Christian W; Magistrado, Pamela A; Nielsen, Morten A

    2009-01-01

    transcribed in the VAR2CSA-expressing parasite line. In addition, two rif genes were found transcribed at early and late intra-erythrocyte stages independently of var gene transcription. Rif genes are organised in groups and inter-genomic conserved gene families, suggesting that RIFIN sub-groups may have......Plasmodium falciparum variant surface antigens (VSA) are targets of protective immunity to malaria. Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) and repetitive interspersed family (RIFIN) proteins are encoded by the two variable multigene families, var and rif genes, respectively...... novel rif gene groups, rifA1 and rifA2, containing inter-genomic conserved rif genes, were identified. All rifA1 genes were orientated head-to-head with a neighbouring Group A var gene whereas rifA2 was present in all parasite genomes as a single copy gene with a unique 5' untranslated region. Rif...

  7. Productivity limits and potentials of the principles of conservation agriculture.

    Science.gov (United States)

    Pittelkow, Cameron M; Liang, Xinqiang; Linquist, Bruce A; van Groenigen, Kees Jan; Lee, Juhwan; Lundy, Mark E; van Gestel, Natasja; Six, Johan; Venterea, Rodney T; van Kessel, Chris

    2015-01-15

    One of the primary challenges of our time is to feed a growing and more demanding world population with reduced external inputs and minimal environmental impacts, all under more variable and extreme climate conditions in the future. Conservation agriculture represents a set of three crop management principles that has received strong international support to help address this challenge, with recent conservation agriculture efforts focusing on smallholder farming systems in sub-Saharan Africa and South Asia. However, conservation agriculture is highly debated, with respect to both its effects on crop yields and its applicability in different farming contexts. Here we conduct a global meta-analysis using 5,463 paired yield observations from 610 studies to compare no-till, the original and central concept of conservation agriculture, with conventional tillage practices across 48 crops and 63 countries. Overall, our results show that no-till reduces yields, yet this response is variable and under certain conditions no-till can produce equivalent or greater yields than conventional tillage. Importantly, when no-till is combined with the other two conservation agriculture principles of residue retention and crop rotation, its negative impacts are minimized. Moreover, no-till in combination with the other two principles significantly increases rainfed crop productivity in dry climates, suggesting that it may become an important climate-change adaptation strategy for ever-drier regions of the world. However, any expansion of conservation agriculture should be done with caution in these areas, as implementation of the other two principles is often challenging in resource-poor and vulnerable smallholder farming systems, thereby increasing the likelihood of yield losses rather than gains. Although farming systems are multifunctional, and environmental and socio-economic factors need to be considered, our analysis indicates that the potential contribution of no-till to the

  8. Conservation of transcription factor binding events predicts gene expression across species

    Science.gov (United States)

    Hemberg, Martin; Kreiman, Gabriel

    2011-01-01

    Recent technological advances have made it possible to determine the genome-wide binding sites of transcription factors (TFs). Comparisons across species have suggested a relatively low degree of evolutionary conservation of experimentally defined TF binding events (TFBEs). Using binding data for six different TFs in hepatocytes and embryonic stem cells from human and mouse, we demonstrate that evolutionary conservation of TFBEs within orthologous proximal promoters is closely linked to function, defined as expression of the target genes. We show that (i) there is a significantly higher degree of conservation of TFBEs when the target gene is expressed in both species; (ii) there is increased conservation of binding events for groups of TFs compared to individual TFs; and (iii) conserved TFBEs have a greater impact on the expression of their target genes than non-conserved ones. These results link conservation of structural elements (TFBEs) to conservation of function (gene expression) and suggest a higher degree of functional conservation than implied by previous studies. PMID:21622661

  9. Identifying human disease genes through cross-species gene mapping of evolutionary conserved processes.

    Directory of Open Access Journals (Sweden)

    Martin Poot

    2011-05-01

    Full Text Available Understanding complex networks that modulate development in humans is hampered by genetic and phenotypic heterogeneity within and between populations. Here we present a method that exploits natural variation in highly diverse mouse genetic reference panels in which genetic and environmental factors can be tightly controlled. The aim of our study is to test a cross-species genetic mapping strategy, which compares data of gene mapping in human patients with functional data obtained by QTL mapping in recombinant inbred mouse strains in order to prioritize human disease candidate genes.We exploit evolutionary conservation of developmental phenotypes to discover gene variants that influence brain development in humans. We studied corpus callosum volume in a recombinant inbred mouse panel (C57BL/6J×DBA/2J, BXD strains using high-field strength MRI technology. We aligned mouse mapping results for this neuro-anatomical phenotype with genetic data from patients with abnormal corpus callosum (ACC development.From the 61 syndromes which involve an ACC, 51 human candidate genes have been identified. Through interval mapping, we identified a single significant QTL on mouse chromosome 7 for corpus callosum volume with a QTL peak located between 25.5 and 26.7 Mb. Comparing the genes in this mouse QTL region with those associated with human syndromes (involving ACC and those covered by copy number variations (CNV yielded a single overlap, namely HNRPU in humans and Hnrpul1 in mice. Further analysis of corpus callosum volume in BXD strains revealed that the corpus callosum was significantly larger in BXD mice with a B genotype at the Hnrpul1 locus than in BXD mice with a D genotype at Hnrpul1 (F = 22.48, p<9.87*10(-5.This approach that exploits highly diverse mouse strains provides an efficient and effective translational bridge to study the etiology of human developmental disorders, such as autism and schizophrenia.

  10. Energy conservation and maximal entropy production in enzyme reactions.

    Science.gov (United States)

    Dobovišek, Andrej; Vitas, Marko; Brumen, Milan; Fajmut, Aleš

    2017-08-01

    A procedure for maximization of the density of entropy production in a single stationary two-step enzyme reaction is developed. Under the constraints of mass conservation, fixed equilibrium constant of a reaction and fixed products of forward and backward enzyme rate constants the existence of maximum in the density of entropy production is demonstrated. In the state with maximal density of entropy production the optimal enzyme rate constants, the stationary concentrations of the substrate and the product, the stationary product yield as well as the stationary reaction flux are calculated. The test, whether these calculated values of the reaction parameters are consistent with their corresponding measured values, is performed for the enzyme Glucose Isomerase. It is found that calculated and measured rate constants agree within an order of magnitude, whereas the calculated reaction flux and the product yield differ from their corresponding measured values for less than 20 % and 5 %, respectively. This indicates that the enzyme Glucose Isomerase, considered in a non-equilibrium stationary state, as found in experiments using the continuous stirred tank reactors, possibly operates close to the state with the maximum in the density of entropy production. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes

    Directory of Open Access Journals (Sweden)

    Lemay Danielle G

    2012-09-01

    Full Text Available Abstract Background In previous studies, gene neighborhoods—spatial clusters of co-expressed genes in the genome—have been defined using arbitrary rules such as requiring adjacency, a minimum number of genes, a fixed window size, or a minimum expression level. In the current study, we developed a Gene Neighborhood Scoring Tool (G-NEST which combines genomic location, gene expression, and evolutionary sequence conservation data to score putative gene neighborhoods across all possible window sizes simultaneously. Results Using G-NEST on atlases of mouse and human tissue expression data, we found that large neighborhoods of ten or more genes are extremely rare in mammalian genomes. When they do occur, neighborhoods are typically composed of families of related genes. Both the highest scoring and the largest neighborhoods in mammalian genomes are formed by tandem gene duplication. Mammalian gene neighborhoods contain highly and variably expressed genes. Co-localized noisy gene pairs exhibit lower evolutionary conservation of their adjacent genome locations, suggesting that their shared transcriptional background may be disadvantageous. Genes that are essential to mammalian survival and reproduction are less likely to occur in neighborhoods, although neighborhoods are enriched with genes that function in mitosis. We also found that gene orientation and protein-protein interactions are partially responsible for maintenance of gene neighborhoods. Conclusions Our experiments using G-NEST confirm that tandem gene duplication is the primary driver of non-random gene order in mammalian genomes. Non-essentiality, co-functionality, gene orientation, and protein-protein interactions are additional forces that maintain gene neighborhoods, especially those formed by tandem duplicates. We expect G-NEST to be useful for other applications such as the identification of core regulatory modules, common transcriptional backgrounds, and chromatin domains. The

  12. Conservation of the rad21 Schizosaccharomyces pombe DNA double-strand break repair gene in mammals

    International Nuclear Information System (INIS)

    McKay, Michael J.; Spek, Peter van der; Kanaar, Roland; Smit, Bep; Bootsma, Dirk; Hoeijmakers, Jan H. J.

    1996-01-01

    Purpose/Objective: Genetic factors are likely to be major determinants of human cellular ionizing radiation sensitivity. DNA double strand breaks (dsbs) are significant ionizing radiation-induced lesions; cellular DNA dsb processing is also important in a number of other contexts. To further the understanding of DNA dsb processing in mammalian cells, we cloned and sequenced mammalian homologs of the rad21 Schizosaccharomyces pombe DNA dsb repair gene. Materials and Methods: The genes were cloned by evolutionary walking, exploiting sequence homology between the yeast and mammalian genes. Results: No major motifs indicative of a particular function were present in the predicted amino acid sequences of the mammalian genes. Alignment of the Rad21 amino acid sequence with its putative homologs showed that similarity was distributed across the length of the proteins, with more highly conserved regions at both termini. The mHR21 sp (mouse homolog ofR ad21, S. pombe) and hHR21 sp (humanh omolog of Rad21, S. pombe) predicted proteins were 96% identical, whereas the human and S. pombe proteins were 25% identical and 47% similar. RNA blot analysis showed that mHR21 sp mRNA was abundant in all adult mouse tissues examined, with highest expression in testis and thymus. In addition to a 3.1kb mRNA transcript in all tissues, an additional 2.2kb transcript was present at a high level in post-meiotic spermatids, white expression of the 3.1kb mRNA in testis was confined to the meiotic compartment. hHR21 sp mRNA was cell cycle regulated in human cells, increasing in late S phase to a peak in G2 phase. The level of hHR21 sp transcripts was not altered by exposure of normal diploid fibroblasts to 10 Gy ionizing radiation. In situ hybridization showed mHR21 sp resided on chromosome 15D3, whereashHR21 sp localized to the syntenic 8q24 region. Conclusion: Cloning these novel mammalian genes and characterization of their protein products should contribute to the understanding of cellular

  13. Evaluation of the conserve flavin reductase gene from three ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-12-15

    Dec 15, 2009 ... means of PCR technique. The nucleic acid sequences of the PCR primers were designed using conserved nucleic acid sequences of the flavin reductase enzyme from. Rhodococcus sp. strain IGTS8. The oligonucleotide primers were as follows: 5'-GAA TTC ATG TCT GAC. AAG CCG AAT GCC-3' (forward) ...

  14. From genes to landscapes: conserving biodiversity at multiple scales.

    Science.gov (United States)

    Sally. Duncan

    2000-01-01

    Biodiversity has at last become a familiar term outside of scientific circles. Ways of measuring it and mapping it are advancing and becoming more complex, but ways of deciding how to conserve it remain mixed at best, and the resources available to manage dimishing biodiversity are themselves scarce. One significant problem is that policy decisions are frequently at...

  15. Eucaryotic operon genes can define highly conserved syntenies

    Czech Academy of Sciences Publication Activity Database

    Trachtulec, Zdeněk

    2004-01-01

    Roč. 50, - (2004), s. 1-6 ISSN 0015-5500 R&D Projects: GA ČR GA204/01/0997; GA MŠk LN00A079 Institutional research plan: CEZ:AV0Z5052915 Keywords : eukaryotic operon * conserved synteny Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.507, year: 2004

  16. Characterization of Conserved and Non-conserved Imprinted Genes in Swine

    Science.gov (United States)

    In order to increase our understanding of the role of imprinted genes in swine reproduction we used two complementary approaches, analysis of imprinting by pyrosequencing, and expression profiling of parthenogenetic fetuses, to carry out a comprehensive analysis of this gene family in swine. Using A...

  17. Conservation in Mammals of Genes Associated with Aggression-Related Behavioral Phenotypes in Honey Bees.

    Science.gov (United States)

    Liu, Hui; Robinson, Gene E; Jakobsson, Eric

    2016-06-01

    The emerging field of sociogenomics explores the relations between social behavior and genome structure and function. An important question is the extent to which associations between social behavior and gene expression are conserved among the Metazoa. Prior experimental work in an invertebrate model of social behavior, the honey bee, revealed distinct brain gene expression patterns in African and European honey bees, and within European honey bees with different behavioral phenotypes. The present work is a computational study of these previous findings in which we analyze, by orthology determination, the extent to which genes that are socially regulated in honey bees are conserved across the Metazoa. We found that the differentially expressed gene sets associated with alarm pheromone response, the difference between old and young bees, and the colony influence on soldier bees, are enriched in widely conserved genes, indicating that these differences have genomic bases shared with many other metazoans. By contrast, the sets of differentially expressed genes associated with the differences between African and European forager and guard bees are depleted in widely conserved genes, indicating that the genomic basis for this social behavior is relatively specific to honey bees. For the alarm pheromone response gene set, we found a particularly high degree of conservation with mammals, even though the alarm pheromone itself is bee-specific. Gene Ontology identification of human orthologs to the strongly conserved honey bee genes associated with the alarm pheromone response shows overrepresentation of protein metabolism, regulation of protein complex formation, and protein folding, perhaps associated with remodeling of critical neural circuits in response to alarm pheromone. We hypothesize that such remodeling may be an adaptation of social animals to process and respond appropriately to the complex patterns of conspecific communication essential for social organization.

  18. Conservation in Mammals of Genes Associated with Aggression-Related Behavioral Phenotypes in Honey Bees.

    Directory of Open Access Journals (Sweden)

    Hui Liu

    2016-06-01

    Full Text Available The emerging field of sociogenomics explores the relations between social behavior and genome structure and function. An important question is the extent to which associations between social behavior and gene expression are conserved among the Metazoa. Prior experimental work in an invertebrate model of social behavior, the honey bee, revealed distinct brain gene expression patterns in African and European honey bees, and within European honey bees with different behavioral phenotypes. The present work is a computational study of these previous findings in which we analyze, by orthology determination, the extent to which genes that are socially regulated in honey bees are conserved across the Metazoa. We found that the differentially expressed gene sets associated with alarm pheromone response, the difference between old and young bees, and the colony influence on soldier bees, are enriched in widely conserved genes, indicating that these differences have genomic bases shared with many other metazoans. By contrast, the sets of differentially expressed genes associated with the differences between African and European forager and guard bees are depleted in widely conserved genes, indicating that the genomic basis for this social behavior is relatively specific to honey bees. For the alarm pheromone response gene set, we found a particularly high degree of conservation with mammals, even though the alarm pheromone itself is bee-specific. Gene Ontology identification of human orthologs to the strongly conserved honey bee genes associated with the alarm pheromone response shows overrepresentation of protein metabolism, regulation of protein complex formation, and protein folding, perhaps associated with remodeling of critical neural circuits in response to alarm pheromone. We hypothesize that such remodeling may be an adaptation of social animals to process and respond appropriately to the complex patterns of conspecific communication essential for

  19. New Genome Similarity Measures based on Conserved Gene Adjacencies.

    Science.gov (United States)

    Doerr, Daniel; Kowada, Luis Antonio B; Araujo, Eloi; Deshpande, Shachi; Dantas, Simone; Moret, Bernard M E; Stoye, Jens

    2017-06-01

    Many important questions in molecular biology, evolution, and biomedicine can be addressed by comparative genomic approaches. One of the basic tasks when comparing genomes is the definition of measures of similarity (or dissimilarity) between two genomes, for example, to elucidate the phylogenetic relationships between species. The power of different genome comparison methods varies with the underlying formal model of a genome. The simplest models impose the strong restriction that each genome under study must contain the same genes, each in exactly one copy. More realistic models allow several copies of a gene in a genome. One speaks of gene families, and comparative genomic methods that allow this kind of input are called gene family-based. The most powerful-but also most complex-models avoid this preprocessing of the input data and instead integrate the family assignment within the comparative analysis. Such methods are called gene family-free. In this article, we study an intermediate approach between family-based and family-free genomic similarity measures. Introducing this simpler model, called gene connections, we focus on the combinatorial aspects of gene family-free genome comparison. While in most cases, the computational costs to the general family-free case are the same, we also find an instance where the gene connections model has lower complexity. Within the gene connections model, we define three variants of genomic similarity measures that have different expression powers. We give polynomial-time algorithms for two of them, while we show NP-hardness for the third, most powerful one. We also generalize the measures and algorithms to make them more robust against recent local disruptions in gene order. Our theoretical findings are supported by experimental results, proving the applicability and performance of our newly defined similarity measures.

  20. Pleiotropic Regulation of Virulence Genes in Streptococcus mutans by the Conserved Small Protein SprV.

    Science.gov (United States)

    Shankar, Manoharan; Hossain, Mohammad S; Biswas, Indranil

    2017-04-15

    Streptococcus mutans , an oral pathogen associated with dental caries, colonizes tooth surfaces as polymicrobial biofilms known as dental plaque. S. mutans expresses several virulence factors that allow the organism to tolerate environmental fluctuations and compete with other microorganisms. We recently identified a small hypothetical protein (90 amino acids) essential for the normal growth of the bacterium. Inactivation of the gene, SMU.2137, encoding this protein caused a significant growth defect and loss of various virulence-associated functions. An S. mutans strain lacking this gene was more sensitive to acid, temperature, osmotic, oxidative, and DNA damage-inducing stresses. In addition, we observed an altered protein profile and defects in biofilm formation, bacteriocin production, and natural competence development, possibly due to the fitness defect associated with SMU.2137 deletion. Transcriptome sequencing revealed that nearly 20% of the S. mutans genes were differentially expressed upon SMU.2137 deletion, thereby suggesting a pleiotropic effect. Therefore, we have renamed this hitherto uncharacterized gene as sprV ( s treptococcal p leiotropic r egulator of v irulence). The transcript levels of several relevant genes in the sprV mutant corroborated the phenotypes observed upon sprV deletion. Owing to its highly conserved nature, inactivation of the sprV ortholog in Streptococcus gordonii also resulted in poor growth and defective UV tolerance and competence development as in the case of S. mutans Our experiments suggest that SprV is functionally distinct from its homologs identified by structure and sequence homology. Nonetheless, our current work is aimed at understanding the importance of SprV in the S. mutans biology. IMPORTANCE Streptococcus mutans employs several virulence factors and stress resistance mechanisms to colonize tooth surfaces and cause dental caries. Bacterial pathogenesis is generally controlled by regulators of fitness that are

  1. The immunomodulatory gene products of myxoma virus

    Indian Academy of Sciences (India)

    Unknown

    273. Keywords. Gene products; myxoma virus; Oryctolagus cuniculus; poxvirus; skin lesions ...... these data is that these viral proteins do not promote class .... Cudmore S, Reckmann I and Way M 1997 Viral manipulations of the actin ...

  2. Energy resources, CO2 production and energy conservation

    International Nuclear Information System (INIS)

    O'Callaghan, P.W.

    1993-01-01

    World fossil fuel reserves, historical and current rates of consumption are reviewed and estimates of indigeneous lives in geographical regions are made. Rates of production and accumulations of carbon dioxide and other greenhouse gases in the atmosphere are calculated and correlations made with measured global mean temperatures and concomitant sea-level rises. It is concluded that, if present rates of global fossil-fuel consumptions continue unabated, the world's fossil-fuel store will be depleted by the year 2050. This would be accompanied by a substantial rise in global mean temperature. The effects of various protocols for the reductions of emissions are examined. It is concluded that there is no alternative than to cease the production and release into the atmosphere of the more damaging man-made greenhouse gases as soon as is practicably possible and to seek a sustained reduction in the rates of combustion of fossil fuels world-wide via energy management and conservation. (author)

  3. Conservation of lipid metabolic gene transcriptional regulatory networks in fish and mammals.

    Science.gov (United States)

    Carmona-Antoñanzas, Greta; Tocher, Douglas R; Martinez-Rubio, Laura; Leaver, Michael J

    2014-01-15

    Lipid content and composition in aquafeeds have changed rapidly as a result of the recent drive to replace ecologically limited marine ingredients, fishmeal and fish oil (FO). Terrestrial plant products are the most economic and sustainable alternative; however, plant meals and oils are devoid of physiologically important cholesterol and long-chain polyunsaturated fatty acids (LC-PUFA), eicosapentaenoic (EPA), docosahexaenoic (DHA) and arachidonic (ARA) acids. Although replacement of dietary FO with vegetable oil (VO) has little effect on growth in Atlantic salmon (Salmo salar), several studies have shown major effects on the activity and expression of genes involved in lipid homeostasis. In vertebrates, sterols and LC-PUFA play crucial roles in lipid metabolism by direct interaction with lipid-sensing transcription factors (TFs) and consequent regulation of target genes. The primary aim of the present study was to elucidate the role of key TFs in the transcriptional regulation of lipid metabolism in fish by transfection and overexpression of TFs. The results show that the expression of genes of LC-PUFA biosynthesis (elovl and fads2) and cholesterol metabolism (abca1) are regulated by Lxr and Srebp TFs in salmon, indicating highly conserved regulatory mechanism across vertebrates. In addition, srebp1 and srebp2 mRNA respond to replacement of dietary FO with VO. Thus, Atlantic salmon adjust lipid metabolism in response to dietary lipid composition through the transcriptional regulation of gene expression. It may be possible to further increase efficient and effective use of sustainable alternatives to marine products in aquaculture by considering these important molecular interactions when formulating diets. © 2013.

  4. Cytogenetics, conserved synteny and evolution of chicken fucosyltransferase genes compared to human

    NARCIS (Netherlands)

    Coullin, P.; Crooijmans, R.P.M.A.; Fillon, V.; Mollicone, R.; Groenen, M.A.M.; Adrien-Dehais, C.; Bernheim, A.; Zoorob, R.; Oriol, R.; Candelier, J.J.

    2003-01-01

    Fucosyltransferases appeared early in evolution, since they are present from bacteria to primates and the genes are well conserved. The aim of this work was to study these genes in the bird group, which is particularly attractive for the comprehension of the evolution of the vertebrate genome.

  5. Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes.

    NARCIS (Netherlands)

    Snel, B.; Noort, V. van; Huynen, M.A.

    2004-01-01

    Differences between species have been suggested to largely reside in the network of connections among the genes. Nevertheless, the rate at which these connections evolve has not been properly quantified. Here, we measure the extent to which co-regulation between pairs of genes is conserved over

  6. Functional conservation of coenzyme Q biosynthetic genes among yeasts, plants, and humans.

    Directory of Open Access Journals (Sweden)

    Kazuhiro Hayashi

    Full Text Available Coenzyme Q (CoQ is an essential factor for aerobic growth and oxidative phosphorylation in the electron transport system. The biosynthetic pathway for CoQ has been proposed mainly from biochemical and genetic analyses of Escherichia coli and Saccharomyces cerevisiae; however, the biosynthetic pathway in higher eukaryotes has been explored in only a limited number of studies. We previously reported the roles of several genes involved in CoQ synthesis in the fission yeast Schizosaccharomyces pombe. Here, we expand these findings by identifying ten genes (dps1, dlp1, ppt1, and coq3-9 that are required for CoQ synthesis. CoQ10-deficient S. pombe coq deletion strains were generated and characterized. All mutant fission yeast strains were sensitive to oxidative stress, produced a large amount of sulfide, required an antioxidant to grow on minimal medium, and did not survive at the stationary phase. To compare the biosynthetic pathway of CoQ in fission yeast with that in higher eukaryotes, the ability of CoQ biosynthetic genes from humans and plants (Arabidopsis thaliana to functionally complement the S. pombe coq deletion strains was determined. With the exception of COQ9, expression of all other human and plant COQ genes recovered CoQ10 production by the fission yeast coq deletion strains, although the addition of a mitochondrial targeting sequence was required for human COQ3 and COQ7, as well as A. thaliana COQ6. In summary, this study describes the functional conservation of CoQ biosynthetic genes between yeasts, humans, and plants.

  7. Conservation

    NARCIS (Netherlands)

    Noteboom, H.P.

    1985-01-01

    The IUCN/WWF Plants Conservation Programme 1984 — 1985. World Wildlife Fund chose plants to be the subject of their fund-raising campaign in the period 1984 — 1985. The objectives were to: 1. Use information techniques to achieve the conservation objectives of the Plants Programme – to save plants;

  8. Conservation.

    Science.gov (United States)

    National Audubon Society, New York, NY.

    This set of teaching aids consists of seven Audubon Nature Bulletins, providing the teacher and student with informational reading on various topics in conservation. The bulletins have these titles: Plants as Makers of Soil, Water Pollution Control, The Ground Water Table, Conservation--To Keep This Earth Habitable, Our Threatened Air Supply,…

  9. Identification of a conserved set of upregulated genes in mouse skeletal muscle hypertrophy and regrowth.

    Science.gov (United States)

    Chaillou, Thomas; Jackson, Janna R; England, Jonathan H; Kirby, Tyler J; Richards-White, Jena; Esser, Karyn A; Dupont-Versteegden, Esther E; McCarthy, John J

    2015-01-01

    The purpose of this study was to compare the gene expression profile of mouse skeletal muscle undergoing two forms of growth (hypertrophy and regrowth) with the goal of identifying a conserved set of differentially expressed genes. Expression profiling by microarray was performed on the plantaris muscle subjected to 1, 3, 5, 7, 10, and 14 days of hypertrophy or regrowth following 2 wk of hind-limb suspension. We identified 97 differentially expressed genes (≥2-fold increase or ≥50% decrease compared with control muscle) that were conserved during the two forms of muscle growth. The vast majority (∼90%) of the differentially expressed genes was upregulated and occurred at a single time point (64 out of 86 genes), which most often was on the first day of the time course. Microarray analysis from the conserved upregulated genes showed a set of genes related to contractile apparatus and stress response at day 1, including three genes involved in mechanotransduction and four genes encoding heat shock proteins. Our analysis further identified three cell cycle-related genes at day and several genes associated with extracellular matrix (ECM) at both days 3 and 10. In conclusion, we have identified a core set of genes commonly upregulated in two forms of muscle growth that could play a role in the maintenance of sarcomere stability, ECM remodeling, cell proliferation, fast-to-slow fiber type transition, and the regulation of skeletal muscle growth. These findings suggest conserved regulatory mechanisms involved in the adaptation of skeletal muscle to increased mechanical loading. Copyright © 2015 the American Physiological Society.

  10. Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes

    Directory of Open Access Journals (Sweden)

    Kohane Isaac

    2005-11-01

    Full Text Available Abstract Background Recent advances in genome sequencing suggest a remarkable conservation in gene content of mammalian organisms. The similarity in gene repertoire present in different organisms has increased interest in studying regulatory mechanisms of gene expression aimed at elucidating the differences in phenotypes. In particular, a proximal promoter region contains a large number of regulatory elements that control the expression of its downstream gene. Although many studies have focused on identification of these elements, a broader picture on the complexity of transcriptional regulation of different biological processes has not been addressed in mammals. The regulatory complexity may strongly correlate with gene function, as different evolutionary forces must act on the regulatory systems under different biological conditions. We investigate this hypothesis by comparing the conservation of promoters upstream of genes classified in different functional categories. Results By conducting a rank correlation analysis between functional annotation and upstream sequence alignment scores obtained by human-mouse and human-dog comparison, we found a significantly greater conservation of the upstream sequence of genes involved in development, cell communication, neural functions and signaling processes than those involved in more basic processes shared with unicellular organisms such as metabolism and ribosomal function. This observation persists after controlling for G+C content. Considering conservation as a functional signature, we hypothesize a higher density of cis-regulatory elements upstream of genes participating in complex and adaptive processes. Conclusion We identified a class of functions that are associated with either high or low promoter conservation in mammals. We detected a significant tendency that points to complex and adaptive processes were associated with higher promoter conservation, despite the fact that they have emerged

  11. 75 FR 52892 - Energy Conservation Program for Consumer Products: Test Procedures for Residential Water Heaters...

    Science.gov (United States)

    2010-08-30

    ... ``Energy Conservation Program for Consumer Products Other Than Automobiles,'' including residential water... final rule revising energy conservation standards for residential water heaters, direct heating.... EERE-2009-BT-TP-0013] RIN 1904-AB95 Energy Conservation Program for Consumer Products: Test Procedures...

  12. Effects of bioenergy production on European nature conservation options

    Science.gov (United States)

    Schleupner, C.; Schneider, U. A.

    2009-04-01

    To increase security of energy supply and reduce greenhouse gas (GHG) emissions the European Commission set out a long-term strategy for renewable energy in the European Union (EU). Bioenergy from forestry and agriculture plays a key role for both. Since the last decade a significant increase of biomass energy plantations has been observed in Europe. Concurrently, the EU agreed to halt the loss of biodiversity within its member states. One measure is the Natura2000 network of important nature sites that actually covers about 20% of the EU land surface. However, to fulfil the biodiversity target more nature conservation and restoration sites need to be designated. There are arising concerns that an increased cultivation of bioenergy crops will decrease the land available for nature reserves and for "traditional" agriculture and forestry. In the following the economic and ecological impacts of structural land use changes are demonstrated by two examples. First, a case study of land use changes on the Eiderstedt peninsula in Schleswig-Holstein/Germany evaluates the impacts of grassland conversion into bioenergy plantations under consideration of selected meadow birds. Scenarios indicate not only a quantitative loss of habitats but also a reduction of habitat quality. The second study assesses the role of bioenergy production in light of possible negative impacts on potential wetland conservation sites in Europe. By coupling the spatial wetland distribution model "SWEDI" (cf. SCHLEUPNER 2007) to the European Forest and Agricultural Sector Optimization Model (EUFASOM; cf. SCHNEIDER ET AL. 2008) economic and environmental aspects of land use are evaluated simultaneously. This way the costs and benefits of the appropriate measures and its consequences for agriculture and forestry are investigated. One aim is to find the socially optimal balance between alternative wetland uses by integrating biological benefits - in this case wetlands - and economic opportunities - here

  13. Characterization of Conserved and Nonconserved Imprinted Genes in Swine

    Science.gov (United States)

    Genomic imprinting results in the silencing of a subset of mammalian alleles due to parent-of-origin inheritance. Due to the nature of their expression patterns they play a critical role in placental and early embryonic development. In order to increase our understanding of imprinted genes specifi...

  14. Conservation and sex-specific splicing of the doublesex gene

    Indian Academy of Sciences (India)

    Genetic control of sex determination in insects has been best characterized in Drosophila melanogaster, where the master gene Sxl codes for RNA that is sex specifically spliced to produce a functional protein only in females. SXL regulates the sex-specific splicing of transformer (tra) RNA which, in turn, regulates the ...

  15. Human cytomegalovirus UL145 gene is highly conserved among ...

    Indian Academy of Sciences (India)

    PRAKASH KUMAR

    capable of causing infections that persist lifelong, and normally ... 1 Virus Laboratory, Affiliated ShengJing Hospital, China Medical University, Shenyang 110004, P. R. China. 2Department of .... Elmer, USA), and negative controls were included in each round of .... variability of the UL145 gene in field isolates. To answer this.

  16. Evolutionary Conservation in Genes Underlying Human Psychiatric Disorders

    Directory of Open Access Journals (Sweden)

    Lisa Michelle Ogawa

    2014-05-01

    Full Text Available Many psychiatric diseases observed in humans have tenuous or absent analogs in other species. Most notable among these are schizophrenia and autism. One hypothesis has posited that these diseases have arisen as a consequence of human brain evolution, for example, that the same processes that led to advances in cognition, language, and executive function also resulted in novel diseases in humans when dysfunctional. Here, the molecular evolution of genes associated with these and other psychiatric disorders are compared among species. Genes associated with psychiatric disorders are drawn from the literature and orthologous sequences are collected from eleven primate species (human, chimpanzee, bonobo, gorilla, orangutan, gibbon, macaque, baboon, marmoset, squirrel monkey, and galago and thirty one non-primate mammalian species. Evolutionary parameters, including dN/dS, are calculated for each gene and compared between disease classes and among species, focusing on humans and primates compared to other mammals and on large-brained taxa (cetaceans, rhinoceros, walrus, bear, and elephant compared to their small-brained sister species. Evidence of differential selection in primates supports the hypothesis that schizophrenia and autism are a cost of higher brain function. Through this work a better understanding of the molecular evolution of the human brain, the pathophysiology of disease, and the genetic basis of human psychiatric disease is gained.

  17. Constraints on genes shape long-term conservation of macro-synteny in metazoan genomes

    Directory of Open Access Journals (Sweden)

    Putnam Nicholas H

    2011-10-01

    Full Text Available Abstract Background Many metazoan genomes conserve chromosome-scale gene linkage relationships (“macro-synteny” from the common ancestor of multicellular animal life 1234, but the biological explanation for this conservation is still unknown. Double cut and join (DCJ is a simple, well-studied model of neutral genome evolution amenable to both simulation and mathematical analysis 5, but as we show here, it is not sufficent to explain long-term macro-synteny conservation. Results We examine a family of simple (one-parameter extensions of DCJ to identify models and choices of parameters consistent with the levels of macro- and micro-synteny conservation observed among animal genomes. Our software implements a flexible strategy for incorporating genomic context into the DCJ model to incorporate various types of genomic context (“DCJ-[C]”, and is available as open source software from http://github.com/putnamlab/dcj-c. Conclusions A simple model of genome evolution, in which DCJ moves are allowed only if they maintain chromosomal linkage among a set of constrained genes, can simultaneously account for the level of macro-synteny conservation and for correlated conservation among multiple pairs of species. Simulations under this model indicate that a constraint on approximately 7% of metazoan genes is sufficient to constrain genome rearrangement to an average rate of 25 inversions and 1.7 translocations per million years.

  18. 78 FR 72533 - Energy Conservation Program: Energy Conservation Standards for Certain Consumer Products

    Science.gov (United States)

    2013-12-03

    ... published on October 23, 2013. That final rule adopted changes to definitions and energy conservation... revised definition and revised energy conservation standards for small duct high velocity central air... Congress has provided in the AEMTCA for the Secretary of Energy to revise definitions and energy...

  19. 75 FR 12144 - Energy Conservation Program for Consumer Products: Energy Conservation Standards for Residential...

    Science.gov (United States)

    2010-03-15

    .... 1. Consensus Agreement On January 26, 2010, the Air-Conditioning, Heating and Refrigeration... subsections. B. History of the Standards Rulemaking for Residential Furnaces 1. Background Energy conservation... recommending minimum energy conservation standards for residential central air conditioners, heat pumps, and...

  20. Evidence for intron length conservation in a set of mammalian genes associated with embryonic development

    LENUS (Irish Health Repository)

    2011-10-05

    Abstract Background We carried out an analysis of intron length conservation across a diverse group of nineteen mammalian species. Motivated by recent research suggesting a role for time delays associated with intron transcription in gene expression oscillations required for early embryonic patterning, we searched for examples of genes that showed the most extreme conservation of total intron content in mammals. Results Gene sets annotated as being involved in pattern specification in the early embryo or containing the homeobox DNA-binding domain, were significantly enriched among genes with highly conserved intron content. We used ancestral sequences reconstructed with probabilistic models that account for insertion and deletion mutations to distinguish insertion and deletion events on lineages leading to human and mouse from their last common ancestor. Using a randomization procedure, we show that genes containing the homeobox domain show less change in intron content than expected, given the number of insertion and deletion events within their introns. Conclusions Our results suggest selection for gene expression precision or the existence of additional development-associated genes for which transcriptional delay is functionally significant.

  1. Evolutionary conservation and network structure characterize genes of phenotypic relevance for mitosis in human.

    Directory of Open Access Journals (Sweden)

    Marek Ostaszewski

    Full Text Available The impact of gene silencing on cellular phenotypes is difficult to establish due to the complexity of interactions in the associated biological processes and pathways. A recent genome-wide RNA knock-down study both identified and phenotypically characterized a set of important genes for the cell cycle in HeLa cells. Here, we combine a molecular interaction network analysis, based on physical and functional protein interactions, in conjunction with evolutionary information, to elucidate the common biological and topological properties of these key genes. Our results show that these genes tend to be conserved with their corresponding protein interactions across several species and are key constituents of the evolutionary conserved molecular interaction network. Moreover, a group of bistable network motifs is found to be conserved within this network, which are likely to influence the network stability and therefore the robustness of cellular functioning. They form a cluster, which displays functional homogeneity and is significantly enriched in genes phenotypically relevant for mitosis. Additional results reveal a relationship between specific cellular processes and the phenotypic outcomes induced by gene silencing. This study introduces new ideas regarding the relationship between genotype and phenotype in the context of the cell cycle. We show that the analysis of molecular interaction networks can result in the identification of genes relevant to cellular processes, which is a promising avenue for future research.

  2. 77 FR 49063 - Energy Conservation Program: Test Procedures for Residential Dishwashers and Cooking Products

    Science.gov (United States)

    2012-08-15

    ... Energy Conservation Program: Test Procedures for Residential Dishwashers and Cooking Products; Proposed...-AC01 Energy Conservation Program: Test Procedures for Residential Dishwashers and Cooking Products... procedures for both dishwashers and conventional cooking products for the measurement of energy use in fan...

  3. 77 FR 28673 - Energy Conservation Program for Consumer Products: Test Procedures for Residential Furnace Fans

    Science.gov (United States)

    2012-05-15

    ... multipliers based on climate, consumer behavior assumptions, and product characteristics (e.g., multi-stage or... Conservation Program for Consumer Products: Test Procedures for Residential Furnace Fans; Proposed Rule #0;#0... Conservation Program for Consumer Products: Test Procedures for Residential Furnace Fans AGENCY: Office of...

  4. Divergent gene expression in the conserved dauer stage of the nematodes Pristionchus pacificus and Caenorhabditis elegans

    Directory of Open Access Journals (Sweden)

    Sinha Amit

    2012-06-01

    Full Text Available Abstract Background An organism can respond to changing environmental conditions by adjusting gene regulation and by forming alternative phenotypes. In nematodes, these mechanisms are coupled because many species will form dauer larvae, a stress-resistant and non-aging developmental stage, when exposed to unfavorable environmental conditions, and execute gene expression programs that have been selected for the survival of the animal in the wild. These dauer larvae represent an environmentally induced, homologous developmental stage across many nematode species, sharing conserved morphological and physiological properties. Hence it can be expected that some core components of the associated transcriptional program would be conserved across species, while others might diverge over the course of evolution. However, transcriptional and metabolic analysis of dauer development has been largely restricted to Caenorhabditis elegans. Here, we use a transcriptomic approach to compare the dauer stage in the evolutionary model system Pristionchus pacificus with the dauer stage in C. elegans. Results We have employed Agilent microarrays, which represent 20,446 P. pacificus and 20,143 C. elegans genes to show an unexpected divergence in the expression profiles of these two nematodes in dauer and dauer exit samples. P. pacificus and C. elegans differ in the dynamics and function of genes that are differentially expressed. We find that only a small number of orthologous gene pairs show similar expression pattern in the dauers of the two species, while the non-orthologous fraction of genes is a major contributor to the active transcriptome in dauers. Interestingly, many of the genes acquired by horizontal gene transfer and orphan genes in P. pacificus, are differentially expressed suggesting that these genes are of evolutionary and functional importance. Conclusion Our data set provides a catalog for future functional investigations and indicates novel insight

  5. Metazoan Remaining Genes for Essential Amino Acid Biosynthesis: Sequence Conservation and Evolutionary Analyses

    Directory of Open Access Journals (Sweden)

    Igor R. Costa

    2014-12-01

    Full Text Available Essential amino acids (EAA consist of a group of nine amino acids that animals are unable to synthesize via de novo pathways. Recently, it has been found that most metazoans lack the same set of enzymes responsible for the de novo EAA biosynthesis. Here we investigate the sequence conservation and evolution of all the metazoan remaining genes for EAA pathways. Initially, the set of all 49 enzymes responsible for the EAA de novo biosynthesis in yeast was retrieved. These enzymes were used as BLAST queries to search for similar sequences in a database containing 10 complete metazoan genomes. Eight enzymes typically attributed to EAA pathways were found to be ubiquitous in metazoan genomes, suggesting a conserved functional role. In this study, we address the question of how these genes evolved after losing their pathway partners. To do this, we compared metazoan genes with their fungal and plant orthologs. Using phylogenetic analysis with maximum likelihood, we found that acetolactate synthase (ALS and betaine-homocysteine S-methyltransferase (BHMT diverged from the expected Tree of Life (ToL relationships. High sequence conservation in the paraphyletic group Plant-Fungi was identified for these two genes using a newly developed Python algorithm. Selective pressure analysis of ALS and BHMT protein sequences showed higher non-synonymous mutation ratios in comparisons between metazoans/fungi and metazoans/plants, supporting the hypothesis that these two genes have undergone non-ToL evolution in animals.

  6. Conserved generation of short products at piRNA loci

    Directory of Open Access Journals (Sweden)

    Khorshid Mohsen

    2011-01-01

    Full Text Available Abstract Background The piRNA pathway operates in animal germ lines to ensure genome integrity through retrotransposon silencing. The Piwi protein-associated small RNAs (piRNAs guide Piwi proteins to retrotransposon transcripts, which are degraded and thereby post-transcriptionally silenced through a ping-pong amplification process. Cleavage of the retrotransposon transcript defines at the same time the 5' end of a secondary piRNA that will in turn guide a Piwi protein to a primary piRNA precursor, thereby amplifying primary piRNAs. Although several studies provided evidence that this mechanism is conserved among metazoa, how the process is initiated and what enzymatic activities are responsible for generating the primary and secondary piRNAs are not entirely clear. Results Here we analyzed small RNAs from three mammalian species, seeking to gain further insight into the mechanisms responsible for the piRNA amplification loop. We found that in all these species piRNA-directed targeting is accompanied by the generation of short sequences that have a very precisely defined length, 19 nucleotides, and a specific spatial relationship with the guide piRNAs. Conclusions This suggests that the processing of the 5' product of piRNA-guided cleavage occurs while the piRNA target is engaged by the Piwi protein. Although they are not stabilized through methylation of their 3' ends, the 19-mers are abundant not only in testes lysates but also in immunoprecipitates of Miwi and Mili proteins. They will enable more accurate identification of piRNA loci in deep sequencing data sets.

  7. Paradoxical DNA repair and peroxide resistance gene conservation in Bacillus pumilus SAFR-032.

    Directory of Open Access Journals (Sweden)

    Jason Gioia

    Full Text Available BACKGROUND: Bacillus spores are notoriously resistant to unfavorable conditions such as UV radiation, gamma-radiation, H2O2, desiccation, chemical disinfection, or starvation. Bacillus pumilus SAFR-032 survives standard decontamination procedures of the Jet Propulsion Lab spacecraft assembly facility, and both spores and vegetative cells of this strain exhibit elevated resistance to UV radiation and H2O2 compared to other Bacillus species. PRINCIPAL FINDINGS: The genome of B. pumilus SAFR-032 was sequenced and annotated. Lists of genes relevant to DNA repair and the oxidative stress response were generated and compared to B. subtilis and B. licheniformis. Differences in conservation of genes, gene order, and protein sequences are highlighted because they potentially explain the extreme resistance phenotype of B. pumilus. The B. pumilus genome includes genes not found in B. subtilis or B. licheniformis and conserved genes with sequence divergence, but paradoxically lacks several genes that function in UV or H2O2 resistance in other Bacillus species. SIGNIFICANCE: This study identifies several candidate genes for further research into UV and H2O2 resistance. These findings will help explain the resistance of B. pumilus and are applicable to understanding sterilization survival strategies of microbes.

  8. Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae

    Science.gov (United States)

    Fauteux, François; Strömvik, Martina V

    2009-01-01

    Background Accurate computational identification of cis-regulatory motifs is difficult, particularly in eukaryotic promoters, which typically contain multiple short and degenerate DNA sequences bound by several interacting factors. Enrichment in combinations of rare motifs in the promoter sequence of functionally or evolutionarily related genes among several species is an indicator of conserved transcriptional regulatory mechanisms. This provides a basis for the computational identification of cis-regulatory motifs. Results We have used a discriminative seeding DNA motif discovery algorithm for an in-depth analysis of 54 seed storage protein (SSP) gene promoters from three plant families, namely Brassicaceae (mustards), Fabaceae (legumes) and Poaceae (grasses) using backgrounds based on complete sets of promoters from a representative species in each family, namely Arabidopsis (Arabidopsis thaliana (L.) Heynh.), soybean (Glycine max (L.) Merr.) and rice (Oryza sativa L.) respectively. We have identified three conserved motifs (two RY-like and one ACGT-like) in Brassicaceae and Fabaceae SSP gene promoters that are similar to experimentally characterized seed-specific cis-regulatory elements. Fabaceae SSP gene promoter sequences are also enriched in a novel, seed-specific E2Fb-like motif. Conserved motifs identified in Poaceae SSP gene promoters include a GCN4-like motif, two prolamin-box-like motifs and an Skn-1-like motif. Evidence of the presence of a variant of the TATA-box is found in the SSP gene promoters from the three plant families. Motifs discovered in SSP gene promoters were used to score whole-genome sets of promoters from Arabidopsis, soybean and rice. The highest-scoring promoters are associated with genes coding for different subunits or precursors of seed storage proteins. Conclusion Seed storage protein gene promoter motifs are conserved in diverse species, and different plant families are characterized by a distinct combination of conserved motifs

  9. Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae

    Directory of Open Access Journals (Sweden)

    Fauteux François

    2009-10-01

    Full Text Available Abstract Background Accurate computational identification of cis-regulatory motifs is difficult, particularly in eukaryotic promoters, which typically contain multiple short and degenerate DNA sequences bound by several interacting factors. Enrichment in combinations of rare motifs in the promoter sequence of functionally or evolutionarily related genes among several species is an indicator of conserved transcriptional regulatory mechanisms. This provides a basis for the computational identification of cis-regulatory motifs. Results We have used a discriminative seeding DNA motif discovery algorithm for an in-depth analysis of 54 seed storage protein (SSP gene promoters from three plant families, namely Brassicaceae (mustards, Fabaceae (legumes and Poaceae (grasses using backgrounds based on complete sets of promoters from a representative species in each family, namely Arabidopsis (Arabidopsis thaliana (L. Heynh., soybean (Glycine max (L. Merr. and rice (Oryza sativa L. respectively. We have identified three conserved motifs (two RY-like and one ACGT-like in Brassicaceae and Fabaceae SSP gene promoters that are similar to experimentally characterized seed-specific cis-regulatory elements. Fabaceae SSP gene promoter sequences are also enriched in a novel, seed-specific E2Fb-like motif. Conserved motifs identified in Poaceae SSP gene promoters include a GCN4-like motif, two prolamin-box-like motifs and an Skn-1-like motif. Evidence of the presence of a variant of the TATA-box is found in the SSP gene promoters from the three plant families. Motifs discovered in SSP gene promoters were used to score whole-genome sets of promoters from Arabidopsis, soybean and rice. The highest-scoring promoters are associated with genes coding for different subunits or precursors of seed storage proteins. Conclusion Seed storage protein gene promoter motifs are conserved in diverse species, and different plant families are characterized by a distinct combination

  10. Evaluation of Conservation Tillage Techniques for Maize Production ...

    African Journals Online (AJOL)

    conservation tillage techniques and evaluate the impacts of the system on ... biological soil manipulation to optimize conditions for seed germination, emergence and ..... planting and weeding operations as total expense and sales from maize ...

  11. Transcriptional dynamics of a conserved gene expression network associated with craniofacial divergence in Arctic charr.

    Science.gov (United States)

    Ahi, Ehsan Pashay; Kapralova, Kalina Hristova; Pálsson, Arnar; Maier, Valerie Helene; Gudbrandsson, Jóhannes; Snorrason, Sigurdur S; Jónsson, Zophonías O; Franzdóttir, Sigrídur Rut

    2014-01-01

    Understanding the molecular basis of craniofacial variation can provide insights into key developmental mechanisms of adaptive changes and their role in trophic divergence and speciation. Arctic charr (Salvelinus alpinus) is a polymorphic fish species, and, in Lake Thingvallavatn in Iceland, four sympatric morphs have evolved distinct craniofacial structures. We conducted a gene expression study on candidates from a conserved gene coexpression network, focusing on the development of craniofacial elements in embryos of two contrasting Arctic charr morphotypes (benthic and limnetic). Four Arctic charr morphs were studied: one limnetic and two benthic morphs from Lake Thingvallavatn and a limnetic reference aquaculture morph. The presence of morphological differences at developmental stages before the onset of feeding was verified by morphometric analysis. Following up on our previous findings that Mmp2 and Sparc were differentially expressed between morphotypes, we identified a network of genes with conserved coexpression across diverse vertebrate species. A comparative expression study of candidates from this network in developing heads of the four Arctic charr morphs verified the coexpression relationship of these genes and revealed distinct transcriptional dynamics strongly correlated with contrasting craniofacial morphologies (benthic versus limnetic). A literature review and Gene Ontology analysis indicated that a significant proportion of the network genes play a role in extracellular matrix organization and skeletogenesis, and motif enrichment analysis of conserved noncoding regions of network candidates predicted a handful of transcription factors, including Ap1 and Ets2, as potential regulators of the gene network. The expression of Ets2 itself was also found to associate with network gene expression. Genes linked to glucocorticoid signalling were also studied, as both Mmp2 and Sparc are responsive to this pathway. Among those, several transcriptional

  12. 78 FR 17648 - Energy Conservation Program for Consumer Products: Representative Average Unit Costs of Energy

    Science.gov (United States)

    2013-03-22

    ... Conservation Program for Consumer Products: Representative Average Unit Costs of Energy'', dated April 26, 2012... DEPARTMENT OF ENERGY Office of Energy Efficiency and Renewable Energy Energy Conservation Program for Consumer Products: Representative Average Unit Costs of Energy AGENCY: Office of Energy Efficiency...

  13. 75 FR 57410 - Energy Conservation Program: Certification, Compliance, and Enforcement for Consumer Products and...

    Science.gov (United States)

    2010-09-21

    ..., regarding the Energy Conservation Program: Certification, Compliance, and Enforcement for Consumer Products... [Docket No. EERE-2010-BT-CE-0014] RIN 1904-AC23 Energy Conservation Program: Certification, Compliance, and Enforcement for Consumer Products and Commercial and Industrial Equipment; Correction AGENCY...

  14. 76 FR 24761 - Energy Conservation Program: Certification, Compliance, and Enforcement for Consumer Products and...

    Science.gov (United States)

    2011-05-02

    ... Conservation Program: Certification, Compliance, and Enforcement for Consumer Products and Commercial and...) Certification. Each manufacturer, before distributing in commerce any basic model of a covered product or.... EERE-2010-BT-CE-0014] RIN 1904-AC23 Energy Conservation Program: Certification, Compliance, and...

  15. 78 FR 65629 - Energy Conservation Program for Consumer Products: Decision and Order Granting a Waiver to...

    Science.gov (United States)

    2013-11-01

    ... representative of consumer behavior. For example, if the number of annual cycles results in greater than a 3-day... Conservation Program for Consumer Products: Decision and Order Granting a Waiver to Whirlpool Corporation From... Conservation Program for Consumer Products Other Than Automobiles, a program covering most major household...

  16. 75 FR 57555 - Energy Conservation Program for Consumer Products: Test Procedure for Residential Clothes Washers

    Science.gov (United States)

    2010-09-21

    ... technologies not covered by the current procedure; (2) more accurately reflect current consumer behavior and... Part II Department of Energy 10 CFR Part 430 Energy Conservation Program for Consumer Products... [Docket No. EERE-2010-BT-TP-0021] RIN 1904-AC08 Energy Conservation Program for Consumer Products: Test...

  17. 75 FR 57556 - Energy Conservation Program for Consumer Products: Test Procedure for Residential Clothes Washers

    Science.gov (United States)

    2010-09-21

    ... technologies not covered by the current procedure; (2) more accurately reflect current consumer behavior and... Part II Department of Energy 10 CFR Part 430 Energy Conservation Program for Consumer Products... [Docket No. EERE-2010-BT-TP-0021] RIN 1904-AC08 Energy Conservation Program for Consumer Products: Test...

  18. Management Approaches to Accomplish Contemporary Livestock Production-Conservation Objectives in Shortgrass Steppe

    Science.gov (United States)

    Traditional rangeland management in the shortgrass steppe has emphasized livestock production with moderate stocking rates, but alternative approaches will be needed to meet production objectives under increasing demands for conservation-oriented management. We investigated the utility of very inten...

  19. Protocols for In Vitro Propagation, Conservation, Synthetic Seed Production, Microrhizome Production, and Molecular Profiling in Turmeric (Curcuma longa L.).

    Science.gov (United States)

    Nirmal Babu, K; Divakaran, Minoo; Pillai, Geetha S; Sumathi, V; Praveen, K; Raj, Rahul P; Akshita, H J; Ravindran, P N; Peter, K V

    2016-01-01

    Turmeric is a rhizomatous herbaceous perennial but cultivated as annual, belonging to the family Zingiberaceae. It is a native of India and South East Asia. The tuberous rhizomes or underground stems of turmeric are used from antiquity as condiments, a dye and as an aromatic stimulant in several medicines. Turmeric is an important crop in India and it is used as a spice, food preservative, coloring agent, cosmetic as well as for its medicinal properties. Propagation is done vegetatively with rhizome bits as seed materials. It is plagued by rhizome rot diseases most of which are mainly spread through infected seed rhizomes. Micropropagation will help in production of disease-free seed. Sexual reproduction is rare in turmeric, making recombinant breeding very difficult. In vitro technology can thus become the preferred choice and it can be utilized for multiplication, conservation of genetic resources, generating variability, gene transfer, molecular tagging, and their utility in crop improvement.

  20. Heterologous Production of an Energy-Conserving Carbon Monoxide Dehydrogenase Complex in the Hyperthermophile Pyrococcus furiosus

    Directory of Open Access Journals (Sweden)

    Gerrit Jan Schut

    2016-01-01

    Full Text Available Carbon monoxide (CO is an important intermediate in anaerobic carbon fixation pathways in acetogenesis and methanogenesis. In addition, some anaerobes can utilize CO as an energy source. In the hyperthermophilic archaeon Thermococcus onnurineus, which grows optimally at 80°C, CO oxidation and energy conservation is accomplished by a respiratory complex encoded by a 16-gene cluster containing a carbon monoxide dehydrogenase, a membrane-bound [NiFe]-hydrogenase and a Na+/H+ antiporter module. This complex oxidizes CO, evolves CO2 and H2, and generates a Na+ motive force that is used to conserve energy by a Na+-dependent ATP synthase. Herein we used a bacterial artificial chromosome to insert the 13.2 kb gene cluster encoding the CO-oxidizing respiratory complex of T. onnurineus into the genome of the heterotrophic archaeon, Pyrococcus furiosus, which grows optimally at 100°C. P. furiosus is normally unable to utilize CO, however, the recombinant strain readily oxidized CO and generated H2 at 80°C. Moreover, CO also served as an energy source and allowed the P. furiosus strain to grow with a limiting concentration of sugar or with peptides as the carbon source. Moreover, CO oxidation by P. furiosus was also coupled to the re-utilization, presumably for biosynthesis, of acetate generated by fermentation. The functional transfer of CO utilization between Thermococcus and Pyrococcus species demonstrated herein is representative of the horizontal gene transfer of an environmentally-relevant metabolic capability. The transfer of CO utilizing, hydrogen-producing genetic modules also has applications for biohydrogen production and a CO-based industrial platform for various thermophilic organisms.

  1. Clusters of conserved beta cell marker genes for assessment of beta cell phenotype

    DEFF Research Database (Denmark)

    Martens, Geert A; Jiang, Lei; Hellemans, Karine H

    2011-01-01

    The aim of this study was to establish a gene expression blueprint of pancreatic beta cells conserved from rodents to humans and to evaluate its applicability to assess shifts in the beta cell differentiated state. Genome-wide mRNA expression profiles of isolated beta cells were compared to those...... of a large panel of other tissue and cell types, and transcripts with beta cell-abundant and -selective expression were identified. Iteration of this analysis in mouse, rat and human tissues generated a panel of conserved beta cell biomarkers. This panel was then used to compare isolated versus laser capture...

  2. Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate Paramecium

    Directory of Open Access Journals (Sweden)

    Lynch Michael

    2010-05-01

    Full Text Available Abstract Background In protozoa, the identification of preserved motifs by comparative genomics is often impeded by difficulties to generate reliable alignments for non-coding sequences. Moreover, the evolutionary dynamics of regulatory elements in 3' untranslated regions (both in protozoa and metazoa remains a virtually unexplored issue. Results By screening Paramecium tetraurelia's 3' untranslated regions for 8-mers that were previously found to be preserved in mammalian 3' UTRs, we detect and characterize a motif that is distinctly conserved in the ribosomal genes of this ciliate. The motif appears to be conserved across Paramecium aurelia species but is absent from the ribosomal genes of four additional non-Paramecium species surveyed, including another ciliate, Tetrahymena thermophila. Motif-free ribosomal genes retain fewer paralogs in the genome and appear to be lost more rapidly relative to motif-containing genes. Features associated with the discovered preserved motif are consistent with this 8-mer playing a role in post-transcriptional regulation. Conclusions Our observations 1 shed light on the evolution of a putative regulatory motif across large phylogenetic distances; 2 are expected to facilitate the understanding of the modulation of ribosomal genes expression in Paramecium; and 3 reveal a largely unexplored--and presumably not restricted to Paramecium--association between the presence/absence of a DNA motif and the evolutionary fate of its host genes.

  3. Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate Paramecium.

    Science.gov (United States)

    Catania, Francesco; Lynch, Michael

    2010-05-04

    In protozoa, the identification of preserved motifs by comparative genomics is often impeded by difficulties to generate reliable alignments for non-coding sequences. Moreover, the evolutionary dynamics of regulatory elements in 3' untranslated regions (both in protozoa and metazoa) remains a virtually unexplored issue. By screening Paramecium tetraurelia's 3' untranslated regions for 8-mers that were previously found to be preserved in mammalian 3' UTRs, we detect and characterize a motif that is distinctly conserved in the ribosomal genes of this ciliate. The motif appears to be conserved across Paramecium aurelia species but is absent from the ribosomal genes of four additional non-Paramecium species surveyed, including another ciliate, Tetrahymena thermophila. Motif-free ribosomal genes retain fewer paralogs in the genome and appear to be lost more rapidly relative to motif-containing genes. Features associated with the discovered preserved motif are consistent with this 8-mer playing a role in post-transcriptional regulation. Our observations 1) shed light on the evolution of a putative regulatory motif across large phylogenetic distances; 2) are expected to facilitate the understanding of the modulation of ribosomal genes expression in Paramecium; and 3) reveal a largely unexplored--and presumably not restricted to Paramecium--association between the presence/absence of a DNA motif and the evolutionary fate of its host genes.

  4. Phylogenetic analysis reveals conservation and diversification of micro RNA166 genes among diverse plant species.

    Science.gov (United States)

    Barik, Suvakanta; SarkarDas, Shabari; Singh, Archita; Gautam, Vibhav; Kumar, Pramod; Majee, Manoj; Sarkar, Ananda K

    2014-01-01

    Similar to the majority of the microRNAs, mature miR166s are derived from multiple members of MIR166 genes (precursors) and regulate various aspects of plant development by negatively regulating their target genes (Class III HD-ZIP). The evolutionary conservation or functional diversification of miRNA166 family members remains elusive. Here, we show the phylogenetic relationships among MIR166 precursor and mature sequences from three diverse model plant species. Despite strong conservation, some mature miR166 sequences, such as ppt-miR166m, have undergone sequence variation. Critical sequence variation in ppt-miR166m has led to functional diversification, as it targets non-HD-ZIPIII gene transcript (s). MIR166 precursor sequences have diverged in a lineage specific manner, and both precursors and mature osa-miR166i/j are highly conserved. Interestingly, polycistronic MIR166s were present in Physcomitrella and Oryza but not in Arabidopsis. The nature of cis-regulatory motifs on the upstream promoter sequences of MIR166 genes indicates their possible contribution to the functional variation observed among miR166 species. Copyright © 2013 Elsevier Inc. All rights reserved.

  5. Conservation, Divergence, and Genome-Wide Distribution of PAL and POX A Gene Families in Plants.

    Science.gov (United States)

    Rawal, H C; Singh, N K; Sharma, T R

    2013-01-01

    Genome-wide identification and phylogenetic and syntenic comparison were performed for the genes responsible for phenylalanine ammonia lyase (PAL) and peroxidase A (POX A) enzymes in nine plant species representing very diverse groups like legumes (Glycine max and Medicago truncatula), fruits (Vitis vinifera), cereals (Sorghum bicolor, Zea mays, and Oryza sativa), trees (Populus trichocarpa), and model dicot (Arabidopsis thaliana) and monocot (Brachypodium distachyon) species. A total of 87 and 1045 genes in PAL and POX A gene families, respectively, have been identified in these species. The phylogenetic and syntenic comparison along with motif distributions shows a high degree of conservation of PAL genes, suggesting that these genes may predate monocot/eudicot divergence. The POX A family genes, present in clusters at the subtelomeric regions of chromosomes, might be evolving and expanding with higher rate than the PAL gene family. Our analysis showed that during the expansion of POX A gene family, many groups and subgroups have evolved, resulting in a high level of functional divergence among monocots and dicots. These results will act as a first step toward the understanding of monocot/eudicot evolution and functional characterization of these gene families in the future.

  6. Conservation, Divergence, and Genome-Wide Distribution of PAL and POX A Gene Families in Plants

    Directory of Open Access Journals (Sweden)

    H. C. Rawal

    2013-01-01

    Full Text Available Genome-wide identification and phylogenetic and syntenic comparison were performed for the genes responsible for phenylalanine ammonia lyase (PAL and peroxidase A (POX A enzymes in nine plant species representing very diverse groups like legumes (Glycine max and Medicago truncatula, fruits (Vitis vinifera, cereals (Sorghum bicolor, Zea mays, and Oryza sativa, trees (Populus trichocarpa, and model dicot (Arabidopsis thaliana and monocot (Brachypodium distachyon species. A total of 87 and 1045 genes in PAL and POX A gene families, respectively, have been identified in these species. The phylogenetic and syntenic comparison along with motif distributions shows a high degree of conservation of PAL genes, suggesting that these genes may predate monocot/eudicot divergence. The POX A family genes, present in clusters at the subtelomeric regions of chromosomes, might be evolving and expanding with higher rate than the PAL gene family. Our analysis showed that during the expansion of POX A gene family, many groups and subgroups have evolved, resulting in a high level of functional divergence among monocots and dicots. These results will act as a first step toward the understanding of monocot/eudicot evolution and functional characterization of these gene families in the future.

  7. Single gene insertion drives bioalcohol production by a thermophilic archaeon

    Energy Technology Data Exchange (ETDEWEB)

    Basen, M; Schut, GJ; Nguyen, DM; Lipscomb, GL; Benn, RA; Prybol, CJ; Vaccaro, BJ; Poole, FL; Kelly, RM; Adams, MWW

    2014-12-09

    Bioethanol production is achieved by only two metabolic pathways and only at moderate temperatures. Herein a fundamentally different synthetic pathway for bioalcohol production at 70 degrees C was constructed by insertion of the gene for bacterial alcohol dehydrogenase (AdhA) into the archaeon Pyrococcus furiosus. The engineered strain converted glucose to ethanol via acetate and acetaldehyde, catalyzed by the host-encoded aldehyde ferredoxin oxidoreductase (AOR) and heterologously expressed AdhA, in an energy-conserving, redox-balanced pathway. Furthermore, the AOR/AdhA pathway also converted exogenously added aliphatic and aromatic carboxylic acids to the corresponding alcohol using glucose, pyruvate, and/or hydrogen as the source of reductant. By heterologous coexpression of a membrane-bound carbon monoxide dehydrogenase, CO was used as a reductant for converting carboxylic acids to alcohols. Redirecting the fermentative metabolism of P. furiosus through strategic insertion of foreign genes creates unprecedented opportunities for thermophilic bioalcohol production. Moreover, the AOR/AdhA pathway is a potentially game-changing strategy for syngas fermentation, especially in combination with carbon chain elongation pathways.

  8. Clusters of conserved beta cell marker genes for assessment of beta cell phenotype

    DEFF Research Database (Denmark)

    Martens, Geert A; Jiang, Lei; Hellemans, Karine H

    2011-01-01

    The aim of this study was to establish a gene expression blueprint of pancreatic beta cells conserved from rodents to humans and to evaluate its applicability to assess shifts in the beta cell differentiated state. Genome-wide mRNA expression profiles of isolated beta cells were compared to those...... of a large panel of other tissue and cell types, and transcripts with beta cell-abundant and -selective expression were identified. Iteration of this analysis in mouse, rat and human tissues generated a panel of conserved beta cell biomarkers. This panel was then used to compare isolated versus laser capture...... microdissected beta cells, monitor adaptations of the beta cell phenotype to fasting, and retrieve possible conserved transcriptional regulators....

  9. Comparative Annotation of Viral Genomes with Non-Conserved Gene Structure

    DEFF Research Database (Denmark)

    de Groot, Saskia; Mailund, Thomas; Hein, Jotun

    2007-01-01

    Motivation: Detecting genes in viral genomes is a complex task. Due to the biological necessity of them being constrained in length, RNA viruses in particular tend to code in overlapping reading frames. Since one amino acid is encoded by a triplet of nucleic acids, up to three genes may be coded...... allows for coding in unidirectional nested and overlapping reading frames, to annotate two homologous aligned viral genomes. Our method does not insist on conserved gene structure between the two sequences, thus making it applicable for the pairwise comparison of more distantly related sequences. Results...... and HIV2, as well as of two different Hepatitis Viruses, attaining results of ~87% sensitivity and ~98.5% specificity. We subsequently incorporate prior knowledge by "knowing" the gene structure of one sequence and annotating the other conditional on it. Boosting accuracy close to perfect we demonstrate...

  10. Conservation

    NARCIS (Netherlands)

    Nooteboom, H.P.

    1987-01-01

    CITES: In February 1987 Singapore finally ratified the Washington Treaty on the international trade in threatened species, exceptions have been made for the trade in crocodile products. A serious breach has now been closed that was of some impediment to the trade between Singapore and many of its

  11. Epstein-Barr Virus BKRF4 Gene Product Is Required for Efficient Progeny Production.

    Science.gov (United States)

    Masud, H M Abdullah Al; Watanabe, Takahiro; Yoshida, Masahiro; Sato, Yoshitaka; Goshima, Fumi; Kimura, Hiroshi; Murata, Takayuki

    2017-12-01

    Epstein-Barr virus (EBV), a member of human gammaherpesvirus, infects mainly B cells. EBV has two alternative life cycles, latent and lytic, and is reactivated occasionally from the latent stage to the lytic cycle. To combat EBV-associated disorders, understanding the molecular mechanisms of the EBV lytic replication cycle is also important. Here, we focused on an EBV lytic gene, BKRF4. Using our anti-BKRF4 antibody, we revealed that the BKRF4 gene product is expressed during the lytic cycle with late kinetics. To characterize the role of BKRF4, we constructed BKRF4-knockout mutants using the bacterial artificial chromosome (BAC) and CRISPR/Cas9 systems. Although disruption of the BKRF4 gene had almost no effect on viral protein expression and DNA synthesis, it significantly decreased progeny virion levels in HEK293 and Akata cells. Furthermore, we show that BKRF4 is involved not only in production of progeny virions but also in increasing the infectivity of the virus particles. Immunoprecipitation assays revealed that BKRF4 interacted with a virion protein, BGLF2. We showed that the C-terminal region of BKRF4 was critical for this interaction and for efficient progeny production. Immunofluorescence analysis revealed that BKRF4 partially colocalized with BGLF2 in the nucleus and perinuclear region. Finally, we showed that BKRF4 is a phosphorylated, possible tegument protein and that the EBV protein kinase BGLF4 may be important for this phosphorylation. Taken together, our data suggest that BKRF4 is involved in the production of infectious virions. IMPORTANCE Although the latent genes of EBV have been studied extensively, the lytic genes are less well characterized. This study focused on one such lytic gene, BKRF4, which is conserved only among gammaherpesviruses (ORF45 of Kaposi's sarcoma-associated herpesvirus or murine herpesvirus 68). After preparing the BKRF4 knockout virus using B95-8 EBV-BAC, we demonstrated that the BKRF4 gene was involved in infectious

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

    Science.gov (United States)

    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.

  13. Conservation of the response regulator gene gacA in Pseudomonas species

    NARCIS (Netherlands)

    Souza, J.T.; Mazzola, M.; Raaijmakers, J.M.

    2003-01-01

    The response regulator gene gacA influences the production of several secondary metabolites in both pathogenic and beneficial Pseudomonas spp. In this study, we developed primers and a probe for the gacA gene of Pseudomonas species and sequenced a 425 bp fragment of gacA from ten Pseudomonas strains

  14. 76 FR 13168 - Energy Conservation Program for Consumer Products: Representative Average Unit Costs of Energy

    Science.gov (United States)

    2011-03-10

    ... average unit costs of residential energy in a Federal Register notice entitled, ``Energy Conservation... DEPARTMENT OF ENERGY Office of Energy Efficiency and Renewable Energy Energy Conservation Program for Consumer Products: Representative Average Unit Costs of Energy AGENCY: Office of Energy Efficiency...

  15. 75 FR 64173 - Energy Conservation Program: Certification, Compliance, and Enforcement for Consumer Products and...

    Science.gov (United States)

    2010-10-19

    ... [Docket No. EERE-2010-BT-CE-0014] RIN 1904-AC23 Energy Conservation Program: Certification, Compliance, and Enforcement for Consumer Products and Commercial and Industrial Equipment AGENCY: Office of Energy... notice of proposed rulemaking, regarding the Energy Conservation Program: Certification, Compliance, and...

  16. 76 FR 16760 - Energy Conservation Program for Consumer Products: Publication of the Petition for Waiver and...

    Science.gov (United States)

    2011-03-25

    ... Conservation Program for Consumer Products: Publication of the Petition for Waiver and Notice of Granting the... Electronics America, Inc. (Samsung) petition for waiver (hereafter, ``petition'') from specified portions of... Authority Title III, part B of the Energy Policy and Conservation Act of 1975 (EPCA), Public Law 94-163 (42...

  17. 76 FR 12825 - Energy Conservation Program for Consumer Products: Test Procedure for Microwave Ovens

    Science.gov (United States)

    2011-03-09

    ... Conservation Program for Consumer Products: Test Procedure for Microwave Ovens AGENCY: Office of Energy.... Department of Energy (DOE) is amending its test procedures for microwave ovens under the Energy Policy and Conservation Act (EPCA) to provide for the measurement of standby mode and off mode power use by microwave...

  18. 75 FR 42612 - Energy Conservation Program for Consumer Products: Test Procedure for Microwave Ovens

    Science.gov (United States)

    2010-07-22

    ... Conservation Program for Consumer Products: Test Procedure for Microwave Ovens AGENCY: Office of Energy... (NOPR) in which DOE proposed test procedures for microwave ovens under the Energy Policy and Conservation Act (EPCA) to measure standby mode and off mode power use by microwave ovens. To address issues...

  19. Knowledge co-production and boundary work to promote implementation of conservation plans.

    Science.gov (United States)

    Nel, Jeanne L; Roux, Dirk J; Driver, Amanda; Hill, Liesl; Maherry, Ashton C; Snaddon, Kate; Petersen, Chantel R; Smith-Adao, Lindie B; Van Deventer, Heidi; Reyers, Belinda

    2016-02-01

    Knowledge co-production and boundary work offer planners a new frame for critically designing a social process that fosters collaborative implementation of resulting plans. Knowledge co-production involves stakeholders from diverse knowledge systems working iteratively toward common vision and action. Boundary work is a means of creating permeable knowledge boundaries that satisfy the needs of multiple social groups while guarding the functional integrity of contributing knowledge systems. Resulting products are boundary objects of mutual interest that maintain coherence across all knowledge boundaries. We examined how knowledge co-production and boundary work can bridge the gap between planning and implementation and promote cross-sectoral cooperation. We applied these concepts to well-established stages in regional conservation planning within a national scale conservation planning project aimed at identifying areas for conserving rivers and wetlands of South Africa and developing an institutional environment for promoting their conservation. Knowledge co-production occurred iteratively over 4 years in interactive stake-holder workshops that included co-development of national freshwater conservation goals and spatial data on freshwater biodiversity and local conservation feasibility; translation of goals into quantitative inputs that were used in Marxan to select draft priority conservation areas; review of draft priority areas; and packaging of resulting map products into an atlas and implementation manual to promote application of the priority area maps in 37 different decision-making contexts. Knowledge co-production stimulated dialogue and negotiation and built capacity for multi-scale implementation beyond the project. The resulting maps and information integrated diverse knowledge types of over 450 stakeholders and represented >1000 years of collective experience. The maps provided a consistent national source of information on priority conservation areas

  20. Functional conservation of the Drosophila gooseberry gene and its evolutionary alleles.

    Directory of Open Access Journals (Sweden)

    Wei Liu

    Full Text Available The Drosophila Pax gene gooseberry (gsb is required for development of the larval cuticle and CNS, survival to adulthood, and male fertility. These functions can be rescued in gsb mutants by two gsb evolutionary alleles, gsb-Prd and gsb-Pax3, which express the Drosophila Paired and mouse Pax3 proteins under the control of gooseberry cis-regulatory region. Therefore, both Paired and Pax3 proteins have conserved all the Gsb functions that are required for survival of embryos to fertile adults, despite the divergent primary sequences in their C-terminal halves. As gsb-Prd and gsb-Pax3 uncover a gsb function involved in male fertility, construction of evolutionary alleles may provide a powerful strategy to dissect hitherto unknown gene functions. Our results provide further evidence for the essential role of cis-regulatory regions in the functional diversification of duplicated genes during evolution.

  1. Energy conservation and dust production in wet rotary cement kilns

    Energy Technology Data Exchange (ETDEWEB)

    Sell, N J; Fischbach, F A

    1976-12-01

    Energy conservation is currently a major concern of the cement industry. A comparison of data supplied by the U.S. Federal Energy Administration with that gathered in an extensive private study incorporating 29 wet cement plants indicates that a significant reduction of the energy consumed can be accomplished by decreasing the amount of dust generated in the process. Energy saving of 8 percent through dust suppression appears possible by increasing the slurry moisture and by using hammermills rather than impactors as the crushing technique.

  2. Evolutionary conservation of essential and highly expressed genes in Pseudomonas aeruginosa

    Directory of Open Access Journals (Sweden)

    Scharfe Maren

    2010-04-01

    Full Text Available Abstract Background The constant increase in development and spread of bacterial resistance to antibiotics poses a serious threat to human health. New sequencing technologies are now on the horizon that will yield massive increases in our capacity for DNA sequencing and will revolutionize the drug discovery process. Since essential genes are promising novel antibiotic targets, the prediction of gene essentiality based on genomic information has become a major focus. Results In this study we demonstrate that pooled sequencing is applicable for the analysis of sequence variations of strain collections with more than 10 individual isolates. Pooled sequencing of 36 clinical Pseudomonas aeruginosa isolates revealed that essential and highly expressed proteins evolve at lower rates, whereas extracellular proteins evolve at higher rates. We furthermore refined the list of experimentally essential P. aeruginosa genes, and identified 980 genes that show no sequence variation at all. Among the conserved nonessential genes we found several that are involved in regulation, motility and virulence, indicating that they represent factors of evolutionary importance for the lifestyle of a successful environmental bacterium and opportunistic pathogen. Conclusion The detailed analysis of a comprehensive set of P. aeruginosa genomes in this study clearly disclosed detailed information of the genomic makeup and revealed a large set of highly conserved genes that play an important role for the lifestyle of this microorganism. Sequencing strain collections enables for a detailed and extensive identification of sequence variations as potential bacterial adaptation processes, e.g., during the development of antibiotic resistance in the clinical setting and thus may be the basis to uncover putative targets for novel treatment strategies.

  3. Fanconi anemia core complex gene promoters harbor conserved transcription regulatory elements.

    Science.gov (United States)

    Meier, Daniel; Schindler, Detlev

    2011-01-01

    The Fanconi anemia (FA) gene family is a recent addition to the complex network of proteins that respond to and repair certain types of DNA damage in the human genome. Since little is known about the regulation of this novel group of genes at the DNA level, we characterized the promoters of the eight genes (FANCA, B, C, E, F, G, L and M) that compose the FA core complex. The promoters of these genes show the characteristic attributes of housekeeping genes, such as a high GC content and CpG islands, a lack of TATA boxes and a low conservation. The promoters functioned in a monodirectional way and were, in their most active regions, comparable in strength to the SV40 promoter in our reporter plasmids. They were also marked by a distinctive transcriptional start site (TSS). In the 5' region of each promoter, we identified a region that was able to negatively regulate the promoter activity in HeLa and HEK 293 cells in isolation. The central and 3' regions of the promoter sequences harbor binding sites for several common and rare transcription factors, including STAT, SMAD, E2F, AP1 and YY1, which indicates that there may be cross-connections to several established regulatory pathways. Electrophoretic mobility shift assays and siRNA experiments confirmed the shared regulatory responses between the prominent members of the TGF-β and JAK/STAT pathways and members of the FA core complex. Although the promoters are not well conserved, they share region and sequence specific regulatory motifs and transcription factor binding sites (TBFs), and we identified a bi-partite nature to these promoters. These results support a hypothesis based on the co-evolution of the FA core complex genes that was expanded to include their promoters.

  4. Fanconi anemia core complex gene promoters harbor conserved transcription regulatory elements.

    Directory of Open Access Journals (Sweden)

    Daniel Meier

    Full Text Available The Fanconi anemia (FA gene family is a recent addition to the complex network of proteins that respond to and repair certain types of DNA damage in the human genome. Since little is known about the regulation of this novel group of genes at the DNA level, we characterized the promoters of the eight genes (FANCA, B, C, E, F, G, L and M that compose the FA core complex. The promoters of these genes show the characteristic attributes of housekeeping genes, such as a high GC content and CpG islands, a lack of TATA boxes and a low conservation. The promoters functioned in a monodirectional way and were, in their most active regions, comparable in strength to the SV40 promoter in our reporter plasmids. They were also marked by a distinctive transcriptional start site (TSS. In the 5' region of each promoter, we identified a region that was able to negatively regulate the promoter activity in HeLa and HEK 293 cells in isolation. The central and 3' regions of the promoter sequences harbor binding sites for several common and rare transcription factors, including STAT, SMAD, E2F, AP1 and YY1, which indicates that there may be cross-connections to several established regulatory pathways. Electrophoretic mobility shift assays and siRNA experiments confirmed the shared regulatory responses between the prominent members of the TGF-β and JAK/STAT pathways and members of the FA core complex. Although the promoters are not well conserved, they share region and sequence specific regulatory motifs and transcription factor binding sites (TBFs, and we identified a bi-partite nature to these promoters. These results support a hypothesis based on the co-evolution of the FA core complex genes that was expanded to include their promoters.

  5. 75 FR 61361 - Energy Conservation Program: Certification, Compliance, and Enforcement for Consumer Products and...

    Science.gov (United States)

    2010-10-05

    .... EERE-2010-BT-CE-0014] RIN 1904-AC24 Energy Conservation Program: Certification, Compliance, and Enforcement for Consumer Products and Commercial and Industrial Equipment Correction In proposed rule document...

  6. 76 FR 21881 - Energy Conservation Program for Consumer Products: Notice of Petition for Waiver of Samsung...

    Science.gov (United States)

    2011-04-19

    ... Conservation Program for Consumer Products: Notice of Petition for Waiver of Samsung Electronics America, Inc... comments. SUMMARY: This notice announces receipt of and publishes the Samsung Electronics America, Inc. (Samsung) petition for waiver and application for [[Page 21882

  7. Blueprint for a minimal photoautotrophic cell: conserved and variable genes in Synechococcus elongatus PCC 7942

    Directory of Open Access Journals (Sweden)

    Peretó Juli

    2011-01-01

    Full Text Available Abstract Background Simpler biological systems should be easier to understand and to engineer towards pre-defined goals. One way to achieve biological simplicity is through genome minimization. Here we looked for genomic islands in the fresh water cyanobacteria Synechococcus elongatus PCC 7942 (genome size 2.7 Mb that could be used as targets for deletion. We also looked for conserved genes that might be essential for cell survival. Results By using a combination of methods we identified 170 xenologs, 136 ORFans and 1401 core genes in the genome of S. elongatus PCC 7942. These represent 6.5%, 5.2% and 53.6% of the annotated genes respectively. We considered that genes in genomic islands could be found if they showed a combination of: a unusual G+C content; b unusual phylogenetic similarity; and/or c a small number of the highly iterated palindrome 1 (HIP1 motif plus an unusual codon usage. The origin of the largest genomic island by horizontal gene transfer (HGT could be corroborated by lack of coverage among metagenomic sequences from a fresh water microbialite. Evidence is also presented that xenologous genes tend to cluster in operons. Interestingly, most genes coding for proteins with a diguanylate cyclase domain are predicted to be xenologs, suggesting a role for horizontal gene transfer in the evolution of Synechococcus sensory systems. Conclusions Our estimates of genomic islands in PCC 7942 are larger than those predicted by other published methods like SIGI-HMM. Our results set a guide to non-essential genes in S. elongatus PCC 7942 indicating a path towards the engineering of a model photoautotrophic bacterial cell.

  8. Differential evolution of members of the rhomboid gene family with conservative and divergent patterns.

    Science.gov (United States)

    Li, Qi; Zhang, Ning; Zhang, Liangsheng; Ma, Hong

    2015-04-01

    Rhomboid proteins are intramembrane serine proteases that are involved in a plethora of biological functions, but the evolutionary history of the rhomboid gene family is not clear. We performed a comprehensive molecular evolutionary analysis of the rhomboid gene family and also investigated the organization and sequence features of plant rhomboids in different subfamilies. Our results showed that eukaryotic rhomboids could be divided into five subfamilies (RhoA-RhoD and PARL). Most orthology groups appeared to be conserved only as single or low-copy genes in all lineages in RhoB-RhoD and PARL, whereas RhoA genes underwent several duplication events, resulting in multiple gene copies. These duplication events were due to whole genome duplications in plants and animals and the duplicates might have experienced functional divergence. We also identified a novel group of plant rhomboid (RhoB1) that might have lost their enzymatic activity; their existence suggests that they might have evolved new mechanisms. Plant and animal rhomboids have similar evolutionary patterns. In addition, there are mutations affecting key active sites in RBL8, RBL9 and one of the Brassicaceae PARL duplicates. This study delineates a possible evolutionary scheme for intramembrane proteins and illustrates distinct fates and a mechanism of evolution of gene duplicates. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

  9. Remarkable sequence conservation of the last intron in the PKD1 gene.

    Science.gov (United States)

    Rodova, Marianna; Islam, M Rafiq; Peterson, Kenneth R; Calvet, James P

    2003-10-01

    The last intron of the PKD1 gene (intron 45) was found to have exceptionally high sequence conservation across four mammalian species: human, mouse, rat, and dog. This conservation did not extend to the comparable intron in pufferfish. Pairwise comparisons for intron 45 showed 91% identity (human vs. dog) to 100% identity (mouse vs. rat) for an average for all four species of 94% identity. In contrast, introns 43 and 44 of the PKD1 gene had average pairwise identities of 57% and 54%, and exons 43, 44, and 45 and the coding region of exon 46 had average pairwise identities of 80%, 84%, 82%, and 80%. Intron 45 is 90 to 95 bp in length, with the major region of sequence divergence being in a central 4-bp to 9-bp variable region. RNA secondary structure analysis of intron 45 predicts a branching stem-loop structure in which the central variable region lies in one loop and the putative branch point sequence lies in another loop, suggesting that the intron adopts a specific stem-loop structure that may be important for its removal. Although intron 45 appears to conform to the class of small, G-triplet-containing introns that are spliced by a mechanism utilizing intron definition, its high sequence conservation may be a reflection of constraints imposed by a unique mechanism that coordinates splicing of this last PKD1 intron with polyadenylation.

  10. Guide to resource conservation and cost savings opportunities in the soap, detergents and related products sector

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-03-01

    The soaps, detergents and related products sector is an important component of the chemical industry within Ontario, as these products are used for cleaning purposes in industrial, institutional and domestic consumer applications. This guide was prepared to assist the sector with cost savings and resource conservation. The guide highlights opportunities for resource conservation through energy and water efficiency improvements, more efficient utilisation of raw materials, and reduction of environmental releases at source. 54 figs.

  11. [Identification of new conserved and variable regions in the 16S rRNA gene of acetic acid bacteria and acetobacteraceae family].

    Science.gov (United States)

    Chakravorty, S; Sarkar, S; Gachhui, R

    2015-01-01

    The Acetobacteraceae family of the class Alpha Proteobacteria is comprised of high sugar and acid tolerant bacteria. The Acetic Acid Bacteria are the economically most significant group of this family because of its association with food products like vinegar, wine etc. Acetobacteraceae are often hard to culture in laboratory conditions and they also maintain very low abundances in their natural habitats. Thus identification of the organisms in such environments is greatly dependent on modern tools of molecular biology which require a thorough knowledge of specific conserved gene sequences that may act as primers and or probes. Moreover unconserved domains in genes also become markers for differentiating closely related genera. In bacteria, the 16S rRNA gene is an ideal candidate for such conserved and variable domains. In order to study the conserved and variable domains of the 16S rRNA gene of Acetic Acid Bacteria and the Acetobacteraceae family, sequences from publicly available databases were aligned and compared. Near complete sequences of the gene were also obtained from Kombucha tea biofilm, a known Acetobacteraceae family habitat, in order to corroborate the domains obtained from the alignment studies. The study indicated that the degree of conservation in the gene is significantly higher among the Acetic Acid Bacteria than the whole Acetobacteraceae family. Moreover it was also observed that the previously described hypervariable regions V1, V3, V5, V6 and V7 were more or less conserved in the family and the spans of the variable regions are quite distinct as well.

  12. 78 FR 77019 - Energy Conservation Program: Energy Conservation Standards for Certain Consumer Products

    Science.gov (United States)

    2013-12-20

    ... air conditioning heat pump'' that were established in section 5 of the American Energy Manufacturing... heat pump'' product class, including the definition and standards. DATES: DOE will accept comments....gov . Table of Contents I. Background and Authority II. Discussion III. Procedural Requirements A...

  13. 75 FR 1121 - Energy Conservation Program: Energy Conservation Standards for Certain Consumer Products...

    Science.gov (United States)

    2010-01-08

    ..., multi-family housing, and on-premises laundry applications led DOE to conduct a sensitivity analysis for... commercial laundry practices likely differ from residential practices,\\5\\ DOE concluded in the October 2008..., and service; (b) adverse impacts on product utility or availability; or (c) adverse impacts on health...

  14. TOPAZ1, a novel germ cell-specific expressed gene conserved during evolution across vertebrates.

    Directory of Open Access Journals (Sweden)

    Adrienne Baillet

    Full Text Available BACKGROUND: We had previously reported that the Suppression Subtractive Hybridization (SSH approach was relevant for the isolation of new mammalian genes involved in oogenesis and early follicle development. Some of these transcripts might be potential new oocyte and granulosa cell markers. We have now characterized one of them, named TOPAZ1 for the Testis and Ovary-specific PAZ domain gene. PRINCIPAL FINDINGS: Sheep and mouse TOPAZ1 mRNA have 4,803 bp and 4,962 bp open reading frames (20 exons, respectively, and encode putative TOPAZ1 proteins containing 1,600 and 1653 amino acids. They possess PAZ and CCCH domains. In sheep, TOPAZ1 mRNA is preferentially expressed in females during fetal life with a peak during prophase I of meiosis, and in males during adulthood. In the mouse, Topaz1 is a germ cell-specific gene. TOPAZ1 protein is highly conserved in vertebrates and specifically expressed in mouse and sheep gonads. It is localized in the cytoplasm of germ cells from the sheep fetal ovary and mouse adult testis. CONCLUSIONS: We have identified a novel PAZ-domain protein that is abundantly expressed in the gonads during germ cell meiosis. The expression pattern of TOPAZ1, and its high degree of conservation, suggests that it may play an important role in germ cell development. Further characterization of TOPAZ1 may elucidate the mechanisms involved in gametogenesis, and particularly in the RNA silencing process in the germ line.

  15. Gene expression in chicken reveals correlation with structural genomic features and conserved patterns of transcription in the terrestrial vertebrates.

    Directory of Open Access Journals (Sweden)

    Haisheng Nie

    Full Text Available BACKGROUND: The chicken is an important agricultural and avian-model species. A survey of gene expression in a range of different tissues will provide a benchmark for understanding expression levels under normal physiological conditions in birds. With expression data for birds being very scant, this benchmark is of particular interest for comparative expression analysis among various terrestrial vertebrates. METHODOLOGY/PRINCIPAL FINDINGS: We carried out a gene expression survey in eight major chicken tissues using whole genome microarrays. A global picture of gene expression is presented for the eight tissues, and tissue specific as well as common gene expression were identified. A Gene Ontology (GO term enrichment analysis showed that tissue-specific genes are enriched with GO terms reflecting the physiological functions of the specific tissue, and housekeeping genes are enriched with GO terms related to essential biological functions. Comparisons of structural genomic features between tissue-specific genes and housekeeping genes show that housekeeping genes are more compact. Specifically, coding sequence and particularly introns are shorter than genes that display more variation in expression between tissues, and in addition intergenic space was also shorter. Meanwhile, housekeeping genes are more likely to co-localize with other abundantly or highly expressed genes on the same chromosomal regions. Furthermore, comparisons of gene expression in a panel of five common tissues between birds, mammals and amphibians showed that the expression patterns across tissues are highly similar for orthologous genes compared to random gene pairs within each pair-wise comparison, indicating a high degree of functional conservation in gene expression among terrestrial vertebrates. CONCLUSIONS: The housekeeping genes identified in this study have shorter gene length, shorter coding sequence length, shorter introns, and shorter intergenic regions, there seems

  16. Comparative genomics of Mycoplasma: analysis of conserved essential genes and diversity of the pan-genome.

    Directory of Open Access Journals (Sweden)

    Wei Liu

    Full Text Available Mycoplasma, the smallest self-replicating organism with a minimal metabolism and little genomic redundancy, is expected to be a close approximation to the minimal set of genes needed to sustain bacterial life. This study employs comparative evolutionary analysis of twenty Mycoplasma genomes to gain an improved understanding of essential genes. By analyzing the core genome of mycoplasmas, we finally revealed the conserved essential genes set for mycoplasma survival. Further analysis showed that the core genome set has many characteristics in common with experimentally identified essential genes. Several key genes, which are related to DNA replication and repair and can be disrupted in transposon mutagenesis studies, may be critical for bacteria survival especially over long period natural selection. Phylogenomic reconstructions based on 3,355 homologous groups allowed robust estimation of phylogenetic relatedness among mycoplasma strains. To obtain deeper insight into the relative roles of molecular evolution in pathogen adaptation to their hosts, we also analyzed the positive selection pressures on particular sites and lineages. There appears to be an approximate correlation between the divergence of species and the level of positive selection detected in corresponding lineages.

  17. Conserved syntenic clusters of protein coding genes are missing in birds.

    Science.gov (United States)

    Lovell, Peter V; Wirthlin, Morgan; Wilhelm, Larry; Minx, Patrick; Lazar, Nathan H; Carbone, Lucia; Warren, Wesley C; Mello, Claudio V

    2014-01-01

    Birds are one of the most highly successful and diverse groups of vertebrates, having evolved a number of distinct characteristics, including feathers and wings, a sturdy lightweight skeleton and unique respiratory and urinary/excretion systems. However, the genetic basis of these traits is poorly understood. Using comparative genomics based on extensive searches of 60 avian genomes, we have found that birds lack approximately 274 protein coding genes that are present in the genomes of most vertebrate lineages and are for the most part organized in conserved syntenic clusters in non-avian sauropsids and in humans. These genes are located in regions associated with chromosomal rearrangements, and are largely present in crocodiles, suggesting that their loss occurred subsequent to the split of dinosaurs/birds from crocodilians. Many of these genes are associated with lethality in rodents, human genetic disorders, or biological functions targeting various tissues. Functional enrichment analysis combined with orthogroup analysis and paralog searches revealed enrichments that were shared by non-avian species, present only in birds, or shared between all species. Together these results provide a clearer definition of the genetic background of extant birds, extend the findings of previous studies on missing avian genes, and provide clues about molecular events that shaped avian evolution. They also have implications for fields that largely benefit from avian studies, including development, immune system, oncogenesis, and brain function and cognition. With regards to the missing genes, birds can be considered ‘natural knockouts’ that may become invaluable model organisms for several human diseases.

  18. Conservation of gene cassettes among diverse viruses of the human gut.

    Directory of Open Access Journals (Sweden)

    Samuel Minot

    Full Text Available Viruses are a crucial component of the human microbiome, but large population sizes, high sequence diversity, and high frequencies of novel genes have hindered genomic analysis by high-throughput sequencing. Here we investigate approaches to metagenomic assembly to probe genome structure in a sample of 5.6 Gb of gut viral DNA sequence from six individuals. Tests showed that a new pipeline based on DeBruijn graph assembly yielded longer contigs that were able to recruit more reads than the equivalent non-optimized, single-pass approach. To characterize gene content, the database of viral RefSeq proteins was compared to the assembled viral contigs, generating a bipartite graph with functional cassettes linking together viral contigs, which revealed a high degree of connectivity between diverse genomes involving multiple genes of the same functional class. In a second step, open reading frames were grouped by their co-occurrence on contigs in a database-independent manner, revealing conserved cassettes of co-oriented ORFs. These methods reveal that free-living bacteriophages, while usually dissimilar at the nucleotide level, often have significant similarity at the level of encoded amino acid motifs, gene order, and gene orientation. These findings thus connect contemporary metagenomic analysis with classical studies of bacteriophage genomic cassettes. Software is available at https://sourceforge.net/projects/optitdba/.

  19. Harmonizing Biodiversity Conservation and Productivity in the Context of Increasing Demands on Landscapes

    Science.gov (United States)

    Seppelt, Ralf; Beckmann, Michael; Ceauşu, Silvia; Cord, Anna F.; Gerstner, Katharina; Gurevitch, Jessica; Kambach, Stephan; Klotz, Stefan; Mendenhall, Chase; Phillips, Helen R. P.; Powell, Kristin; Verburg, Peter H.; Verhagen, Willem; Winter, Marten; Newbold, Tim

    2016-01-01

    Abstract Biodiversity conservation and agricultural production are often seen as mutually exclusive objectives. Strategies for reconciling them are intensely debated. We argue that harmonization between biodiversity conservation and crop production can be improved by increasing our understanding of the underlying relationships between them. We provide a general conceptual framework that links biodiversity and agricultural production through the separate relationships between land use and biodiversity and between land use and production. Hypothesized relationships are derived by synthesizing existing empirical and theoretical ecological knowledge. The framework suggests nonlinear relationships caused by the multifaceted impacts of land use (composition, configuration, and intensity). We propose solutions for overcoming the apparently dichotomous aims of maximizing either biodiversity conservation or agricultural production and suggest new hypotheses that emerge from our proposed framework. PMID:29599534

  20. Erva-mate production and conservation of Araucaria Forest

    Directory of Open Access Journals (Sweden)

    Pablo Signor

    2015-09-01

    Full Text Available This study aims to characterize a native production area (native erval through silvicultural procedures, productivity and density of Ilex paraguariensis St.-Hil. (erva-mate and also the floristic, phytosociology, and diameter structure. To identify the silvicultural procedures, we used semi-structured interviews. For productivity assessment, the commercial biomass of I. paraguariensis was determined. For vegetation assessment, two permanent sample plots totaling 1.25 ha were installed, considering all individuals with circumference at 1.30 m above soil level (CBH ≥ 31.4 cm, for which it was registered CBH, botanical identification, XY coordinates in the plot, and all the individuals of I. paraguariensis composing the production system. Silvicultural procedures were characterized by mowing, canopy opening and conduct of natural regeneration, promoting I. paraguariensis, Araucaria angustifolia (Bert. Kuntze, and cattle. I. paraguariensis density was 634 trees.ha-1, with 2,030 kg.ha-1 of productivity in three-year crops. We found 22 species, with a predominance of Myrtaceae and Aquifoliaceae. The species of highest importance value and coverage was A. angustifolia. The diameter distribution showed a higher concentration of individuals in the smaller classes.

  1. Unusual conservation of mitochondrial gene order in Crassostrea oysters: evidence for recent speciation in Asia

    Science.gov (United States)

    2010-01-01

    Background Oysters are morphologically plastic and hence difficult subjects for taxonomic and evolutionary studies. It is long been suspected, based on the extraordinary species diversity observed, that Asia Pacific is the epicenter of oyster speciation. To understand the species diversity and its evolutionary history, we collected five Crassostrea species from Asia and sequenced their complete mitochondrial (mt) genomes in addition to two newly released Asian oysters (C. iredalei and Saccostrea mordax) for a comprehensive analysis. Results The six Asian Crassostrea mt genomes ranged from 18,226 to 22,446 bp in size, and all coded for 39 genes (12 proteins, 2 rRNAs and 25 tRNAs) on the same strand. Their genomes contained a split of the rrnL gene and duplication of trnM, trnK and trnQ genes. They shared the same gene order that differed from an Atlantic sister species by as many as nine tRNA changes (6 transpositions and 3 duplications) and even differed significantly from S. mordax in protein-coding genes. Phylogenetic analysis indicates that the six Asian Crassostrea species emerged between 3 and 43 Myr ago, while the Atlantic species evolved 83 Myr ago. Conclusions The complete conservation of gene order in the six Asian Crassostrea species over 43 Myr is highly unusual given the remarkable rate of rearrangements in their sister species and other bivalves. It provides strong evidence for the recent speciation of the six Crassostrea species in Asia. It further indicates that changes in mt gene order may not be strictly a function of time but subject to other constraints that are presently not well understood. PMID:21189147

  2. On conservation of renewable resources with stock-dependent return and non-concave production

    International Nuclear Information System (INIS)

    Olson, Lars J.; Roy, Santanu

    1994-05-01

    An analysis is presented of the intertemporal choice foundations underlying the conservation or extinction of renewable resources when the resource production function is non-concave and the immediate return function depends on both current consumption and the size of the resource stock. This case may exhibit nonlinear dynamics and extinction is possible from high stocks even if conservation occurs from lower stocks. The paper focusses on the influence of preferences and the production function on the efficiency of: global conservation, the existence of a safe standard of conservation, or extinction. We show that conservation is efficient under weaker conditions than the 'δ-productivity' requirements derived in models where return function is not stock-dependent. The marginal rate of substitution between investment and the stock plays an important role in addition to the discount factor and the marginal productivity of the resource. Extinction need not be optimal even if the intrinsic growth rate of the resource is less than the external rate of return. Our analysis demonstrates the potential role of taxes, subsidies, demand forces, and harvest costs in determining the efficiency of conservation or extinction. 3 figs., 1 appendix, 24 refs

  3. On conservation of renewable resources with stock-dependent return and non-concave production

    Energy Technology Data Exchange (ETDEWEB)

    Olson, Lars J. [Department of Agricultural and Resource Economics, University of Maryland, College Park, MD (United States); Roy, Santanu [Econometric Institute, Erasmus University, Rotterdam (Netherlands)

    1994-05-01

    An analysis is presented of the intertemporal choice foundations underlying the conservation or extinction of renewable resources when the resource production function is non-concave and the immediate return function depends on both current consumption and the size of the resource stock. This case may exhibit nonlinear dynamics and extinction is possible from high stocks even if conservation occurs from lower stocks. The paper focusses on the influence of preferences and the production function on the efficiency of: global conservation, the existence of a safe standard of conservation, or extinction. We show that conservation is efficient under weaker conditions than the `{delta}-productivity` requirements derived in models where return function is not stock-dependent. The marginal rate of substitution between investment and the stock plays an important role in addition to the discount factor and the marginal productivity of the resource. Extinction need not be optimal even if the intrinsic growth rate of the resource is less than the external rate of return. Our analysis demonstrates the potential role of taxes, subsidies, demand forces, and harvest costs in determining the efficiency of conservation or extinction. 3 figs., 1 appendix, 24 refs.

  4. Will intensification of beef production deliver conservation outcomes in the Brazilian Amazon?

    Directory of Open Access Journals (Sweden)

    Frank Merry

    2017-05-01

    Full Text Available The intensification of beef production has become a conservation target based on the idea of land sparing and the assumption that in order to contain deforestation and meet increasing beef demand we must increase productivity. There is also increasing attention and conservation credit being given to supply chain management in beef production. Based on a historical comparison between the US, a fully intensive system, and Brazil, one moving in that direction, we suggest that cattle ranching will intensify as a result of conservation investments (reductions in capital and land subsidies rather than intensifying in order to produce conservation results. If the comparison holds, the new intensive system, however, will continue to require large natural resource inputs, government subsidies, and be plagued by social and conservation problems. It will also be held in thrall by a few large processing companies, which exert undue influence over both producers and consumers. Therefore, we suggest that closer attention be paid to attribution in the claim of conservation outcomes from intensive beef production.

  5. Comparisons of Copy Number, Genomic Structure, and Conserved Motifs for α-Amylase Genes from Barley, Rice, and Wheat

    Directory of Open Access Journals (Sweden)

    Qisen Zhang

    2017-10-01

    Full Text Available Barley is an important crop for the production of malt and beer. However, crops such as rice and wheat are rarely used for malting. α-amylase is the key enzyme that degrades starch during malting. In this study, we compared the genomic properties, gene copies, and conserved promoter motifs of α-amylase genes in barley, rice, and wheat. In all three crops, α-amylase consists of four subfamilies designated amy1, amy2, amy3, and amy4. In wheat and barley, members of amy1 and amy2 genes are localized on chromosomes 6 and 7, respectively. In rice, members of amy1 genes are found on chromosomes 1 and 2, and amy2 genes on chromosome 6. The barley genome has six amy1 members and three amy2 members. The wheat B genome contains four amy1 members and three amy2 members, while the rice genome has three amy1 members and one amy2 member. The B genome has mostly amy1 and amy2 members among the three wheat genomes. Amy1 promoters from all three crop genomes contain a GA-responsive complex consisting of a GA-responsive element (CAATAAA, pyrimidine box (CCTTTT and TATCCAT/C box. This study has shown that amy1 and amy2 from both wheat and barley have similar genomic properties, including exon/intron structures and GA-responsive elements on promoters, but these differ in rice. Like barley, wheat should have sufficient amy activity to degrade starch completely during malting. Other factors, such as high protein with haze issues and the lack of husk causing Lauting difficulty, may limit the use of wheat for brewing.

  6. EST analysis in Ginkgo biloba: an assessment of conserved developmental regulators and gymnosperm specific genes

    Directory of Open Access Journals (Sweden)

    Runko Suzan J

    2005-10-01

    Full Text Available Abstract Background Ginkgo biloba L. is the only surviving member of one of the oldest living seed plant groups with medicinal, spiritual and horticultural importance worldwide. As an evolutionary relic, it displays many characters found in the early, extinct seed plants and extant cycads. To establish a molecular base to understand the evolution of seeds and pollen, we created a cDNA library and EST dataset from the reproductive structures of male (microsporangiate, female (megasporangiate, and vegetative organs (leaves of Ginkgo biloba. Results RNA from newly emerged male and female reproductive organs and immature leaves was used to create three distinct cDNA libraries from which 6,434 ESTs were generated. These 6,434 ESTs from Ginkgo biloba were clustered into 3,830 unigenes. A comparison of our Ginkgo unigene set against the fully annotated genomes of rice and Arabidopsis, and all available ESTs in Genbank revealed that 256 Ginkgo unigenes match only genes among the gymnosperms and non-seed plants – many with multiple matches to genes in non-angiosperm plants. Conversely, another group of unigenes in Gingko had highly significant homology to transcription factors in angiosperms involved in development, including MADS box genes as well as post-transcriptional regulators. Several of the conserved developmental genes found in Ginkgo had top BLAST homology to cycad genes. We also note here the presence of ESTs in G. biloba similar to genes that to date have only been found in gymnosperms and an additional 22 Ginkgo genes common only to genes from cycads. Conclusion Our analysis of an EST dataset from G. biloba revealed genes potentially unique to gymnosperms. Many of these genes showed homology to fully sequenced clones from our cycad EST dataset found in common only with gymnosperms. Other Ginkgo ESTs are similar to developmental regulators in higher plants. This work sets the stage for future studies on Ginkgo to better understand seed and

  7. Designing Conservation Corridors in Production Landscapes: Assessment Methods, Implementation Issues, and Lessons Learned

    Directory of Open Access Journals (Sweden)

    Amanda T. Lombard

    2010-09-01

    Full Text Available Designing broad-scale conservation corridors has become increasingly common as a way of conducting an assessment for achieving targets for the representation and persistence of nature. However, since many of these corridors must traverse agricultural and other production landscapes, planning and implementation are not trivial tasks. Most approaches to conservation assessments in the dynamic world of production landscapes are data-intensive and analytically complex. However, in the real world, donor and other external requirements impose time and budget constraints, and dictate strong stakeholder involvement in the entire planning process. In order to accommodate this, assessments must be rapid, cheap, and the approach and products must be comprehensible and acceptable to stakeholders. Here we describe such an assessment aimed at identifying and implementing a network of conservation corridors in the Gouritz Initiative project domain of South Africa's Cape Floristic Region hotspot. We used empirical data and expert knowledge to identify a corridor network hypothesized to sustain key ecological and evolutionary processes. We also consulted experts to provide a spatially explicit assessment of the opportunity costs of conservation associated with agriculture, the predominant land use in the region. We used these products to identify categories of land requiring different actions and instruments to achieve conservation goals, thereby moving from the "where" to the "how" of conservation. This information was then fed into the collaborative strategy development process for the Gouritz Initiative. Our discussion emphasizes the lessons that we learnt from undertaking this assessment, particularly lessons regarding the implementation of the planning products. We conclude that at the outset of any planning project, a consensus on the vision must be achieved, a detailed social assessment of appropriate institutions must be undertaken, and a learning

  8. Department of Energy programs and objectives: energy conservation in agricultural production

    Energy Technology Data Exchange (ETDEWEB)

    1977-12-01

    This document describes the current Department of Energy agriculture research program as it relates to the research recommendations submitted by a 1976 workshop on energy conservation in agricultural production. In-depth discussions on fertilizers, irrigation, crop drying, fuel substitution, crop and animal production systems, greenhouses, materials handling, and transport systems are included. (MCW)

  9. 76 FR 21813 - Energy Conservation Program: Certification, Compliance, and Enforcement for Consumer Products and...

    Science.gov (United States)

    2011-04-19

    ..., as set forth below: PART 429--CERTIFICATION, COMPLIANCE, AND ENFORCEMENT FOR CONSUMER PRODUCTS AND...: EERE-2010-BT-CE-0014] RIN 1904-AC23 Energy Conservation Program: Certification, Compliance, and Enforcement for Consumer Products and Commercial and Industrial Equipment AGENCY: Office of Energy Efficiency...

  10. 77 FR 74559 - Energy Conservation Program for Consumer Products: Test Procedures for Residential Water Heaters...

    Science.gov (United States)

    2012-12-17

    ... Conservation Program for Consumer Products: Test Procedures for Residential Water Heaters, Direct Heating... Energy (DOE) is amending its test procedures for residential water heaters, direct heating equipment (DHE... necessary for residential water heaters, because the existing test procedures for those products already...

  11. 76 FR 19902 - Energy Conservation Program for Consumer Products: Decision and Order Granting 180-Day Extension...

    Science.gov (United States)

    2011-04-11

    ... Furnace Company; (16) New Yorker Residential Heating Boilers; (17) Nordyne; (18) NY Thermal Inc.; (19... Products LLC; (24) Trane; (25) Triangle Tube; (26) US Boiler Company; and (27) Weil-McLain. In the same... Conservation Program for Consumer Products: Decision and Order Granting 180-Day Extension of Compliance Date...

  12. Maximal conservation and minimal usage of blood products in open heart surgery.

    Science.gov (United States)

    Newland, P E; Pastoriza-Pinol, J; McMillan, J; Smith, B F; Stirling, G R

    1980-05-01

    Open heart surgery has previously been associated with the use of large volumes of blood products. This paper describes methods of blood conservation and a simple method of intraoperative autotransfusion that together have resulted in minimal blood product usage in elective open heart surgery cases. This has reduced our dependence on blood bank supplies for the performance of elective open heart surgery.

  13. 75 FR 62127 - Energy Conservation Program for Consumer Products: Decision and Order Granting a Waiver to...

    Science.gov (United States)

    2010-10-07

    ... requirements for covered consumer products when (1) the petitioner's basic model for which the petition for... petition, discussed below. Whirlpool claims that water softeners can prevent consumer behaviors that... Conservation Program for Consumer Products: Decision and Order Granting a Waiver to Whirlpool Corporation From...

  14. Differential conservation and divergence of fertility genes boule and dazl in the rainbow trout.

    Directory of Open Access Journals (Sweden)

    Mingyou Li

    Full Text Available BACKGROUND: The genes boule and dazl are members of the DAZ (Deleted in Azoospermia family encoding RNA binding proteins essential for germ cell development. Although dazl exhibits bisexual expression in mitotic and meiotic germ cells in diverse animals, boule shows unisexual meiotic expression in invertebrates and mammals but a bisexual mitotic and meiotic expression in medaka. How boule and dazl have evolved different expression patterns in diverse organisms has remained unknown. METHODOLOGY AND PRINCIPAL FINDINGS: Here we chose the fish rainbow trout (Oncorhynchus mykiss as a second lower vertebrate model to investigate the expression of boule and dazl. By molecular cloning and sequence comparison, we identified cDNAs encoding the trout Boule and Dazl proteins, which have a conserved RNA-recognition motif and a maximal similarity to their homologs. By RT-PCR analysis, adult RNA expression of trout boule and dazl is restricted to the gonads of both sexes. By chromogenic and two-color fluorescence in situ hybridization, we revealed bisexual and germline-specific expression of boule and dazl. We found that dazl displays conserved expression throughout gametogenesis and concentrates in the Balbinani's body of early oocytes and the chromatoid body of sperm. Surprisingly, boule exhibits mitotic and meiotic expression in the male but meiosis-specific expression in the female. CONCLUSIONS: Our data underscores differential conservation and divergence of DAZ family genes during vertebrate evolution. We propose a model in which the diversity of boule expression in sex and stage specificity might have resulted from selective loss or gain of its expression in one sex and mitotic germ cells.

  15. Genes of the most conserved WOX clade in plants affect root and flower development in Arabidopsis

    Directory of Open Access Journals (Sweden)

    Moreau Hervé

    2008-10-01

    Full Text Available Abstract Background The Wuschel related homeobox (WOX family proteins are key regulators implicated in the determination of cell fate in plants by preventing cell differentiation. A recent WOX phylogeny, based on WOX homeodomains, showed that all of the Physcomitrella patens and Selaginella moellendorffii WOX proteins clustered into a single orthologous group. We hypothesized that members of this group might preferentially share a significant part of their function in phylogenetically distant organisms. Hence, we first validated the limits of the WOX13 orthologous group (WOX13 OG using the occurrence of other clade specific signatures and conserved intron insertion sites. Secondly, a functional analysis using expression data and mutants was undertaken. Results The WOX13 OG contained the most conserved plant WOX proteins including the only WOX detected in the highly proliferating basal unicellular and photosynthetic organism Ostreococcus tauri. A large expansion of the WOX family was observed after the separation of mosses from other land plants and before monocots and dicots have arisen. In Arabidopsis thaliana, AtWOX13 was dynamically expressed during primary and lateral root initiation and development, in gynoecium and during embryo development. AtWOX13 appeared to affect the floral transition. An intriguing clade, represented by the functional AtWOX14 gene inside the WOX13 OG, was only found in the Brassicaceae. Compared to AtWOX13, the gene expression profile of AtWOX14 was restricted to the early stages of lateral root formation and specific to developing anthers. A mutational insertion upstream of the AtWOX14 homeodomain sequence led to abnormal root development, a delay in the floral transition and premature anther differentiation. Conclusion Our data provide evidence in favor of the WOX13 OG as the clade containing the most conserved WOX genes and established a functional link to organ initiation and development in Arabidopsis, most

  16. The Aspergillus flavus Homeobox Gene, hbx1, Is Required for Development and Aflatoxin Production

    Directory of Open Access Journals (Sweden)

    Jeffrey W. Cary

    2017-10-01

    Full Text Available Homeobox proteins, a class of well conserved transcription factors, regulate the expression of targeted genes, especially those involved in development. In filamentous fungi, homeobox genes are required for normal conidiogenesis and fruiting body formation. In the present study, we identified eight homeobox (hbx genes in the aflatoxin-producing ascomycete, Aspergillus flavus, and determined their respective role in growth, conidiation and sclerotial production. Disruption of seven of the eight genes had little to no effect on fungal growth and development. However, disruption of the homeobox gene AFLA_069100, designated as hbx1, in two morphologically different A. flavus strains, CA14 and AF70, resulted in complete loss of production of conidia and sclerotia as well as aflatoxins B1 and B2, cyclopiazonic acid and aflatrem. Microscopic examination showed that the Δhbx1 mutants did not produce conidiophores. The inability of Δhbx1 mutants to produce conidia was related to downregulation of brlA (bristle and abaA (abacus, regulatory genes for conidiophore development. These mutants also had significant downregulation of the aflatoxin pathway biosynthetic genes aflC, aflD, aflM and the cluster-specific regulatory gene, aflR. Our results demonstrate that hbx1 not only plays a significant role in controlling A. flavus development but is also critical for the production of secondary metabolites, such as aflatoxins.

  17. Setulang forest conservation strategy in safeguarding the conservation of non-timber forest products in Malinau District

    Science.gov (United States)

    Hutauruk, T. R.; Lahjie, A. M.; Simarangkir, B. D. A. S.; Aipassa, M. I.; Ruslim, Y.

    2018-04-01

    Some research on human relationships with forests shows that human activities for the forests are sufficient to meet demand or to meet demand. Both will directly or indirectly change the perceptions of the people who exploit them against the forests being utilized. Setulang community one of the community groups that intensively utilize NTFP as one of the source of fulfillment and fulfill the demand of handicraft product. For needs and demand of livelihood the people of Setulang choose to make the existing forest in the Tane Olen area into. The analysis method used in this research with Stength Weakness Opportunity and Threat (SWOT). The results of this study show the extent to which the commitment of Setulang community and the conservation efforts of Setulang community both self-help and donor assistance and the local government, as well as what strategic steps can be taken by the stakeholders to conserve so that the village forest can provide benefits in the short or long term. Strategic measures need to be set up save Setulang State Forest from degradation and deforestation occurring around the village.

  18. Conservation of the Duchenne muscular dystrophy gene in mice and humans

    Energy Technology Data Exchange (ETDEWEB)

    Hoffman, E.P.; Monaco, A.P.; Feener, C.C.; Kunkel, L.M.

    1987-10-16

    A portion of the Duchenne muscular dystrophy (DMD) gene transcript from human fetal skeletal muscle and mouse adult heart was sequence, representing approximately 25 percent of the total, 14-kb DMD transcript. The nucleic acid and predicted amino acid sequences from the two species are nearly 90 percent homologous. The amino acid sequence that is predicted from this portion of the DMD gene indicates that the protein product might serve a structural role in muscle, but the abundance and tissue distribution of the messenger RNA suggest that the DMD protein is not nebulin.

  19. Revealing gene action for production characteristics by inbreeding ...

    African Journals Online (AJOL)

    Revealing gene action for production characteristics by inbreeding, based on a long-term selection ... The gene action involved in the expression of production characters was investigated, using the effect of the theoretical inbreeding ..... and predicted selection responses for growth, fat and lean traits in mice. J. Anim. Sci.

  20. Duplication of the IGFBP-2 gene in teleost fish: protein structure and functionality conservation and gene expression divergence.

    Directory of Open Access Journals (Sweden)

    Jianfeng Zhou

    Full Text Available BACKGROUND: Insulin-like growth factor binding protein-2 (IGFBP-2 is a secreted protein that binds and regulates IGF actions in controlling growth, development, reproduction, and aging. Elevated expression of IGFBP-2 is often associated with progression of many types of cancers. METHODOLOGY/PRINCIPAL FINDINGS: We report the identification and characterization of two IGFBP-2 genes in zebrafish and four other teleost fish. Comparative genomics and structural analyses suggest that they are co-orthologs of the human IGFBP-2 gene. Biochemical assays show that both zebrafish igfbp-2a and -2b encode secreted proteins that bind IGFs. These two genes exhibit distinct spatiotemporal expression patterns. During embryogenesis, IGFBP-2a mRNA is initially detected in the lens, then in the brain boundary vasculature, and subsequently becomes highly expressed in the liver. In the adult stage, liver has the highest levels of IGFBP-2a mRNA, followed by the brain. Low levels of IGFBP-2a mRNA were detected in muscle and in the gonad in male adults only. IGFBP-2b mRNA is detected initially in all tissues at low levels, but later becomes abundant in the liver. In adult males, IGFBP-2b mRNA is only detected in the liver. In adult females, it is also found in the gut, kidney, ovary, and muscle. To gain insights into how the IGFBP-2 genes may have evolved through partitioning of ancestral functions, functional and mechanistic studies were carried out. Expression of zebrafish IGFBP-2a and -2b caused significant decreases in the growth and developmental rates and their effects are comparable to that of human IGFBP-2. IGFBP-2 mutants with altered IGF binding-, RGD-, and heparin-binding sites were generated and their actions examined. While mutating the RGD and heparin binding sites had little effect, altering the IGF binding site abolished its biological activity. CONCLUSIONS/SIGNIFICANCE: These results suggest that IGFBP-2 is a conserved regulatory protein and it inhibits

  1. LEVERAGING RURAL LIVELIHOODS WITH FOREST CONSERVATION IN NIGERIA: THE ROLE OF NON-TIMBER FOREST PRODUCTS

    Directory of Open Access Journals (Sweden)

    Egbe BASSEY ETOWA

    2015-03-01

    Full Text Available In recent times some economists view Non-Timber Forest Products (NTFPs extraction and marketing as a better alternative to timber exploitation as a rural livelihood strategy. Harvesting and sale of NTFPs have the potential for accomplishing the dual goals of natural forest conservation and income generation for the rural inhabitants. Meanwhile, realization of these dual goals in Nigeria, require an understanding of how NTFPs functions in the face of marketing, ecological, geographic and institutional constraints. Following a conceptualization of NTFPs, this paper provides a vivid overview of the simultaneous roles of NTFPs in rural livelihood enhancement and forest conservation in Nigeria. It highlights governmental initiatives with respect to conservation, the challenges and prospects of NTFPs as a conservation strategy. Conclusively, the paper suggests that appropriate NTFPs development policies are required to simultaneously address forest depletion and poverty in rural areas of Nigeria.

  2. Integrating Ontological Knowledge and Textual Evidence in Estimating Gene and Gene Product Similarity

    Energy Technology Data Exchange (ETDEWEB)

    Sanfilippo, Antonio P.; Posse, Christian; Gopalan, Banu; Tratz, Stephen C.; Gregory, Michelle L.

    2006-06-08

    With the rising influence of the Gene On-tology, new approaches have emerged where the similarity between genes or gene products is obtained by comparing Gene Ontology code annotations associ-ated with them. So far, these approaches have solely relied on the knowledge en-coded in the Gene Ontology and the gene annotations associated with the Gene On-tology database. The goal of this paper is to demonstrate that improvements to these approaches can be obtained by integrating textual evidence extracted from relevant biomedical literature.

  3. Correlating Information Contents of Gene Ontology Terms to Infer Semantic Similarity of Gene Products

    Directory of Open Access Journals (Sweden)

    Mingxin Gan

    2014-01-01

    Full Text Available Successful applications of the gene ontology to the inference of functional relationships between gene products in recent years have raised the need for computational methods to automatically calculate semantic similarity between gene products based on semantic similarity of gene ontology terms. Nevertheless, existing methods, though having been widely used in a variety of applications, may significantly overestimate semantic similarity between genes that are actually not functionally related, thereby yielding misleading results in applications. To overcome this limitation, we propose to represent a gene product as a vector that is composed of information contents of gene ontology terms annotated for the gene product, and we suggest calculating similarity between two gene products as the relatedness of their corresponding vectors using three measures: Pearson’s correlation coefficient, cosine similarity, and the Jaccard index. We focus on the biological process domain of the gene ontology and annotations of yeast proteins to study the effectiveness of the proposed measures. Results show that semantic similarity scores calculated using the proposed measures are more consistent with known biological knowledge than those derived using a list of existing methods, suggesting the effectiveness of our method in characterizing functional relationships between gene products.

  4. Single-copy genes define a conserved order between rice and wheat for understanding differences caused by duplication, deletion, and transposition of genes.

    Science.gov (United States)

    Singh, Nagendra K; Dalal, Vivek; Batra, Kamlesh; Singh, Binay K; Chitra, G; Singh, Archana; Ghazi, Irfan A; Yadav, Mahavir; Pandit, Awadhesh; Dixit, Rekha; Singh, Pradeep K; Singh, Harvinder; Koundal, Kirpa R; Gaikwad, Kishor; Mohapatra, Trilochan; Sharma, Tilak R

    2007-01-01

    The high-quality rice genome sequence is serving as a reference for comparative genome analysis in crop plants, especially cereals. However, early comparisons with bread wheat showed complex patterns of conserved synteny (gene content) and colinearity (gene order). Here, we show the presence of ancient duplicated segments in the progenitor of wheat, which were first identified in the rice genome. We also show that single-copy (SC) rice genes, those representing unique matches with wheat expressed sequence tag (EST) unigene contigs in the whole rice genome, show more than twice the proportion of genes mapping to syntenic wheat chromosome as compared to the multicopy (MC) or duplicated rice genes. While 58.7% of the 1,244 mapped SC rice genes were located in single syntenic wheat chromosome groups, the remaining 41.3% were distributed randomly to the other six non-syntenic wheat groups. This could only be explained by a background dispersal of genes in the genome through transposition or other unknown mechanism. The breakdown of rice-wheat synteny due to such transpositions was much greater near the wheat centromeres. Furthermore, the SC rice genes revealed a conserved primordial gene order that gives clues to the origin of rice and wheat chromosomes from a common ancestor through polyploidy, aneuploidy, centromeric fusions, and translocations. Apart from the bin-mapped wheat EST contigs, we also compared 56,298 predicted rice genes with 39,813 wheat EST contigs assembled from 409,765 EST sequences and identified 7,241 SC rice gene homologs of wheat. Based on the conserved colinearity of 1,063 mapped SC rice genes across the bins of individual wheat chromosomes, we predicted the wheat bin location of 6,178 unmapped SC rice gene homologs and validated the location of 213 of these in the telomeric bins of 21 wheat chromosomes with 35.4% initial success. This opens up the possibility of directed mapping of a large number of conserved SC rice gene homologs in wheat

  5. Low Energy Technology. A Unit of Instruction on Energy Conservation in Field Crop Production.

    Science.gov (United States)

    Davis, George; Scanlon, Dennis C.

    This unit of instruction on energy conservation in field crop production was designed for use by agribusiness and natural resources teachers in Florida high schools and by agricultural extension agents as they work with adults and students. It is one of a series of 11 instructional units (see note) written to help teachers and agents to educate…

  6. Natural Fostering in Fritillaria cirrhosa: Integrating herbal medicine production with biodiversity conservation

    Directory of Open Access Journals (Sweden)

    Xiwen Li

    2012-02-01

    Full Text Available Protected areas are generally regarded as a power tool to conserve biodiversity. Nonetheless, few protected areas could address three crucial problems simultaneously, namely funding, public participation and rural living. Here, we introduced a new protective approach, Natural Fostering, which integrated herbal medicine production with community conservation. The principles of Natural Fostering adopted species–species interaction at community level. Most effective chemical components of herbal medicine are derived from such interaction. Fritillaria cirrhosa was selected as an economic botany, one of herbal medicines, to carry out Natural Fostering. Community habitats, herbal medicine production, funding and income of local family were investigated to verify the feasibility of Natural Fostering for biodiversity. We found the density of plant populations and the annual average personal income of rural people increased. F. cirrhosa production could provide sufficient funds for sustainable conservation. Local people gradually changed their life style of wild collection and overgrazing, instead of herbal medicine production. The fostering area set up a good sustainable economic cycle. Natural Fostering can be presented as an effective and pragmatic way to conserve biological diversity and sustainable utilization of traditional medicinal resources.

  7. 76 FR 46202 - Energy Conservation Program: Certification, Compliance, and Enforcement for Consumer Products and...

    Science.gov (United States)

    2011-08-02

    ... DEPARTMENT OF ENERGY 10 CFR Parts 429 and 430 [Docket No. EERE-2010-BT-CE-0014] RIN 1904-AC23 Energy Conservation Program: Certification, Compliance, and Enforcement for Consumer Products and Commercial and Industrial Equipment; Correction Correction In rule document 2011-10401 appearing on pages...

  8. 76 FR 56347 - Energy Conservation Program for Consumer Products: Test Procedures for Residential Water Heaters...

    Science.gov (United States)

    2011-09-13

    ... Conservation Program for Consumer Products: Test Procedures for Residential Water Heaters, Direct Heating... proposed to amend, where appropriate, its test procedures for residential water heaters, direct heating... notes that the test procedure and metric for residential water heaters currently address and incorporate...

  9. 77 FR 38743 - Energy Efficiency Program for Consumer Products: Energy Conservation Standards for Battery...

    Science.gov (United States)

    2012-06-29

    ... Efficiency Program for Consumer Products: Energy Conservation Standards for Battery Chargers and External Power Supplies AGENCY: Office of Energy Efficiency and Renewable Energy, Department of Energy. ACTION... Energy Efficiency and Renewable Energy, Building Technologies Program, EE-2J, 1000 Independence Avenue SW...

  10. 78 FR 9631 - Energy Efficiency Program for Consumer Products: Energy Conservation Standards for Residential...

    Science.gov (United States)

    2013-02-11

    ... Efficiency Program for Consumer Products: Energy Conservation Standards for Residential Boilers AGENCY: Office of Energy Efficiency and Renewable Energy, Department of Energy. ACTION: Notice of public meeting.... Department of Energy, Office of Energy Efficiency and Renewable Energy, Building Technologies Program, EE-2J...

  11. 77 FR 35299 - Energy Conservation Program for Consumer Products and Certain Commercial and Industrial Equipment...

    Science.gov (United States)

    2012-06-13

    ... Conservation Program for Consumer Products Other Than Automobiles,\\2\\ a program covering most major household... polluting than sources that must be used during peak demand times. The utilities indicated that a survey... customarily treated as confidential within the industry; (3) whether the information is generally known by or...

  12. 75 FR 19959 - Energy Conservation Program for Consumer Products: Notice of Petition for Waiver of Samsung...

    Science.gov (United States)

    2010-04-16

    ... Conservation Program for Consumer Products: Notice of Petition for Waiver of Samsung Electronics America, Inc.... SUMMARY: This notice announces receipt of and publishes the Samsung Electronics America, Inc. (Samsung... refrigerator-freezers to additional Samsung basic models. Through this document, DOE also solicits comments...

  13. 75 FR 13120 - Energy Conservation Program for Consumer Products: Decision and Order Granting a Waiver to...

    Science.gov (United States)

    2010-03-18

    ... Conservation Program for Consumer Products: Decision and Order Granting a Waiver to Samsung Electronics America... (Case No. RF-011) that grants to Samsung Electronics America, Inc. (Samsung) a waiver from the DOE... humidity sensors and adaptive control anti-sweat heaters. Under today's decision and order, Samsung shall...

  14. 75 FR 57937 - Energy Conservation Program for Consumer Products: Notice of Petition for Waiver of Samsung...

    Science.gov (United States)

    2010-09-23

    ... Conservation Program for Consumer Products: Notice of Petition for Waiver of Samsung Electronics America, Inc... announces receipt of and publishes the Samsung Electronics America, Inc. (Samsung) petition for waiver... clothes washer test procedure. Through this notice, DOE also solicits comments with respect to the Samsung...

  15. 75 FR 45623 - Energy Conservation Program for Consumer Products: Decision and Order Granting a Waiver to...

    Science.gov (United States)

    2010-08-03

    ... Conservation Program for Consumer Products: Decision and Order Granting a Waiver to Samsung Electronics America...-014) that grants to Samsung Electronics America, Inc. (Samsung) a waiver from the DOE electric... decision and order, Samsung shall be required to test and rate these refrigerator- freezers equipped with...

  16. Conservation, spillover and gene flow within a network of Northern European marine protected areas.

    Directory of Open Access Journals (Sweden)

    Mats Brockstedt Olsen Huserbråten

    Full Text Available To ensure that marine protected areas (MPAs benefit conservation and fisheries, the effectiveness of MPA designs has to be evaluated in field studies. Using an interdisciplinary approach, we empirically assessed the design of a network of northern MPAs where fishing for European lobster (Homarusgammarus is prohibited. First, we demonstrate a high level of residency and survival (50% for almost a year (363 days within MPAs, despite small MPA sizes (0.5-1 km(2. Second, we demonstrate limited export (4.7% of lobsters tagged within MPAs (N = 1810 to neighbouring fished areas, over a median distance of 1.6 km out to maximum 21 km away from MPA centres. In comparison, median movement distance of lobsters recaptured within MPAs was 164 m, and recapture rate was high (40%. Third, we demonstrate a high level of gene flow within the study region, with an estimated F ST of less than 0.0001 over a ≈ 400 km coastline. Thus, the restricted movement of older life stages, combined with a high level of gene flow suggests that connectivity is primarily driven by larval drift. Larval export from the MPAs can most likely affect areas far beyond their borders. Our findings are of high importance for the design of MPA networks for sedentary species with pelagic early life stages.

  17. An evolutionarily conserved gene family encodes proton-selective ion channels.

    Science.gov (United States)

    Tu, Yu-Hsiang; Cooper, Alexander J; Teng, Bochuan; Chang, Rui B; Artiga, Daniel J; Turner, Heather N; Mulhall, Eric M; Ye, Wenlei; Smith, Andrew D; Liman, Emily R

    2018-03-02

    Ion channels form the basis for cellular electrical signaling. Despite the scores of genetically identified ion channels selective for other monatomic ions, only one type of proton-selective ion channel has been found in eukaryotic cells. By comparative transcriptome analysis of mouse taste receptor cells, we identified Otopetrin1 (OTOP1), a protein required for development of gravity-sensing otoconia in the vestibular system, as forming a proton-selective ion channel. We found that murine OTOP1 is enriched in acid-detecting taste receptor cells and is required for their zinc-sensitive proton conductance. Two related murine genes, Otop2 and Otop3 , and a Drosophila ortholog also encode proton channels. Evolutionary conservation of the gene family and its widespread tissue distribution suggest a broad role for proton channels in physiology and pathophysiology. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  18. Approaches to gene pool conservation of medicinal plant Oxytropis lanata (Pall. DC. (Fabaceae

    Directory of Open Access Journals (Sweden)

    A. B. Kholina

    2015-05-01

    Full Text Available In order to preserve the gene pool of medicinal plant Oxytropis lanata (Pall. DC. we analyzed allozyme polymorphism and identified reliable and informative marker enzyme systems of this species; also we studied the response of seeds to deep freezing in liquid nitrogen (–196 ºС. Population has an average level of polymorphism (P95 = 41,2 %, P99 = 52,9 %, A = 1,58, Ho = 0,158, He = 0,171 in general typical for herbaceous legumes, and can serve as a source of material for gene pool conservation of the species. Deep freezing has not led to the death of the seeds; it was marked stimulatory effect of ultralow temperatures, expressed as an acceleration of germination and sharp increase of germinability (98,6 ± 2,3 % compared to the control (12,0 ± 3,5 % that is associated with overcoming physical dormancy. There were no abnormalities in the development of seedlings from seeds passed cryopreservation.

  19. Violation of energy–momentum conservation in Mueller–Navelet jets production

    Energy Technology Data Exchange (ETDEWEB)

    Ducloué, B. [LPT, Université Paris-Sud, CNRS, 91405, Orsay (France); Szymanowski, L. [National Centre for Nuclear Research (NCBJ), Warsaw (Poland); Wallon, S., E-mail: wallon@th.u-psud.fr [LPT, Université Paris-Sud, CNRS, 91405, Orsay (France); UPMC Univ. Paris 06, Faculté de Physique, 4 place Jussieu, 75252 Paris Cedex 05 (France)

    2014-11-10

    We study effects related to violation of energy–momentum conservation inherent to the BFKL approach, in the particular case of Mueller–Navelet jets production. We argue, based on the comparison of the lowest order non-trivial corrections O(α{sub s}{sup 3}) to the cross section with predictions of an exact calculation, that the inclusion of next-to-leading order BFKL corrections to the jet production vertex significantly reduces the importance of these effects.

  20. Violation of energy–momentum conservation in Mueller–Navelet jets production

    International Nuclear Information System (INIS)

    Ducloué, B.; Szymanowski, L.; Wallon, S.

    2014-01-01

    We study effects related to violation of energy–momentum conservation inherent to the BFKL approach, in the particular case of Mueller–Navelet jets production. We argue, based on the comparison of the lowest order non-trivial corrections O(α s 3 ) to the cross section with predictions of an exact calculation, that the inclusion of next-to-leading order BFKL corrections to the jet production vertex significantly reduces the importance of these effects

  1. Comprehensive analysis of coding-lncRNA gene co-expression network uncovers conserved functional lncRNAs in zebrafish.

    Science.gov (United States)

    Chen, Wen; Zhang, Xuan; Li, Jing; Huang, Shulan; Xiang, Shuanglin; Hu, Xiang; Liu, Changning

    2018-05-09

    Zebrafish is a full-developed model system for studying development processes and human disease. Recent studies of deep sequencing had discovered a large number of long non-coding RNAs (lncRNAs) in zebrafish. However, only few of them had been functionally characterized. Therefore, how to take advantage of the mature zebrafish system to deeply investigate the lncRNAs' function and conservation is really intriguing. We systematically collected and analyzed a series of zebrafish RNA-seq data, then combined them with resources from known database and literatures. As a result, we obtained by far the most complete dataset of zebrafish lncRNAs, containing 13,604 lncRNA genes (21,128 transcripts) in total. Based on that, a co-expression network upon zebrafish coding and lncRNA genes was constructed and analyzed, and used to predict the Gene Ontology (GO) and the KEGG annotation of lncRNA. Meanwhile, we made a conservation analysis on zebrafish lncRNA, identifying 1828 conserved zebrafish lncRNA genes (1890 transcripts) that have their putative mammalian orthologs. We also found that zebrafish lncRNAs play important roles in regulation of the development and function of nervous system; these conserved lncRNAs present a significant sequential and functional conservation, with their mammalian counterparts. By integrative data analysis and construction of coding-lncRNA gene co-expression network, we gained the most comprehensive dataset of zebrafish lncRNAs up to present, as well as their systematic annotations and comprehensive analyses on function and conservation. Our study provides a reliable zebrafish-based platform to deeply explore lncRNA function and mechanism, as well as the lncRNA commonality between zebrafish and human.

  2. The importance of immune gene variability (MHC in evolutionary ecology and conservation

    Directory of Open Access Journals (Sweden)

    Sommer Simone

    2005-10-01

    Full Text Available Abstract Genetic studies have typically inferred the effects of human impact by documenting patterns of genetic differentiation and levels of genetic diversity among potentially isolated populations using selective neutral markers such as mitochondrial control region sequences, microsatellites or single nucleotide polymorphism (SNPs. However, evolutionary relevant and adaptive processes within and between populations can only be reflected by coding genes. In vertebrates, growing evidence suggests that genetic diversity is particularly important at the level of the major histocompatibility complex (MHC. MHC variants influence many important biological traits, including immune recognition, susceptibility to infectious and autoimmune diseases, individual odours, mating preferences, kin recognition, cooperation and pregnancy outcome. These diverse functions and characteristics place genes of the MHC among the best candidates for studies of mechanisms and significance of molecular adaptation in vertebrates. MHC variability is believed to be maintained by pathogen-driven selection, mediated either through heterozygote advantage or frequency-dependent selection. Up to now, most of our knowledge has derived from studies in humans or from model organisms under experimental, laboratory conditions. Empirical support for selective mechanisms in free-ranging animal populations in their natural environment is rare. In this review, I first introduce general information about the structure and function of MHC genes, as well as current hypotheses and concepts concerning the role of selection in the maintenance of MHC polymorphism. The evolutionary forces acting on the genetic diversity in coding and non-coding markers are compared. Then, I summarise empirical support for the functional importance of MHC variability in parasite resistance with emphasis on the evidence derived from free-ranging animal populations investigated in their natural habitat. Finally, I

  3. Conserved repertoire of orthologous vomeronasal type 1 receptor genes in ruminant species

    Directory of Open Access Journals (Sweden)

    Okamura Hiroaki

    2009-09-01

    Full Text Available Abstract Background In mammals, pheromones play an important role in social and innate reproductive behavior within species. In rodents, vomeronasal receptor type 1 (V1R, which is specifically expressed in the vomeronasal organ, is thought to detect pheromones. The V1R gene repertoire differs dramatically between mammalian species, and the presence of species-specific V1R subfamilies in mouse and rat suggests that V1R plays a profound role in species-specific recognition of pheromones. In ruminants, however, the molecular mechanism(s for pheromone perception is not well understood. Interestingly, goat male pheromone, which can induce out-of-season ovulation in anestrous females, causes the same pheromone response in sheep, and vice versa, suggesting that there may be mechanisms for detecting "inter-species" pheromones among ruminant species. Results We isolated 23 goat and 21 sheep intact V1R genes based on sequence similarity with 32 cow V1R genes in the cow genome database. We found that all of the goat and sheep V1R genes have orthologs in their cross-species counterparts among these three ruminant species and that the sequence identity of V1R orthologous pairs among these ruminants is much higher than that of mouse-rat V1R orthologous pairs. Furthermore, all goat V1Rs examined thus far are expressed not only in the vomeronasal organ but also in the main olfactory epithelium. Conclusion Our results suggest that, compared with rodents, the repertoire of orthologous V1R genes is remarkably conserved among the ruminants cow, sheep and goat. We predict that these orthologous V1Rs can detect the same or closely related chemical compound(s within each orthologous set/pair. Furthermore, all identified goat V1Rs are expressed in the vomeronasal organ and the main olfactory epithelium, suggesting that V1R-mediated ligand information can be detected and processed by both the main and accessory olfactory systems. The fact that ruminant and rodent V1Rs

  4. Short-range order and local conservation of quantum numbers in multiparticle production

    International Nuclear Information System (INIS)

    Le Bellac, M.

    1976-01-01

    These lectures discuss the implications of the hypotheses of short-range order (SRO) and local conservation of quantum numbers (LCQN) for multiple production of elementary particles at high energies. The consequences of SRO for semi-inclusive correlations and the distribution of rapidity gaps are derived, essentially in the framework of the cluster model. Then the experimental status of local conservation of charge and transverse momentum is reviewed. Finally, by making use of the unitarity relation, it is shown that LCQN has important consequences for the elastic amplitude. The derivation is given both in a model-independent way, and in specific multiperiheral models. (Author)

  5. Enhancing Conservation with High Resolution Productivity Datasets for the Conterminous United States

    Science.gov (United States)

    Robinson, Nathaniel Paul

    Human driven alteration of the earth's terrestrial surface is accelerating through land use changes, intensification of human activity, climate change, and other anthropogenic pressures. These changes occur at broad spatio-temporal scales, challenging our ability to effectively monitor and assess the impacts and subsequent conservation strategies. While satellite remote sensing (SRS) products enable monitoring of the earth's terrestrial surface continuously across space and time, the practical applications for conservation and management of these products are limited. Often the processes driving ecological change occur at fine spatial resolutions and are undetectable given the resolution of available datasets. Additionally, the links between SRS data and ecologically meaningful metrics are weak. Recent advances in cloud computing technology along with the growing record of high resolution SRS data enable the development of SRS products that quantify ecologically meaningful variables at relevant scales applicable for conservation and management. The focus of my dissertation is to improve the applicability of terrestrial gross and net primary productivity (GPP/NPP) datasets for the conterminous United States (CONUS). In chapter one, I develop a framework for creating high resolution datasets of vegetation dynamics. I use the entire archive of Landsat 5, 7, and 8 surface reflectance data and a novel gap filling approach to create spatially continuous 30 m, 16-day composites of the normalized difference vegetation index (NDVI) from 1986 to 2016. In chapter two, I integrate this with other high resolution datasets and the MOD17 algorithm to create the first high resolution GPP and NPP datasets for CONUS. I demonstrate the applicability of these products for conservation and management, showing the improvements beyond currently available products. In chapter three, I utilize this dataset to evaluate the relationships between land ownership and terrestrial production

  6. Characterization, expression profiles, intracellular distribution and association analysis of porcine PNAS-4 gene with production traits

    Directory of Open Access Journals (Sweden)

    Wang Heng

    2008-06-01

    Full Text Available Abstract Background In a previous screen to identify differentially expressed genes associated with embryonic development, the porcine PNAS-4 gene had been found. Considering differentially expressed genes in early stages of muscle development are potential candidate genes to improve meat quality and production efficiency, we determined how porcine PNAS-4 gene regulates meat production. Therefore, this gene has been sequenced, expression analyzed and associated with meat production traits. Results We cloned the full-length cDNA of porcine PNAS-4 gene encoding a protein of 194 amino acids which was expressed in the Golgi complex. This gene was mapped to chromosome 10, q11–16, in a region of conserved synteny with human chromosome 1 where the human homologous gene was localized. Real-time PCR revealed that PNAS-4 mRNA was widely expressed with highest expression levels in skeletal muscle followed by lymph, liver and other tissues, and showed a down-regulated expression pattern during prenatal development while a up-regulated expression pattern after weaning. Association analysis revealed that allele C of SNP A1813C was prevalent in Chinese indigenous breeds whereas A was dominant allele in Landrace and Large White, and the pigs with homozygous CC had a higher fat content than those of the pigs with other genotypes (P Conclusion Porcine PNAS-4 protein tagged with green fluorescent protein accumulated in the Golgi complex, and its mRNA showed a widespread expression across many tissues and organs in pigs. It may be an important factor affecting the meat production efficiency, because its down-regulated expression pattern during early embryogenesis suggests involvement in increase of muscle fiber number. In addition, the SNP A1813C associated with fat traits might be a genetic marker for molecular-assisted selection in animal breeding.

  7. An evolutionarily conserved gene, FUWA, plays a role in determining panicle architecture, grain shape and grain weight in rice.

    Science.gov (United States)

    Chen, Jun; Gao, He; Zheng, Xiao-Ming; Jin, Mingna; Weng, Jian-Feng; Ma, Jin; Ren, Yulong; Zhou, Kunneng; Wang, Qi; Wang, Jie; Wang, Jiu-Lin; Zhang, Xin; Cheng, Zhijun; Wu, Chuanyin; Wang, Haiyang; Wan, Jian-Min

    2015-08-01

    Plant breeding relies on creation of novel allelic combinations for desired traits. Identification and utilization of beneficial alleles, rare alleles and evolutionarily conserved genes in the germplasm (referred to as 'hidden' genes) provide an effective approach to achieve this goal. Here we show that a chemically induced null mutation in an evolutionarily conserved gene, FUWA, alters multiple important agronomic traits in rice, including panicle architecture, grain shape and grain weight. FUWA encodes an NHL domain-containing protein, with preferential expression in the root meristem, shoot apical meristem and inflorescences, where it restricts excessive cell division. Sequence analysis revealed that FUWA has undergone a bottleneck effect, and become fixed in landraces and modern cultivars during domestication and breeding. We further confirm a highly conserved role of FUWA homologs in determining panicle architecture and grain development in rice, maize and sorghum through genetic transformation. Strikingly, knockdown of the FUWA transcription level by RNA interference results in an erect panicle and increased grain size in both indica and japonica genetic backgrounds. This study illustrates an approach to create new germplasm with improved agronomic traits for crop breeding by tapping into evolutionary conserved genes. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

  8. Enhanced citrate production through gene insertion in Aspergillus niger

    DEFF Research Database (Denmark)

    Jongh, Wian de; Nielsen, Jens

    2007-01-01

    The effect of inserting genes involved in the reductive branch of the tricarboxylic acid (TCA) cycle on citrate production by Aspergillus niger was evaluated. Several different genes were inserted individually and in combination, i.e. malate dehydrogenase (mdh2) from Saccharomyces cerevisiae, two...

  9. Radiochemical identification of the kil gene product of bacteriophage lambda

    International Nuclear Information System (INIS)

    Greer, H.; Ausubel, F.M.

    1979-01-01

    The coliphage lambda kil gene product has been identified using a differential labeling technique . The kil gene polypeptide has a molecular weight of about 16,000, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Gel filtration of the kil protein indicates that it may exist as a tetramer in native form

  10. Candidate genes for drought tolerance and improved productivity in ...

    Indian Academy of Sciences (India)

    Madhu

    Improving drought tolerance and productivity is one of the most difficult tasks for ... Keywords. Candidate gene; mapping population; polymerase chain reaction; single marker analysis. .... ple and the mean value computed. 2.4 Isolation of DNA.

  11. Dynamic Gene-Resource Landscape Management of Norway Spruce: Combining Utilization and Conservation

    Directory of Open Access Journals (Sweden)

    Milan Lstibůrek

    2017-10-01

    Full Text Available Traditional gene-resource management programs for forest trees are long-term endeavors requiring sustained organizational commitment covering extensive landscapes. While successful in maintaining adaptation, genetic diversity and capturing traditional growth attributes gains, these programs are dependent on rigid methods requiring elaborate mating schemes, thus making them slow in coping with climate change challenges. Here, we review the significance of Norway spruce in the boreal region and its current management practices. Next, we discuss opportunities offered by novel technologies and, with the use of computer simulations, we propose and evaluate a dynamic landscape gene-resource management in Norway. Our suggested long-term management approach capitalizes on: (1 existing afforestation activities, natural crosses, and DNA-based pedigree assembly to create structured pedigree for evaluation, thus traditional laborious control crosses are avoided and (2 landscape level genetic evaluation, rather than localized traditional progeny trials, allowing for screening of adapted individuals across multiple environmental gradients under changing climate. These advantages lead to greater genetic response to selection in adaptive traits without the traditional breeding and testing scheme, facilitating conservation of genetic resources within the breeding population of the most important forest tree species in Norway. The use of in situ selection from proven material exposed to realistic conditions over vast territories has not been conducted in forestry before. Our proposed approach is in contrast to worldwide current programs, where genetic evaluation is constrained by the range of environments where testing is conducted, which may be insufficient to capture the broad environmental variation necessary to tackle adaptation under changing climate.

  12. Variable gene dispersal conditions and spatial deforestation patterns can interact to affect tropical tree conservation outcomes.

    Directory of Open Access Journals (Sweden)

    Yamini Kashimshetty

    Full Text Available Tropical lowland rain forest (TLRF biodiversity is under threat from anthropogenic factors including deforestation which creates forest fragments of different sizes that can further undergo various internal patterns of logging. Such interventions can modify previous equilibrium abundance and spatial distribution patterns of offspring recruitment and/or pollen dispersal. Little is known about how these aspects of deforestation and fragmentation might synergistically affect TLRF tree recovery demographics and population genetics in newly formed forest fragments. To investigate these TLRF anthropogenic disturbance processes we used the computer program NEWGARDEN (NG, which models spatially-explicit, individual-based plant populations, to simulate 10% deforestation in six different spatial logging patterns for the plant functional type of a long-lived TLRF canopy tree species. Further, each logging pattern was analyzed under nine varying patterns of offspring versus pollen dispersal distances that could have arisen post-fragmentation. Results indicated that gene dispersal condition (especially via offspring had a greater effect on population growth and genetic diversity retention (explaining 98.5% and 88.8% of the variance respectively than spatial logging pattern (0.2% and 4.7% respectively, with 'Near' distance dispersal maximizing population growth and genetic diversity relative to distant dispersal. Within logged regions of the fragment, deforestation patterns closer to fragment borders more often exhibited lower population recovery rates and founding genetic diversity retention relative to more centrally located logging. These results suggest newly isolated fragments have populations that are more sensitive to the way in which their offspring and pollen dispersers are affected than the spatial pattern in which subsequent logging occurs, and that large variation in the recovery rates of different TLRF tree species attributable to altered gene

  13. Variable gene dispersal conditions and spatial deforestation patterns can interact to affect tropical tree conservation outcomes.

    Science.gov (United States)

    Kashimshetty, Yamini; Pelikan, Stephan; Rogstad, Steven H

    2015-01-01

    Tropical lowland rain forest (TLRF) biodiversity is under threat from anthropogenic factors including deforestation which creates forest fragments of different sizes that can further undergo various internal patterns of logging. Such interventions can modify previous equilibrium abundance and spatial distribution patterns of offspring recruitment and/or pollen dispersal. Little is known about how these aspects of deforestation and fragmentation might synergistically affect TLRF tree recovery demographics and population genetics in newly formed forest fragments. To investigate these TLRF anthropogenic disturbance processes we used the computer program NEWGARDEN (NG), which models spatially-explicit, individual-based plant populations, to simulate 10% deforestation in six different spatial logging patterns for the plant functional type of a long-lived TLRF canopy tree species. Further, each logging pattern was analyzed under nine varying patterns of offspring versus pollen dispersal distances that could have arisen post-fragmentation. Results indicated that gene dispersal condition (especially via offspring) had a greater effect on population growth and genetic diversity retention (explaining 98.5% and 88.8% of the variance respectively) than spatial logging pattern (0.2% and 4.7% respectively), with 'Near' distance dispersal maximizing population growth and genetic diversity relative to distant dispersal. Within logged regions of the fragment, deforestation patterns closer to fragment borders more often exhibited lower population recovery rates and founding genetic diversity retention relative to more centrally located logging. These results suggest newly isolated fragments have populations that are more sensitive to the way in which their offspring and pollen dispersers are affected than the spatial pattern in which subsequent logging occurs, and that large variation in the recovery rates of different TLRF tree species attributable to altered gene dispersal

  14. Primary structure and promoter analysis of leghemoglobin genes of the stem-nodulated tropical legume Sesbania rostrata: conserved coding sequences, cis-elements and trans-acting factors

    DEFF Research Database (Denmark)

    Metz, B A; Welters, P; Hoffmann, H J

    1988-01-01

    The primary structure of a leghemoglobin (lb) gene from the stem-nodulated, tropical legume Sesbania rostrata and two lb gene promoter regions was analysed. The S. rostrata lb gene structure and Lb amino acid composition were found to be highly conserved with previously described lb genes and Lb ...

  15. Structure of genes for dermaseptins B, antimicrobial peptides from frog skin. Exon 1-encoded prepropeptide is conserved in genes for peptides of highly different structures and activities.

    Science.gov (United States)

    Vouille, V; Amiche, M; Nicolas, P

    1997-09-01

    We cloned the genes of two members of the dermaseptin family, broad-spectrum antimicrobial peptides isolated from the skin of the arboreal frog Phyllomedusa bicolor. The dermaseptin gene Drg2 has a 2-exon coding structure interrupted by a small 137-bp intron, wherein exon 1 encoded a 22-residue hydrophobic signal peptide and the first three amino acids of the acidic propiece; exon 2 contained the 18 additional acidic residues of the propiece plus a typical prohormone processing signal Lys-Arg and a 32-residue dermaseptin progenitor sequence. The dermaseptin genes Drg2 and Drg1g2 have conserved sequences at both untranslated ends and in the first and second coding exons. In contrast, Drg1g2 comprises a third coding exon for a short version of the acidic propiece and a second dermaseptin progenitor sequence. Structural conservation between the two genes suggests that Drg1g2 arose recently from an ancestral Drg2-like gene through amplification of part of the second coding exon and 3'-untranslated region. Analysis of the cDNAs coding precursors for several frog skin peptides of highly different structures and activities demonstrates that the signal peptides and part of the acidic propieces are encoded by conserved nucleotides encompassed by the first coding exon of the dermaseptin genes. The organization of the genes that belong to this family, with the signal peptide and the progenitor sequence on separate exons, permits strikingly different peptides to be directed into the secretory pathway. The recruitment of such a homologous 'secretory' exon by otherwise non-homologous genes may have been an early event in the evolution of amphibian.

  16. Bombyx mori nucleopolyhedrovirus BM5 protein regulates progeny virus production and viral gene expression

    International Nuclear Information System (INIS)

    Kokusho, Ryuhei; Koh, Yoshikazu; Fujimoto, Masaru; Shimada, Toru; Katsuma, Susumu

    2016-01-01

    Bombyx mori nucleopolyhedrovirus (BmNPV) orf5 (Bm5) is a core gene of lepidopteran baculoviruses and encodes the protein with the conserved amino acid residues (DUF3627) in its C-terminus. Here, we found that Bm5 disruption resulted in lower titers of budded viruses and fewer numbers of occlusion bodies (OBs) in B. mori cultured cells and larvae, although viral genome replication was not affected. Bm5 disruption also caused aberrant expression of various viral genes at the very late stage of infection. Immunocytochemical analysis revealed that BM5 localized to the nuclear membrane. We also found that DUF3627 is important for OB production, transcriptional regulation of viral genes, and subcellular localization of BM5. Compared with wild-type BmNPV infection, larval death was delayed when B. mori larvae were infected with Bm5 mutants. These results suggest that BM5 is involved in progeny virus production and regulation of viral gene expression at the very late stage of infection. -- Highlights: •The role of BmNPV BM5 protein was examined in B. mori cultured cells and larvae. •BM5 contributes to efficient production of budded viruses and occlusion bodies. •BM5 regulates viral gene expression at the very late stage of infection. •BM5 dominantly localizes to the nuclear membrane. •Bm5 mutant showed v-cath down-regulation and resulting delay of larval death.

  17. Bombyx mori nucleopolyhedrovirus BM5 protein regulates progeny virus production and viral gene expression

    Energy Technology Data Exchange (ETDEWEB)

    Kokusho, Ryuhei, E-mail: kokusho@ss.ab.a.u-tokyo.ac.jp; Koh, Yoshikazu; Fujimoto, Masaru; Shimada, Toru; Katsuma, Susumu, E-mail: katsuma@ss.ab.a.u-tokyo.ac.jp

    2016-11-15

    Bombyx mori nucleopolyhedrovirus (BmNPV) orf5 (Bm5) is a core gene of lepidopteran baculoviruses and encodes the protein with the conserved amino acid residues (DUF3627) in its C-terminus. Here, we found that Bm5 disruption resulted in lower titers of budded viruses and fewer numbers of occlusion bodies (OBs) in B. mori cultured cells and larvae, although viral genome replication was not affected. Bm5 disruption also caused aberrant expression of various viral genes at the very late stage of infection. Immunocytochemical analysis revealed that BM5 localized to the nuclear membrane. We also found that DUF3627 is important for OB production, transcriptional regulation of viral genes, and subcellular localization of BM5. Compared with wild-type BmNPV infection, larval death was delayed when B. mori larvae were infected with Bm5 mutants. These results suggest that BM5 is involved in progeny virus production and regulation of viral gene expression at the very late stage of infection. -- Highlights: •The role of BmNPV BM5 protein was examined in B. mori cultured cells and larvae. •BM5 contributes to efficient production of budded viruses and occlusion bodies. •BM5 regulates viral gene expression at the very late stage of infection. •BM5 dominantly localizes to the nuclear membrane. •Bm5 mutant showed v-cath down-regulation and resulting delay of larval death.

  18. A new measure for functional similarity of gene products based on Gene Ontology

    Directory of Open Access Journals (Sweden)

    Lengauer Thomas

    2006-06-01

    Full Text Available Abstract Background Gene Ontology (GO is a standard vocabulary of functional terms and allows for coherent annotation of gene products. These annotations provide a basis for new methods that compare gene products regarding their molecular function and biological role. Results We present a new method for comparing sets of GO terms and for assessing the functional similarity of gene products. The method relies on two semantic similarity measures; simRel and funSim. One measure (simRel is applied in the comparison of the biological processes found in different groups of organisms. The other measure (funSim is used to find functionally related gene products within the same or between different genomes. Results indicate that the method, in addition to being in good agreement with established sequence similarity approaches, also provides a means for the identification of functionally related proteins independent of evolutionary relationships. The method is also applied to estimating functional similarity between all proteins in Saccharomyces cerevisiae and to visualizing the molecular function space of yeast in a map of the functional space. A similar approach is used to visualize the functional relationships between protein families. Conclusion The approach enables the comparison of the underlying molecular biology of different taxonomic groups and provides a new comparative genomics tool identifying functionally related gene products independent of homology. The proposed map of the functional space provides a new global view on the functional relationships between gene products or protein families.

  19. G-NEST: A gene neighborhood scoring tool to identify co-conserved, co-expressed genes

    Science.gov (United States)

    In previous studies, gene neighborhoods--spatial clusters of co-expressed genes in the genome--have been defined using arbitrary rules such as requiring adjacency, a minimum number of genes, a fixed window size, or a minimum expression level. In the current study, we developed a Gene Neighborhood Sc...

  20. Unbinned maximum likelihood fit for the CP conserving couplings for W + photon production at CDF

    International Nuclear Information System (INIS)

    Lannon, K.

    1994-01-01

    We present an unbinned maximum likelihood fit as an alternative to the currently used fit for the CP conserving couplings W plus photon production studied at CDF. We show that a four parameter double exponential fits the E T spectrum of the photon very well. We also show that the fit parameters can be related to and by a second order polynomial. Finally, we discuss various conclusions we have reasoned from our results to the fit so far

  1. Physical and chemical effects of ionizing radiation, application for conservation of food products

    International Nuclear Information System (INIS)

    Foos, J.

    1986-01-01

    The author sets about ''defining the parameters'' and ''describing the systems'' by means of which ionizing radiation can be used to conserve food products and make them more healthy. After defining the different types of radiation, he goes on to examine interactions between these types of radiation and the food to be processed, including the chemical reactions caused by the ionization and excitation processes [fr

  2. Discovery of Conservation and Diversification of miR171 Genes by Phylogenetic Analysis based on Global Genomes

    Directory of Open Access Journals (Sweden)

    Xudong Zhu

    2015-07-01

    Full Text Available The microRNA171 (miR171 family is widely distributed and highly conserved in a range of species and plays critical roles in regulating plant growth and development through repressing expression of ( transcription factors. However, information on the evolutionary conservation and functional diversification of the miRNA171 family members remains scanty. We reconstructed the phylogenetic relationships among miR171 precursor and mature sequences so as to investigate the extent and degree of evolutionary conservation of miR171 in (L. Heynh. (ath, grape ( L. (vvi, poplar ( Torr. & A.Gray ex Hook. (ptc, and rice ( L. (osa. Despite strong conservation of over 80%, some mature miR171 sequences, such as , and and , -, and -, have undergone critical sequence variation, leading to functional diversification, since they target non gene transcript(s. Phylogenetic analyses revealed a combination of old ancestral relationships and recent lineage-specific diversification in the miR171 family within the four model plants. The -regulatory motifs on the upstream promoter sequences of genes were highly divergent and shared some similar elements, indicating their possible contribution to the functional variation observed within the miR171 family. This study will buttress our understanding of the functional differentiation of miRNAs and the relationships of miRNA–target pairs based on the evolutionary history of genes.

  3. Soil Tillage Conservation and its Effect on Soil Properties Bioremediation and Sustained Production of Crops

    Science.gov (United States)

    Rusu, Teodor; Ioana Moraru, Paula; Muresan, Liliana; Andriuca, Valentina; Cojocaru, Olesea

    2017-04-01

    Soil Tillage Conservation (STC) is considered major components of agricultural technology for soil conservation strategies and part of Sustainable Agriculture (SA). Human action upon soil by tillage determines important morphological, physical-chemical and biological changes, with different intensities and evaluative directions. Nowadays, internationally is unanimous accepted the fact that global climatic changes are the results of human intervention in the bio-geo-chemical water and material cycle, and the sequestration of carbon in soil is considered an important intervention to limit these changes. STC involves reducing the number of tillage's (minimum tillage) to direct sowing (no-tillage) and plant debris remains at the soil surface in the ratio of at least 30%. Plant debris left on the soil surface or superficial incorporated contributes to increased biological activity and is an important source of carbon sequestration. STC restore soil structure and improve overall soil drainage, allowing more rapid infiltration of water into soil. The result is a soil bioremediation, more productive, better protected against wind and water erosion and requires less fuel for preparing the germinative bed. Carbon sequestration in soil is net advantageous, improving the productivity and sustainability. We present the influence of conventional plough tillage system on soil, water and organic matter conservation in comparison with an alternative minimum tillage (paraplow, chisel plow and rotary harrow) and no-tillage system. The application of STC increased the organic matter content 0.8 to 22.1% and water stabile aggregate content from 1.3 to 13.6%, in the 0-30 cm depth, as compared to the conventional system. For the organic matter content and the wet aggregate stability, the statistical analysis of the data showed, increasing positive significance of STC. While the soil fertility and the wet aggregate stability were initially low, the effect of conservation practices on the

  4. The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima

    Science.gov (United States)

    Chipman, Ariel D.; Ferrier, David E. K.; Brena, Carlo; Qu, Jiaxin; Hughes, Daniel S. T.; Schröder, Reinhard; Torres-Oliva, Montserrat; Znassi, Nadia; Jiang, Huaiyang; Almeida, Francisca C.; Alonso, Claudio R.; Apostolou, Zivkos; Aqrawi, Peshtewani; Arthur, Wallace; Barna, Jennifer C. J.; Blankenburg, Kerstin P.; Brites, Daniela; Capella-Gutiérrez, Salvador; Coyle, Marcus; Dearden, Peter K.; Du Pasquier, Louis; Duncan, Elizabeth J.; Ebert, Dieter; Eibner, Cornelius; Erikson, Galina; Evans, Peter D.; Extavour, Cassandra G.; Francisco, Liezl; Gabaldón, Toni; Gillis, William J.; Goodwin-Horn, Elizabeth A.; Green, Jack E.; Griffiths-Jones, Sam; Grimmelikhuijzen, Cornelis J. P.; Gubbala, Sai; Guigó, Roderic; Han, Yi; Hauser, Frank; Havlak, Paul; Hayden, Luke; Helbing, Sophie; Holder, Michael; Hui, Jerome H. L.; Hunn, Julia P.; Hunnekuhl, Vera S.; Jackson, LaRonda; Javaid, Mehwish; Jhangiani, Shalini N.; Jiggins, Francis M.; Jones, Tamsin E.; Kaiser, Tobias S.; Kalra, Divya; Kenny, Nathan J.; Korchina, Viktoriya; Kovar, Christie L.; Kraus, F. Bernhard; Lapraz, François; Lee, Sandra L.; Lv, Jie; Mandapat, Christigale; Manning, Gerard; Mariotti, Marco; Mata, Robert; Mathew, Tittu; Neumann, Tobias; Newsham, Irene; Ngo, Dinh N.; Ninova, Maria; Okwuonu, Geoffrey; Ongeri, Fiona; Palmer, William J.; Patil, Shobha; Patraquim, Pedro; Pham, Christopher; Pu, Ling-Ling; Putman, Nicholas H.; Rabouille, Catherine; Ramos, Olivia Mendivil; Rhodes, Adelaide C.; Robertson, Helen E.; Robertson, Hugh M.; Ronshaugen, Matthew; Rozas, Julio; Saada, Nehad; Sánchez-Gracia, Alejandro; Scherer, Steven E.; Schurko, Andrew M.; Siggens, Kenneth W.; Simmons, DeNard; Stief, Anna; Stolle, Eckart; Telford, Maximilian J.; Tessmar-Raible, Kristin; Thornton, Rebecca; van der Zee, Maurijn; von Haeseler, Arndt; Williams, James M.; Willis, Judith H.; Wu, Yuanqing; Zou, Xiaoyan; Lawson, Daniel; Muzny, Donna M.; Worley, Kim C.; Gibbs, Richard A.; Akam, Michael; Richards, Stephen

    2014-01-01

    Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific

  5. Effects of soil and water conservation on crop productivity: Evidences from Anjenie watershed, Ethiopia

    Science.gov (United States)

    Adgo, Enyew; Teshome, Akalu

    2014-05-01

    Widespread soil and water conservation activities have been implemented in many parts of eastern Africa to control soil erosion by water and improve land productivity for the last few decades. Following the 1974 severe drought, soil and water conservation became more important to Ethiopia and the approach shifted to watershed based land management initiatives since the 1980s. To capture long-term impacts of these initiatives, a study was conducted in Anjenie Watershed of Ethiopia, assessing fanya juu terraces and grass strips constructed in a pilot project in 1984, and which are still functional nearly 30 years later. Data were collected from government records, field observations and questionnaire surveys administered to 60 farmers. Half of the respondents had terraced farms in the watershed former project area (with terrace technology) and the rest were outside the terraced area. The crops assessed were teff, barley and maize. Cost-benefit analyses were used to determine the economic benefits with and without terraces, including gross and net profit values, returns on labour, water productivity and impacts on poverty. The results indicated that soil and water conservation had improved crop productivity. The average yield on terraced fields was 0.95 t ha-1 for teff (control 0.49), 1.86 t ha-1 for barley (control 0.61), and 1.73 t ha-1 for maize (control 0.77). The net benefit was significantly higher on terraced fields, recording US 20.9 (US -112 control) for teff, US 185 (US -41 control) for barley and US -34.5 (US - 101 control) ha-1 yr-1 for maize. The returns on family labour were 2.33 for barley, 1.01 for teff, and 0.739 US per person-day for maize grown on terraced plots, compared to US 0.44, 0.27 and 0.16 per person-day for plots without terraces, respectively. Using a discount rate of 10%, the average net present value (NPV) of barley production with terrace was found to be about US 1542 over a period of 50 years. In addition, the average financial

  6. Gene analogue finder: a GRID solution for finding functionally analogous gene products

    Directory of Open Access Journals (Sweden)

    Licciulli Flavio

    2007-09-01

    Full Text Available Abstract Background To date more than 2,1 million gene products from more than 100000 different species have been described specifying their function, the processes they are involved in and their cellular localization using a very well defined and structured vocabulary, the gene ontology (GO. Such vast, well defined knowledge opens the possibility of compare gene products at the level of functionality, finding gene products which have a similar function or are involved in similar biological processes without relying on the conventional sequence similarity approach. Comparisons within such a large space of knowledge are highly data and computing intensive. For this reason this project was based upon the use of the computational GRID, a technology offering large computing and storage resources. Results We have developed a tool, GENe AnaloGue FINdEr (ENGINE that parallelizes the search process and distributes the calculation and data over the computational GRID, splitting the process into many sub-processes and joining the calculation and the data on the same machine and therefore completing the whole search in about 3 days instead of occupying one single machine for more than 5 CPU years. The results of the functional comparison contain potential functional analogues for more than 79000 gene products from the most important species. 46% of the analyzed gene products are well enough described for such an analysis to individuate functional analogues, such as well-known members of the same gene family, or gene products with similar functions which would never have been associated by standard methods. Conclusion ENGINE has produced a list of potential functionally analogous relations between gene products within and between species using, in place of the sequence, the gene description of the GO, thus demonstrating the potential of the GO. However, the current limiting factor is the quality of the associations of many gene products from non

  7. Candidate genes for drought tolerance and improved productivity in ...

    Indian Academy of Sciences (India)

    Madhu

    tropics. Improving drought tolerance and productivity is one of the most difficult tasks for cereal breeders. The diffi- culty arises from the diverse strategies adopted by plants themselves to combat drought stress depending on the timing,. Candidate genes for drought tolerance and improved productivity in rice (Oryza sativa L.).

  8. Landscape genetics as a tool for conservation planning: predicting the effects of landscape change on gene flow.

    Science.gov (United States)

    van Strien, Maarten J; Keller, Daniela; Holderegger, Rolf; Ghazoul, Jaboury; Kienast, Felix; Bolliger, Janine

    2014-03-01

    For conservation managers, it is important to know whether landscape changes lead to increasing or decreasing gene flow. Although the discipline of landscape genetics assesses the influence of landscape elements on gene flow, no studies have yet used landscape-genetic models to predict gene flow resulting from landscape change. A species that has already been severely affected by landscape change is the large marsh grasshopper (Stethophyma grossum), which inhabits moist areas in fragmented agricultural landscapes in Switzerland. From transects drawn between all population pairs within maximum dispersal distance (landscape composition as well as some measures of habitat configuration. Additionally, a complete sampling of all populations in our study area allowed incorporating measures of population topology. These measures together with the landscape metrics formed the predictor variables in linear models with gene flow as response variable (F(ST) and mean pairwise assignment probability). With a modified leave-one-out cross-validation approach, we selected the model with the highest predictive accuracy. With this model, we predicted gene flow under several landscape-change scenarios, which simulated construction, rezoning or restoration projects, and the establishment of a new population. For some landscape-change scenarios, significant increase or decrease in gene flow was predicted, while for others little change was forecast. Furthermore, we found that the measures of population topology strongly increase model fit in landscape genetic analysis. This study demonstrates the use of predictive landscape-genetic models in conservation and landscape planning.

  9. Multi-species sequence comparison reveals conservation of ghrelin gene-derived splice variants encoding a truncated ghrelin peptide.

    Science.gov (United States)

    Seim, Inge; Jeffery, Penny L; Thomas, Patrick B; Walpole, Carina M; Maugham, Michelle; Fung, Jenny N T; Yap, Pei-Yi; O'Keeffe, Angela J; Lai, John; Whiteside, Eliza J; Herington, Adrian C; Chopin, Lisa K

    2016-06-01

    The peptide hormone ghrelin is a potent orexigen produced predominantly in the stomach. It has a number of other biological actions, including roles in appetite stimulation, energy balance, the stimulation of growth hormone release and the regulation of cell proliferation. Recently, several ghrelin gene splice variants have been described. Here, we attempted to identify conserved alternative splicing of the ghrelin gene by cross-species sequence comparisons. We identified a novel human exon 2-deleted variant and provide preliminary evidence that this splice variant and in1-ghrelin encode a C-terminally truncated form of the ghrelin peptide, termed minighrelin. These variants are expressed in humans and mice, demonstrating conservation of alternative splicing spanning 90 million years. Minighrelin appears to have similar actions to full-length ghrelin, as treatment with exogenous minighrelin peptide stimulates appetite and feeding in mice. Forced expression of the exon 2-deleted preproghrelin variant mirrors the effect of the canonical preproghrelin, stimulating cell proliferation and migration in the PC3 prostate cancer cell line. This is the first study to characterise an exon 2-deleted preproghrelin variant and to demonstrate sequence conservation of ghrelin gene-derived splice variants that encode a truncated ghrelin peptide. This adds further impetus for studies into the alternative splicing of the ghrelin gene and the function of novel ghrelin peptides in vertebrates.

  10. An evolutionary conserved region (ECR in the human dopamine receptor D4 gene supports reporter gene expression in primary cultures derived from the rat cortex

    Directory of Open Access Journals (Sweden)

    Haddley Kate

    2011-05-01

    Full Text Available Abstract Background Detecting functional variants contributing to diversity of behaviour is crucial for dissecting genetics of complex behaviours. At a molecular level, characterisation of variation in exons has been studied as they are easily identified in the current genome annotation although the functional consequences are less well understood; however, it has been difficult to prioritise regions of non-coding DNA in which genetic variation could also have significant functional consequences. Comparison of multiple vertebrate genomes has allowed the identification of non-coding evolutionary conserved regions (ECRs, in which the degree of conservation can be comparable with exonic regions suggesting functional significance. Results We identified ECRs at the dopamine receptor D4 gene locus, an important gene for human behaviours. The most conserved non-coding ECR (D4ECR1 supported high reporter gene expression in primary cultures derived from neonate rat frontal cortex. Computer aided analysis of the sequence of the D4ECR1 indicated the potential transcription factors that could modulate its function. D4ECR1 contained multiple consensus sequences for binding the transcription factor Sp1, a factor previously implicated in DRD4 expression. Co-transfection experiments demonstrated that overexpression of Sp1 significantly decreased the activity of the D4ECR1 in vitro. Conclusion Bioinformatic analysis complemented by functional analysis of the DRD4 gene locus has identified a a strong enhancer that functions in neurons and b a transcription factor that may modulate the function of that enhancer.

  11. Regulation of Cell and Gene Therapy Medicinal Products in Taiwan.

    Science.gov (United States)

    Lin, Yi-Chu; Wang, Po-Yu; Tsai, Shih-Chih; Lin, Chien-Liang; Tai, Hsuen-Yung; Lo, Chi-Fang; Wu, Shiow-Ing; Chiang, Yu-Mei; Liu, Li-Ling

    2015-01-01

    Owing to the rapid and mature development of emerging biotechnology in the fields of cell culture, cell preservation, and recombinant DNA technology, more and more cell or gene medicinal therapy products have been approved for marketing, to treat serious diseases which have been challenging to treat with current medical practice or medicine. This chapter will briefly introduce the Taiwan Food and Drug Administration (TFDA) and elaborate regulation of cell and gene therapy medicinal products in Taiwan, including regulatory history evolution, current regulatory framework, application and review procedures, and relevant jurisdictional issues. Under the promise of quality, safety, and efficacy of medicinal products, it is expected the regulation and environment will be more flexible, streamlining the process of the marketing approval of new emerging cell or gene therapy medicinal products and providing diverse treatment options for physicians and patients.

  12. Protocols for In Vitro Propagation, Conservation, Synthetic Seed Production, Embryo Rescue, Microrhizome Production, Molecular Profiling, and Genetic Transformation in Ginger (Zingiber officinale Roscoe.).

    Science.gov (United States)

    Nirmal Babu, K; Samsudeen, K; Divakaran, Minoo; Pillai, Geetha S; Sumathi, V; Praveen, K; Ravindran, P N; Peter, K V

    2016-01-01

    Ginger is a rhizomatous plant that belongs to the family Zingiberaceae. It is a herbaceous perennial but cultivated as annual, with crop duration of 7-10 months. Ginger is native to India and Tropical South Asia. The tuberous rhizomes or underground stems of ginger are used as condiment, an aromatic stimulant, and food preservative as well as in traditional medicine. Ginger is propagated vegetatively with rhizome bits as seed material. Cultivation of ginger is plagued by rhizome rot diseases, most of which are mainly spread through infected seed rhizomes. Micropropagation will help in production of disease-free planting material. Sexual reproduction is absent in ginger, making recombinant breeding very impossible. In vitro technology can thus become the preferred choice as it can be utilized for multiplication, conservation of genetic resources, generating variability, gene transfer, molecular tagging, and their utility in crop improvement of these crops.

  13. Combining Human Epigenetics and Sleep Studies in Caenorhabditis elegans: A Cross-Species Approach for Finding Conserved Genes Regulating Sleep.

    Science.gov (United States)

    Huang, Huiyan; Zhu, Yong; Eliot, Melissa N; Knopik, Valerie S; McGeary, John E; Carskadon, Mary A; Hart, Anne C

    2017-06-01

    We aimed to test a combined approach to identify conserved genes regulating sleep and to explore the association between DNA methylation and sleep length. We identified candidate genes associated with shorter versus longer sleep duration in college students based on DNA methylation using Illumina Infinium HumanMethylation450 BeadChip arrays. Orthologous genes in Caenorhabditis elegans were identified, and we examined whether their loss of function affected C. elegans sleep. For genes whose perturbation affected C. elegans sleep, we subsequently undertook a small pilot study to re-examine DNA methylation in an independent set of human participants with shorter versus longer sleep durations. Eighty-seven out of 485,577 CpG sites had significant differential methylation in young adults with shorter versus longer sleep duration, corresponding to 52 candidate genes. We identified 34 C. elegans orthologs, including NPY/flp-18 and flp-21, which are known to affect sleep. Loss of five additional genes alters developmentally timed C. elegans sleep (B4GALT6/bre-4, DOCK180/ced-5, GNB2L1/rack-1, PTPRN2/ida-1, ZFYVE28/lst-2). For one of these genes, ZFYVE28 (also known as hLst2), the pilot replication study again found decreased DNA methylation associated with shorter sleep duration at the same two CpG sites in the first intron of ZFYVE28. Using an approach that combines human epigenetics and C. elegans sleep studies, we identified five genes that play previously unidentified roles in C. elegans sleep. We suggest sleep duration in humans may be associated with differential DNA methylation at specific sites and that the conserved genes identified here likely play roles in C. elegans sleep and in other species. © Sleep Research Society 2017. Published by Oxford University Press on behalf of the Sleep Research Society. All rights reserved. For permissions, please e-mail journals.permissions@oup.com.

  14. The Role of Biotechnology for Conservation and Biologically Active Substances Production of Rhodiola rosea: Endangered Medicinal Species

    Science.gov (United States)

    Tasheva, Krasimira; Kosturkova, Georgina

    2012-01-01

    At present, more than 50 000 plant species are used in phytotherapy and medicine. About 2/3 of them are harvested from nature leading to local extinction of many species or degradation of their habitats. Biotechnological methods offer possibilities not only for faster cloning and conservation of the genotype of the plants but for modification of their gene information, regulation, and expression for production of valuable substances in higher amounts or with better properties. Rhodiola rosea is an endangered medicinal species with limited distribution. It has outstanding importance for pharmaceutical industry for prevention and cure of cancer, heart and nervous system diseases, and so forth. Despite the great interest in golden root and the wide investigations in the area of phytochemistry, plant biotechnology remained less endeavoured and exploited. The paper presents research on initiation of in vitro cultures in Rhodiola rosea and some other Rhodiola species. Achievements in induction of organogenic and callus cultures, regeneration, and micropropagation varied but were a good basis for alternative in vitro synthesis of the desired metabolites and for the development of efficient systems for micropropagation for conservation of the species. PMID:22666097

  15. Expression conservation within the circadian clock of a monocot: natural variation at barley Ppd-H1 affects circadian expression of flowering time genes, but not clock orthologs.

    Science.gov (United States)

    Campoli, Chiara; Shtaya, Munqez; Davis, Seth J; von Korff, Maria

    2012-06-21

    The circadian clock is an endogenous mechanism that coordinates biological processes with daily changes in the environment. In plants, circadian rhythms contribute to both agricultural productivity and evolutionary fitness. In barley, the photoperiod response regulator and flowering-time gene Ppd-H1 is orthologous to the Arabidopsis core-clock gene PRR7. However, relatively little is known about the role of Ppd-H1 and other components of the circadian clock in temperate crop species. In this study, we identified barley clock orthologs and tested the effects of natural genetic variation at Ppd-H1 on diurnal and circadian expression of clock and output genes from the photoperiod-response pathway. Barley clock orthologs HvCCA1, HvGI, HvPRR1, HvPRR37 (Ppd-H1), HvPRR73, HvPRR59 and HvPRR95 showed a high level of sequence similarity and conservation of diurnal and circadian expression patterns, when compared to Arabidopsis. The natural mutation at Ppd-H1 did not affect diurnal or circadian cycling of barley clock genes. However, the Ppd-H1 mutant was found to be arrhythmic under free-running conditions for the photoperiod-response genes HvCO1, HvCO2, and the MADS-box transcription factor and vernalization responsive gene Vrn-H1. We suggest that the described eudicot clock is largely conserved in the monocot barley. However, genetic differentiation within gene families and differences in the function of Ppd-H1 suggest evolutionary modification in the angiosperm clock. Our data indicates that natural variation at Ppd-H1 does not affect the expression level of clock genes, but controls photoperiodic output genes. Circadian control of Vrn-H1 in barley suggests that this vernalization responsive gene is also controlled by the photoperiod-response pathway. Structural and functional characterization of the barley circadian clock will set the basis for future studies of the adaptive significance of the circadian clock in Triticeae species.

  16. An Intelligent Method of Product Scheme Design Based on Product Gene

    Directory of Open Access Journals (Sweden)

    Qing Song Ai

    2013-01-01

    Full Text Available Nowadays, in order to have some featured products, many customers tend to buy customized products instead of buying common ones in supermarket. The manufacturing enterprises, with the purpose of improving their competitiveness, are focusing on providing customized products with high quality and low cost as well. At present, how to produce customized products rapidly and cheaply has been the key challenge to manufacturing enterprises. In this paper, an intelligent modeling approach applied to supporting the modeling of customized products is proposed, which may improve the efficiency during the product design process. Specifically, the product gene (PG method, which is an analogy of biological evolution in engineering area, is employed to model products in a new way. Based on product gene, we focus on the intelligent modeling method to generate product schemes rapidly and automatically. The process of our research includes three steps: (1 develop a product gene model for customized products; (2 find the obtainment and storage method for product gene; and (3 propose a specific genetic algorithm used for calculating the solution of customized product and generating new product schemes. Finally, a case study is applied to test the usefulness of our study.

  17. Integrating gene flow, crop biology, and farm management in on-farm conservation of avocado (Persea americana, Lauraceae).

    Science.gov (United States)

    Birnbaum, Kenneth; Desalle, Rob; Peters, Charles M; Benfey, Philip N

    2003-11-01

    Maintaining crop diversity on farms where cultivars can evolve is a conservation goal, but few tools are available to assess the long-term maintenance of genetic diversity on farms. One important issue for on-farm conservation is gene flow from crops with a narrow genetic base into related populations that are genetically diverse. In a case study of avocado (Persea americana var. americana) in one of its centers of diversity (San Jerónimo, Costa Rica), we used 10 DNA microsatellite markers in a parentage analysis to estimate gene flow from commercialized varieties into a traditional crop population. Five commercialized genotypes comprised nearly 40% of orchard trees, but they contributed only about 14.5% of the gametes to the youngest cohort of trees. Although commercialized varieties and the diverse population were often planted on the same farm, planting patterns appeared to keep the two types of trees separated on small scales, possibly explaining the limited gene flow. In a simulation that combined gene flow estimates, crop biology, and graft tree management, loss of allelic diversity was less than 10% over 150 yr, and selection was effective in retaining desirable alleles in the diverse subpopulation. Simulations also showed that, in addition to gene flow, managing the genetic makeup and life history traits of the invasive commercialized varieties could have a significant impact on genetic diversity in the target population. The results support the feasibility of on-farm crop conservation, but simulations also showed that higher levels of gene flow could lead to severe losses of genetic diversity even if farmers continue to plant diverse varieties.

  18. Ethnopharmacology, food production, nutrition and biodiversity conservation: towards a sustainable future for indigenous peoples.

    Science.gov (United States)

    Heywood, Vernon H

    2011-09-01

    It is becoming increasingly clear that ethnopharmacology cannot be disassociated from food production, human nutrition and the conservation of the biodiversity that constitutes its resource base. This paper aims to provide a perspective of ethnopharmacology that explicitly extends the range of disciplines it covers so as to embrace food and nutrition and the biodiversity basis, both wild and agricultural, and also places it in the context of the dramatic changes to our planet that we are experiencing during a period of rapid global change and the impacts that these changes are having on human health and nutrition and on its resource base. A review is made of recent initiatives and developments that show linkages between ethnopharmacology, agriculture, food production, nutrition and biodiversity conservation. Ethnopharmacology, biodiversity, agriculture, food and nutrition are inextricably linked but suffer from compartmentalization and a lack of communication which have to be overcome if progress is to be made. Fortunately, a convergence of interest between the agricultural biodiversity and the biodiversity conservation sectors has emerged in recent years and there is an increased appreciation of the need to adopt a wider approach to human nutrition than the conventional agricultural model allows; there is also a greater awareness of the important role played by diversity of crops, especially local species, and consumption of wild species in achieving balanced nutrition. An increased recognition of the key role of local communities in managing agricultural biodiversity is evident. While ethnopharmacologists have expressed concern at the relentless loss of biodiversity, there has been little direct involvement but it is perhaps now time to consider a more proactive role. Attention is also drawn to the need to assess the implications of global change for ethnopharmacology. Ethnopharmacologists need to take much more cognizance of the fate of the resource base - the

  19. Electricity demand and conservation potential in the Chinese nonmetallic mineral products industry

    International Nuclear Information System (INIS)

    Lin, Boqiang; Ouyang, Xiaoling

    2014-01-01

    As the high energy-consuming manufacturing industry, electricity consumption of nonmetallic mineral products in China accounted for 7.93% of industrial, 5.84% of national and 1.33% of global electricity consumption in 2010. This study attempts to specify the determinants of sectoral electricity demand, forecast future electricity consumption by creating a model using the Johansen cointegration methodology and estimate the sectoral electricity conservation potential. Results indicate that GDP per capita is the leading force explaining the sectoral electricity consumption increase, while value-added per worker, R and D intensity and electricity price are the main factors contributing to the sectoral electricity consumption decrease. Results demonstrate that sectoral electricity consumption in 2020 will be 369.79–464.83 billion kWh under the low-growth scenario and 530.14–666.39 billion kWh under the high-growth scenario. Moreover, under the low-growth scenario, the sectoral electricity conservation potential in 2020 will be 33.72–95.03 billion kWh, accounting for 0.45–1.26% of China's total electricity demand in 2020; under the high-growth scenario, the sectoral electricity conservation potential in 2020 will be 48.34–136.24 billion kWh, accounting for 0.26–0.74% of world's total electricity consumption in 2010 respectively. Finally, we provide some policy recommendations for encouraging energy conservation in China's nonmetallic mineral products industry. - Highlights: • A long-term relationship of electricity demand in nonmetallic minerals industry is established. • Determinants of the sectoral electricity consumption are specified. • The sectoral electricity demand and saving potential are analyzed using scenarios analysis. • Electricity saving potential will be 48.34–136.24 billion kWh under the high-growth scenario

  20. Conservation and Sex-Specific Splicing of the transformer Gene in the Calliphorids Cochliomyia hominivorax, Cochliomyia macellaria and Lucilia sericata

    Science.gov (United States)

    Li, Fang; Vensko, Steven P.; Belikoff, Esther J.; Scott, Maxwell J.

    2013-01-01

    Transformer (TRA) promotes female development in several dipteran species including the Australian sheep blowfly Lucilia cuprina, the Mediterranean fruit fly, housefly and Drosophila melanogaster. tra transcripts are sex-specifically spliced such that only the female form encodes full length functional protein. The presence of six predicted TRA/TRA2 binding sites in the sex-specific female intron of the L. cuprina gene suggested that tra splicing is auto-regulated as in medfly and housefly. With the aim of identifying conserved motifs that may play a role in tra sex-specific splicing, here we have isolated and characterized the tra gene from three additional blowfly species, L. sericata, Cochliomyia hominivorax and C. macellaria. The blowfly adult male and female transcripts differ in the choice of splice donor site in the first intron, with males using a site downstream of the site used in females. The tra genes all contain a single TRA/TRA2 site in the male exon and a cluster of four to five sites in the male intron. However, overall the sex-specific intron sequences are poorly conserved in closely related blowflies. The most conserved regions are around the exon/intron junctions, the 3′ end of the intron and near the cluster of TRA/TRA2 sites. We propose a model for sex specific regulation of tra splicing that incorporates the conserved features identified in this study. In L. sericata embryos, the male tra transcript was first detected at around the time of cellular blastoderm formation. RNAi experiments showed that tra is required for female development in L. sericata and C. macellaria. The isolation of the tra gene from the New World screwworm fly C. hominivorax, a major livestock pest, will facilitate the development of a “male-only” strain for genetic control programs. PMID:23409170

  1. A two-cassette reporter system for assessing target gene translation and target gene product inclusion body formation

    DEFF Research Database (Denmark)

    2016-01-01

    The present invention relates to a dual cassette reporter system capable of assessing target gene translation and target gene product folding. The present invention further relates to vectors and host cells comprising the dual cassette reporter system. In addition the invention relates to the use...... of the dual cassette reporter system for assessing target gene translation and target gene product folding....

  2. Conservation agriculture practices in rainfed uplands of India improve maize-based system productivity and profitability

    Directory of Open Access Journals (Sweden)

    Aliza Pradhan

    2016-07-01

    Full Text Available Traditional agriculture in rainfed uplands of India has been experiencing low agricultural productivity as the lands suffer from poor soil fertility, susceptibility to water erosion and other external pressures of development and climate change. A shift towards more sustainable cropping systems such as conservation agriculture production systems (CAPS may help in maintaining soil quality as well as improving crop production and farmer’s net economic benefit. This research assessed the effects over three years (2011-2014 of reduced tillage, intercropping, and cover cropping practices customized for maize-based production systems in upland areas of Odisha, India. The study focused on crop yield, system productivity and profitability through maize equivalent yield and dominance analysis. Results showed that maize grain yield did not differ significantly over time or among CAPS treatments while cowpea yield was considered as an additional yield in intercropping systems. Mustard and horsegram grown in plots after maize cowpea intercropping recorded higher grain yields of 25 and 37%, respectively, as compared to those without intercropping. Overall, the full CAPS implementation i.e. minimum tillage, maize-cowpea intercropping and mustard residue retention had significantly higher system productivity and net benefits than traditional farmer practices, i.e. conventional tillage, sole maize cropping, and no mustard residue retention. The dominance analysis demonstrated increasing benefits of combining conservation practices that exceeded thresholds for farmer adoption. Given the use of familiar crops and technologies and the magnitude of yield and income improvements, these types of CAPS should be acceptable and attractive for smallholder farmers in the area. This in turn should support a move toward sustainable intensification of crop production to meet future household income and nutritional needs.

  3. Conservation Agriculture Practices in Rainfed Uplands of India Improve Maize-Based System Productivity and Profitability

    Science.gov (United States)

    Pradhan, Aliza; Idol, Travis; Roul, Pravat K.

    2016-01-01

    Traditional agriculture in rainfed uplands of India has been experiencing low agricultural productivity as the lands suffer from poor soil fertility, susceptibility to water erosion and other external pressures of development and climate change. A shift toward more sustainable cropping systems such as conservation agriculture production systems (CAPSs) may help in maintaining soil quality as well as improving crop production and farmer’s net economic benefit. This research assessed the effects over 3 years (2011–2014) of reduced tillage, intercropping, and cover cropping practices customized for maize-based production systems in upland areas of Odisha, India. The study focused on crop yield, system productivity and profitability through maize equivalent yield and dominance analysis. Results showed that maize grain yield did not differ significantly over time or among CAPS treatments while cowpea yield was considered as an additional yield in intercropping systems. Mustard and horsegram grown in plots after maize cowpea intercropping recorded higher grain yields of 25 and 37%, respectively, as compared to those without intercropping. Overall, the full CAPS implementation, i.e., minimum tillage, maize–cowpea intercropping and mustard residue retention had significantly higher system productivity and net benefits than traditional farmer practices, i.e., conventional tillage, sole maize cropping, and no mustard residue retention. The dominance analysis demonstrated increasing benefits of combining conservation practices that exceeded thresholds for farmer adoption. Given the use of familiar crops and technologies and the magnitude of yield and income improvements, these types of CAPS should be acceptable and attractive for smallholder farmers in the area. This in turn should support a move toward sustainable intensification of crop production to meet future household income and nutritional needs. PMID:27471508

  4. Conservation Agriculture Practices in Rainfed Uplands of India Improve Maize-Based System Productivity and Profitability.

    Science.gov (United States)

    Pradhan, Aliza; Idol, Travis; Roul, Pravat K

    2016-01-01

    Traditional agriculture in rainfed uplands of India has been experiencing low agricultural productivity as the lands suffer from poor soil fertility, susceptibility to water erosion and other external pressures of development and climate change. A shift toward more sustainable cropping systems such as conservation agriculture production systems (CAPSs) may help in maintaining soil quality as well as improving crop production and farmer's net economic benefit. This research assessed the effects over 3 years (2011-2014) of reduced tillage, intercropping, and cover cropping practices customized for maize-based production systems in upland areas of Odisha, India. The study focused on crop yield, system productivity and profitability through maize equivalent yield and dominance analysis. Results showed that maize grain yield did not differ significantly over time or among CAPS treatments while cowpea yield was considered as an additional yield in intercropping systems. Mustard and horsegram grown in plots after maize cowpea intercropping recorded higher grain yields of 25 and 37%, respectively, as compared to those without intercropping. Overall, the full CAPS implementation, i.e., minimum tillage, maize-cowpea intercropping and mustard residue retention had significantly higher system productivity and net benefits than traditional farmer practices, i.e., conventional tillage, sole maize cropping, and no mustard residue retention. The dominance analysis demonstrated increasing benefits of combining conservation practices that exceeded thresholds for farmer adoption. Given the use of familiar crops and technologies and the magnitude of yield and income improvements, these types of CAPS should be acceptable and attractive for smallholder farmers in the area. This in turn should support a move toward sustainable intensification of crop production to meet future household income and nutritional needs.

  5. Variation in MHC class II B genes in marbled murrelets: implications for delineating conservation units

    Science.gov (United States)

    C. Vásquez-Carrillo; V. Friesen; L. Hall; M.Z. Peery

    2013-01-01

    Conserving genetic variation is critical for maintaining the evolutionary potential and viability of a species. Genetic studies seeking to delineate conservation units, however, typically focus on characterizing neutral genetic variation and may not identify populations harboring local adaptations. Here, variation at two major histocompatibility complex (MHC) class II...

  6. 78 FR 43974 - Energy and Water Use Labeling for Consumer Products Under the Energy Policy and Conservation Act...

    Science.gov (United States)

    2013-07-23

    ... FEDERAL TRADE COMMISSION 16 CFR Part 305 [3084-AB15] Energy and Water Use Labeling for Consumer Products Under the Energy Policy and Conservation Act (Energy Labeling Rule) AGENCY: Federal Trade...'') in 1979,\\1\\ pursuant to the Energy Policy and Conservation Act of 1975 (EPCA).\\2\\ The Rule requires...

  7. Neutral Higgs production at proton colliders in the CP-conserving NMSSM

    International Nuclear Information System (INIS)

    Liebler, Stefan

    2015-02-01

    We discuss neutral Higgs boson production through gluon fusion and bottom-quark annihilation in the CP-conserving Z 3 -invariant Next-to-Minimal Supersymmetric Standard Model (NMSSM) at proton colliders. For gluon fusion we adapt known asymptotic expansions in supersymmetric particles for the inclusion of next-to-leading order contributions of squarks and gluinos from the Minimal Supersymmetric Standard Model (MSSM) and include electro-weak corrections involving light quarks. Together with the resummation of higher order sbottom contributions in the bottom-quark Yukawa coupling for both production processes we thus present accurate cross section predictions implemented in a new release of the code SusHi. We elaborate on the new features of an additional SU(2) L singlet in the production of CP-even and -odd Higgs bosons with respect to the MSSM and include a short discussion of theory uncertainties.

  8. Coupling movement and landscape ecology for animal conservation in production landscapes.

    Science.gov (United States)

    Doherty, Tim S; Driscoll, Don A

    2018-01-10

    Habitat conversion in production landscapes is among the greatest threats to biodiversity, not least because it can disrupt animal movement. Using the movement ecology framework, we review animal movement in production landscapes, including areas managed for agriculture and forestry. We consider internal and external drivers of altered animal movement and how this affects navigation and motion capacities and population dynamics. Conventional management approaches in fragmented landscapes focus on promoting connectivity using structural changes in the landscape. However, a movement ecology perspective emphasizes that manipulating the internal motivations or navigation capacity of animals represents untapped opportunities to improve movement and the effectiveness of structural connectivity investments. Integrating movement and landscape ecology opens new opportunities for conservation management in production landscapes. © 2018 The Authors.

  9. Comparative analysis of alternative co-production approaches to conservation science in Alaska

    Science.gov (United States)

    Trammell, E. J.

    2017-12-01

    Co-production has been suggested as an important tool for reducing the gap between science and management. Although co-production can require substantial investments in time and relationship building, there are a range of possible approaches that can be utilized that honor the focus and intent of co-production. I present here a comparison of three efforts that range from relatively simple, to complex and exhaustive, that illustrate diverse approaches to co-production of conservation science in Alaska. The first example highlights a workshop-based approach to identify long-term environmental monitoring needs in Alaska, while the second example describes stakeholder-driven scenarios that identified stressors to salmon in southcentral Alaska. The third example describes a 2-year cooperative agreement to develop management questions as part of a rapid ecoregional assessment in central Alaska. Results suggest that careful stakeholder selection is essential to successful co-production. Additionally, all three examples highlight the potential disconnect between management questions and specific management decisions, even when working directly with resource managers. As the focus of the Alaska Climate Science Center will be on co-production of climate science over the next 5 years, I conclude with some key pathways forward for successful co-production efforts in the future.

  10. Transcriptome profiling in conifers and the PiceaGenExpress database show patterns of diversification within gene families and interspecific conservation in vascular gene expression

    Directory of Open Access Journals (Sweden)

    Raherison Elie

    2012-08-01

    Full Text Available Abstract Background Conifers have very large genomes (13 to 30 Gigabases that are mostly uncharacterized although extensive cDNA resources have recently become available. This report presents a global overview of transcriptome variation in a conifer tree and documents conservation and diversity of gene expression patterns among major vegetative tissues. Results An oligonucleotide microarray was developed from Picea glauca and P. sitchensis cDNA datasets. It represents 23,853 unique genes and was shown to be suitable for transcriptome profiling in several species. A comparison of secondary xylem and phelloderm tissues showed that preferential expression in these vascular tissues was highly conserved among Picea spp. RNA-Sequencing strongly confirmed tissue preferential expression and provided a robust validation of the microarray design. A small database of transcription profiles called PiceaGenExpress was developed from over 150 hybridizations spanning eight major tissue types. In total, transcripts were detected for 92% of the genes on the microarray, in at least one tissue. Non-annotated genes were predominantly expressed at low levels in fewer tissues than genes of known or predicted function. Diversity of expression within gene families may be rapidly assessed from PiceaGenExpress. In conifer trees, dehydrins and late embryogenesis abundant (LEA osmotic regulation proteins occur in large gene families compared to angiosperms. Strong contrasts and low diversity was observed in the dehydrin family, while diverse patterns suggested a greater degree of diversification among LEAs. Conclusion Together, the oligonucleotide microarray and the PiceaGenExpress database represent the first resource of this kind for gymnosperm plants. The spruce transcriptome analysis reported here is expected to accelerate genetic studies in the large and important group comprised of conifer trees.

  11. Conserving marine biodiversity: insights from life-history trait candidate genes in Atlantic cod (Gadus morhua)

    DEFF Research Database (Denmark)

    Hansen, Jakob Hemmer; Therkildsen, Nina Overgaard; Meldrup, Dorte

    2014-01-01

    Recent technological developments have facilitated an increased focus on identifying genomic regions underlying adaptive trait variation in natural populations, and it has been advocated that this information should be important for designating population units for conservation. In marine fishes...... are under selection in natural populations of Atlantic cod. Furthermore, we find that patterns of variation in outlier markers do not align with those observed at selectively neutral markers, and that outlier markers identify conservation units on finer geographical scales than those revealed when analysing...... only neutral markers. Accordingly, results also suggest that information about adaptive genetic variation will be useful for targeted conservation and management in this and other marine species...

  12. Nuclear cGMP-dependent kinase regulates gene expression via activity-dependent recruitment of a conserved histone deacetylase complex.

    Directory of Open Access Journals (Sweden)

    Yan Hao

    2011-05-01

    Full Text Available Elevation of the second messenger cGMP by nitric oxide (NO activates the cGMP-dependent protein kinase PKG, which is key in regulating cardiovascular, intestinal, and neuronal functions in mammals. The NO-cGMP-PKG signaling pathway is also a major therapeutic target for cardiovascular and male reproductive diseases. Despite widespread effects of PKG activation, few molecular targets of PKG are known. We study how EGL-4, the Caenorhabditis elegans PKG ortholog, modulates foraging behavior and egg-laying and seeks the downstream effectors of EGL-4 activity. Using a combination of unbiased forward genetic screen and proteomic analysis, we have identified a conserved SAEG-1/SAEG-2/HDA-2 histone deacetylase complex that is specifically recruited by activated nuclear EGL-4. Gene expression profiling by microarrays revealed >40 genes that are sensitive to EGL-4 activity in a SAEG-1-dependent manner. We present evidence that EGL-4 controls egg laying via one of these genes, Y45F10C.2, which encodes a novel protein that is expressed exclusively in the uterine epithelium. Our results indicate that, in addition to cytoplasmic functions, active EGL-4/PKG acts in the nucleus via a conserved Class I histone deacetylase complex to regulate gene expression pertinent to behavioral and physiological responses to cGMP. We also identify transcriptional targets of EGL-4 that carry out discrete components of the physiological response.

  13. Conservation of transcription factor binding events predicts gene expression across species

    OpenAIRE

    Hemberg, Martin; Kreiman, Gabriel

    2011-01-01

    Recent technological advances have made it possible to determine the genome-wide binding sites of transcription factors (TFs). Comparisons across species have suggested a relatively low degree of evolutionary conservation of experimentally defined TF binding events (TFBEs). Using binding data for six different TFs in hepatocytes and embryonic stem cells from human and mouse, we demonstrate that evolutionary conservation of TFBEs within orthologous proximal promoters is closely linked to funct...

  14. DnaB gene product-independence of DNA polymerase III-directed repair synthesis in Escherichia coli K-12

    International Nuclear Information System (INIS)

    Billen, D.; Hellermann, G.R.

    1977-01-01

    An investigation has been carried out into the role of dnaB gene product in X-ray-induced repair synthesis carried out by DNA polymerase III in toluene-treated Escherichia coli K-12. A polAl polBlOO dnaB mutant deficient in both DNA polymerase I and II activities was used, and it was shown that the level of X-ray-induced, ATP-dependent, non-conservative DNA synthesis was, unlike semi-conservative DNA synthesis, unaffected by a temperature shift from 30 0 to 42 0 C. The dnaB gene product was not therefore necessary for DNA polymerase III-directed repair synthesis, which occurred in the absence of replicative synthesis. (U.K.)

  15. Conserved-peptide upstream open reading frames (CPuORFs are associated with regulatory genes in angiosperms

    Directory of Open Access Journals (Sweden)

    Richard A Jorgensen

    2012-08-01

    Full Text Available Upstream open reading frames (uORFs are common in eukaryotic transcripts, but those that encode conserved peptides (CPuORFs occur in less than 1% of transcripts. The peptides encoded by three plant CPuORF families are known to control translation of the downstream ORF in response to a small signal molecule (sucrose, polyamines and phosphocholine. In flowering plants, transcription factors are statistically over-represented among genes that possess CPuORFs, and in general it appeared that many CPuORF genes also had other regulatory functions, though the significance of this suggestion was uncertain (Hayden and Jorgensen, 2007. Five years later the literature provides much more information on the functions of many CPuORF genes. Here we reassess the functions of 27 known CPuORF gene families and find that 22 of these families play a variety of different regulatory roles, from transcriptional control to protein turnover, and from small signal molecules to signal transduction kinases. Clearly then, there is indeed a strong association of CPuORFs with regulatory genes. In addition, 16 of these families play key roles in a variety of different biological processes. Most strikingly, the core sucrose response network includes three different CPuORFs, creating the potential for sophisticated balancing of the network in response to three different molecular inputs. We propose that the function of most CPuORFs is to modulate translation of a downstream major ORF (mORF in response to a signal molecule recognized by the conserved peptide and that because the mORFs of CPuORF genes generally encode regulatory proteins, many of them centrally important in the biology of plants, CPuORFs play key roles in balancing such regulatory networks.

  16. Id-1 gene and gene products as therapeutic targets for treatment of breast cancer and other types of carcinoma

    Science.gov (United States)

    Desprez, Pierre-Yves; Campisi, Judith

    2014-08-19

    A method for treatment of breast cancer and other types of cancer. The method comprises targeting and modulating Id-1 gene expression, if any, for the Id-1 gene, or gene products in breast or other epithelial cancers in a patient by delivering products that modulate Id-1 gene expression. When expressed, Id-1 gene is a prognostic indicator that cancer cells are invasive and metastatic.

  17. Patterns of genetic differentiation at MHC class I genes and microsatellites identify conservation units in the giant panda.

    Science.gov (United States)

    Zhu, Ying; Wan, Qiu-Hong; Yu, Bin; Ge, Yun-Fa; Fang, Sheng-Guo

    2013-10-22

    Evaluating patterns of genetic variation is important to identify conservation units (i.e., evolutionarily significant units [ESUs], management units [MUs], and adaptive units [AUs]) in endangered species. While neutral markers could be used to infer population history, their application in the estimation of adaptive variation is limited. The capacity to adapt to various environments is vital for the long-term survival of endangered species. Hence, analysis of adaptive loci, such as the major histocompatibility complex (MHC) genes, is critical for conservation genetics studies. Here, we investigated 4 classical MHC class I genes (Aime-C, Aime-F, Aime-I, and Aime-L) and 8 microsatellites to infer patterns of genetic variation in the giant panda (Ailuropoda melanoleuca) and to further define conservation units. Overall, we identified 24 haplotypes (9 for Aime-C, 1 for Aime-F, 7 for Aime-I, and 7 for Aime-L) from 218 individuals obtained from 6 populations of giant panda. We found that the Xiaoxiangling population had the highest genetic variation at microsatellites among the 6 giant panda populations and higher genetic variation at Aime-MHC class I genes than other larger populations (Qinling, Qionglai, and Minshan populations). Differentiation index (FST)-based phylogenetic and Bayesian clustering analyses for Aime-MHC-I and microsatellite loci both supported that most populations were highly differentiated. The Qinling population was the most genetically differentiated. The giant panda showed a relatively higher level of genetic diversity at MHC class I genes compared with endangered felids. Using all of the loci, we found that the 6 giant panda populations fell into 2 ESUs: Qinling and non-Qinling populations. We defined 3 MUs based on microsatellites: Qinling, Minshan-Qionglai, and Daxiangling-Xiaoxiangling-Liangshan. We also recommended 3 possible AUs based on MHC loci: Qinling, Minshan-Qionglai, and Daxiangling-Xiaoxiangling-Liangshan. Furthermore, we recommend

  18. Regulatory Oversight of Cell and Gene Therapy Products in Canada.

    Science.gov (United States)

    Ridgway, Anthony; Agbanyo, Francisca; Wang, Jian; Rosu-Myles, Michael

    2015-01-01

    Health Canada regulates gene therapy products and many cell therapy products as biological drugs under the Canadian Food and Drugs Act and its attendant regulations. Cellular products that meet certain criteria, including minimal manipulation and homologous use, may be subjected to a standards-based approach under the Safety of Human Cells, Tissues and Organs for Transplantation Regulations. The manufacture and clinical testing of cell and gene therapy products (CGTPs) presents many challenges beyond those for protein biologics. Cells cannot be subjected to pathogen removal or inactivation procedures and must frequently be administered shortly after final formulation. Viral vector design and manufacturing control are critically important to overall product quality and linked to safety and efficacy in patients through concerns such as replication competence, vector integration, and vector shedding. In addition, for many CGTPs, the value of nonclinical studies is largely limited to providing proof of concept, and the first meaningful data relating to appropriate dosing, safety parameters, and validity of surrogate or true determinants of efficacy must come from carefully designed clinical trials in patients. Addressing these numerous challenges requires application of various risk mitigation strategies and meeting regulatory expectations specifically adapted to the product types. Regulatory cooperation and harmonisation at an international level are essential for progress in the development and commercialisation of these products. However, particularly in the area of cell therapy, new regulatory paradigms may be needed to harness the benefits of clinical progress in situations where the resources and motivation to pursue a typical drug product approval pathway may be lacking.

  19. A conserved gene family encodes transmembrane proteins with fibronectin, immunoglobulin and leucine-rich repeat domains (FIGLER

    Directory of Open Access Journals (Sweden)

    Haga Christopher L

    2007-09-01

    Full Text Available Abstract Background In mouse the cytokine interleukin-7 (IL-7 is required for generation of B lymphocytes, but human IL-7 does not appear to have this function. A bioinformatics approach was therefore used to identify IL-7 receptor related genes in the hope of identifying the elusive human cytokine. Results Our database search identified a family of nine gene candidates, which we have provisionally named fibronectin immunoglobulin leucine-rich repeat (FIGLER. The FIGLER 1–9 genes are predicted to encode type I transmembrane glycoproteins with 6–12 leucine-rich repeats (LRR, a C2 type Ig domain, a fibronectin type III domain, a hydrophobic transmembrane domain, and a cytoplasmic domain containing one to four tyrosine residues. Members of this multichromosomal gene family possess 20–47% overall amino acid identity and are differentially expressed in cell lines and primary hematopoietic lineage cells. Genes for FIGLER homologs were identified in macaque, orangutan, chimpanzee, mouse, rat, dog, chicken, toad, and puffer fish databases. The non-human FIGLER homologs share 38–99% overall amino acid identity with their human counterpart. Conclusion The extracellular domain structure and absence of recognizable cytoplasmic signaling motifs in members of the highly conserved FIGLER gene family suggest a trophic or cell adhesion function for these molecules.

  20. Importance of nuclear technology in the conservation and production of nutritional fungi

    International Nuclear Information System (INIS)

    Sajet, A.S.

    2008-01-01

    The shortfall in food and field crops due to bad weather and the incidence of insects and microbes during harvesting, handling and storage under non-suitable conditions, called the attention of researchers to try to minimize the damage happening and by various means, whether to develop sources of new food, such as producing nutritional fungi, or by following non-traditional methods of anti-microbes and insects such as the use of radiation as a safe and successful way to save the food without any toxic effects. Permits have been issued for food irradiation by many international organizations including IAEA, World Health Organization and FAO. Nutritional fungi is one of the food sources used as food fit for human consumption in various countries around the world due to their importance which includes many aspects: the nutritional and health value; medical significance; environmental importance and industrial importance. Nuclear technology has contributed in many of the developments in the production and conservation of nutritional fungi, notably, biological studies of nutritional fungi, production technology of fungus, the role of radiation in the preparation and improvement of the nutritional media, improvement of the fungus strains, the use of radiation in the conservation of nutritional fungi and the detection of irradiated nutritional fungus.

  1. Chemical production from waste carbon monoxide: its potential for energy conservation

    Energy Technology Data Exchange (ETDEWEB)

    Rohrmann, C.A.; Schiefelbein, G.F.; Molton, P.M.; Li, C.T.; Elliott, D.C.; Baker, E.G.

    1977-11-01

    Results of a study of the potential for energy conservation by producing chemicals from by-product or waste carbon monoxide (CO) from industrial sources are summarized. Extensive compilations of both industrial sources and uses for carbon monoxide were developed and included. Reviews of carbon monoxide purification and concentration technology and preliminary economic evaluations of carbon monoxide concentration, pipeline transportation and utilization of CO in the synthesis of ammonia and methanol are included. Preliminary technical and economic feasibility studies were made of producing ammonia and methanol from the by-product CO produced by a typical elemental phosphorus plant. Methanol synthesis appears to be more attractive than ammonia synthesis when using CO feedstock because of reduced water gas shift and carbon dioxide removal requirements. The economic studies indicate that methanol synthesis from CO appears to be competitive with conventional technology when the price of natural gas exceeds $0.82/million Btu, while ammonia synthesis from CO is probably not competitive until the price of natural gas exceeds $1.90/million Btu. It is concluded that there appears to be considerable potential for energy conservation in the chemical industry, by collecting CO rather than flaring it, and using it to make major chemicals such as ammonia and methanol.

  2. Resource conservation approached with an appropriate collection and upgrade-remanufacturing for used electronic products.

    Science.gov (United States)

    Zlamparet, Gabriel I; Tan, Quanyin; Stevels, A B; Li, Jinhui

    2018-03-01

    This comparative research represents an example for a better conservation of resources by reducing the amount of waste (kg) and providing it more value under the umbrella of remanufacturing. The three discussed cases will expose three issues already addressed separately in the literature. The generation of waste electrical and electronic equipment (WEEE) interacts with the environmental depletion. In this article, we gave the examples of addressed issues under the concept of remanufacturing. Online collection opportunity eliminating classical collection, a business to business (B2B) implementation for remanufactured servers and medical devices. The material reuse (recycling), component sustainability, reuse (part harvesting), product reuse (after repair/remanufacturing) indicates the recovery potential using remanufacturing tool for a better conservation of resources adding more value to the products. Our findings can provide an overview of new system organization for the general collection, market potential and the technological advantages using remanufacturing instead of recycling of WEEE or used electrical and electronic equipment. Copyright © 2017. Published by Elsevier Ltd.

  3. Effects of 24 Years of Conservation Tillage Systems on Soil Organic Carbon and Soil Productivity

    Directory of Open Access Journals (Sweden)

    Kenneth R. Olson

    2013-01-01

    Full Text Available The 24-year study was conducted in southern Illinois (USA on land similar to that being removed from Conservation Reserve Program (CRP to evaluate the effects of conservation tillage systems on: (1 amount and rates of soil organic carbon (SOC storage and retention, (2 the long-term corn and soybean yields, and (3 maintenance and restoration of soil productivity of previously eroded soils. The no-till (NT plots did store and retain 7.8 Mg C ha−1 more and chisel plow (CP −1.6 Mg C ha−1 less SOC in the soil than moldboard plow (MP during the 24 years. However, no SOC sequestration occurred in the sloping and eroding NT, CP, and MP plots since the SOC level of the plot area was greater at the start of the experiment than at the end. The NT plots actually lost a total of −1.2 Mg C ha−1, the CP lost −9.9 Mg C ha−1, and the MP lost −8.2 Mg C ha−1 during the 24-year study. The long-term productivity of NT compared favorably with that of MP and CP systems.

  4. Effect of resource conserving techniques on crop productivity in rice-wheat cropping system

    International Nuclear Information System (INIS)

    Mann, R.A.; Munir, M.; Haqqani, A.M.

    2004-01-01

    Rice-wheat cropping system is the most important one in Pakistan. The system provides food and livelihood for more than 15 million people in the country. The productivity of the system is much lower than the potential yields of both rice and wheat crops. With the traditional methods, rice-wheat system is not a profitable one to many farmers. Hence, Cost of cultivation must be reduced and at the same time, efficiency of resources like irrigation water, fuel, and fertilizers must be improved to make the crop production system more viable and eco- friendly. Resource conserving technology (RCT) must figure highly in this equation, since they play a major role in achieving the above goals. The RCT include laser land leveling, zero-tillage, bed furrow irrigation method and crop residue management. These technologies were evaluated in irrigated areas of Punjab where rice follows wheat. The results showed that paddy yield was not affected by the new methods. Direct seeding of rice crop saved irrigation water by 13% over the conventionally planted crop. Weeds were the major problem indirect seeded crop, which could be eliminated through cultural, mechanical and chemical means. Wheat crop on beds produced the highest yield but cost of production was minimum in the zero-till wheat crop. Planting of wheat on raised beds in making headway in low- lying and poorly drained areas. Thus, resource conserving tillage technology provides a tool for making progress towards improving and sustaining wheat production system, helping with food security and poverty alleviation in Pakistan in the next few decades. (author)

  5. MicroRNA genes preferentially expressed in dendritic cells contain sites for conserved transcription factor binding motifs in their promoters

    Directory of Open Access Journals (Sweden)

    Huynen Martijn A

    2011-06-01

    Full Text Available Abstract Background MicroRNAs (miRNAs play a fundamental role in the regulation of gene expression by translational repression or target mRNA degradation. Regulatory elements in miRNA promoters are less well studied, but may reveal a link between their expression and a specific cell type. Results To explore this link in myeloid cells, miRNA expression profiles were generated from monocytes and dendritic cells (DCs. Differences in miRNA expression among monocytes, DCs and their stimulated progeny were observed. Furthermore, putative promoter regions of miRNAs that are significantly up-regulated in DCs were screened for Transcription Factor Binding Sites (TFBSs based on TFBS motif matching score, the degree to which those TFBSs are over-represented in the promoters of the up-regulated miRNAs, and the extent of conservation of the TFBSs in mammals. Conclusions Analysis of evolutionarily conserved TFBSs in DC promoters revealed preferential clustering of sites within 500 bp upstream of the precursor miRNAs and that many mRNAs of cognate TFs of the conserved TFBSs were indeed expressed in the DCs. Taken together, our data provide evidence that selected miRNAs expressed in DCs have evolutionarily conserved TFBSs relevant to DC biology in their promoters.

  6. Identification of conserved drought stress responsive gene-network across tissues and developmental stages in rice.

    Science.gov (United States)

    Smita, Shuchi; Katiyar, Amit; Pandey, Dev Mani; Chinnusamy, Viswanathan; Archak, Sunil; Bansal, Kailash Chander

    2013-01-01

    Identification of genes that are coexpressed across various tissues and environmental stresses is biologically interesting, since they may play coordinated role in similar biological processes. Genes with correlated expression patterns can be best identified by using coexpression network analysis of transcriptome data. In the present study, we analyzed the temporal-spatial coordination of gene expression in root, leaf and panicle of rice under drought stress and constructed network using WGCNA and Cytoscape. Total of 2199 differentially expressed genes (DEGs) were identified in at least three or more tissues, wherein 88 genes have coordinated expression profile among all the six tissues under drought stress. These 88 highly coordinated genes were further subjected to module identification in the coexpression network. Based on chief topological properties we identified 18 hub genes such as ABC transporter, ATP-binding protein, dehydrin, protein phosphatase 2C, LTPL153 - Protease inhibitor, phosphatidylethanolaminebinding protein, lactose permease-related, NADP-dependent malic enzyme, etc. Motif enrichment analysis showed the presence of ABRE cis-elements in the promoters of > 62% of the coordinately expressed genes. Our results suggest that drought stress mediated upregulated gene expression was coordinated through an ABA-dependent signaling pathway across tissues, at least for the subset of genes identified in this study, while down regulation appears to be regulated by tissue specific pathways in rice.

  7. Conservation value of low-productivity forests measured as the amount and diversity of dead wood and saproxylic beetles.

    Science.gov (United States)

    Hämäläinen, Aino; Strengbom, Joachim; Ranius, Thomas

    2018-06-01

    In many managed landscapes, low-productivity land comprises most of the remaining relatively untouched areas, and is often over-represented within protected areas. The relationship between the productivity and conservational value of a site is poorly known; however, it has been hypothesized that biodiversity increases with productivity due to higher resource abundance or heterogeneity, and that the species communities of low-productivity land are a nested subset of communities from more productive land. We tested these hypotheses for dead-wood-dependent beetles by comparing their species richness and composition, as well as the amount and diversity of dead wood, between low-productivity (potential forest growth dead wood, but volume appeared to be a better predictor than diversity for the higher species richness in set-asides. Beetle species composition was similar among stand types, and the assemblages in low-productivity stands were largely subsets of those in high-productivity set-asides. However, 11% of all species and 40% of red-listed species only occurred in high-productivity stands, while no species were unique to low-productivity stands. We conclude that low-productivity forests are less valuable for conservation than high-productivity forest land. Given the generally similar species composition among stand types, a comparable conservational effect could be obtained by setting aside a larger area of low-productivity forest in comparison to the high-productivity. In terms of dead wood volumes, 1.8-3.6 ha of low-productivity forest has the same value as 1 ha of unmanaged high-productivity forest. This figure can be used to estimate the conservation value of low-productivity forests; however, as high-productivity forests harbored some unique species, they are not completely exchangeable. © 2018 The Authors. Ecological Applications published by Wiley Periodicals, Inc. on behalf of Ecological Society of America.

  8. Energy indices in irrigated wheat production under conservation and conventional tillage and planting methods

    Directory of Open Access Journals (Sweden)

    S. M Hosseini

    2016-04-01

    Full Text Available Introduction: Conservation tillage system was recommended for soil erosion control in North America for the first time 60 years ago (Wang et al., 2006. Using this tillage system including minimum and zero tillage has been rapidly developed in recent years. Thearea covered by zero tillage in 2006 was 95 million ha all over the world (Dumanski et al., 2006. In addition to saving soil and water resources, conservation tillage system reduces energy consumption and improves energy indices by combining different tillage and planting operations. Results of research conducted in Fars province shows that conservation tillage saves fuel consumption for 77% compared to the conventional system (Afzalinia et al., 2009. Conservation tillage also reduces energy consumption from 23.6 to 42.8% in comparison to the conventional tillage (Rusu, 2005. Since energy indices would be affected by reduced input energies in conservation tillage, this research was conducted to evaluate the effect of different tillage and planting methods on energy inputs and energy indices in irrigated wheat production in Eghlid region. Materials and Methods: This research was performed to evaluate and compare the energy indices in irrigated wheat production under different tillage and planting methods. The study was conducted in the form of a randomized complete block experimental design with five treatments and three replications in Eghlid region. The treatments were included, conventional tillage and seed broadcasting (A, conventional tillage and planting with Machine Barzegar grain drill (B, reduced tillage and seeding with Roto-seeder (C, direct seeding with Jairan Sanaat grain drill (D, and direct seeding with Sfoggia direct drill (E. Experimental plots with 10 by 50 m dimensions were used in this study. Loss crop residues were taken out of the experimental plots and standing crop residues were retained in the plots. In the conventional tillage method, primary tillage was performed

  9. Use of galerina marginata genes and proteins for peptide production

    Science.gov (United States)

    Hallen-Adams, Heather E.; Scott-Craig, John S.; Walton, Jonathan D.; Luo, Hong

    2018-04-03

    The present invention relates to compositions and methods comprising genes and peptides associated with cyclic peptides and cyclic peptide production in mushrooms. In particular, the present invention relates to using genes and proteins from Galerina species encoding peptides specifically relating to amatoxins in addition to proteins involved with processing cyclic peptide toxins. In a preferred embodiment, the present invention also relates to methods for making small peptides and small cyclic peptides including peptides similar to amanitin. Further, the present inventions relate to providing kits for making small peptides.

  10. Use of Galerina marginata genes and proteins for peptide production

    Energy Technology Data Exchange (ETDEWEB)

    Hallen-Adams, Heather E.; Scott-Craig, John S.; Walton, Jonathan D.; Luo, Hong

    2017-03-21

    The present invention relates to compositions and methods comprising genes and peptides associated with cyclic peptides and cyclic peptide production in mushrooms. In particular, the present invention relates to using genes and proteins from Galerina species encoding peptides specifically relating to amatoxins in addition to proteins involved with processing cyclic peptide toxins. In a preferred embodiment, the present invention also relates to methods for making small peptides and small cyclic peptides including peptides similar to amanitin. Further, the present inventions relate to providing kits for making small peptides.

  11. Evolution and Origin of HRS, a Protein Interacting with Merlin, the Neurofibromatosis 2 Gene Product

    Directory of Open Access Journals (Sweden)

    Leonid V. Omelyanchuk

    2009-10-01

    Full Text Available Hepatocyte growth factor receptor tyrosine kinase substrate (HRS is an endosomal protein required for trafficking receptor tyrosine kinases from the early endosome to the lysosome. HRS interacts with Merlin, the Neurofibromatosis 2 (NF2 gene product, and this interaction may be important for Merlin’s tumor suppressor activity. Understanding the evolution, origin, and structure of HRS may provide new insight into Merlin function. We show that HRS homologs are present across a wide range of Metazoa with the yeast Vps27 protein as their most distant ancestor. The phylogenetic tree of the HRS family coincides with species evolution and divergence, suggesting a unique function for HRS. Sequence alignment shows that various protein domains of HRS, including the VHS domain, the FYVE domain, the UIM domain, and the clathrin-binding domain, are conserved from yeast to multicellular organisms. The evolutionary transition from unicellular to multicellular organisms was accompanied by the appearance of a binding site for Merlin, which emerges in the early Metazoa after its separation from flatworms. In addition to the region responsible for growth suppression, the Merlin-binding and STAM-binding domains of HRS are conserved among multicellular organisms. The residue equivalent to tyrosine-377, which is phosphorylated in the human HRS protein, is highly conserved throughout the HRS family. Three additional conserved boxes lacking assigned functions are found in the HRS proteins of Metazoa. While boxes 1 and 3 may constitute the Eps-15- and Snx1-binding sites, respectively, box 2, containing the residue equivalent to tyrosine-377, is likely to be important for HRS phosphorylation. While several functional domains are conserved throughout the HRS family, the STAM-binding, Merlin-binding, and growth suppression domains evolved in the early Metazoa around the time the Merlin protein emerged. As these domains appear during the transition to multicellularity

  12. Effort to Increase Oil Palm Production through Application Technique of Soil and Water Conservation

    Directory of Open Access Journals (Sweden)

    Kukuh Murtilaksono

    2009-05-01

    Full Text Available The study was carried out at block 375, 415, and 414 (block 1, 2, and 3 Afdeling III, Mangement Unit of Rejosari, PT Perkebunan Nusantara VII, Lampung from June 2005 until December 2007. Objective of the study is to examine the effect of soil and water conservation measurement, namely bund terrace and silt pit that are combined with retarded-water hole on production of oil palm. Sampled trees of each block were randomly selected as much as 36 trees. Parameters of vegetative growth (additional new frond, total of frond, number of new bunch, production (number of bunch, fresh fruit bunch (TBS, and average of bunch weigh (RBT were observed and recorded every two weeks. Production of palm oil of each block was also recorded every harvesting schedule of Afdeling. Tabular data were analyzed descriptively by logical comparison among the blocks as result of application of bund terrace and silt pit. Although the data of sampled trees were erratic, bund terrace and silt pit generally increasing number of frond, number of bunch, average of bunch weight, and fresh fruit bunch. Bund terrace gived the highest production of TBS (25.2 t ha-1 compared to silt pit application (23.6 t ha-1, and it has better effect on TBS than block control (20.8 t ha-1. Aside from that, RBT is the highest (21 kg at bund terrace block compared to silt pit block (20 kg and control block (19 kg.

  13. Overexpression screens identify conserved dosage chromosome instability genes in yeast and human cancer

    Science.gov (United States)

    Duffy, Supipi; Fam, Hok Khim; Wang, Yi Kan; Styles, Erin B.; Kim, Jung-Hyun; Ang, J. Sidney; Singh, Tejomayee; Larionov, Vladimir; Shah, Sohrab P.; Andrews, Brenda; Boerkoel, Cornelius F.; Hieter, Philip

    2016-01-01

    Somatic copy number amplification and gene overexpression are common features of many cancers. To determine the role of gene overexpression on chromosome instability (CIN), we performed genome-wide screens in the budding yeast for yeast genes that cause CIN when overexpressed, a phenotype we refer to as dosage CIN (dCIN), and identified 245 dCIN genes. This catalog of genes reveals human orthologs known to be recurrently overexpressed and/or amplified in tumors. We show that two genes, TDP1, a tyrosyl-DNA-phosphdiesterase, and TAF12, an RNA polymerase II TATA-box binding factor, cause CIN when overexpressed in human cells. Rhabdomyosarcoma lines with elevated human Tdp1 levels also exhibit CIN that can be partially rescued by siRNA-mediated knockdown of TDP1. Overexpression of dCIN genes represents a genetic vulnerability that could be leveraged for selective killing of cancer cells through targeting of an unlinked synthetic dosage lethal (SDL) partner. Using SDL screens in yeast, we identified a set of genes that when deleted specifically kill cells with high levels of Tdp1. One gene was the histone deacetylase RPD3, for which there are known inhibitors. Both HT1080 cells overexpressing hTDP1 and rhabdomyosarcoma cells with elevated levels of hTdp1 were more sensitive to histone deacetylase inhibitors valproic acid (VPA) and trichostatin A (TSA), recapitulating the SDL interaction in human cells and suggesting VPA and TSA as potential therapeutic agents for tumors with elevated levels of hTdp1. The catalog of dCIN genes presented here provides a candidate list to identify genes that cause CIN when overexpressed in cancer, which can then be leveraged through SDL to selectively target tumors. PMID:27551064

  14. Detection of biosurfactants in Bacillus species: genes and products identification.

    Science.gov (United States)

    Płaza, G; Chojniak, J; Rudnicka, K; Paraszkiewicz, K; Bernat, P

    2015-10-01

    To screen environmental Bacillus strains for detection of genes encoding the enzymes involved in biosurfactant synthesis and to evaluate their products e.g. surfactin, iturin and fengycin. The taxonomic identification of isolated from the environment Bacillus strains was performed by Microgene ID Bacillus panel and GEN III Biolog system. The polymerase chain reaction (PCR) strategy for screening of genes in Bacillus strains was set up. Liquid chromatography-mass spectrometry (LC-MS/MS) method was used for the identification of lipopeptides (LPs). All studied strains exhibited the presence of srfAA gene and produced surfactin mostly as four homologues (C13 to C16). Moreover, in 2 strains (KP7, T'-1) simultaneous co-production of 3 biosurfactants: surfactin, iturin and fengycin was observed. Additionally, it was found out that isolate identified as Bacillus subtilis ssp. subtilis (KP7), beside LPs co-production, synthesizes surfactin with the efficiency much higher than other studied strains (40·2 mg l(-1) ) and with the yield ranging from 0·8 to 8·3 mg l(-1) . We showed that the combined methodology based on PCR and LC-MS/MS technique is an optimal tool for the detection of genes encoding enzymes involved in biosurfactant synthesis as well as their products, e.g. surfactin, iturin and fengycin. This approach improves the screening and the identification of environmental Bacillus co-producing biosurfactants-stimulating and facilitating the development of this area of science. The findings of this work will help to improve screening of biosurfactant producers. Discovery of novel biosurfactants and biosurfactants co-production ability has shed light on their new application fields and for the understanding of their interactions and properties. © 2015 The Society for Applied Microbiology.

  15. Can conservation tillage reduce N2O emissions on cropland transitioning to organic vegetable production?

    Science.gov (United States)

    Chen, Guihua; Kolb, Lauren; Cavigelli, Michel A; Weil, Ray R; Hooks, Cerruti R R

    2018-03-15

    Nitrous oxide (N 2 O) is an important greenhouse gas and a catalyst of stratospheric ozone decay. Agricultural soils are the source of 75% of anthropogenic N 2 O emissions globally. Recently, significant attention has been directed at examining effects of conservation tillage on carbon sequestration in agricultural systems. However, limited knowledge is available regarding how these practices impact N 2 O emissions, especially for organic vegetable production systems. In this context, a three-year study was conducted in a well-drained sandy loam field transitioning to organic vegetable production in the Mid-Atlantic coastal plain of USA to investigate impacts of conservation tillage [strip till (ST) and no-till (NT)] and conventional tillage (CT) [with black plastic mulch (CT-BP) and bare-ground (CT-BG)] on N 2 O emissions. Each year, a winter cover crop mixture (forage radish: Raphanus sativus var. longipinnatus, crimson clover: Trifolium incarnatum L., and rye: Secale cereale L.) was grown and flail-mowed in the spring. Nearly 80% of annual N 2 O-nitrogen (N) emissions occurred during the vegetable growing season for all treatments. Annual N 2 O-N emissions were greater in CT-BP than in ST and NT, and greater in CT-BG than in NT, but not different between CT-BG and CT-BP, ST and NT, or CT-BG and ST. Conventional tillage promoted N mineralization and plastic mulch increased soil temperature, which contributed to greater N 2 O-N fluxes. Though water filled porosity in NT was higher and correlated well with N 2 O-N fluxes, annual N 2 O-N emissions were lowest in NT suggesting a lack of substrates for nitrification and denitrification processes. Crop yield was lowest in NT in Year 1 and CT-BP in Year 3 but yield-scaled N 2 O-N emissions were consistently greatest in CT-BP and lowest in NT each year. Our results suggest that for coarse-textured soils in the coastal plain with winter cover crops, conservation tillage practices may reduce N 2 O emissions in organic

  16. Evolutionary history of the recruitment of conserved developmental genes in association to the formation and diversification of a novel trait

    Directory of Open Access Journals (Sweden)

    Shirai Leila T

    2012-02-01

    Full Text Available Abstract Background The origin and modification of novel traits are important aspects of biological diversification. Studies combining concepts and approaches of developmental genetics and evolutionary biology have uncovered many examples of the recruitment, or co-option, of genes conserved across lineages for the formation of novel, lineage-restricted traits. However, little is known about the evolutionary history of the recruitment of those genes, and of the relationship between them -for example, whether the co-option involves whole or parts of existing networks, or whether it occurs by redeployment of individual genes with de novo rewiring. We use a model novel trait, color pattern elements on butterfly wings called eyespots, to explore these questions. Eyespots have greatly diversified under natural and sexual selection, and their formation involves genetic circuitries shared across insects. Results We investigated the evolutionary history of the recruitment and co-recruitment of four conserved transcription regulators to the larval wing disc region where circular pattern elements develop. The co-localization of Antennapedia, Notch, Distal-less, and Spalt with presumptive (eyespot organizers was examined in 13 butterfly species, providing the largest comparative dataset available for the system. We found variation between families, between subfamilies, and between tribes. Phylogenetic reconstructions by parsimony and maximum likelihood methods revealed an unambiguous evolutionary history only for Antennapedia, with a resolved single origin of eyespot-associated expression, and many homoplastic events for Notch, Distal-less, and Spalt. The flexibility in the (co-recruitment of the targeted genes includes cases where different gene combinations are associated with morphologically similar eyespots, as well as cases where identical protein combinations are associated with very different phenotypes. Conclusions The evolutionary history of gene

  17. Associating transcription factors and conserved RNA structures with gene regulation in the human brain

    DEFF Research Database (Denmark)

    Hecker, Nikolai; Seemann, Stefan E.; Silahtaroglu, Asli

    2017-01-01

    Anatomical subdivisions of the human brain can be associated with different neuronal functions. This functional diversification is reflected by differences in gene expression. By analyzing post-mortem gene expression data from the Allen Brain Atlas, we investigated the impact of transcription fac...

  18. Modeling the impact of conservation agriculture on crop production and soil properties in Mediterranean climate

    Science.gov (United States)

    Moussadek, Rachid; Mrabet, Rachid; Dahan, Rachid; Laghrour, Malika; Lembiad, Ibtissam; ElMourid, Mohamed

    2015-04-01

    In Morocco, rainfed agriculture is practiced in the majority of agricultural land. However, the intensive land use coupled to the irregular rainfall constitutes a serious threat that affect country's food security. Conservation agriculture (CA) represents a promising alternative to produce more and sustainably. In fact, the direct seeding showed high yield in arid regions of Morocco but its extending to other more humid agro-ecological zones (rainfall > 350mm) remains scarce. In order to promote CA in Morocco, differents trials have been installed in central plateau of Morocco, to compare CA to conventional tillage (CT). The yields of the main practiced crops (wheat, lentil and checkpea) under CA and CT were analyzed and compared in the 3 soils types (Vertisol, Cambisol and Calcisol). Also, we studied the effect of CA on soil organic matter (SOM) and soil losses (SL) in the 3 different sites. The APSIM model was used to model the long term impact of CA compared to CT. The results obtained in this research have shown favorable effects of CA on crop production, SOM and soil erosion. Key words: Conservation agriculture, yield, soil properties, modeling, APSIM, Morocco.

  19. A Protocol for Producing Virus-Free Artichoke Genetic Resources for Conservation, Breeding, and Production

    Directory of Open Access Journals (Sweden)

    Roberta Spanò

    2018-03-01

    Full Text Available The potential of the globe artichoke biodiversity in the Mediterranean area is enormous but at risk of genetic erosion because only a limited number of varieties are vegetatively propagated and grown. In Apulia (southern Italy, the Regional Government launched specific actions to rescue and preserve biodiversity of woody and vegetable crops in the framework of the Rural Development Program. Many globe artichoke ecotypes have remained neglected and unnoticed for a long time and have been progressively eroded by several causes, which include a poor phytosanitary status. Sanitation of such ecotypes from infections of vascular fungi and viruses may be a solution for their ex situ conservation and multiplication in nursery plants in conformity to the current EU Directives 93/61/CEE and 93/62/CEE that enforce nursery productions of virus-free and true-to-type certified stocks. Five Apulian ecotypes, Bianco di Taranto, Francesina, Locale di Mola, Verde di Putignano and Violetto di Putignano, were sanitized from artichoke Italian latent virus (AILV, artichoke latent virus (ArLV and tomato infectious chlorosis virus (TICV by meristem-tip culture and in vitro thermotherapy through a limited number of subcultures to reduce the risk of “pastel variants” induction of and loss of earliness. A total of 25 virus-free primary sources were obtained and conserved ex situ in a nursery.

  20. The Conserved Actinobacterial Two-Component System MtrAB Coordinates Chloramphenicol Production with Sporulation in Streptomyces venezuelae NRRL B-65442

    Directory of Open Access Journals (Sweden)

    Nicolle F. Som

    2017-06-01

    Full Text Available Streptomyces bacteria make numerous secondary metabolites, including half of all known antibiotics. Production of antibiotics is usually coordinated with the onset of sporulation but the cross regulation of these processes is not fully understood. This is important because most Streptomyces antibiotics are produced at low levels or not at all under laboratory conditions and this makes large scale production of these compounds very challenging. Here, we characterize the highly conserved actinobacterial two-component system MtrAB in the model organism Streptomyces venezuelae and provide evidence that it coordinates production of the antibiotic chloramphenicol with sporulation. MtrAB are known to coordinate DNA replication and cell division in Mycobacterium tuberculosis where TB-MtrA is essential for viability but MtrB is dispensable. We deleted mtrB in S. venezuelae and this resulted in a global shift in the metabolome, including constitutive, higher-level production of chloramphenicol. We found that chloramphenicol is detectable in the wild-type strain, but only at very low levels and only after it has sporulated. ChIP-seq showed that MtrA binds upstream of DNA replication and cell division genes and genes required for chloramphenicol production. dnaA, dnaN, oriC, and wblE (whiB1 are DNA binding targets for MtrA in both M. tuberculosis and S. venezuelae. Intriguingly, over-expression of TB-MtrA and gain of function TB- and Sv-MtrA proteins in S. venezuelae also switched on higher-level production of chloramphenicol. Given the conservation of MtrAB, these constructs might be useful tools for manipulating antibiotic production in other filamentous actinomycetes.

  1. Transcriptional regulation of genes related to progesterone production.

    Science.gov (United States)

    Mizutani, Tetsuya; Ishikane, Shin; Kawabe, Shinya; Umezawa, Akihiro; Miyamoto, Kaoru

    2015-01-01

    Steroid hormones are synthesized from cholesterol in various tissues, mainly in the adrenal glands and gonads. Because these lipid-soluble steroid hormones immediately diffuse through the cells in which they are produced, their secretion directly reflects the activity of the genes related to their production. Progesterone is important not only for luteinization and maintenance of pregnancy, but also as a substrate for most other steroids. Steroidogenic acute regulatory protein (STAR), cytochrome P450 cholesterol side-chain cleavage enzyme (P450scc), and 3β-hydroxysteroid dehydrogenase/Δ(5)-Δ(4) isomerase (3β-HSD) are well-known proteins essential for progesterone production. In addition to them, glutathione S-transferase A1-1 and A3-3 are shown to exert Δ(5)-Δ(4) isomerization activity to produce progesterone in a cooperative fashion with 3β-HSD. 5-Aminolevulinic acid synthase 1, ferredoxin 1, and ferredoxin reductase also play a role in steroidogenesis as accessory factors. Members of the nuclear receptor 5A (NR5A) family (steroidogenic factor 1 and liver receptor homolog 1) play a crucial role in the transcriptional regulation of these genes. The NR5A family activates these genes by binding to NR5A responsive elements present within their promoter regions, as well as to the elements far from their promoters. In addition, various NR5A-interacting proteins including peroxisome proliferator-activated receptor-γ coactivator-1α (PGC-1α), nuclear receptor subfamily 0, group B, member 1 (DAX-1), and CCAAT/enhancer-binding proteins (C/EBP) are involved in the transcription of NR5A target genes and regulate the transcription either positively or negatively under both basal and tropic hormone-stimulated conditions. In this review, we describe the transcriptional regulation of genes related to progesterone production.

  2. From biophysical to social-ecological trade-offs: integrating biodiversity conservation and agricultural production in the Argentine Dry Chaco

    Directory of Open Access Journals (Sweden)

    Matias E. Mastrangelo

    2015-03-01

    Full Text Available Agricultural intensification in rural areas of developing countries compromises the provision of ecosystem services. Social conflict arises among landholders with different preferences for ecosystem services and land-use practices in agricultural frontiers of the Argentine Dry Chaco. We explored policy and management options by assessing the actual and potential outcomes of alternative land-use systems and scenarios. We first constructed the efficiency frontier for avian habitat and agricultural productivity to analyze the combinations of ecosystem services that can be achieved under different land-use intensities. A nonlinear, concave efficiency frontier indicated opportunities to achieve large gains for production with small losses for conservation, for instance, by transitioning from low- to intermediate-intensity systems. Second, we projected production and conservation outcomes, which can be achieved through the implementation of five alternative policy options. The land sharing with conservation scenario, 70% of the landscape covered by intermediate-intensity systems and 30% by undisturbed forests, yielded the higher combination of avian habitat and agricultural productivity. Third, we constructed indifference curves of three landholder groups, i.e., preproductivist, multifunctional, and productivist, by assessing their intentions (proxies for preferences to conserve and convert remnant forests in their landholdings. Multifunctional landholders showed balanced preferences for conserving and converting forests in their landholdings, and maintaining intermediate-intensity systems. A general willingness to conserve forests coexisted in preproductivist landholders with the intention to clear some portions of the landholding and intensify landuse, indicating the potential of an endogenously motivated transition toward a multifunctional regime. Such transition may increase their productivity by 35-65% without compromising avian habitat

  3. Overall requirements for an advanced underground coal extraction system. [environment effects, miner health and safety, production cost, and coal conservation

    Science.gov (United States)

    Goldsmith, M.; Lavin, M. L.

    1980-01-01

    Underground mining systems suitable for coal seams expoitable in the year 2000 are examined with particular relevance to the resources of Central Appalachia. Requirements for such systems may be summarized as follows: (1) production cost; (2)miner safety; (3) miner health; (4) environmental impact; and (5) coal conservation. No significant trade offs between production cost and other performance indices were found.

  4. Management and conservation of tropical acid soils for sustainable crop production. Proceedings of a consultants meeting

    International Nuclear Information System (INIS)

    2000-06-01

    Forests of the tropics are invaluable ecosystems of global, regional and local importance, particularly in terms of protection and conservation of biodiversity and water resources. The indiscriminate conversion of tropical forests into agricultural land as a result of intense human activities - logging and modem shifting cultivation - continues to cause soil erosion and degradation. However, the acid savannahs of the world, such as the cerrado of Brazil, the Llanos in Venezuela and Colombia, the savannahs of Africa, and the largely anthropic savannahs of tropical Asia, encompass vast areas of potentially arable land. The acid soils of the savannahs are mostly considered marginal because of low inherent fertility and susceptibility to rapid degradation. These constraints for agricultural development are exacerbated by the poverty of new settlers who try to cultivate such areas after deforestation. Low- or minimum-input systems are not sustainable on these tropical acid soils but, with sufficient investment and adequate technologies, they can be highly productive. Thus, there is a need to develop management practices for sustainable agricultural production systems on such savannah acid soils. The Soil and Water Management and Crop Nutrition Sub-programme of the Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture strongly supports an integrated approach to soil, water and nutrient management within cropping systems. In this context, nuclear and related techniques can be used to better understand the processes and factors influencing the productivity of agricultural production systems, and improve them through the use of better soil, water and nutrient management practices. A panel of experts actively engaged in field projects on acid soils of savannah agro-ecosystems in the humid and sub-humid tropics convened in March 1999 in Vienna to review and discuss recent research progress, along the following main lines of investigation: (i) utilization of

  5. The Drosophila wings apart gene anchors a novel, evolutionarily conserved pathway of neuromuscular development.

    Science.gov (United States)

    Morriss, Ginny R; Jaramillo, Carmelita T; Mikolajczak, Crystal M; Duong, Sandy; Jaramillo, Maryann S; Cripps, Richard M

    2013-11-01

    wings apart (wap) is a recessive, semilethal gene located on the X chromosome in Drosophila melanogaster, which is required for normal wing-vein patterning. We show that the wap mutation also results in loss of the adult jump muscle. We use complementation mapping and gene-specific RNA interference to localize the wap locus to the proximal X chromosome. We identify the annotated gene CG14614 as the gene affected by the wap mutation, since one wap allele contains a non-sense mutation in CG14614, and a genomic fragment containing only CG14614 rescues the jump-muscle phenotypes of two wap mutant alleles. The wap gene lies centromere-proximal to touch-insensitive larva B and centromere-distal to CG14619, which is tentatively assigned as the gene affected in introverted mutants. In mutant wap animals, founder cell precursors for the jump muscle are specified early in development, but are later lost. Through tissue-specific knockdowns, we demonstrate that wap function is required in both the musculature and the nervous system for normal jump-muscle formation. wap/CG14614 is homologous to vertebrate wdr68, DDB1 and CUL4 associated factor 7, which also are expressed in neuromuscular tissues. Thus, our findings provide insight into mechanisms of neuromuscular development in higher animals and facilitate the understanding of neuromuscular diseases that may result from mis-expression of muscle-specific or neuron-specific genes.

  6. Preclinical and clinical experience in vascular gene therapy: advantages over conservative/standard therapy.

    Science.gov (United States)

    Nikol, S; Huehns, T Y

    2001-04-01

    No systemic pharmacological treatment has been shown to convincingly reduce the incidence of restenosis after angioplasty or increase the formation of collaterals in ischemic tissue in patients. The lack of success of many pharmaceutical agents in reducing restenosis rates or in inducing angiogenesis post-angioplasty and following stent implantation has encouraged the development of new technological treatment approaches. Gene therapy is a novel strategy with the potential to prevent some of the sequelae after arterial injury, particularly cell proliferation, and to induce growth of new vessels or remodeling of pre-existing vessel branches, which may help patients with critical ischemia. Gene therapy strategies have the advantage of minimizing systemic side effects and may have a long-term effect as the encoded protein is released. Most clinical trials investigating gene therapy for vascular disease have been uncontrolled phase I and IIa trials. Gene therapy into vessels with the genes for growth factors has been demonstrated to be feasible and efficient. Local drug delivery devices have been used in combination with gene therapy in several trials to maximize safety and efficiency. Data from experimental animal work indicates that gene therapy may modify intimal hyperplasia after arterial injury, but there are few clinical trials on restenosis in patients. Preliminary clinical results show only limited success in altering restenosis rates. In vitro and experimental in vivo investigations into gene therapy for angiogenesis demonstrate increased formation of collaterals and functional improvement of limb ischemia. There is some evidence of increased collateral formation and clinical improvement in patients with critical limb ischemia. Results of placebo-controlled and double-blind trials of gene therapy for vascular disease are awaited.

  7. Residue management practices and planter attachments for corn production in a conservation agriculture system

    Directory of Open Access Journals (Sweden)

    J. Nejadi

    2013-11-01

    Full Text Available Seed placement and failure to establish a uniform plant stand are critical problems associated with production of corn (Zea mays following wheat (Triticum aestivum in a conservation agriculture system in Iran. Our objectives were to evaluate the performance of a corn row- crop planter equipped with two planter attachments (smooth/toothed coulters at six wheat residue management systems (three tillage systems and two levels of surface residue at two forward speeds of 5 and 7 km h-1. Residue retained after planting, seeding depth, emergence rate index (ERI and seed spacing indices were determined. The baled residue plots tilled by chisel plow followed by disc harrow (BRCD resulted in minimum residue after planting as compared to other residue treatments. Furthermore, the maximum values of the ERI and uniformity of plant spacing pertained to this treatment. Other results showed that the ERI increased up to 18% for the toothed coulter as compared to the smooth coulter. The toothed coulter also established a deeper seed placement as compared to the smooth coulter. Planting at forward speed of 5 km h-1 resulted in deeper seeding depth as compared to a forward speed of 7 km h-1. However, lower values of miss and precision indices were obtained at forward speed of 7 km h-1, indicating a more uniformity of plant spacing. Results of this study showed that equipping the conventional planter with toothed coulter and planting in soil prepared under the BRCD residue management system can result in a satisfactory conservation crop production system.

  8. The human homolog of S. cerevisiae CDC27, CDC27 Hs, is encoded by a highly conserved intronless gene present in multiple copies in the human genome

    Energy Technology Data Exchange (ETDEWEB)

    Devor, E.J.; Dill-Devor, R.M. [Univ. of Iowa College of Medicine, Iowa City (United States)

    1994-09-01

    We have obtained a number of unique sequences via PCR amplification of human genomic DNA using degenerate primers under low stringency (42{degrees}C). One of these, an 853 bp product, has been identified as a partial genomic sequence of the human homolog of the S. cerevisiae CDC27 gene, CDC27Hs (GenBank No. U00001). This gene, reported by Turgendreich et al. is also designated EST00556 from Adams et al. We have undertaken a more detailed examination of our sequence, MCP34N, and have found that: 1. the genomic sequence is nearly identical to CDC27Hs over its entire 853 bp length; 2. an MCP34N-specific PCR assay of several non-human primate species reveals amplification products in chimpanzee and gorilla genomes having greater than 90% sequence identity with CDC27Hs; and 3. an MCP34N-specific PCR assay of the BIOS hybrid cell line panel gives a discordancy pattern suggesting multiple loci. Based upon these data, we present the following initial characterization: 1. the complete MCP34N sequence identity with CDC27Hs indicates that the latter is encoded by an intronless gene; 2. CDC27Hs is highly conserved among higher primates; and 3. CDC27Hs is present in multiple copies in the human genome. These characteristics, taken together with those initially reported for CDC27Hs, suggest that this is an old gene that carries out an important but, as yet, unknown function in the human brain.

  9. Supporting food security in the 21st century through resource-conserving increases in agricultural production

    Directory of Open Access Journals (Sweden)

    Uphoff Norman

    2012-12-01

    Full Text Available Abstract The Green Revolution was accomplished under a set of demographic, economic, climatic and other conditions in the 20th century that have been changing and will surely be different and more difficult in the decades ahead. The suitability and sustainability of any given agricultural technology depends on factors like resource availability and productivity, energy costs, and environmental constraints. The achievements of Green Revolution technologies in the 1960s and 1970s came at a critical time of impending food shortages, and the world’s people would be worse off without them. However, the rate of yield improvement for cereal production has been slowing since the mid-1980s. Looking ahead at the foreseeable circumstances under which 21st century agricultural producers must try to assure food security, there will be need for technologies that are less dependent on resources that are becoming relatively scarcer, like arable land and water, or becoming relatively more costly, like energy and petrochemical-based inputs. This paper considers agroecologically-based innovations that reduce farmers’ dependence on external inputs, relying more on endogenous processes and existing potentials in plants and soil systems. Such resource-conserving production represents a different approach to meeting food security goals. While these innovations are not yet fully understood and are still being researched, there are good agronomic reasons to account for their effectiveness, and scientific validations are accumulating. Enough successes have been recorded from making changes in the management of plants, soil, water and nutrients that more attention from researchers, policy-makers and practitioners is warranted, especially given the need to adapt to, and to mitigate the effects of, climate change. The same agroecological concepts and management methods that are enhancing factor productivity in rice production are giving similar results with other crops

  10. Anxa4 Genes are Expressed in Distinct Organ Systems in Xenopus laevis and tropicalis But are Functionally Conserved

    Science.gov (United States)

    Massé, Karine L; Collins, Robert J; Bhamra, Surinder; Seville, Rachel A

    2007-01-01

    Anxa4 belongs to the multigenic annexin family of proteins which are characterized by their ability to interact with membranes in a calcium-dependent manner. Defined as a marker for polarized epithelial cells, Anxa4 is believed to be involved in many cellular processes but its functions in vivo are still poorly understood. Previously, we cloned Xanx4 in Xenopus laevis (now referred to as anxa4a) and demonstrated its role during organogenesis of the pronephros, providing the first evidence of a specific function for this protein during the development of a vertebrate. Here, we describe the strict conservation of protein sequence and functional domains of anxa4 during vertebrate evolution. We also identify the paralog of anxa4a, anxa4b and show its specific temporal and spatial expression pattern is different from anxa4a. We show that anxa4 orthologs in X. laevis and tropicalis display expression domains in different organ systems. Whilst the anxa4a gene is mainly expressed in the kidney, Xt anxa4 is expressed in the liver. Finally, we demonstrate Xt anxa4 and anxa4a can display conserved function during kidney organogenesis, despite the fact that Xt anxa4 transcripts are not expressed in this domain. This study highlights the divergence of expression of homologous genes during Xenopus evolution and raises the potential problems of using X. tropicalis promoters in X. laevis. PMID:19279706

  11. Soil Conservation Unit for the Advanced Crop Production and Marketing Course. Student Reference. AGDEX 570.

    Science.gov (United States)

    Stewart, Bob R.; And Others

    This student reference booklet is designed to accompany lessons outlined in the companion instructor's guide on soil conservation. The soil conservation unit builds on competencies gained in Agricultural Science I and II. Informative material is provided for these eight lessons: benefits of conservation, land utilization, how soils are eroded,…

  12. Novel cancer gene variants and gene fusions of triple-negative breast cancers (TNBCs) reveal their molecular diversity conserved in the patient-derived xenograft (PDX) model.

    Science.gov (United States)

    Jung, Jaeyun; Jang, Kiwon; Ju, Jung Min; Lee, Eunji; Lee, Jong Won; Kim, Hee Jung; Kim, Jisun; Lee, Sae Byul; Ko, Beom Seok; Son, Byung Ho; Lee, Hee Jin; Gong, Gyungyup; Ahn, Sei Yeon; Choi, Jung Kyoon; Singh, Shree Ram; Chang, Suhwan

    2018-04-20

    Despite the improved 5-year survival rate of breast cancer, triple-negative breast cancer (TNBC) remains a challenge due to lack of effective targeted therapy and higher recurrence and metastasis than other subtypes. To identify novel druggable targets and to understand its unique biology, we tried to implement 24 patient-derived xenografts (PDXs) of TNBC. The overall success rate of PDX implantation was 45%, much higher than estrogen receptor (ER)-positive cases. Immunohistochemical analysis revealed conserved ER/PR/Her2 negativity (with two exceptions) between the original and PDX tumors. Genomic analysis of 10 primary tumor-PDX pairs with Ion AmpliSeq CCP revealed high degree of variant conservation (85.0% to 96.9%) between primary and PDXs. Further analysis showed 44 rare variants with a predicted high impact in 36 genes including Trp53, Pten, Notch1, and Col1a1. Among them, we confirmed frequent Notch1 variant. Furthermore, RNA-seq analysis of 24 PDXs revealed 594 gene fusions, of which 163 were in-frame, including AZGP1-GJC3 and NF1-AARSD1. Finally, western blot analysis of oncogenic signaling proteins supporting molecular diversity of TNBC PDXs. Overall, our report provides a molecular basis for the usefulness of the TNBC PDX model in preclinical study. Copyright © 2018. Published by Elsevier B.V.

  13. Climate-Driven Reshuffling of Species and Genes: Potential Conservation Roles for Species Translocations and Recombinant Hybrid Genotypes.

    Science.gov (United States)

    Scriber, Jon Mark

    2013-12-24

    Comprising 50%-75% of the world's fauna, insects are a prominent part of biodiversity in communities and ecosystems globally. Biodiversity across all levels of biological classifications is fundamentally based on genetic diversity. However, the integration of genomics and phylogenetics into conservation management may not be as rapid as climate change. The genetics of hybrid introgression as a source of novel variation for ecological divergence and evolutionary speciation (and resilience) may generate adaptive potential and diversity fast enough to respond to locally-altered environmental conditions. Major plant and herbivore hybrid zones with associated communities deserve conservation consideration. This review addresses functional genetics across multi-trophic-level interactions including "invasive species" in various ecosystems as they may become disrupted in different ways by rapid climate change. "Invasive genes" (into new species and populations) need to be recognized for their positive creative potential and addressed in conservation programs. "Genetic rescue" via hybrid translocations may provide needed adaptive flexibility for rapid adaptation to environmental change. While concerns persist for some conservationists, this review emphasizes the positive aspects of hybrids and hybridization. Specific implications of natural genetic introgression are addressed with a few examples from butterflies, including transgressive phenotypes and climate-driven homoploid recombinant hybrid speciation. Some specific examples illustrate these points using the swallowtail butterflies (Papilionidae) with their long-term historical data base (phylogeographical diversity changes) and recent (3-decade) climate-driven temporal and genetic divergence in recombinant homoploid hybrids and relatively recent hybrid speciation of Papilio appalachiensis in North America. Climate-induced "reshuffling" (recombinations) of species composition, genotypes, and genomes may become

  14. Guidelines for the naming of genes, gene products, and mutants in the opportunistic protists.

    Science.gov (United States)

    Limper, Andrew H; Weiss, Louis M

    2011-01-01

    The opportunistic protists encompass a wide diversity of organisms including Pneumocystis, Toxoplasma, cryptosporidia, microsporidia, and related genera. Recent advances in the molecular biology and cellular biochemistry of these organisms have led to the identification of an ever growing numbers of key genes and their cognate proteins. Until now, these molecules have not been designated using any consistent nomenclature system, leading to considerable confusion. The participants of the 11th International Workshop on Opportunistic Protists met on August 3, 2010 to reach consensus of a nomenclature system for genes, gene products, and mutants in the opportunistic protists. The following summary reports the consensus agreement to move toward a unified nomenclature system for these organisms. The system is adapted from that used for Saccharomyces cerevisiae. © 2011 The Author(s). Journal of Eukaryotic Microbiology © 2011 International Society of Protistologists.

  15. A zebrafish screen for craniofacial mutants identifies wdr68 as a highly conserved gene required for endothelin-1 expression

    Directory of Open Access Journals (Sweden)

    Amsterdam Adam

    2006-06-01

    identification of approximately 25% of the essential genes required for craniofacial development. The identification of zebrafish models for two human disease syndromes indicates that homologs to the other genes are likely to also be relevant for human craniofacial development. The initial characterization of wdr68 suggests an important role in craniofacial development for the highly conserved Wdr68-Dyrk1 protein complexes.

  16. Weed Dynamics during Transition to Conservation Agriculture in Western Kenya Maize Production.

    Directory of Open Access Journals (Sweden)

    Judith A Odhiambo

    Full Text Available Weed competition is a significant problem in maize (Zea mays, L. production in Sub-Saharan Africa. Better understanding of weed management and costs in maize intercropped with beans (Phaseolus vulgaris, L. during transition to conservation agricultural systems is needed. Changes in weed population and maize growth were assessed for a period of three years at Bungoma where crops are grown twice per year and at Trans-Nzoia where crops are grown once per year. Treatments included three tillage practices: minimum (MT, no-till (NT and conventional (CT applied to three cropping systems: continuous maize/bean intercropping (TYPICAL, maize/bean intercropping with relayed mucuna after bean harvest (RELAY and maize, bean and mucuna planted in a strip intercropping arrangement (STRIP. Herbicides were used in NT, shallow hand hoeing and herbicides were used in MT and deep hoeing with no herbicides were used in CT. Weed and maize performance in the maize phase of each cropping system were assessed at both locations and costs of weed control were estimated at Manor House only. Weed density of grass and forb species declined significantly under MT and NT at Manor House and of grass species only at Mabanga. The greatest declines of more than 50% were observed as early as within one year of the transition to MT and NT in STRIP and TYPICAL cropping systems at Manor House. Transitioning to conservation based systems resulted in a decline of four out of five most dominant weed species. At the same time, no negative impact of MT or NT on maize growth was observed. Corresponding costs of weed management were reduced by $148.40 ha(-1 in MT and $149.60 ha(-1 in NT compared with CT. In conclusion, farmers can benefit from effective and less expensive weed management alternatives early in the process of transitioning to reduced tillage operations.

  17. Weed Dynamics during Transition to Conservation Agriculture in Western Kenya Maize Production.

    Science.gov (United States)

    Odhiambo, Judith A; Norton, Urszula; Ashilenje, Dennis; Omondi, Emmanuel C; Norton, Jay B

    2015-01-01

    Weed competition is a significant problem in maize (Zea mays, L.) production in Sub-Saharan Africa. Better understanding of weed management and costs in maize intercropped with beans (Phaseolus vulgaris, L.) during transition to conservation agricultural systems is needed. Changes in weed population and maize growth were assessed for a period of three years at Bungoma where crops are grown twice per year and at Trans-Nzoia where crops are grown once per year. Treatments included three tillage practices: minimum (MT), no-till (NT) and conventional (CT) applied to three cropping systems: continuous maize/bean intercropping (TYPICAL), maize/bean intercropping with relayed mucuna after bean harvest (RELAY) and maize, bean and mucuna planted in a strip intercropping arrangement (STRIP). Herbicides were used in NT, shallow hand hoeing and herbicides were used in MT and deep hoeing with no herbicides were used in CT. Weed and maize performance in the maize phase of each cropping system were assessed at both locations and costs of weed control were estimated at Manor House only. Weed density of grass and forb species declined significantly under MT and NT at Manor House and of grass species only at Mabanga. The greatest declines of more than 50% were observed as early as within one year of the transition to MT and NT in STRIP and TYPICAL cropping systems at Manor House. Transitioning to conservation based systems resulted in a decline of four out of five most dominant weed species. At the same time, no negative impact of MT or NT on maize growth was observed. Corresponding costs of weed management were reduced by $148.40 ha(-1) in MT and $149.60 ha(-1) in NT compared with CT. In conclusion, farmers can benefit from effective and less expensive weed management alternatives early in the process of transitioning to reduced tillage operations.

  18. Trade-offs between cattle production and bird conservation in an agricultural frontier of the Gran Chaco of Argentina.

    Science.gov (United States)

    Mastrangelo, Matias E; Gavin, Michael C

    2012-12-01

    Intensification of food production in tropical landscapes in the absence of land-use planning can pose a major threat to biological diversity. Decisions on whether to spatially integrate or segregate lands for production and conservation depend in part on the functional relations between biological diversity and agricultural productivity. We measured diversity, density, and species composition of birds along a gradient of production intensification on an agricultural frontier of the Argentine Chaco, where dry tropical forests are cleared for cattle production. Bird species diversity in intact forests was higher than in any type of cattle-production system. Bird species richness decreased nonlinearly as cattle yield increased. Intermediate-intensity silvopastoral systems, those in which forest understory is selectively cleared to grow pastures of non-native plants beneath the tree canopy, produced 80% of the mean cattle yield obtained in pastures on cleared areas and were occupied by 70-90% of the number of bird species present in the nearest forest fragments. Densities of >50% of bird species were significantly lower in open pastures than in silvopastoral systems. Therefore, intermediate-intensity silvopastoral systems may have the greatest potential to sustain cattle yield and conserve a large percentage of bird species. However, compared with low-intensity production systems, in which forest structure and extent were intact, intermediate-intensity silvopastoral systems supported significantly fewer forest-restricted bird species and fewer frugivorous birds. These data suggest that the integration of production and conservation through intermediate-intensity silvopastoral systems combined with the protection of forest fragments may be required to maintain cattle yield, bird diversity, and conservation of forest-restricted species in this agricultural frontier. ©2012 Society for Conservation Biology.

  19. Synteny of orthologous genes conserved in human, mouse, snake, Drosophila, nematode, and fission yeast

    Czech Academy of Sciences Publication Activity Database

    Trachtulec, Zdeněk; Forejt, Jiří

    2001-01-01

    Roč. 12, č. 3 (2001), s. 227-231 ISSN 0938-8990 Institutional research plan: CEZ:AV0Z5052915 Keywords : synteny of orthologous genes Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.318, year: 2001

  20. Extended region of nodulation genes in Rhizobium meliloti 1021. II. Nucleotide sequence, transcription start sites and protein products

    International Nuclear Information System (INIS)

    Fisher, R.F.; Swanson, J.A.; Mulligan, J.T.; Long, S.R.

    1987-01-01

    The authors have established the DNA sequence and analyzed the transcription and translation products of a series of putative nodulation (nod) genes in Rhizobium meliloti strain 1021. Four loci have been designated nodF, nodE, nodG and nodH. The correlation of transposon insertion positions with phenotypes and open reading frames was confirmed by sequencing the insertion junctions of the transposons. The protein products of these nod genes were visualized by in vitro expression of cloned DNA segments in a R. meliloti transcription-translation system. In addition, the sequence for nodG was substantiated by creating translational fusions in all three reading frames at several points in the sequence; the resulting fusions were expressed in vitro in both E. coli and R. meliloti transcription-translation systems. A DNA segment bearing several open reading frames downstream of nodG corresponds to the putative nod gene mutated in strain nod-216. The transcription start sites of nodF and nodH were mapped by primer extension of RNA from cells induced with the plant flavone, luteolin. Initiation of transcription occurs approximately 25 bp downstream from the conserved sequence designated the nod box, suggesting that this conserved sequence acts as an upstream regulator of inducible nod gene expression. Its distance from the transcription start site is more suggestive of an activator binding site rather than an RNA polymerase binding site

  1. Carbon debt of Conservation Reserve Program (CRP) grasslands converted to bioenergy production.

    Science.gov (United States)

    Gelfand, Ilya; Zenone, Terenzio; Jasrotia, Poonam; Chen, Jiquan; Hamilton, Stephen K; Robertson, G Philip

    2011-08-16

    Over 13 million ha of former cropland are enrolled in the US Conservation Reserve Program (CRP), providing well-recognized biodiversity, water quality, and carbon (C) sequestration benefits that could be lost on conversion back to agricultural production. Here we provide measurements of the greenhouse gas consequences of converting CRP land to continuous corn, corn-soybean, or perennial grass for biofuel production. No-till soybeans preceded the annual crops and created an initial carbon debt of 10.6 Mg CO(2) equivalents (CO(2)e)·ha(-1) that included agronomic inputs, changes in C stocks, altered N(2)O and CH(4) fluxes, and foregone C sequestration less a fossil fuel offset credit. Total debt, which includes future debt created by additional changes in soil C stocks and the loss of substantial future soil C sequestration, can be constrained to 68 Mg CO(2)e·ha(-1) if subsequent crops are under permanent no-till management. If tilled, however, total debt triples to 222 Mg CO(2)e·ha(-1) on account of further soil C loss. Projected C debt repayment periods under no-till management range from 29 to 40 y for corn-soybean and continuous corn, respectively. Under conventional tillage repayment periods are three times longer, from 89 to 123 y, respectively. Alternatively, the direct use of existing CRP grasslands for cellulosic feedstock production would avoid C debt entirely and provide modest climate change mitigation immediately. Incentives for permanent no till and especially permission to harvest CRP biomass for cellulosic biofuel would help to blunt the climate impact of future CRP conversion.

  2. Isolation and expression analysis of EcbZIP17 from different finger millet genotypes shows conserved nature of the gene.

    Science.gov (United States)

    Chopperla, Ramakrishna; Singh, Sonam; Mohanty, Sasmita; Reddy, Nanja; Padaria, Jasdeep C; Solanke, Amolkumar U

    2017-10-01

    Basic leucine zipper (bZIP) transcription factors comprise one of the largest gene families in plants. They play a key role in almost every aspect of plant growth and development and also in biotic and abiotic stress tolerance. In this study, we report isolation and characterization of EcbZIP17 , a group B bZIP transcription factor from a climate smart cereal, finger millet ( Eleusine coracana L.). The genomic sequence of EcbZIP17 is 2662 bp long encompassing two exons and one intron with ORF of 1722 bp and peptide length of 573 aa. This gene is homologous to AtbZIP17 ( Arabidopsis ), ZmbZIP17 (maize) and OsbZIP60 (rice) which play a key role in endoplasmic reticulum (ER) stress pathway. In silico analysis confirmed the presence of basic leucine zipper (bZIP) and transmembrane (TM) domains in the EcbZIP17 protein. Allele mining of this gene in 16 different genotypes by Sanger sequencing revealed no variation in nucleotide sequence, including the 618 bp long intron. Expression analysis of EcbZIP17 under heat stress exhibited similar pattern of expression in all the genotypes across time intervals with highest upregulation after 4 h. The present study established the conserved nature of EcbZIP17 at nucleotide and expression level.

  3. Exploring strategies for the production of ultracold RbYb molecules in conservative traps

    Energy Technology Data Exchange (ETDEWEB)

    Bruni, Cristian

    2015-07-14

    Within the scope of this thesis, the production of ultracold molecules at a temperature of a few μK with various isotopes of rubidium (Rb) and ytterbium (Yb) was examined by means of photoassociation spectroscopy and magnetic Feshbach resonances in combined conservative traps. The long-term goal of this experiment is the production of ultracold RbYb molecules in the rovibronic ground state. It was possible to produce electronically excited {sup 87}Rb {sup 176}Yb molecules in a novel hybrid trap (HT) at a combined temperature of 1.7 μK by means of 1-photon photoassociation close to the Rb D1 line at 795 nm. This HT takes advantage of the different magnetic properties of Rb and Yb and allows for independent trapping and manipulation of the atomic species. It combines an Ioffe-Pritchard type magnetic trap for Rb and a near-resonant optical dipole trap for Yb. The excited molecular {sup 2}Π{sub 1/2} state could be characterized further extending previous works in a combined MOT and vibrational levels reaching binding energies up to E{sub b}=-h x 2.2 THz could be assigned by trap-loss spectroscopy. Almost every detected vibrational state consists of two resonances that could be assigned to the molecular analogue of the hyperfine structure of {sup 87}Rb. An important experimental observation is a decrease in hyperfine splitting with increasing binding energy of a vibrational level. For the deepest found vibrational state the hyperfine splitting amounts only 70 % of the atomic value (817 MHz) which emphasizes a gradual passage from weakly to tightly bound molecules. Furthermore, detailed attempts were undertaken to induce magnetic Feshbach resonances in {sup 85}Rb and different Yb isotopes, especially {sup 171}Yb in a crossed optical dipole trap at 1064 nm at temperatures of 10 μK. For this purpose, a homogeneous magnetic field was applied and scanned in small steps over the range of 495 G ∼ 640 G. Unfortunately, our efforts were without success. Additionally, well

  4. 76 FR 9028 - Guidance for Industry: Potency Tests for Cellular and Gene Therapy Products; Availability

    Science.gov (United States)

    2011-02-16

    ...] Guidance for Industry: Potency Tests for Cellular and Gene Therapy Products; Availability AGENCY: Food and... Therapy Products'' dated January 2011. The guidance document provides manufacturers of cellular and gene... for Industry: Potency Tests for Cellular and Gene Therapy Products'' dated January 2011. The guidance...

  5. Conserved role of the Vsx genes supports a monophyletic origin for bilaterian visual systems.

    Science.gov (United States)

    Erclik, Ted; Hartenstein, Volker; Lipshitz, Howard D; McInnes, Roderick R

    2008-09-09

    Components of the genetic network specifying eye development are conserved from flies to humans, but homologies between individual neuronal cell types have been difficult to identify. In the vertebrate retina, the homeodomain-containing transcription factor Chx10 is required for both progenitor cell proliferation and the development of the bipolar interneurons, which transmit visual signals from photoreceptors to ganglion cells. We show that dVsx1 and dVsx2, the two Drosophila homologs of Chx10, play a conserved role in visual-system development. DVSX1 is expressed in optic-lobe progenitor cells, and, in dVsx1 mutants, progenitor cell proliferation is defective, leading to hypocellularity. Subsequently, DVSX1 and DVSX2 are coexpressed in a subset of neurons in the medulla, including the transmedullary neurons that transmit visual information from photoreceptors to deeper layers of the visual system. In dVsx mutant adults, the optic lobe is reduced in size, and the medulla is small or absent. These results suggest that the progenitor cells and photoreceptor target neurons of the vertebrate retina and fly optic lobe are ancestrally related. Genetic and functional homology may extend to the neurons directly downstream of the bipolar and transmedullary neurons, the vertebrate ganglion cells and fly lobula projection neurons. Both cell types project to visual-processing centers in the brain, and both sequentially express the Math5/ATO and Brn3b/ACJ6 transcription factors during their development. Our findings support a monophyletic origin for the bilaterian visual system in which the last common ancestor of flies and vertebrates already contained a primordial visual system with photoreceptors, interneurons, and projection neurons.

  6. Assessment of Benefits of Conservation Agriculture on Soil Functions in Arable Production Systems in Europe

    Directory of Open Access Journals (Sweden)

    Bhim Bahadur Ghaley

    2018-03-01

    Full Text Available Conventional farming (CONV is the norm in European farming, causing adverse effects on some of the five major soil functions, viz. primary productivity, carbon sequestration and regulation, nutrient cycling and provision, water regulation and purification, and habitat for functional and intrinsic biodiversity. Conservation agriculture (CA is an alternative to enhance soil functions. However, there is no analysis of CA benefits on the five soil functions as most studies addressed individual soil functions. The objective was to compare effects of CA and CONV practices on the five soil functions in four major environmental zones (Atlantic North, Pannonian, Continental and Mediterranean North in Europe by applying expert scoring based on synthesis of existing literature. In each environmental zone, a team of experts scored the five soil functions due to CA and CONV treatments and median scores indicated the overall effects on five soil functions. Across the environmental zones, CONV had overall negative effects on soil functions with a median score of 0.50 whereas CA had overall positive effects with median score ranging from 0.80 to 0.83. The study proposes the need for field-based investigations, policies and subsidy support to benefit from CA adoption to enhance the five soil functions.

  7. Identification of gene pools used in restoration and conservation by chloroplast microsatellite markers in Iberian pine species

    Directory of Open Access Journals (Sweden)

    Enrique Hernández-Tecles

    2017-10-01

    Full Text Available Aim of study: To contribute to the characterization of the origin of material used in afforestation, restoration or conservation activities by using Cp-SSR markers. Area of study: We used information from the natural range of Iberian pines, from Spain. Materials and methods: We used Iberian pines as an example to undertook gene pool characterization based on a wide Iberian sample of 97 populations from five Pinus species (Pinus halepensis, Pinus pinaster, Pinus nigra, Pinus sylvestris and Pinus uncinata. Haplotypes from each analyzed tree (derived from nine chloroplast microsatellites markers in P. halepensis and six in the rest of the species were obtained. Based on this information we subdivided each species in regions (considering both genetic structure and its application in afforestation, restoration and conservation programs and tested the assignation of populations to the different groups based on the genetic distance among samples. Main results: The rate of successful identification of populations among the different species was very high (> 94 % for P. nigra, P. sylvestris and P. uncinata, high (81 % for P. pinaster, and low (< 65 % for P. halepensis. Research highlights: Chloroplast DNA markers from extensive population datasets can be used to assign the origin of the forest reproductive material in some pine species.

  8. Identification of gene pools used in restoration and conservation by chloroplast microsatellite markers in Iberian pine species

    International Nuclear Information System (INIS)

    Hernández-Tecles, Enrique; De las Heras, Jorge; Lorenzo, Zaida; Navascués, Miguel; Alia, Ricardo

    2017-01-01

    Aim of study: To contribute to the characterization of the origin of material used in afforestation, restoration or conservation activities by using Cp-SSR markers. Area of study: We used information from the natural range of Iberian pines, from Spain. Materials and methods: We used Iberian pines as an example to undertook gene pool characterization based on a wide Iberian sample of 97 populations from five Pinus species (Pinus halepensis, Pinus pinaster, Pinus nigra, Pinus sylvestris and Pinus uncinata). Haplotypes from each analyzed tree (derived from nine chloroplast microsatellites markers in P. halepensis and six in the rest of the species) were obtained. Based on this information we subdivided each species in regions (considering both genetic structure and its application in afforestation, restoration and conservation programs) and tested the assignation of populations to the different groups based on the genetic distance among samples. Main results: The rate of successful identification of populations among the different species was very high (> 94 %) for P. nigra, P. sylvestris and P. uncinata, high (81 %) for P. pinaster, and low (< 65 %) for P. halepensis. Research highlights: Chloroplast DNA markers from extensive population datasets can be used to assign the origin of the forest reproductive material in some pine species.

  9. Identification of gene pools used in restoration and conservation by chloroplast microsatellite markers in Iberian pine species

    Energy Technology Data Exchange (ETDEWEB)

    Hernández-Tecles, Enrique; De las Heras, Jorge; Lorenzo, Zaida; Navascués, Miguel; Alia, Ricardo

    2017-11-01

    Aim of study: To contribute to the characterization of the origin of material used in afforestation, restoration or conservation activities by using Cp-SSR markers. Area of study: We used information from the natural range of Iberian pines, from Spain. Materials and methods: We used Iberian pines as an example to undertook gene pool characterization based on a wide Iberian sample of 97 populations from five Pinus species (Pinus halepensis, Pinus pinaster, Pinus nigra, Pinus sylvestris and Pinus uncinata). Haplotypes from each analyzed tree (derived from nine chloroplast microsatellites markers in P. halepensis and six in the rest of the species) were obtained. Based on this information we subdivided each species in regions (considering both genetic structure and its application in afforestation, restoration and conservation programs) and tested the assignation of populations to the different groups based on the genetic distance among samples. Main results: The rate of successful identification of populations among the different species was very high (> 94 %) for P. nigra, P. sylvestris and P. uncinata, high (81 %) for P. pinaster, and low (< 65 %) for P. halepensis. Research highlights: Chloroplast DNA markers from extensive population datasets can be used to assign the origin of the forest reproductive material in some pine species.

  10. Quantum Correlation Properties in Composite Parity-Conserved Matrix Product States

    Science.gov (United States)

    Zhu, Jing-Min

    2016-09-01

    We give a new thought for constructing long-range quantum correlation in quantum many-body systems. Our proposed composite parity-conserved matrix product state has long-range quantum correlation only for two spin blocks where their spin-block length larger than 1 compared to any subsystem only having short-range quantum correlation, and we investigate quantum correlation properties of two spin blocks varying with environment parameter and spacing spin number. We also find that the geometry quantum discords of two nearest-neighbor spin blocks and two next-nearest-neighbor spin blocks become smaller and for other conditions the geometry quantum discord becomes larger than that in any subcomponent, i.e., the increase or the production of the long-range quantum correlation is at the cost of reducing the short-range quantum correlation compared to the corresponding classical correlation and total correlation having no any characteristic of regulation. For nearest-neighbor and next-nearest-neighbor all the correlations take their maximal values at the same points, while for other conditions no whether for spacing same spin number or for different spacing spin numbers all the correlations taking their maximal values are respectively at different points which are very close. We believe that our work is helpful to comprehensively and deeply understand the organization and structure of quantum correlation especially for long-range quantum correlation of quantum many-body systems; and further helpful for the classification, the depiction and the measure of quantum correlation of quantum many-body systems.

  11. Ancient Exaptation of a CORE-SINE Retroposon into a Highly Conserved Mammalian Neuronal Enhancer of the Proopiomelanocortin Gene

    Science.gov (United States)

    Bumaschny, Viviana F; Low, Malcolm J; Rubinstein, Marcelo

    2007-01-01

    The proopiomelanocortin gene (POMC) is expressed in the pituitary gland and the ventral hypothalamus of all jawed vertebrates, producing several bioactive peptides that function as peripheral hormones or central neuropeptides, respectively. We have recently determined that mouse and human POMC expression in the hypothalamus is conferred by the action of two 5′ distal and unrelated enhancers, nPE1 and nPE2. To investigate the evolutionary origin of the neuronal enhancer nPE2, we searched available vertebrate genome databases and determined that nPE2 is a highly conserved element in placentals, marsupials, and monotremes, whereas it is absent in nonmammalian vertebrates. Following an in silico paleogenomic strategy based on genome-wide searches for paralog sequences, we discovered that opossum and wallaby nPE2 sequences are highly similar to members of the superfamily of CORE-short interspersed nucleotide element (SINE) retroposons, in particular to MAR1 retroposons that are widely present in marsupial genomes. Thus, the neuronal enhancer nPE2 originated from the exaptation of a CORE-SINE retroposon in the lineage leading to mammals and remained under purifying selection in all mammalian orders for the last 170 million years. Expression studies performed in transgenic mice showed that two nonadjacent nPE2 subregions are essential to drive reporter gene expression into POMC hypothalamic neurons, providing the first functional example of an exapted enhancer derived from an ancient CORE-SINE retroposon. In addition, we found that this CORE-SINE family of retroposons is likely to still be active in American and Australian marsupial genomes and that several highly conserved exonic, intronic and intergenic sequences in the human genome originated from the exaptation of CORE-SINE retroposons. Together, our results provide clear evidence of the functional novelties that transposed elements contributed to their host genomes throughout evolution. PMID:17922573

  12. Segment polarity gene expression in a myriapod reveals conserved and diverged aspects of early head patterning in arthropods.

    Science.gov (United States)

    Janssen, Ralf

    2012-09-01

    Arthropods show two kinds of developmental mode. In the so-called long germ developmental mode (as exemplified by the fly Drosophila), all segments are formed almost simultaneously from a preexisting field of cells. In contrast, in the so-called short germ developmental mode (as exemplified by the vast majority of arthropods), only the anterior segments are patterned similarly as in Drosophila, and posterior segments are added in a single or double segmental periodicity from a posterior segment addition zone (SAZ). The addition of segments from the SAZ is controlled by dynamic waves of gene activity. Recent studies on a spider have revealed that a similar dynamic process, involving expression of the segment polarity gene (SPG) hedgehog (hh), is involved in the formation of the anterior head segments. The present study shows that in the myriapod Glomeris marginata the early expression of hh is also in a broad anterior domain, but this domain corresponds only to the ocular and antennal segment. It does not, like in spiders, represent expression in the posterior adjacent segment. In contrast, the anterior hh pattern is conserved in Glomeris and insects. All investigated myriapod SPGs and associated factors are expressed with delay in the premandibular (tritocerebral) segment. This delay is exclusively found in insects and myriapods, but not in chelicerates, crustaceans and onychophorans. Therefore, it may represent a synapomorphy uniting insects and myriapods (Atelocerata hypothesis), contradicting the leading opinion that suggests a sister relationship of crustaceans and insects (Pancrustacea hypothesis). In Glomeris embryos, the SPG engrailed is first expressed in the mandibular segment. This feature is conserved in representatives of all arthropod classes suggesting that the mandibular segment may have a special function in anterior patterning.

  13. Ancient exaptation of a CORE-SINE retroposon into a highly conserved mammalian neuronal enhancer of the proopiomelanocortin gene.

    Directory of Open Access Journals (Sweden)

    Andrea M Santangelo

    2007-10-01

    Full Text Available The proopiomelanocortin gene (POMC is expressed in the pituitary gland and the ventral hypothalamus of all jawed vertebrates, producing several bioactive peptides that function as peripheral hormones or central neuropeptides, respectively. We have recently determined that mouse and human POMC expression in the hypothalamus is conferred by the action of two 5' distal and unrelated enhancers, nPE1 and nPE2. To investigate the evolutionary origin of the neuronal enhancer nPE2, we searched available vertebrate genome databases and determined that nPE2 is a highly conserved element in placentals, marsupials, and monotremes, whereas it is absent in nonmammalian vertebrates. Following an in silico paleogenomic strategy based on genome-wide searches for paralog sequences, we discovered that opossum and wallaby nPE2 sequences are highly similar to members of the superfamily of CORE-short interspersed nucleotide element (SINE retroposons, in particular to MAR1 retroposons that are widely present in marsupial genomes. Thus, the neuronal enhancer nPE2 originated from the exaptation of a CORE-SINE retroposon in the lineage leading to mammals and remained under purifying selection in all mammalian orders for the last 170 million years. Expression studies performed in transgenic mice showed that two nonadjacent nPE2 subregions are essential to drive reporter gene expression into POMC hypothalamic neurons, providing the first functional example of an exapted enhancer derived from an ancient CORE-SINE retroposon. In addition, we found that this CORE-SINE family of retroposons is likely to still be active in American and Australian marsupial genomes and that several highly conserved exonic, intronic and intergenic sequences in the human genome originated from the exaptation of CORE-SINE retroposons. Together, our results provide clear evidence of the functional novelties that transposed elements contributed to their host genomes throughout evolution.

  14. 78 FR 79419 - Energy Conservation Program for Consumer Products and Commercial and Industrial Equipment: Effect...

    Science.gov (United States)

    2013-12-30

    ...\\ Present value Discount rate Category (million 2012$) (percent) Benefits Operating Cost Savings 1,848 7 3... Energy Conservation Standards \\5\\ Present value Discount rate Category (million 2012$) (percent) Benefits... Conservation Standards \\6\\ Present value Discount rate Category (billion 2012$) (percent) Benefits Operating...

  15. 77 FR 76972 - Energy Conservation Program for Consumer Products and Certain Commercial and Industrial Equipment...

    Science.gov (United States)

    2012-12-31

    ... motors and pumps and certain other industrial equipment to conserve the energy resources of the nation... the efficiency of electric motors, pumps and certain other industrial equipment to conserve the energy... electric motors as covered equipment. A compressor may have some or all of the following components: piston...

  16. O-linked glycosylation of retroviral envelope gene products

    Energy Technology Data Exchange (ETDEWEB)

    Pinter, A.; Honnen, W.J. (Public Health Research Institute of the City of New York Inc., NY (USA))

    1988-03-01

    Treatment of ({sup 3}H)glucosamine-labeled Friend mink cell focus-forming virus (FrMCF) gp70 with excess peptide:N-glycanase F (PNGase F) resulted in removal of the expected seven N-linked oligosaccharide chains; however, approximately 10% of the glucosamine label was retained in the resulting 49,000-M{sub r} (49K) product. For ({sup 3}H)mannose-labeled gp70, similar treatment led to removal of all the carbohydrate label from the protein. Prior digestion of the PNGase F-treated gp70 with neuraminidase resulted in an addition size shift, and treatment with O-glycanase led to the removal of almost all of the PNGase F-resistant sugars. These results indicate that gp70 possesses sialic acid-containing O-linked oligosaccharides. Analysis of intracellular env precursors demonstrated that O-linked sugars were present in gPr90{sup env}, the polyprotein intermediate which contains complex sugars, but not in the primary translation product, gPr80{sup env}, and proteolytic digestion studies allowed localization of the O-linked carbohydrates to a 10K region near the center of the gp70 molecule. similar substituents were detected on the gp70s of ecotropic and xenotropic murine leukemia viruses and two subgroups of feline leukemia virus, indicting that O-linked glycosylation is a conserved feature of retroviral env proteins.

  17. O-linked glycosylation of retroviral envelope gene products

    International Nuclear Information System (INIS)

    Pinter, A.; Honnen, W.J.

    1988-01-01

    Treatment of [ 3 H]glucosamine-labeled Friend mink cell focus-forming virus (FrMCF) gp70 with excess peptide:N-glycanase F (PNGase F) resulted in removal of the expected seven N-linked oligosaccharide chains; however, approximately 10% of the glucosamine label was retained in the resulting 49,000-M r (49K) product. For [ 3 H]mannose-labeled gp70, similar treatment led to removal of all the carbohydrate label from the protein. Prior digestion of the PNGase F-treated gp70 with neuraminidase resulted in an addition size shift, and treatment with O-glycanase led to the removal of almost all of the PNGase F-resistant sugars. These results indicate that gp70 possesses sialic acid-containing O-linked oligosaccharides. Analysis of intracellular env precursors demonstrated that O-linked sugars were present in gPr90 env , the polyprotein intermediate which contains complex sugars, but not in the primary translation product, gPr80 env , and proteolytic digestion studies allowed localization of the O-linked carbohydrates to a 10K region near the center of the gp70 molecule. similar substituents were detected on the gp70s of ecotropic and xenotropic murine leukemia viruses and two subgroups of feline leukemia virus, indicting that O-linked glycosylation is a conserved feature of retroviral env proteins

  18. Energy conservation in ethanol production from renewable resources and non-petroleum energy sources

    Energy Technology Data Exchange (ETDEWEB)

    1981-03-01

    The dry milling process for the conversion of grain to fuel ethanol is reviewed for the application of energy conservation technology, which will reduce the energy consumption to 70,000 Btu per gallon, a reduction of 42% from a distilled spirits process. Specific energy conservation technology applications are outlined and guidelines for the owner/engineer for fuel ethanol plants to consider in the selection on the basis of energy conservation economics of processing steps and equipment are provided. The process was divided into 5 sections and the energy consumed in each step was determined based on 3 sets of conditions; a conventional distilled spirits process; a modern process incorporating commercially proven energy conservation; and a second generation process incorporating advanced conservation technologies which have not yet been proven. Steps discussed are mash preparation and cooking, fermentation, distillation, and distillers dried grains processing. The economics of cogeneration of electricity on fuel ethanol plants is also studied. (MCW)

  19. Gene Coexpression and Evolutionary Conservation Analysis of the Human Preimplantation Embryos

    Directory of Open Access Journals (Sweden)

    Tiancheng Liu

    2015-01-01

    Full Text Available Evolutionary developmental biology (EVO-DEVO tries to decode evolutionary constraints on the stages of embryonic development. Two models—the “funnel-like” model and the “hourglass” model—have been proposed by investigators to illustrate the fluctuation of selective pressure on these stages. However, selective indices of stages corresponding to mammalian preimplantation embryonic development (PED were undetected in previous studies. Based on single cell RNA sequencing of stages during human PED, we used coexpression method to identify gene modules activated in each of these stages. Through measuring the evolutionary indices of gene modules belonging to each stage, we observed change pattern of selective constraints on PED for the first time. The selective pressure decreases from the zygote stage to the 4-cell stage and increases at the 8-cell stage and then decreases again from 8-cell stage to the late blastocyst stages. Previous EVO-DEVO studies concerning the whole embryo development neglected the fluctuation of selective pressure in these earlier stages, and the fluctuation was potentially correlated with events of earlier stages, such as zygote genome activation (ZGA. Such oscillation in an earlier stage would further affect models of the evolutionary constraints on whole embryo development. Therefore, these earlier stages should be measured intensively in future EVO-DEVO studies.

  20. Loss of a highly conserved sterile alpha motif domain gene (WEEP) results in pendulous branch growth in peach trees.

    Science.gov (United States)

    Hollender, Courtney A; Pascal, Thierry; Tabb, Amy; Hadiarto, Toto; Srinivasan, Chinnathambi; Wang, Wanpeng; Liu, Zhongchi; Scorza, Ralph; Dardick, Chris

    2018-05-15

    Plant shoots typically grow upward in opposition to the pull of gravity. However, exceptions exist throughout the plant kingdom. Most conspicuous are trees with weeping or pendulous branches. While such trees have long been cultivated and appreciated for their ornamental value, the molecular basis behind the weeping habit is not known. Here, we characterized a weeping tree phenotype in Prunus persica (peach) and identified the underlying genetic mutation using a genomic sequencing approach. Weeping peach tree shoots exhibited a downward elliptical growth pattern and did not exhibit an upward bending in response to 90° reorientation. The causative allele was found to be an uncharacterized gene, Ppa013325 , having a 1.8-Kb deletion spanning the 5' end. This gene, dubbed WEEP , was predominantly expressed in phloem tissues and encodes a highly conserved 129-amino acid protein containing a sterile alpha motif (SAM) domain. Silencing WEEP in the related tree species Prunus domestica (plum) resulted in more outward, downward, and wandering shoot orientations compared to standard trees, supporting a role for WEEP in directing lateral shoot growth in trees. This previously unknown regulator of branch orientation, which may also be a regulator of gravity perception or response, provides insights into our understanding of how tree branches grow in opposition to gravity and could serve as a critical target for manipulating tree architecture for improved tree shape in agricultural and horticulture applications. Copyright © 2018 the Author(s). Published by PNAS.

  1. Expression regulation of design process gene in product design

    DEFF Research Database (Denmark)

    Li, Bo; Fang, Lusheng; Li, Bo

    2011-01-01

    To improve the design process efficiency, this paper proposes the principle and methodology that design process gene controls the characteristics of design process under the framework of design process reuse and optimization based on design process gene. First, the concept of design process gene...... is proposed and analyzed, as well as its three categories i.e., the operator gene, the structural gene and the regulator gene. Second, the trigger mechanism that design objectives and constraints trigger the operator gene is constructed. Third, the expression principle of structural gene is analyzed...... with the example of design management gene. Last, the regulation mode that the regulator gene regulates the expression of the structural gene is established and it is illustrated by taking the design process management gene as an example. © (2011) Trans Tech Publications....

  2. Structural and functional analysis of mouse Msx1 gene promoter: sequence conservation with human MSX1 promoter points at potential regulatory elements.

    Science.gov (United States)

    Gonzalez, S M; Ferland, L H; Robert, B; Abdelhay, E

    1998-06-01

    Vertebrate Msx genes are related to one of the most divergent homeobox genes of Drosophila, the muscle segment homeobox (msh) gene, and are expressed in a well-defined pattern at sites of tissue interactions. This pattern of expression is conserved in vertebrates as diverse as quail, zebrafish, and mouse in a range of sites including neural crest, appendages, and craniofacial structures. In the present work, we performed structural and functional analyses in order to identify potential cis-acting elements that may be regulating Msx1 gene expression. To this end, a 4.9-kb segment of the 5'-flanking region was sequenced and analyzed for transcription-factor binding sites. Four regions showing a high concentration of these sites were identified. Transfection assays with fragments of regulatory sequences driving the expression of the bacterial lacZ reporter gene showed that a region of 4 kb upstream of the transcription start site contains positive and negative elements responsible for controlling gene expression. Interestingly, a fragment of 130 bp seems to contain the minimal elements necessary for gene expression, as its removal completely abolishes gene expression in cultured cells. These results are reinforced by comparison of this region with the human Msx1 gene promoter, which shows extensive conservation, including many consensus binding sites, suggesting a regulatory role for them.

  3. Mouse transgenesis identifies conserved functional enhancers and cis-regulatory motif in the vertebrate LIM homeobox gene Lhx2 locus.

    Directory of Open Access Journals (Sweden)

    Alison P Lee

    Full Text Available The vertebrate Lhx2 is a member of the LIM homeobox family of transcription factors. It is essential for the normal development of the forebrain, eye, olfactory system and liver as well for the differentiation of lymphoid cells. However, despite the highly restricted spatio-temporal expression pattern of Lhx2, nothing is known about its transcriptional regulation. In mammals and chicken, Crb2, Dennd1a and Lhx2 constitute a conserved linkage block, while the intervening Dennd1a is lost in the fugu Lhx2 locus. To identify functional enhancers of Lhx2, we predicted conserved noncoding elements (CNEs in the human, mouse and fugu Crb2-Lhx2 loci and assayed their function in transgenic mouse at E11.5. Four of the eight CNE constructs tested functioned as tissue-specific enhancers in specific regions of the central nervous system and the dorsal root ganglia (DRG, recapitulating partial and overlapping expression patterns of Lhx2 and Crb2 genes. There was considerable overlap in the expression domains of the CNEs, which suggests that the CNEs are either redundant enhancers or regulating different genes in the locus. Using a large set of CNEs (810 CNEs associated with transcription factor-encoding genes that express predominantly in the central nervous system, we predicted four over-represented 8-mer motifs that are likely to be associated with expression in the central nervous system. Mutation of one of them in a CNE that drove reporter expression in the neural tube and DRG abolished expression in both domains indicating that this motif is essential for expression in these domains. The failure of the four functional enhancers to recapitulate the complete expression pattern of Lhx2 at E11.5 indicates that there must be other Lhx2 enhancers that are either located outside the region investigated or divergent in mammals and fishes. Other approaches such as sequence comparison between multiple mammals are required to identify and characterize such enhancers.

  4. The assessment of soil conservation technologies for sustainable agricultural production. Report of the FAO/IAEA consultants meeting. Working material

    International Nuclear Information System (INIS)

    2001-01-01

    A Consultants' Meeting on 'The assessment of soil conservation technologies for sustainable agricultural production' was held in Vienna at the IAEA Headquarters from May 28-30, 2001. The consultants' presentations reviewed recent advances in the use of fallout radionuclides to measure soil erosion as well as approaches and technologies applied for soil conservation worldwide. Also, activities and experiences of FAO and UNEP in the field of land degradation, soil conservation and related issues were presented. Based on the information provided by the Scientific Secretary, a full project proposal was prepared during the second part of the Consultants' Meeting. The consultants also provided recommendations on the formulation and implementation of a future CRP on the subject

  5. Sponge non-metastatic Group I Nme gene/protein - structure and function is conserved from sponges to humans

    Science.gov (United States)

    2011-01-01

    Background Nucleoside diphosphate kinases NDPK are evolutionarily conserved enzymes present in Bacteria, Archaea and Eukarya, with human Nme1 the most studied representative of the family and the first identified metastasis suppressor. Sponges (Porifera) are simple metazoans without tissues, closest to the common ancestor of all animals. They changed little during evolution and probably provide the best insight into the metazoan ancestor's genomic features. Recent studies show that sponges have a wide repertoire of genes many of which are involved in diseases in more complex metazoans. The original function of those genes and the way it has evolved in the animal lineage is largely unknown. Here we report new results on the metastasis suppressor gene/protein homolog from the marine sponge Suberites domuncula, NmeGp1Sd. The purpose of this study was to investigate the properties of the sponge Group I Nme gene and protein, and compare it to its human homolog in order to elucidate the evolution of the structure and function of Nme. Results We found that sponge genes coding for Group I Nme protein are intron-rich. Furthermore, we discovered that the sponge NmeGp1Sd protein has a similar level of kinase activity as its human homolog Nme1, does not cleave negatively supercoiled DNA and shows nonspecific DNA-binding activity. The sponge NmeGp1Sd forms a hexamer, like human Nme1, and all other eukaryotic Nme proteins. NmeGp1Sd interacts with human Nme1 in human cells and exhibits the same subcellular localization. Stable clones expressing sponge NmeGp1Sd inhibited the migratory potential of CAL 27 cells, as already reported for human Nme1, which suggests that Nme's function in migratory processes was engaged long before the composition of true tissues. Conclusions This study suggests that the ancestor of all animals possessed a NmeGp1 protein with properties and functions similar to evolutionarily recent versions of the protein, even before the appearance of true tissues

  6. Genes related to xylose fermentation and methods of using same for enhanced biofuel production

    Science.gov (United States)

    Wohlbach, Dana J.; Gasch, Audrey P.

    2014-08-05

    The present invention provides isolated gene sequences involved in xylose fermentation and related recombinant yeast which are useful in methods of enhanced biofuel production, particularly ethanol production. Methods of bioengineering recombinant yeast useful for biofuel production are also provided.

  7. Energy indices in irrigated wheat production under conservation and conventional tillage and planting methods

    OpenAIRE

    S. M Hosseini; S Afzalinia; K Mollaei

    2016-01-01

    Introduction: Conservation tillage system was recommended for soil erosion control in North America for the first time 60 years ago (Wang et al., 2006). Using this tillage system including minimum and zero tillage has been rapidly developed in recent years. Thearea covered by zero tillage in 2006 was 95 million ha all over the world (Dumanski et al., 2006). In addition to saving soil and water resources, conservation tillage system reduces energy consumption and improves energy indices by com...

  8. Mutations in the evolutionarily highly conserved KEOPS complex genes cause nephrotic syndrome with microcephaly

    Science.gov (United States)

    Braun, Daniela A.; Rao, Jia; Mollet, Geraldine; Schapiro, David; Daugeron, Marie-Claire; Tan, Weizhen; Gribouval, Olivier; Boyer, Olivia; Revy, Patrick; Jobst-Schwan, Tilman; Schmidt, Johanna Magdalena; Lawson, Jennifer A.; Schanze, Denny; Ashraf, Shazia; Boddaert, Nathalie; Collinet, Bruno; Martin, Gaëlle; Liger, Dominique; Lovric, Svjetlana; Furlano, Monica; Guerrera, I. Chiara; Sanchez-Ferras, Oraly; Menten, Björn; Vergult, Sarah; De Rocker, Nina; Airik, Merlin; Hermle, Tobias; Shril, Shirlee; Widmeier, Eugen; Gee, Heon Yung; Choi, Won-Il; Sadowski, Carolin E.; Pabst, Werner L.; Warejko, Jillian; Daga, Ankana; LeBerre, Tamara Basta; Matejas, Verena; Behnam, Babak; Beeson, Brendan; Begtrup, Amber; Bruce, Malcolm; Ch'ng, Gaik-Siew; Lin, Shuan-Pei; Chang, Jui-Hsing; Chen, Chao-Huei; Cho, Megan T.; Gipson, Patrick E.; Hsu, Chyong-Hsin; Kari, Jameela A.; Ke, Yu-Yuan; Kiraly-Borri, Cathy; Lai, Wai-ming; Lemyre, Emmanuelle; Littlejohn, Rebecca Okasha; Masri, Amira; Moghtaderi, Mastaneh; Nakamura, Kazuyuki; Praet, Marleen; Prasad, Chitra; Prytula, Agnieszka; Roeder, Elizabeth; Rump, Patrick; Schnur, Rhonda E.; Shiihara, Takashi; Sinha, Manish; Soliman, Neveen A; Soulami, Kenza; Sweetser, David A.; Tsai, Wen-Hui; Tsai, Jeng-Daw; Vester, Udo; Viskochil, David H.; Vatanavicharn, Nithiwat; Waxler, Jessica L.; Wolf, Matthias T.F.; Wong, Sik-Nin; Poduri, Annapurna; Truglio, Gessica; Mane, Shrikant; Lifton, Richard P.; Bouchard, Maxime; Kannu, Peter; Chitayat, David; Magen, Daniella; Calleweart, Bert; van Tilbeurgh, Herman; Zenker, Martin; Antignac, Corinne; Hildebrandt, Friedhelm

    2018-01-01

    Galloway-Mowat syndrome (GAMOS) is a severe autosomal-recessive disease characterized by the combination of early-onset steroid-resistant nephrotic syndrome (SRNS) and microcephaly with brain anomalies. To date, mutations of WDR73 are the only known monogenic cause of GAMOS and in most affected individuals the molecular diagnosis remains elusive. We here identify recessive mutations of OSGEP, TP53RK, TPRKB, or LAGE3, encoding the 4 subunits of the KEOPS complex in 33 individuals of 30 families with GAMOS. CRISPR/Cas9 knockout in zebrafish and mice recapitulates the human phenotype of microcephaly and results in early lethality. Knockdown of OSGEP, TP53RK, or TPRKB inhibits cell proliferation, which human mutations fail to rescue, and knockdown of either gene activates DNA damage response signaling and induces apoptosis. OSGEP and TP53RK molecularly interact and co-localize with the actin-regulating ARP2/3 complex. Furthermore, knockdown of OSGEP and TP53RK induces defects of the actin cytoskeleton and reduces migration rate of human podocytes, an established intermediate phenotype of SRNS. We thus identify 4 novel monogenic causes of GAMOS, describe the first link between KEOPS function and human disease, and delineate potential pathogenic mechanisms. PMID:28805828

  9. Restoration of degraded arid farmland at Project Wadi Attir: Impact of conservation on biological productivity and soil organic matter

    Science.gov (United States)

    Mor-Mussery, Amir; Helman, David; Ben Eli, Michael; Leu, Stefan

    2017-04-01

    The Israeli Negev Desert, as most Mediterranean drylands, is profoundly degraded. We have been documenting degradation and successful rehabilitation approaches in recent research, aiming at maximizing environmental and economic benefits while restoring healthy dryland soils and perennial vegetation to act as carbon sinks. These methods have been implemented for rehabilitation of Project Wadi Attir's. 50 hectares of heavily degraded farmland suffering from intensive soil erosion (expressed in dense gullies net and massive overland flow). Project Wadi Attir is a groundbreaking initiative of the Bedouin community in the Negev, for establishing a model sustainable agricultural operation. The project was initiated by the US-based Sustainability Laboratory and the Hura Municipal Council. The project is designed to demonstrate implementation of holistic sustainability principles developed by The Lab. The project's ecosystem restoration component involves site development, erosion control, soil conservation and improvement, planting of native and agroforestry trees, together with conservation and protection of biodiversity hotspots and avoiding grazing have, within three years, revealed the high biodiversity and productivity potential of this arid/semi-arid landscape. A number of shrublands and loess plots were subject to strict conservation, avoiding tilling and grazing. Soil fertility, productivity and biodiversity of these conserved plots inside the farm boundaries was compared to similar unprotected plots outside the farm fences by sampling in the field and by using satellite imaging. Our findings indicate a gradual improvement of SOM content specifically in the conserved shrubland area. Water infiltration, herbaceous biomass productivity and ants' activity of the protected plots also significantly increased within 3 years compared to the unprotected control areas. Starting from similar soil organic matter content in 2013 (3.3%) in the rocky slopes, in 2016 1% higher

  10. How to reconcile wood production and biodiversity conservation? The Pan-European boreal forest history gradient as an "experiment".

    Science.gov (United States)

    Naumov, Vladimir; Manton, Michael; Elbakidze, Marine; Rendenieks, Zigmars; Priednieks, Janis; Uhlianets, Siarhei; Yamelynets, Taras; Zhivotov, Anton; Angelstam, Per

    2018-07-15

    There are currently competing demands on Europe's forests and the finite resources and services that they can offer. Forestry intensification that aims at mitigating climate change and biodiversity conservation is one example. Whether or not these two objectives compete can be evaluated by comparative studies of forest landscapes with different histories. We test the hypothesis that indicators of wood production and biodiversity conservation are inversely related in a gradient of long to short forestry intensification histories. Forest management data containing stand age, volume and tree species were used to model the opportunity for wood production and biodiversity conservation in five north European forest regions representing a gradient in landscape history from very long in the West and short in the East. Wood production indicators captured the supply of coniferous wood and total biomass, as well as current accessibility by transport infrastructure. Biodiversity conservation indicators were based on modelling habitat network functionality for focal bird species dependent on different combinations of stand age and tree species composition representing naturally dynamic forests. In each region we randomly sampled 25 individual 100-km 2 areas with contiguous forest cover. Regarding wood production, Sweden's Bergslagen region had the largest areas of coniferous wood, followed by Vitebsk in Belarus and Zemgale in Latvia. NW Russia's case study regions in Pskov and Komi had the lowest values, except for the biomass indicator. The addition of forest accessibility for transportation made the Belarusian and Swedish study region most suitable for wood and biomass production, followed by Latvia and two study regions in NW Russian. Regarding biodiversity conservation, the overall rank among regions was opposite. Mixed and deciduous habitats were functional in Russia, Belarus and Latvia. Old Scots pine and Norway spruce habitats were only functional in Komi. Thus

  11. Evolution and origin of merlin, the product of the Neurofibromatosis type 2 (NF2 tumor-suppressor gene

    Directory of Open Access Journals (Sweden)

    Omelyanchuk Leonid V

    2005-12-01

    Full Text Available Abstract Background Merlin, the product of the Neurofibromatosis type 2 (NF2 tumor suppressor gene, belongs to the ezrin-radixin-moesin (ERM subgroup of the protein 4.1 superfamily, which links cell surface glycoproteins to the actin cytoskeleton. While merlin's functional activity has been examined in mammalian and Drosophila models, little is understood about its evolution, diversity, and overall distribution among different taxa. Results By combining bioinformatic and phylogenetic approaches, we demonstrate that merlin homologs are present across a wide range of metazoan lineages. While the phylogenetic tree shows a monophyletic origin of the ERM family, the origin of the merlin proteins is robustly separated from that of the ERM proteins. The derivation of merlin is thought to be in early metazoa. We have also observed the expansion of the ERM-like proteins within the vertebrate clade, which occurred after its separation from Urochordata (Ciona intestinalis. Amino acid sequence alignment reveals the absence of an actin-binding site in the C-terminal region of all merlin proteins from various species but the presence of a conserved internal binding site in the N-terminal domain of the merlin and ERM proteins. In addition, a more conserved pattern of amino acid residues is found in the region containing the so-called "Blue Box," although some amino acid substitutions in this region exist in the merlin sequences of worms, fish, and Ciona. Examination of sequence variability at functionally significant sites, including the serine-518 residue, the phosphorylation of which modulates merlin's intra-molecular association and function as a tumor suppressor, identifies several potentially important sites that are conserved among all merlin proteins but divergent in the ERM proteins. Secondary structure prediction reveals the presence of a conserved α-helical domain in the central to C-terminal region of the merlin proteins of various species. The

  12. Environmental sex determination in the branchiopod crustacean Daphnia magna: deep conservation of a Doublesex gene in the sex-determining pathway.

    Directory of Open Access Journals (Sweden)

    Yasuhiko Kato

    2011-03-01

    Full Text Available Sex-determining mechanisms are diverse among animal lineages and can be broadly divided into two major categories: genetic and environmental. In contrast to genetic sex determination (GSD, little is known about the molecular mechanisms underlying environmental sex determination (ESD. The Doublesex (Dsx genes play an important role in controlling sexual dimorphism in genetic sex-determining organisms such as nematodes, insects, and vertebrates. Here we report the identification of two Dsx genes from Daphnia magna, a freshwater branchiopod crustacean that parthenogenetically produces males in response to environmental cues. One of these genes, designated DapmaDsx1, is responsible for the male trait development when expressed during environmental sex determination. The domain organization of DapmaDsx1 was similar to that of Dsx from insects, which are thought to be the sister group of branchiopod crustaceans. Intriguingly, the molecular basis for sexually dimorphic expression of DapmaDsx1 is different from that of insects. Rather than being regulated sex-specifically at the level of pre-mRNA splicing in the coding region, DapmaDsx1 exhibits sexually dimorphic differences in the abundance of its transcripts. During embryogenesis, expression of DapmaDsx1 was increased only in males and its transcripts were primarily detected in male-specific structures. Knock-down of DapmaDsx1 in male embryos resulted in the production of female traits including ovarian maturation, whereas ectopic expression of DapmaDsx1 in female embryos resulted in the development of male-like phenotypes. Expression patterns of another D. magna Dsx gene, DapmaDsx2, were similar to those of DapmaDsx1, but silencing and overexpression of this gene did not induce any clear phenotypic changes. These results establish DapmaDsx1 as a key regulator of the male phenotype. Our findings reveal how ESD is implemented by selective expression of a fundamental genetic component that is

  13. Spatially conserved regulatory elements identified within human and mouse Cd247 gene using high-throughput sequencing data from the ENCODE project

    DEFF Research Database (Denmark)

    Pundhir, Sachin; Hannibal, Tine Dahlbæk; Bang-Berthelsen, Claus Heiner

    2014-01-01

    . In this study, we have utilized the wealth of high-throughput sequencing data produced during the Encyclopedia of DNA Elements (ENCODE) project to identify spatially conserved regulatory elements within the Cd247 gene from human and mouse. We show the presence of two transcription factor binding sites...

  14. Enhanced biosurfactant production through cloning of three genes and role of esterase in biosurfactant release

    Science.gov (United States)

    2011-01-01

    Background Biosurfactants have been reported to utilize a number of immiscible substrates and thereby facilitate the biodegradation of panoply of polyaromatic hydrocarbons. Olive oil is one such carbon source which has been explored by many researchers. However, studying the concomitant production of biosurfactant and esterase enzyme in the presence of olive oil in the Bacillus species and its recombinants is a relatively novel approach. Results Bacillus species isolated from endosulfan sprayed cashew plantation soil was cultivated on a number of hydrophobic substrates. Olive oil was found to be the best inducer of biosurfactant activity. The protein associated with the release of the biosurfactant was found to be an esterase. There was a twofold increase in the biosurfactant and esterase activities after the successful cloning of the biosurfactant genes from Bacillus subtilis SK320 into E.coli. Multiple sequence alignment showed regions of similarity and conserved sequences between biosurfactant and esterase genes, further confirming the symbiotic correlation between the two. Biosurfactants produced by Bacillus subtilis SK320 and recombinant strains BioS a, BioS b, BioS c were found to be effective emulsifiers, reducing the surface tension of water from 72 dynes/cm to as low as 30.7 dynes/cm. Conclusion The attributes of enhanced biosurfactant and esterase production by hyper-producing recombinant strains have many utilities from industrial viewpoint. This study for the first time has shown a possible association between biosurfactant production and esterase activity in any Bacillus species. Biosurfactant-esterase complex has been found to have powerful emulsification properties, which shows promising bioremediation, hydrocarbon biodegradation and pharmaceutical applications. PMID:21707984

  15. Vasopressin Gene-Related Products in the Management of Breast Cancer

    National Research Council Canada - National Science Library

    North, William

    1998-01-01

    .... The VP gene is expressed by seemingly all breast cancers and by all DCIS, and this information coupled with an absence of VP gene-related products from fibrocystic disease potentially provides us...

  16. Gene Delivery into Plant Cells for Recombinant Protein Production

    Directory of Open Access Journals (Sweden)

    Qiang Chen

    2015-01-01

    Full Text Available Recombinant proteins are primarily produced from cultures of mammalian, insect, and bacteria cells. In recent years, the development of deconstructed virus-based vectors has allowed plants to become a viable platform for recombinant protein production, with advantages in versatility, speed, cost, scalability, and safety over the current production paradigms. In this paper, we review the recent progress in the methodology of agroinfiltration, a solution to overcome the challenge of transgene delivery into plant cells for large-scale manufacturing of recombinant proteins. General gene delivery methodologies in plants are first summarized, followed by extensive discussion on the application and scalability of each agroinfiltration method. New development of a spray-based agroinfiltration and its application on field-grown plants is highlighted. The discussion of agroinfiltration vectors focuses on their applications for producing complex and heteromultimeric proteins and is updated with the development of bridge vectors. Progress on agroinfiltration in Nicotiana and non-Nicotiana plant hosts is subsequently showcased in context of their applications for producing high-value human biologics and low-cost and high-volume industrial enzymes. These new advancements in agroinfiltration greatly enhance the robustness and scalability of transgene delivery in plants, facilitating the adoption of plant transient expression systems for manufacturing recombinant proteins with a broad range of applications.

  17. Enhancing Productivity and Resource Conservation by Eliminating Inefficiency of Thai Rice Farmers: A Zero Inefficiency Stochastic Frontier Approach

    Directory of Open Access Journals (Sweden)

    Jianxu Liu

    2017-05-01

    Full Text Available The study first identified fully efficient farmers and then estimated technical efficiency of inefficient farmers, identifying their determinants by applying a Zero Inefficiency Stochastic Frontier Model (ZISFM on a sample of 300 rice farmers from central-northern Thailand. Next, the study developed scenarios of potential production increase and resource conservation if technical inefficiency was eliminated. Results revealed that 13% of the sampled farmers were fully efficient, thereby justifying the use of our approach. The estimated mean technical efficiency was 91%, implying that rice production can be increased by 9%, by reallocating resources. Land and labor were the major productivity drivers. Education significantly improved technical efficiency. Farmers who transplanted seedlings were relatively technically efficient as compared to those who practised manual and/or mechanical direct seeding methods. Elimination of technical inefficiency could increase output by 8.64% per ha, or generate 5.7–6.4 million tons of additional rice output for Thailand each year. Similarly, elimination of technical inefficiency would potentially conserve 19.44% person-days of labor, 11.95% land area, 11.46% material inputs and 8.67% mechanical power services for every ton of rice produced. This translates into conservation of 2.9–3.0 million person-days of labor, 3.7–4.5 thousand km2 of land, 10.0–14.5 billion baht of material input and 7.6–12.8 billion baht of mechanical power costs to produce current level of rice output in Thailand each year. Policy implications include investment into educating farmers, and improving technical knowledge of seeding technology, to boost rice production and conserve scarce resources in Thailand.

  18. Restriction fragment length polymorphism (RFLP) analysis of PCR products amplified from 18S ribosomal RNA gene of Trypanosoma congolense

    International Nuclear Information System (INIS)

    Osanyo, A.; Majiwa, P.W.

    2006-01-01

    Oligonucleotide primers were designed from the conserved nucleotide sequences of 18S ribosomal RNA (18S rRNA) gene of protozoans: Trypanosoma brucei, Leishmania donovani, Triponema aequale and Lagenidium gigantum. The primers were used in polymerace chain reaction (PCR) to generate PCR products of approximately 1 Kb using genomic DNA from T. brucei and the four genotypic groups of T. congolense as template. The five PCR products so produced were digested with several restriction enzymes and hybridized to a DNA probe made from T. brucei PCR product of the same 18S rRNA gene region. Most restriction enzyme digests revealed polymorphism with respect to the location of their recognition sites on the five PCR products. The restriction fragment length polymorphism (RFLP) pattern observed indicate that the 18S rRNA gene sequences of trypanosomes: T. brucei and the four genotypes of T.congolence group are heterogeneous. The results further demonstrate that the region that was amplified can be used in specific identification of trypanosomes species and subspecies.(author)

  19. Expression of cocoa genes in Saccharomyces cerevisiae improves cocoa butter production

    DEFF Research Database (Denmark)

    Wei, Yongjun; Bergenholm, David; Gossing, Michael

    2018-01-01

    Background: Cocoa butter (CB) extracted from cocoa beans (Theobroma cacao) is the main raw material for chocolate production, but CB supply is insufficient due to the increased chocolate demand and limited CB production. CB is mainly composed of three different kinds of triacylglycerols (TAGs), 1......), and it is essential to modulate the yeast TAG biosynthetic pathway for higher CBL production.Results: We cloned seven GPAT genes and three LPAT genes from cocoa cDNA, in order to screen for CBL biosynthetic gene candidates. By expressing these cloned cocoa genes and two synthesized cocoa DGAT genes in S. cerevisiae......, we successfully increased total fatty acid production, TAG production and CBL production in some of the strains. In the best producer, the potential CBL content was eightfold higher than the control strain, suggesting the cocoa genes expressed in this strain were functional and might be responsible...

  20. Isolation of BAC Clones Containing Conserved Genes from Libraries of Three Distantly Related Moths: A Useful Resource for Comparative Genomics of Lepidoptera

    Directory of Open Access Journals (Sweden)

    Yuji Yasukochi

    2011-01-01

    Full Text Available Lepidoptera, butterflies and moths, is the second largest animal order and includes numerous agricultural pests. To facilitate comparative genomics in Lepidoptera, we isolated BAC clones containing conserved and putative single-copy genes from libraries of three pests, Heliothis virescens, Ostrinia nubilalis, and Plutella xylostella, harboring the haploid chromosome number, =31, which are not closely related with each other or with the silkworm, Bombyx mori, (=28, the sequenced model lepidopteran. A total of 108–184 clones representing 101–182 conserved genes were isolated for each species. For 79 genes, clones were isolated from more than two species, which will be useful as common markers for analysis using fluorescence in situ hybridization (FISH, as well as for comparison of genome sequence among multiple species. The PCR-based clone isolation method presented here is applicable to species which lack a sequenced genome but have a significant collection of cDNA or EST sequences.

  1. 77 FR 24940 - Energy Conservation Program for Consumer Products: Representative Average Unit Costs of Energy

    Science.gov (United States)

    2012-04-26

    ... 5-year average ratio with heating oil prices published in the Monthly Energy Review, but the propane... DEPARTMENT OF ENERGY Office of Energy Efficiency and Renewable Energy Energy Conservation Program... and Renewable Energy, Department of Energy. ACTION: Notice. SUMMARY: In this notice, the U.S...

  2. 78 FR 62970 - Energy Conservation Program for Consumer Products and Certain Commercial and Industrial Equipment...

    Science.gov (United States)

    2013-10-23

    ... Standard E. Definition of Basic Model F. Statistical Sampling Plans G. Information To Be Provided in... administrative convenience based on their nature or type. Under EPCA, the energy conservation program consists... Reference of Standards 5. Basic Models 6. Statistical Sampling Plans 7. Information To Be Provided in...

  3. 75 FR 27170 - Energy Conservation Program for Consumer Products: Determination Concerning the Potential for...

    Science.gov (United States)

    2010-05-14

    ... Points for a 203-Watt Multiple-Voltage EPS for a Video Game Console Efficiency- Reference point for... would likely benefit economically from the imposition of energy conservation standards for non-Class A... projected savings and national NPV considers only the direct financial costs and benefits to consumers of...

  4. 76 FR 37678 - Energy Conservation Program for Consumer Products and Certain Commercial and Industrial Equipment...

    Science.gov (United States)

    2011-06-28

    ... Laboratory study, which determined the energy use based on conservative estimates on number of fume hood... issue a Family Policymaking Assessment for any rule that may affect family well-being. This proposed determination would not have any impact on the autonomy or integrity of the family as an institution...

  5. The role of herbicides for enhancing productivity and conserving land for biodiversity in North America

    Science.gov (United States)

    Robert G. Wagner; Michael Newton; Elizabeth C. Cole; James H. Miller; Barry D. Shiver

    2004-01-01

    Herbicide technology has evolved with forest management in North America over the past 60 years and has become an integral part of modern forestry practice. Forest managers have prescribed herbicides to increase reforestation success and long-term timber yields. Wildlife managers and others interested in conserving biodi- versity, however, have often viewed herbicide...

  6. 75 FR 42579 - Energy Conservation Program for Consumer Products: Test Procedure for Microwave Ovens; Repeal of...

    Science.gov (United States)

    2010-07-22

    ... provided in paragraph (i)(2) of this section, for each basic model of conventional cooking tops, and... the cooking efficiency test procedure for microwave ovens under the Energy Policy and Conservation Act (EPCA). DOE has determined that the microwave oven test procedure to measure the cooking efficiency does...

  7. 77 FR 76952 - Energy Conservation Program for Consumer Products: Association of Home Appliance Manufacturers...

    Science.gov (United States)

    2012-12-31

    ... dishwashers. Given that 65 percent of all standard dishwashers currently on the market meet or exceed the..., standard, or criteria for that determination. It is a textbook arbitrary and capricious determination. As... the market meet or exceed the minimum energy conservation standards established in the direct final...

  8. 78 FR 63410 - Energy Conservation Program for Consumer Products: Test Procedures for Direct Heating Equipment...

    Science.gov (United States)

    2013-10-24

    ... test procedures for direct heating equipment and pool heaters established under the Energy Policy and... U.S.C. 6293(e)(2)) The current energy conservation standards for direct heating equipment and pool... DEPARTMENT OF ENERGY 10 CFR Part 430 [Docket Number EERE-2013-BT-TP-0004] RIN 1904-AC94 Energy...

  9. 78 FR 16443 - Energy Efficiency Program for Consumer Products: Energy Conservation Standards for Ceiling Fans...

    Science.gov (United States)

    2013-03-15

    ... Standards for Ceiling Fans and Ceiling Fan Light Kits AGENCY: Office of Energy Efficiency and Renewable... consider amending the energy conservation standards for ceiling fans and ceiling fan light kits. DOE also....gov . Follow the instructions for submitting comments. Email: CeilingFan[email protected

  10. 75 FR 13123 - Energy Conservation Program for Consumer Products: Representative Average Unit Costs of Energy

    Science.gov (United States)

    2010-03-18

    ... that of heating oil, based on the 2004-2008 averages for these two fuels. The source for these price... DEPARTMENT OF ENERGY Office of Energy Efficiency and Renewable Energy Energy Conservation Program... and Renewable Energy, Department of Energy. ACTION: Notice. SUMMARY: In this notice, the U.S...

  11. 76 FR 971 - Energy Conservation Program for Consumer Products: Test Procedures for Clothes Dryers and Room...

    Science.gov (United States)

    2011-01-06

    .... Detergent Specifications for Clothes Dryer Test Cloth Preconditioning 5. Changes To Reflect Current Usage... conservation standard; (3) updated detergent specifications for clothes dryer test cloth preconditioning; (4... detergent specifications for clothes dryer test cloth preconditioning; (7) update the references to external...

  12. Neuropeptide Y receptor genes on human chromosome 4q31-q32 map to conserved linkage groups on mouse chromosomes 3 and 8

    Energy Technology Data Exchange (ETDEWEB)

    Lutz, C.M.; Frankel, W.N. [Jackson Lab., Bar Harbor, ME (United States); Richards, J.E. [Univ. of Michigan Medical School, Ann Arbor, MI (United States)] [and others

    1997-05-01

    Npy1r and Npy2r, the genes encoding mouse type 1 and type 2 neuropeptide Y receptors, have been mapped by interspecific backcross analysis. Previous studies have localized the human genes encoding these receptors to chromosome 4q31-q32. We have now assigned Npy1r and Npy2r to conserved linkage groups on mouse Chr 8 and Chr 3, respectively, which correspond to the distal region of human chromosome 4q. Using yeast artificial chromosomes, we have estimated the distance between the human genes to be approximately 6 cM. Although ancient tandem duplication events may account for some closely spaced G-protein-coupled receptor genes, the large genetic distance between the human type 1 and type 2 neuropeptide Y receptor genes raises questions about whether this mechanism accounts for their proximity. 20 refs., 1 fig.

  13. 75 FR 56795 - Energy Conservation Program: Certification, Compliance, and Enforcement for Consumer Products and...

    Science.gov (United States)

    2010-09-16

    ...: Certification, Compliance, and Enforcement for Consumer Products and Commercial and Industrial Equipment... product, additional provisions for imports, voluntary industry certification programs (VICP), verification... DOE intends to apply certification, compliance, and enforcement regulations to all covered products...

  14. Cloning of the cDNA for murine von Willebrand factor and identification of orthologous genes reveals the extent of conservation among diverse species.

    Science.gov (United States)

    Chitta, Mohan S; Duhé, Roy J; Kermode, John C

    2007-05-01

    Interaction of von Willebrand factor (VWF) with circulating platelets promotes hemostasis when a blood vessel is injured. The A1 domain of VWF is responsible for the initial interaction with platelets and is well conserved among species. Knowledge of the cDNA and genomic DNA sequences for human VWF allowed us to predict the cDNA sequence for murine VWF in silico and amplify its entire coding region by RT-PCR. The murine VWF cDNA has an open reading frame of 8,442 bp, encoding a protein of 2,813 amino acid residues with 83% identity to human pre-pro-VWF. The same strategy was used to predict in silico the cDNA sequence for the ortholog of VWF in a further six species. Many of these predictions diverged substantially from the putative Reference Sequences derived by ab initio methods. Our predicted sequences indicated that the VWF gene has a conserved structure of 52 exons in all seven mammalian species examined, as well as in the chicken. There is a minor structural variation in the pufferfish Takifugu rubripes insofar as the VWF gene in this species has 53 exons. Comparison of the translated amino acid sequences also revealed a high degree of conservation. In particular, the cysteine residues are conserved precisely throughout both the pro-peptide and the mature VWF sequence in all species, with a minor exception in the pufferfish VWF ortholog where two adjacent cysteine residues are omitted. The marked conservation of cysteine residues emphasizes the importance of the intricate pattern of disulfide bonds in governing the structure of pro-VWF and regulating the function of the mature VWF protein. It should also be emphasized that many of the conserved features of the VWF gene and protein were obscured when the comparison among species was based on the putative Reference Sequences instead of our predicted cDNA sequences.

  15. The L locus, one of complementary genes required for anthocyanin production in onions (Allium cepa), encodes anthocyanidin synthase.

    Science.gov (United States)

    Kim, Sunggil; Jones, Rick; Yoo, Kil-Sun; Pike, Leonard M

    2005-06-01

    Bulb color in onions (Allium cepa) is an important trait, but its complex, unclear mechanism of inheritance has been a limiting factor in onion cultivar improvement. The identity of the L locus, which is involved in the color difference between Brazilian yellow and red onions, is revealed in this study. A cross was made between a US-type yellow breeding line and a Brazilian yellow cultivar. The segregation ratio of nine red to seven yellow onions in the F(2) population supports the involvement of two complementary genes in anthocyanin production in the F(1) hybrids. The high-performance liquid chromatography (HPLC) and reverse-transcriptase (RT)-PCR analysis of the Brazilian yellow onions indicated that the genes are involved late in the anthocyanin synthesis pathway. The genomic sequence of the anthocyanidin synthase (ANS) gene in Brazilian yellow onions showed a point mutation, which results in an amino acid change of a glycine to an arginine at residue 229. Because this residue is located adjacent to a highly conserved iron-binding active site, this mutation is likely responsible for the inactivation of the ANS gene in Brazilian yellow onions. Following the isolation of the promoter sequence of the mutant allele, a PCR-based marker for allelic selection of the ANS gene was designed. This assay is based on an insertion (larger than 3 kb) mutation. The marker perfectly co-segregated with the color phenotypes in the F(2) populations, thereby indicating that the L locus encodes ANS.

  16. Comparative anatomy of the human APRT gene and enzyme: nucleotide sequence divergence and conservation of a nonrandom CpG dinucleotide arrangement

    International Nuclear Information System (INIS)

    Broderick, T.P.; Schaff, D.A.; Bertino, A.M.; Dush, M.K.; Tischfield, J.A.; Stambrook, P.J.

    1987-01-01

    The functional human adenine phosphoribosyltransferase (APRT) gene is <2.6 kilobases in length and contains five exons. The amino acid sequences of APRTs have been highly conserved throughout evolution. The human enzyme is 82%, 90%, and 40% identical to the mouse, hamster, and Escherichia coli enzymes, respectively. The promoter region of the human APRT gene, like that of several other housekeeping genes, lacks TATA and CCAAT boxes but contains five GC boxes that are potential binding sites for the Sp1 transcription factor. The distal three, however, are dispensable for gene expression. Comparison between human and mouse APRT gene nucleotide sequences reveals a high degree of homology within protein coding regions but an absence of significant homology in 5' flanking, 3' untranslated, and intron sequences, except for similarly positioned GC boxes in the promoter region and a 26-base-pair region in intron 3. This 26-base-pair sequence is 92% identical with a similarly positioned sequence in the mouse gene and is also found in intron 3 of the hamster gene, suggesting that its retention may be a consequence of stringent selection. The positions of all introns have been precisely retained in the human and both rodent genes. Retention of an elevated CpG dinucleotide content, despite loss of sequence homology, suggests that there may be selection for CpG dinucleotides in these regions and that their maintenance may be important for APRT gene function

  17. Trade-offs between pasture production and farmland bird conservation: exploration of options using a dynamic farm model.

    Science.gov (United States)

    Sabatier, R; Teillard, F; Rossing, W A H; Doyen, L; Tichit, M

    2015-05-01

    In European grassland landscapes, grazing and mowing play a key role for the maintenance of high-quality habitats that host important bird populations. As grasslands are also key resources for cattle feeding, there is a need to develop management strategies that achieve the double objective of production and biodiversity conservation. The objective of this study was to use a modelling approach to generate recognisable patterns of bird dynamics in farms composed of different land use proportions, and to compare their production and ecological dimensions. We developed a dynamic model, which linked grassland management to bird population dynamics at the field and farm levels. The model was parameterised for two types of suckling farms corresponding to contrasting levels of grassland intensification and for two bird species of high conservation value. A viability algorithm was used to define and assess viable management strategies for production and ecological performance so as to draw the shape of the relationship between both types of performances for the two types of farms. Our results indicated that, at the farm level, there was a farming system effect with a negative and non-linear relationship linking performance. Improving bird population maintenance was less costly in extensive farms compared with intensive farms. At the field level, the model predicted the timing and intensity of land use, maximising either production or ecological performance. The results suggested that multi-objective grassland management would benefit from public policies that consider levels of organisation higher than the field level, such as the farm or the landscape.

  18. Comparative Bioinformatics Analysis of Transcription Factor Genes Indicates Conservation of Key Regulatory Domains among Babesia bovis, Babesia microti, and Theileria equi.

    Science.gov (United States)

    Alzan, Heba F; Knowles, Donald P; Suarez, Carlos E

    2016-11-01

    Apicomplexa tick-borne hemoparasites, including Babesia bovis, Babesia microti, and Theileria equi are responsible for bovine and human babesiosis and equine theileriosis, respectively. These parasites of vast medical, epidemiological, and economic impact have complex life cycles in their vertebrate and tick hosts. Large gaps in knowledge concerning the mechanisms used by these parasites for gene regulation remain. Regulatory genes coding for DNA binding proteins such as members of the Api-AP2, HMG, and Myb families are known to play crucial roles as transcription factors. Although the repertoire of Api-AP2 has been defined and a HMG gene was previously identified in the B. bovis genome, these regulatory genes have not been described in detail in B. microti and T. equi. In this study, comparative bioinformatics was used to: (i) identify and map genes encoding for these transcription factors among three parasites' genomes; (ii) identify a previously unreported HMG gene in B. microti; (iii) define a repertoire of eight conserved Myb genes; and (iv) identify AP2 correlates among B. bovis and the better-studied Plasmodium parasites. Searching the available transcriptome of B. bovis defined patterns of transcription of these three gene families in B. bovis erythrocyte stage parasites. Sequence comparisons show conservation of functional domains and general architecture in the AP2, Myb, and HMG proteins, which may be significant for the regulation of common critical parasite life cycle transitions in B. bovis, B. microti, and T. equi. A detailed understanding of the role of gene families encoding DNA binding proteins will provide new tools for unraveling regulatory mechanisms involved in B. bovis, B. microti, and T. equi life cycles and environmental adaptive responses and potentially contributes to the development of novel convergent strategies for improved control of babesiosis and equine piroplasmosis.

  19. Comparative Bioinformatics Analysis of Transcription Factor Genes Indicates Conservation of Key Regulatory Domains among Babesia bovis, Babesia microti, and Theileria equi.

    Directory of Open Access Journals (Sweden)

    Heba F Alzan

    2016-11-01

    Full Text Available Apicomplexa tick-borne hemoparasites, including Babesia bovis, Babesia microti, and Theileria equi are responsible for bovine and human babesiosis and equine theileriosis, respectively. These parasites of vast medical, epidemiological, and economic impact have complex life cycles in their vertebrate and tick hosts. Large gaps in knowledge concerning the mechanisms used by these parasites for gene regulation remain. Regulatory genes coding for DNA binding proteins such as members of the Api-AP2, HMG, and Myb families are known to play crucial roles as transcription factors. Although the repertoire of Api-AP2 has been defined and a HMG gene was previously identified in the B. bovis genome, these regulatory genes have not been described in detail in B. microti and T. equi. In this study, comparative bioinformatics was used to: (i identify and map genes encoding for these transcription factors among three parasites' genomes; (ii identify a previously unreported HMG gene in B. microti; (iii define a repertoire of eight conserved Myb genes; and (iv identify AP2 correlates among B. bovis and the better-studied Plasmodium parasites. Searching the available transcriptome of B. bovis defined patterns of transcription of these three gene families in B. bovis erythrocyte stage parasites. Sequence comparisons show conservation of functional domains and general architecture in the AP2, Myb, and HMG proteins, which may be significant for the regulation of common critical parasite life cycle transitions in B. bovis, B. microti, and T. equi. A detailed understanding of the role of gene families encoding DNA binding proteins will provide new tools for unraveling regulatory mechanisms involved in B. bovis, B. microti, and T. equi life cycles and environmental adaptive responses and potentially contributes to the development of novel convergent strategies for improved control of babesiosis and equine piroplasmosis.

  20. Production of Recombinant Adenovirus Containing Human Interlukin-4 Gene

    OpenAIRE

    Mojarrad, Majid; Abdolazimi, Yassan; Hajati, Jamshid; Modarressi, Mohammad Hossein

    2011-01-01

    Objective(s) Recombinant adenoviruses are currently used for a variety of purposes, including in vitro gene transfer, in vivo vaccination, and gene therapy. Ability to infect many cell types, high efficiency in gene transfer, entering both dividing and non dividing cells, and growing to high titers make this virus a good choice for using in various experiments. In the present experiment, a recombinant adenovirus containing human IL-4 coding sequence was made. IL-4 has several characteristics ...

  1. Molecular phylogeny of the genus Saguinus (Platyrrhini, Primates based on the ND1 mitochondrial gene and implications for conservation

    Directory of Open Access Journals (Sweden)

    Claudia Helena Tagliaro

    2005-03-01

    Full Text Available The systematics of the subfamily Callitrichinae (Platyrrhini, Primates, a group of small monkeys from South America and Panama, remains an area of considerable discussion despite many investigations, there being continuing controversy over subgeneric taxonomic classifications based on morphological characters. The purpose of our research was to help elucidate the phylogenetic relationships within the monkey genus Saguinus (Callitrichinae using a molecular approach to discover whether or not the two different sections containing hairy-faced and bare-faced species are monophyletic, whether Saguinus midas midas and Saguinus bicolor are more closely related than are S. midas midas and Saguinus midas niger, and if Saguinus fuscicollis melanoleucus and Saguinus fuscicollis weddelli really are different species. We sequenced the 957 bp ND1 mitochondrial gene of 21 Saguinus monkeys (belonging to six species and nine morphotypes and one Cebus monkey (the outgroup and constructed phylogenetic trees using maximum parsimony, neighbor joining, and maximum likelihood methods. The phylogenetic trees obtained divided the genus Saguinus into two groups, one containing the small-bodied species S. fuscicollis and the other, the large-bodied species S. mystax, S. leucopus, S. oedipus, S. midas, S. bicolor. The most derived taxa, S. midas and S. bicolor, grouped together, while S. fuscicollis melanoleucus and S. f. weddelli showed divergence values that did not support the division of these morphotypes into subspecies. On the other hand, S. midas individuals showed divergence compatible with the existence of three subspecies, two of them with the same morphotype as the subspecies S. midas niger. The results of our study suggest that there is at least one Saguinus subspecies that has not yet been described and that the conservation status of Saguinus species and subspecies should be carefully revised using modern molecular approaches.

  2. 76 FR 19077 - Energy Conservation Program for Consumer Products: Decision and Order Granting a Waiver to...

    Science.gov (United States)

    2011-04-06

    ... technology. Specifically, DOE granted GE, Whirlpool, Electrolux (3 waivers), LG, Samsung (2 waivers), and...- freezer products for compliance, marketing, or other purposes only to the extent that such products have...

  3. 76 FR 38287 - Energy Conservation Program: Certification, Compliance, and Enforcement for Consumer Products and...

    Science.gov (United States)

    2011-06-30

    ... Program: Certification, Compliance, and Enforcement for Consumer Products and Commercial and Industrial... products will be required to submit certification reports no later than December 31, 2012. DATES: This rule... some certification requirements for these products but make those requirements [[Page 38289

  4. Evolutionary conservation advice for despotic populations: habitat heterogeneity favours conflict and reduces productivity in Seychelles magpie robins.

    Science.gov (United States)

    López-Sepulcre, Andrés; Kokko, Hanna; Norris, Ken

    2010-11-22

    Individual preferences for good habitat are often thought to have a beneficial stabilizing effect for populations. However, if individuals preferentially compete for better-quality territories, these may become hotspots of conflict. We show that, in an endangered species, this process decreases the productivity of favoured territories to the extent that differences in productivity between territories disappear. Unlike predictions from current demographic theory on site-dependent population regulation (ideal despotic distribution), we show that population productivity is reduced if resources are distributed unevenly in space. Competition for high-quality habitat can thus have detrimental consequences for populations even though it benefits individuals. Manipulating conflict (e.g. by reducing variation in habitat quality) can therefore prove an effective conservation measure in species with strong social or territorial conflict.

  5. The genome sequence of the commercially cultivated mushroom Agrocybe aegerita reveals a conserved repertoire of fruiting-related genes and a versatile suite of biopolymer-degrading enzymes.

    Science.gov (United States)

    Gupta, Deepak K; Rühl, Martin; Mishra, Bagdevi; Kleofas, Vanessa; Hofrichter, Martin; Herzog, Robert; Pecyna, Marek J; Sharma, Rahul; Kellner, Harald; Hennicke, Florian; Thines, Marco

    2018-01-15

    Agrocybe aegerita is an agaricomycete fungus with typical mushroom features, which is commercially cultivated for its culinary use. In nature, it is a saprotrophic or facultative pathogenic fungus causing a white-rot of hardwood in forests of warm and mild climate. The ease of cultivation and fructification on solidified media as well as its archetypal mushroom fruit body morphology render A. aegerita a well-suited model for investigating mushroom developmental biology. Here, the genome of the species is reported and analysed with respect to carbohydrate active genes and genes known to play a role during fruit body formation. In terms of fruit body development, our analyses revealed a conserved repertoire of fruiting-related genes, which corresponds well to the archetypal fruit body morphology of this mushroom. For some genes involved in fruit body formation, paralogisation was observed, but not all fruit body maturation-associated genes known from other agaricomycetes seem to be conserved in the genome sequence of A. aegerita. In terms of lytic enzymes, our analyses suggest a versatile arsenal of biopolymer-degrading enzymes that likely account for the flexible life style of this species. Regarding the amount of genes encoding CAZymes relevant for lignin degradation, A. aegerita shows more similarity to white-rot fungi than to litter decomposers, including 18 genes coding for unspecific peroxygenases and three dye-decolourising peroxidase genes expanding its lignocellulolytic machinery. The genome resource will be useful for developing strategies towards genetic manipulation of A. aegerita, which will subsequently allow functional genetics approaches to elucidate fundamentals of fruiting and vegetative growth including lignocellulolysis.

  6. Analysis of the grape MYB R2R3 subfamily reveals expanded wine quality-related clades and conserved gene structure organization across Vitis and Arabidopsis genomes

    Science.gov (United States)

    Matus, José Tomás; Aquea, Felipe; Arce-Johnson, Patricio

    2008-01-01

    Background The MYB superfamily constitutes the most abundant group of transcription factors described in plants. Members control processes such as epidermal cell differentiation, stomatal aperture, flavonoid synthesis, cold and drought tolerance and pathogen resistance. No genome-wide characterization of this family has been conducted in a woody species such as grapevine. In addition, previous analysis of the recently released grape genome sequence suggested expansion events of several gene families involved in wine quality. Results We describe and classify 108 members of the grape R2R3 MYB gene subfamily in terms of their genomic gene structures and similarity to their putative Arabidopsis thaliana orthologues. Seven gene models were derived and analyzed in terms of gene expression and their DNA binding domain structures. Despite low overall sequence homology in the C-terminus of all proteins, even in those with similar functions across Arabidopsis and Vitis, highly conserved motif sequences and exon lengths were found. The grape epidermal cell fate clade is expanded when compared with the Arabidopsis and rice MYB subfamilies. Two anthocyanin MYBA related clusters were identified in chromosomes 2 and 14, one of which includes the previously described grape colour locus. Tannin related loci were also detected with eight candidate homologues in chromosomes 4, 9 and 11. Conclusion This genome wide transcription factor analysis in Vitis suggests that clade-specific grape R2R3 MYB genes are expanded while other MYB genes could be well conserved compared to Arabidopsis. MYB gene abundance, homology and orientation within particular loci also suggests that expanded MYB clades conferring quality attributes of grapes and wines, such as colour and astringency, could possess redundant, overlapping and cooperative functions. PMID:18647406

  7. Analysis of the grape MYB R2R3 subfamily reveals expanded wine quality-related clades and conserved gene structure organization across Vitis and Arabidopsis genomes

    Directory of Open Access Journals (Sweden)

    Arce-Johnson Patricio

    2008-07-01

    Full Text Available Abstract Background The MYB superfamily constitutes the most abundant group of transcription factors described in plants. Members control processes such as epidermal cell differentiation, stomatal aperture, flavonoid synthesis, cold and drought tolerance and pathogen resistance. No genome-wide characterization of this family has been conducted in a woody species such as grapevine. In addition, previous analysis of the recently released grape genome sequence suggested expansion events of several gene families involved in wine quality. Results We describe and classify 108 members of the grape R2R3 MYB gene subfamily in terms of their genomic gene structures and similarity to their putative Arabidopsis thaliana orthologues. Seven gene models were derived and analyzed in terms of gene expression and their DNA binding domain structures. Despite low overall sequence homology in the C-terminus of all proteins, even in those with similar functions across Arabidopsis and Vitis, highly conserved motif sequences and exon lengths were found. The grape epidermal cell fate clade is expanded when compared with the Arabidopsis and rice MYB subfamilies. Two anthocyanin MYBA related clusters were identified in chromosomes 2 and 14, one of which includes the previously described grape colour locus. Tannin related loci were also detected with eight candidate homologues in chromosomes 4, 9 and 11. Conclusion This genome wide transcription factor analysis in Vitis suggests that clade-specific grape R2R3 MYB genes are expanded while other MYB genes could be well conserved compared to Arabidopsis. MYB gene abundance, homology and orientation within particular loci also suggests that expanded MYB clades conferring quality attributes of grapes and wines, such as colour and astringency, could possess redundant, overlapping and cooperative functions.

  8. RNA-seq of the aging brain in the short-lived fish N. furzeri - conserved pathways and novel genes associated with neurogenesis.

    Science.gov (United States)

    Baumgart, Mario; Groth, Marco; Priebe, Steffen; Savino, Aurora; Testa, Giovanna; Dix, Andreas; Ripa, Roberto; Spallotta, Francesco; Gaetano, Carlo; Ori, Michela; Terzibasi Tozzini, Eva; Guthke, Reinhard; Platzer, Matthias; Cellerino, Alessandro

    2014-12-01

    The brains of teleost fish show extensive adult neurogenesis and neuronal regeneration. The patterns of gene regulation during fish brain aging are unknown. The short-lived teleost fish Nothobranchius furzeri shows markers of brain aging including reduced learning performances, gliosis, and reduced adult neurogenesis. We used RNA-seq to quantify genome-wide transcript regulation and sampled five different time points to characterize whole-genome transcript regulation during brain aging of N. furzeri. Comparison with human datasets revealed conserved up-regulation of ribosome, lysosome, and complement activation and conserved down-regulation of synapse, mitochondrion, proteasome, and spliceosome. Down-regulated genes differ in their temporal profiles: neurogenesis and extracellular matrix genes showed rapid decay, synaptic and axonal genes a progressive decay. A substantial proportion of differentially expressed genes (~40%) showed inversion of their temporal profiles in the last time point: spliceosome and proteasome showed initial down-regulation and stress-response genes initial up-regulation. Extensive regulation was detected for chromatin remodelers of the DNMT and CBX families as well as members of the polycomb complex and was mirrored by an up-regulation of the H3K27me3 epigenetic mark. Network analysis showed extensive coregulation of cell cycle/DNA synthesis genes with the uncharacterized zinc-finger protein ZNF367 as central hub. In situ hybridization showed that ZNF367 is expressed in neuronal stem cell niches of both embryonic zebrafish and adult N. furzeri. Other genes down-regulated with age, not previously associated with adult neurogenesis and with similar patterns of expression are AGR2, DNMT3A, KRCP, MEX3A, SCML4, and CBX1. CBX7, on the other hand, was up-regulated with age. © 2014 The Authors. Aging cell published by the Anatomical Society and John Wiley & Sons Ltd.

  9. Form gene clustering method about pan-ethnic-group products based on emotional semantic

    Science.gov (United States)

    Chen, Dengkai; Ding, Jingjing; Gao, Minzhuo; Ma, Danping; Liu, Donghui

    2016-09-01

    The use of pan-ethnic-group products form knowledge primarily depends on a designer's subjective experience without user participation. The majority of studies primarily focus on the detection of the perceptual demands of consumers from the target product category. A pan-ethnic-group products form gene clustering method based on emotional semantic is constructed. Consumers' perceptual images of the pan-ethnic-group products are obtained by means of product form gene extraction and coding and computer aided product form clustering technology. A case of form gene clustering about the typical pan-ethnic-group products is investigated which indicates that the method is feasible. This paper opens up a new direction for the future development of product form design which improves the agility of product design process in the era of Industry 4.0.

  10. Production process reproducibility and product quality consistency of transient gene expression in HEK293 cells with anti-PD1 antibody as the model protein.

    Science.gov (United States)

    Ding, Kai; Han, Lei; Zong, Huifang; Chen, Junsheng; Zhang, Baohong; Zhu, Jianwei

    2017-03-01

    Demonstration of reproducibility and consistency of process and product quality is one of the most crucial issues in using transient gene expression (TGE) technology for biopharmaceutical development. In this study, we challenged the production consistency of TGE by expressing nine batches of recombinant IgG antibody in human embryonic kidney 293 cells to evaluate reproducibility including viable cell density, viability, apoptotic status, and antibody yield in cell culture supernatant. Product quality including isoelectric point, binding affinity, secondary structure, and thermal stability was assessed as well. In addition, major glycan forms of antibody from different batches of production were compared to demonstrate glycosylation consistency. Glycan compositions of the antibody harvested at different time periods were also measured to illustrate N-glycan distribution over the culture time. From the results, it has been demonstrated that different TGE batches are reproducible from lot to lot in overall cell growth, product yield, and product qualities including isoelectric point, binding affinity, secondary structure, and thermal stability. Furthermore, major N-glycan compositions are consistent among different TGE batches and conserved during cell culture time.

  11. In vitro conservation and sustained production of breadfruit ( Artocarpus altilis, Moraceae): modern technologies for a traditional tropical crop

    Science.gov (United States)

    Murch, Susan J.; Ragone, Diane; Shi, Wendy Lei; Alan, Ali R.; Saxena, Praveen K.

    2008-02-01

    Breadfruit ( Artocarpus altilis, Moraceae) is a traditionally cultivated, high-energy, high-yield crop, but widespread use of the plant for food is limited by poor quality and poor storage properties of the fruit. A unique field genebank of breadfruit species and cultivars exists at the National Tropical Botanical Garden in the Hawaiian Islands and is an important global resource for conservation and sustainable use of breadfruit. However, this plant collection could be damaged by a random natural disaster such as a hurricane. We have developed a highly efficient in vitro plant propagation system to maintain, conserve, mass propagate, and distribute elite varieties of this important tree species. Mature axillary shoot buds were collected from three different cultivars of breadfruit and proliferated using a cytokinin-supplemented medium. The multiple shoots were maintained as stock cultures and repeatedly used to develop whole plants after root differentiation on a basal or an auxin-containing medium. The plantlets were successfully grown under greenhouse conditions and were reused to initiate additional shoot cultures for sustained production of plants. Flow cytometry was used to determine the nuclear deoxyribonucleic acid content and the ploidy status of the in vitro grown population. The efficacy of the micropropagation protocols developed in this study represents a significant advancement in the conservation and sustained mass propagation of breadfruit germplasm in a controlled environment free from contamination.

  12. A parametrization of two-dimensional turbulence based on a maximum entropy production principle with a local conservation of energy

    International Nuclear Information System (INIS)

    Chavanis, Pierre-Henri

    2014-01-01

    In the context of two-dimensional (2D) turbulence, we apply the maximum entropy production principle (MEPP) by enforcing a local conservation of energy. This leads to an equation for the vorticity distribution that conserves all the Casimirs, the energy, and that increases monotonically the mixing entropy (H-theorem). Furthermore, the equation for the coarse-grained vorticity dissipates monotonically all the generalized enstrophies. These equations may provide a parametrization of 2D turbulence. They do not generally relax towards the maximum entropy state. The vorticity current vanishes for any steady state of the 2D Euler equation. Interestingly, the equation for the coarse-grained vorticity obtained from the MEPP turns out to coincide, after some algebraic manipulations, with the one obtained with the anticipated vorticity method. This shows a connection between these two approaches when the conservation of energy is treated locally. Furthermore, the newly derived equation, which incorporates a diffusion term and a drift term, has a nice physical interpretation in terms of a selective decay principle. This sheds new light on both the MEPP and the anticipated vorticity method. (paper)

  13. Non-timber Forest Products, Their Vulnerability and Conservation in a Designated UNESCO Heritage Site of Arunanchal Pradesh, India

    Directory of Open Access Journals (Sweden)

    Kaushalendra Kumar JHA

    2015-12-01

    Full Text Available The Apatani, non-nomadic tribe, have evolved an ecologically sustainable system of rural forestry in Ziro Valley, a proposed heritage site of UNESCO. They have been using non-timber forest products (NTFPs grown in homestead and nearby forests for a very long period. The present study was aimed at identification of priority NTFPs and uses, their availability status and availability trend, conservation need, and sustainability interventions. Qualitative methods of research like, exploratory survey, questionnaire survey, focus group discussion, semi-structured interview of key informants, etc. were employed for data collection. The Apatani used 112 priority NTFPs for food supplement, herbal medicine, house building material and other purposes. However, on the basis of ecological importance such NTFPs were categorized as very low, low, moderate, high, and very high vulnerable species. Twenty vulnerable species like Antiitari ayi (Actinidia callosa, Biiling (Choerospondias axillaris, Henchi (Rubus niveus, Jojuru ayi (Coccinia grandis, Ngiilyang Khiiko (Centella asiatica etc. should be conserved and seventeen not vulnerable species at this stage like, Padii hamang (Cardamine hirsute, Sankhe (Quercus griffithii, Bije (Phyllostachys manii, Hiigu hamang (Oenanthe javanica, Kiira (Quercus dealbata , etc. could be commercialized. However, a balance needed to be struck between commercialization and conservation by adopting a comprehensive policy based on scientific and traditional Apatani knowledge for harvesting and regeneration of NTFPs. Homegardening or community farming is recommended for sustainable supply of commercially important species to be domasticated.

  14. Identification of potentially hazardous human gene products in GMO risk assessment.

    Science.gov (United States)

    Bergmans, Hans; Logie, Colin; Van Maanen, Kees; Hermsen, Harm; Meredyth, Michelle; Van Der Vlugt, Cécile

    2008-01-01

    Genetically modified organisms (GMOs), e.g. viral vectors, could threaten the environment if by their release they spread hazardous gene products. Even in contained use, to prevent adverse consequences, viral vectors carrying genes from mammals or humans should be especially scrutinized as to whether gene products that they synthesize could be hazardous in their new context. Examples of such potentially hazardous gene products (PHGPs) are: protein toxins, products of dominant alleles that have a role in hereditary diseases, gene products and sequences involved in genome rearrangements, gene products involved in immunomodulation or with an endocrine function, gene products involved in apoptosis, activated proto-oncogenes. For contained use of a GMO that carries a construct encoding a PHGP, the precautionary principle dictates that safety measures should be applied on a "worst case" basis, until the risks of the specific case have been assessed. The potential hazard of cloned genes can be estimated before empirical data on the actual GMO become available. Preliminary data may be used to focus hazard identification and risk assessment. Both predictive and empirical data may also help to identify what further information is needed to assess the risk of the GMO. A two-step approach, whereby a PHGP is evaluated for its conceptual dangers, then checked by data bank searches, is delineated here.

  15. Pyrenean meadows in Natura 2000 network: grass production and plant biodiversity conservation

    Energy Technology Data Exchange (ETDEWEB)

    Reine, R.; Barrantes, O.; Chocarro, C.; Juarez, A.; Broca, A.; Maestro, M.; Ferrer, C.

    2014-06-01

    In semi-natural mountain meadows, yield and forage quality must be reconciled with plant biodiversity conservation. This study was performed to analyze the relationships between these three parameters. To quantify plant biodiversity and pastoral value (PV), phyto sociological inventories were performed in 104 semi-natural meadows in the Central Spanish Pyrenees included in the Natura 2000 network. Forage yields were calculated and forage samples were analyzed for relative feed value (RFV). We identified two main types of meadows: (i) those that had more intensive management, relatively close to farm buildings, with little or no slope, dominated by grasses, with low plant biodiversity, high PV and yield, but low forage quality and (ii) those that had less intensive management, distant from farm buildings, on slopes, richer in other forbs, with high plant biodiversity and forage quality, but low PV and yield. Conservation policies should emphasize less intensive management practices to maintain plant diversity in the semi-natural meadows in the Pyrenees. The widespread view that other forbs have low nutritional value should be revised in future research. These species often are undervalued by the PV method, because their nutritional quality, digestibility and intake are poorly understood. (Author)

  16. Pyrenean meadows in Natura 2000 network: grass production and plant biodiversity conservation

    Directory of Open Access Journals (Sweden)

    Ramón Reiné

    2014-02-01

    Full Text Available In semi-natural mountain meadows, yield and forage quality must be reconciled with plant biodiversity conservation. This study was performed to analyze the relationships between these three parameters. To quantify plant biodiversity and pastoral value (PV, phytosociological inventories were performed in 104 semi-natural meadows in the Central Spanish Pyrenees included in the Natura 2000 network. Forage yields were calculated and forage samples were analyzed for relative feed value (RFV. We identified two main types of meadows: (i those that had “more intensive management,” relatively close to farm buildings, with little or no slope, dominated by grasses, with low plant biodiversity, high PV and yield, but low forage quality and (ii those that had “less intensive management,” distant from farm buildings, on slopes, richer in “other forbs”, with high plant biodiversity and forage quality, but low PV and yield. Conservation policies should emphasize less intensive management practices to maintain plant diversity in the semi-natural meadows in the Pyrenees. The widespread view that “other forbs” have low nutritional value should be revised in future research. These species often are undervalued by the PV method, because their nutritional quality, digestibility and intake are poorly understood.

  17. Weaver gene 3'UTR novel mutations: Associations with production ...

    African Journals Online (AJOL)

    use

    2011-11-21

    Nov 21, 2011 ... College of Animal Science and Technology, Northwest A&F University, Shaanxi ... To further understand the effects of weaver gene variant on fat, protein, .... one kid, but does that lambed twins were also part of the dataset.

  18. 75 FR 6013 - Energy Conservation Program for Consumer Products: Decision and Order Granting a Waiver to...

    Science.gov (United States)

    2010-02-05

    ... decision and order is effective February 5, 2010. FOR FURTHER INFORMATION CONTACT: Dr. Michael G. Raymond... variable-speed or digital compressor. Hallowell's product deviates from the anticipated form--a system... conditioners and heat pump products, for compliance, marketing, or other purposes, only to the extent that such...

  19. 77 FR 3559 - Energy Conservation Program for Consumer Products: Test Procedures for Refrigerators...

    Science.gov (United States)

    2012-01-25

    ... Long-Time and Variable Defrost Test Method To Fully Capture Energy Use for Temperature Recovery D... product classes. 55 FR 42845 (October 24, 1990). DOE again updated the performance standards for...: (1) Compartment temperature changes; (2) modified volume calculation methods; (3) products that...

  20. 76 FR 69147 - Energy Conservation Program for Consumer Products: Proposed Determination To Treat Non-Compressor...

    Science.gov (United States)

    2011-11-08

    ... use for such products, (e.g., thermoelectric wine chillers) is likely to exceed the 100 kilowatt-hour.... DOE's analysis describes both the burdens and benefits of potential standards, pursuant to 42 U.S.C... efforts to amend the standards for these products, interested parties urged DOE to include wine chillers...

  1. 75 FR 78809 - Energy Conservation Program for Consumer Products: Test Procedures for Refrigerators...

    Science.gov (United States)

    2010-12-16

    ... discusses the treatment of combination wine storage-freezer products that were the subject of a recent test... interim final rule incorporate by reference into part 430 the following industry standards: (1) ANSI/AHAM... Rule III. Discussion A. Products Covered by the Proposed Revisions B. Combination Wine Storage-Freezer...

  2. Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences

    Directory of Open Access Journals (Sweden)

    De Marzo Angelo M

    2011-06-01

    Full Text Available Abstract Background DNA methylation has been linked to genome regulation and dysregulation in health and disease respectively, and methods for characterizing genomic DNA methylation patterns are rapidly emerging. We have developed/refined methods for enrichment of methylated genomic fragments using the methyl-binding domain of the human MBD2 protein (MBD2-MBD followed by analysis with high-density tiling microarrays. This MBD-chip approach was used to characterize DNA methylation patterns across all non-repetitive sequences of human chromosomes 21 and 22 at high-resolution in normal and malignant prostate cells. Results Examining this data using computational methods that were designed specifically for DNA methylation tiling array data revealed widespread methylation of both gene promoter and non-promoter regions in cancer and normal cells. In addition to identifying several novel cancer hypermethylated 5' gene upstream regions that mediated epigenetic gene silencing, we also found several hypermethylated 3' gene downstream, intragenic and intergenic regions. The hypermethylated intragenic regions were highly enriched for overlap with intron-exon boundaries, suggesting a possible role in regulation of alternative transcriptional start sites, exon usage and/or splicing. The hypermethylated intergenic regions showed significant enrichment for conservation across vertebrate species. A sampling of these newly identified promoter (ADAMTS1 and SCARF2 genes and non-promoter (downstream or within DSCR9, C21orf57 and HLCS genes hypermethylated regions were effective in distinguishing malignant from normal prostate tissues and/or cell lines. Conclusions Comparison of chromosome-wide DNA methylation patterns in normal and malignant prostate cells revealed significant methylation of gene-proximal and conserved intergenic sequences. Such analyses can be easily extended for genome-wide methylation analysis in health and disease.

  3. Comparison of effects of machine performance parameters and energy indices of soybean production in conservation and conventional tillage systems

    Directory of Open Access Journals (Sweden)

    A Sharifi

    2016-09-01

    Full Text Available Introduction Nowadays, agricultural systems are seeking economic, ecological and bioenvironmental goals for production of agricultural crops with protection and sustainability of the environment. Therefore, there is need to extend sustainable agricultural systems such as conservation agriculture. One of the principles of conservation agriculture is conservation tillage. Conservation tillage is a kind of tillage that retains crop residues on the soil surface or mixes it with soil using related machines. It could also affect on machine performance parameters. Energy consumption for producing one kilogram crop could be studied for conservation tillage. Several researchers have conducted studies on this issue for production of different crops including wheat, sunflower and forage crops. This study conducted to assess machine performance parameters and energy indices of conservation tillage systems for soybean cultivation in Golestan province. Materials and Methods This study was conducted to investigate the effects of conservation tillage systems on machine performance and energy indices in soybean production at the Gorgan research station of Golestan Agricultural and Natural Resource Research Center in 2012. The precipitation was 450 mm. Soil texture was silty clay loam. Treatments were four tillage methods, including no-till using row crop direct planter, no-till using grain direct drill, conventional tillage usin a disk harrow with working depth of 10-15 cm and minimum tillage using chisel packer with a working depth of 20 cm. Machine performance parameters and energy indices studied in a farm covered by wheat residues in a randomized complete block design (RCBD with four treatments and four replications. Machine performance parameters consisted of field efficiency, field capacity, total field capacity and planting uniformity index were measured. Energy indices such as energy ratio, energy productivity, energy intensity and net energy gain were

  4. Can we conserve trans-resveratrol content and antioxidant activity during industrial production of chocolate?

    Science.gov (United States)

    Salvador, Izabela; Massarioli, Adna P; Silva, Anna Paula S; Malaguetta, Heloísa; Melo, Priscilla S; Alencar, Severino M

    2018-05-23

    Cocoa exhibits high content of phenolic compounds, among which trans-resveratrol stands out, associated with several bioactive activities such as antioxidant properties. Chocolate contains reduced amounts of these bioactive compounds due to losses during the production process. Therefore, this study aimed to assess changes in total phenolic content and specifically trans-resveratrol, as well as in the antioxidant activity of cocoa and its products during industrial production of chocolate. A total of ten different cocoa products were analyzed. The processes of fermentation and roasting caused significant loss of total phenolic compounds and antioxidant activity. However, due to high temperature, roasting had a major influence on this loss (71% for total phenolic compounds and 53% to 77% for antioxidant activity), except for trans-resveratrol. The content of trans-resveratrol formed after fermentation (9.8 μg kg -1 ) showed little variation during the processes, and it was detected in higher concentrations both in natural (11.4 μg kg -1 ) and in alkalized cocoa powder (13.5 μg kg -1 ). Alkalization of cocoa products led to loss of capacity of deactivating superoxide radical. These findings contribute to the optimization of the production process of chocolate and other food products containing cocoa and its derivatives aiming to better preserve their bioactive compounds. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  5. The mitochondrial genome of the stingless bee Melipona bicolor (Hymenoptera, Apidae, Meliponini: sequence, gene organization and a unique tRNA translocation event conserved across the tribe Meliponini

    Directory of Open Access Journals (Sweden)

    Daniela Silvestre

    2008-01-01

    Full Text Available At present a complete mtDNA sequence has been reported for only two hymenopterans, the Old World honey bee, Apis mellifera and the sawfly Perga condei. Among the bee group, the tribe Meliponini (stingless bees has some distinction due to its Pantropical distribution, great number of species and large importance as main pollinators in several ecosystems, including the Brazilian rain forest. However few molecular studies have been conducted on this group of bees and few sequence data from mitochondrial genomes have been described. In this project, we PCR amplified and sequenced 78% of the mitochondrial genome of the stingless bee Melipona bicolor (Apidae, Meliponini. The sequenced region contains all of the 13 mitochondrial protein-coding genes, 18 of 22 tRNA genes, and both rRNA genes (one of them was partially sequenced. We also report the genome organization (gene content and order, gene translation, genetic code, and other molecular features, such as base frequencies, codon usage, gene initiation and termination. We compare these characteristics of M. bicolor to those of the mitochondrial genome of A. mellifera and other insects. A highly biased A+T content is a typical characteristic of the A. mellifera mitochondrial genome and it was even more extreme in that of M. bicolor. Length and compositional differences between M. bicolor and A. mellifera genes were detected and the gene order was compared. Eleven tRNA gene translocations were observed between these two species. This latter finding was surprising, considering the taxonomic proximity of these two bee tribes. The tRNA Lys gene translocation was investigated within Meliponini and showed high conservation across the Pantropical range of the tribe.

  6. Crop-to-wild gene flow and its fitness consequences for a wild fruit tree: Towards a comprehensive conservation strategy of the wild apple in Europe.

    Science.gov (United States)

    Feurtey, Alice; Cornille, Amandine; Shykoff, Jacqui A; Snirc, Alodie; Giraud, Tatiana

    2017-02-01

    Crop-to-wild gene flow can reduce the fitness and genetic integrity of wild species. Malus sylvestris , the European crab-apple fruit tree in particular, is threatened by the disappearance of its habitat and by gene flow from its domesticated relative , Malus domestica . With the aims of evaluating threats for M. sylvestris and of formulating recommendations for its conservation, we studied here, using microsatellite markers and growth experiments: (i) hybridization rates in seeds and trees from a French forest and in seeds used for replanting crab apples in agrosystems and in forests, (ii) the impact of the level of M. domestica ancestry on individual tree fitness and (iii) pollen dispersal abilities in relation to crop-to-wild gene flow. We found substantial contemporary crop-to-wild gene flow in crab-apple tree populations and superior fitness of hybrids compared to wild seeds and seedlings. Using paternity analyses, we showed that pollen dispersal could occur up to 4 km and decreased with tree density. The seed network furnishing the wild apple reintroduction agroforestry programmes was found to suffer from poor genetic diversity, introgressions and species misidentification. Overall, our findings indicate supported threats for the European wild apple steering us to provide precise recommendations for its conservation.

  7. Hormone-induced protection against mammary tumorigenesis is conserved in multiple rat strains and identifies a core gene expression signature induced by pregnancy.

    Science.gov (United States)

    Blakely, Collin M; Stoddard, Alexander J; Belka, George K; Dugan, Katherine D; Notarfrancesco, Kathleen L; Moody, Susan E; D'Cruz, Celina M; Chodosh, Lewis A

    2006-06-15

    Women who have their first child early in life have a substantially lower lifetime risk of breast cancer. The mechanism for this is unknown. Similar to humans, rats exhibit parity-induced protection against mammary tumorigenesis. To explore the basis for this phenomenon, we identified persistent pregnancy-induced changes in mammary gene expression that are tightly associated with protection against tumorigenesis in multiple inbred rat strains. Four inbred rat strains that exhibit marked differences in their intrinsic susceptibilities to carcinogen-induced mammary tumorigenesis were each shown to display significant protection against methylnitrosourea-induced mammary tumorigenesis following treatment with pregnancy levels of estradiol and progesterone. Microarray expression profiling of parous and nulliparous mammary tissue from these four strains yielded a common 70-gene signature. Examination of the genes constituting this signature implicated alterations in transforming growth factor-beta signaling, the extracellular matrix, amphiregulin expression, and the growth hormone/insulin-like growth factor I axis in pregnancy-induced alterations in breast cancer risk. Notably, related molecular changes have been associated with decreased mammographic density, which itself is strongly associated with decreased breast cancer risk. Our findings show that hormone-induced protection against mammary tumorigenesis is widely conserved among divergent rat strains and define a gene expression signature that is tightly correlated with reduced mammary tumor susceptibility as a consequence of a normal developmental event. Given the conservation of this signature, these pathways may contribute to pregnancy-induced protection against breast cancer.

  8. Conservation of AtTZF1, AtTZF2 and AtTZF3 homolog gene regulation by salt stress in evolutionarily distant plant species

    Directory of Open Access Journals (Sweden)

    Fabio eD'Orso

    2015-06-01

    Full Text Available Arginine-rich tandem zinc-finger proteins (RR-TZF participate in a wide range of plant developmental processes and adaptive responses to abiotic stress, such as cold, salt and drought. This study investigates the conservation of the genes AtTZF1-5 at the level of their sequences and expression across plant species. The genomic sequences of the two RR-TZF genes TdTZF1-A and TdTZF1-B were isolated in durum wheat and assigned to chromosomes 3A and 3B, respectively. Sequence comparisons revealed that they encode proteins that are highly homologous to AtTZF1, AtTZF2 and AtTZF3. The expression profiles of these RR-TZF durum wheat and Arabidopsis proteins support a common function in the regulation of seed germination and responses to abiotic stress. In particular, analysis of plants with attenuated and overexpressed AtTZF3 indicate that AtTZF3 is a negative regulator of seed germination under conditions of salt stress. Finally, comparative sequence analyses establish that the RR-TZF genes are encoded by lower plants, including the bryophyte Physcomitrella patens and the alga Chlamydomonas reinhardtii. The regulation of the Physcomitrella AtTZF1-2-3-like genes by salt stress strongly suggests that a subgroup of the RR-TZF proteins has a function that has been conserved throughout evolution.

  9. 78 FR 65223 - Energy Conservation Program for Consumer Products: Proposed Determination of Miscellaneous...

    Science.gov (United States)

    2013-10-31

    ... defined these items in terms of their ability to safely store fresh food. In so doing, the agency has.... (2013). ``U.S. Residential Miscellaneous Refrigeration Products: Results from Amazon Mechanical Turk...

  10. 75 FR 75289 - Energy Conservation Program for Consumer Products: Test Procedures for Residential Dishwashers...

    Science.gov (United States)

    2010-12-02

    ... revisions: (1) The addition of a method to rate the efficiency of soil-sensing products; (2) the addition of... means and discharges to the plumbing drainage system.'' 10 CFR 430.2. Today's proposed amendments to the...

  11. 75 FR 41167 - Energy Conservation Program for Consumer Products: Notice of Petition for Waiver of Whirlpool...

    Science.gov (United States)

    2010-07-15

    ... Products Other Than Automobiles.'' (42 U.S.C. 6291-6309) Part A includes definitions, test procedures... consumers. 1. Petitioner. Whirlpool Corporation is the world's leading manufacturer and marketer of major...

  12. 75 FR 22586 - Energy Conservation Program for Consumer Products: Notice of Petition for Waiver of General...

    Science.gov (United States)

    2010-04-29

    ... Appliances Corp. (Bosch-Siemens Hausgerate GmbH), Electrolux Home Products, Equator, Fisher & Paykel... Corp. filed and was granted its waiver petition, \\2\\ as was Electrolux \\3\\ and Samsung.\\4\\ \\1\\ FR Vol...

  13. 77 FR 31742 - Energy Conservation Program for Consumer Products and Certain Commercial and Industrial Equipment...

    Science.gov (United States)

    2012-05-30

    ... product is prescribed, no manufacturer may make any representation with respect to water usage of such... or plastic plate that requires the testing laboratory to adapt its test depending on the specific...

  14. 75 FR 81258 - Energy Conservation Program for Consumer Products: Notice of Petition for Waiver of Electrolux...

    Science.gov (United States)

    2010-12-27

    ... associate General Counsel, Electrolux Home Products, Inc., 20445 Emerald Parkway, SW., Suite 250, P.O. Box... insight, to meet the real needs of consumers and professionals. Electrolux's principal clothes washer...

  15. The presence of two S-layer-protein-encoding genes is conserved among species related to Lactobacillus acidophilus

    NARCIS (Netherlands)

    Boot, H.J.; Kolen, C.P.A.M.; Pot, B.; Kersters, K.; Pouwels, P.H.

    1996-01-01

    Previously we have shown that the type strain of Lactobacillus acidophilus possesses two S-protein-encoding genes, one of which is silent, on a chromosomal segment of 6 kb. The S-protein-encoding gene in the expression site can be exchanged for the silent S-protein-encoding gene by inversion of this

  16. Project AProWa: a national view on managing trade-offs between agricultural production and conservation of aquatic ecosystems

    Science.gov (United States)

    Dietzel, Anne; Rahn, Eric; Stamm, Christian

    2014-05-01

    Swiss agriculture is legally committed to fulfill several, partially conflicting goals such as agricultural production on the one hand and the conservation of natural resources on the other hand. In the context of the research project AProWa ("Agricultural Production and Water"), the relationships between the production aspect and the conservation of aquatic ecosystems is analyzed with a holistic approach. Agricultural production and the protection of water resources have high potential for conflicts: Farmers use ground and surface water to irrigate their fields. On the other hand, drainage systems enable the production on otherwise unfavorably wet soils. These in turn often affect ground water recharge and divert precipitation directly into surface waters, which changes their hydrological regime. Typically, drainage systems also elevate the input of nutrients and pesticides into the water bodies. In general, applied fertilizers, plant protection products, veterinary drugs and phytohormones of cultivated plants are introduced into the ground and surface waters through different processes such as drift, leaching, runoff, preferential flow or erosion. They influence the nutrient cycles and ecological health of aquatic systems. The nutrient and pesticide loss processes themselves can be altered by tillage operations and other agricultural practices. Furthermore, the competition for space can lead to additional conflicts between agriculture and the protection of aquatic ecosystems. For example, channelized or otherwise morphologically changed rivers do not have a natural discharge pattern and are often not suitable for the local flora and fauna; but naturally meandering rivers need space that cannot be used for agriculture. In a highly industrialized and densely populated country like Switzerland, all these potential conflicts are of importance. Although it is typically seen as a water-rich country, local and seasonal overexploitation of rivers through water extraction

  17. Functional conservation and divergence of four ginger AP1/AGL9 MADS-box genes revealed by analysis of their expression and protein-protein interaction, and ectopic expression of AhFUL gene in Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Xiumei Li

    Full Text Available Alpinia genus are known generally as ginger-lilies for showy flowers in the ginger family, Zingiberaceae, and their floral morphology diverges from typical monocotyledon flowers. However, little is known about the functions of ginger MADS-box genes in floral identity. In this study, four AP1/AGL9 MADS-box genes were cloned from Alpinia hainanensis, and protein-protein interactions (PPIs and roles of the four genes in floral homeotic conversion and in floral evolution are surveyed for the first time. AhFUL is clustered to the AP1 lineage, AhSEP4 and AhSEP3b to the SEP lineage, and AhAGL6-like to the AGL6 lineage. The four genes showed conserved and divergent expression patterns, and their encoded proteins were localized in the nucleus. Seven combinations of PPI (AhFUL-AhSEP4, AhFUL-AhAGL6-like, AhFUL-AhSEP3b, AhSEP4-AhAGL6-like, AhSEP4-AhSEP3b, AhAGL6-like-AhSEP3b, and AhSEP3b-AhSEP3b were detected, and the PPI patterns in the AP1/AGL9 lineage revealed that five of the 10 possible combinations are conserved and three are variable, while conclusions cannot yet be made regarding the other two. Ectopic expression of AhFUL in Arabidopsis thaliana led to early flowering and floral organ homeotic conversion to sepal-like or leaf-like. Therefore, we conclude that the four A. hainanensis AP1/AGL9 genes show functional conservation and divergence in the floral identity from other MADS-box genes.

  18. Water conservation and improved production efficiency using closed-loop evaporative cooling systems

    Energy Technology Data Exchange (ETDEWEB)

    Marchetta, C. [Niagara Blower Co., Buffalo, NY (United States)

    2009-07-01

    This paper described wet surface air coolers (WSAC) that can be used in refineries and hydrocarbon processing plants to address water use issues. These closed-loop evaporative cooling systems are a cost-effective technology for both heat transfer and water conservation. WSACs can help deliver required cooling water temperatures and improve plant performance while using water streams currently considered to be unusable with conventional towers and heat exchangers. WSACs are versatile and can provide solutions to water use, water quality, and outlet temperature. The benefits of the WSAC include capital cost savings, reduced system pressures, lower carbon footprint, and the ability to use poor quality water as makeup. Water makeup can be blowdown from other equipment, plant effluent, reclaimed water, produced water, flue gas desulphurization (FGD) wastewater, and even seawater. Units can be manufactured with a wide variety of materials depending on water quality, water treatment, and cycles of concentration. This paper also provided comparisons to other alternative technologies, capital and operating cost savings, and site specific case studies. Two other system designs can accommodate closed-loop heat transfer applications, notably an open tower with a heat exchanger and a dry, air-cooled system. A WSAC system is an efficient and effective heat rejection technology for several reasons. The WSAC cooler or condenser utilizes latent cooling, which is far more efficient than sensible cooling. This means that a WSAC system can cool the same heat load with a smaller footprint than all-dry systems. 6 figs.

  19. Enrichment of conserved synaptic activity-responsive element in neuronal genes predicts a coordinated response of MEF2, CREB and SRF.

    Directory of Open Access Journals (Sweden)

    Fernanda M Rodríguez-Tornos

    Full Text Available A unique synaptic activity-responsive element (SARE sequence, composed of the consensus binding sites for SRF, MEF2 and CREB, is necessary for control of transcriptional upregulation of the Arc gene in response to synaptic activity. We hypothesize that this sequence is a broad mechanism that regulates gene expression in response to synaptic activation and during plasticity; and that analysis of SARE-containing genes could identify molecular mechanisms involved in brain disorders. To search for conserved SARE sequences in the mammalian genome, we used the SynoR in silico tool, and found the SARE cluster predominantly in the regulatory regions of genes expressed specifically in the nervous system; most were related to neural development and homeostatic maintenance. Two of these SARE sequences were tested in luciferase assays and proved to promote transcription in response to neuronal activation. Supporting the predictive capacity of our candidate list, up-regulation of several SARE containing genes in response to neuronal activity was validated using external data and also experimentally using primary cortical neurons and quantitative real time RT-PCR. The list of SARE-containing genes includes several linked to mental retardation and cognitive disorders, and is significantly enriched in genes that encode mRNA targeted by FMRP (fragile X mental retardation protein. Our study thus supports the idea that SARE sequences are relevant transcriptional regulatory elements that participate in plasticity. In addition, it offers a comprehensive view of how activity-responsive transcription factors coordinate their actions and increase the selectivity of their targets. Our data suggest that analysis of SARE-containing genes will reveal yet-undescribed pathways of synaptic plasticity and additional candidate genes disrupted in mental disease.

  20. Prediction and characterisation of a highly conserved, remote and cAMP responsive enhancer that regulates Msx1 gene expression in cardiac neural crest and outflow tract.

    Science.gov (United States)

    Miller, Kerry Ann; Davidson, Scott; Liaros, Angela; Barrow, John; Lear, Marissa; Heine, Danielle; Hoppler, Stefan; MacKenzie, Alasdair

    2008-05-15

    Double knockouts of the Msx1 and Msx2 genes in the mouse result in severe cardiac outflow tract malformations similar to those frequently found in newborn infants. Despite the known role of the Msx genes in cardiac formation little is known of the regulatory systems (ligand receptor, signal transduction and protein-DNA interactions) that regulate the tissue-specific expression of the Msx genes in mammals during the formation of the outflow tract. In the present study we have used a combination of multi-species comparative genomics, mouse transgenic analysis and in-situ hybridisation to predict and validate the existence of a remote ultra-conserved enhancer that supports the expression of the Msx1 gene in migrating mouse cardiac neural crest and the outflow tract primordia. Furthermore, culturing of embryonic explants derived from transgenic lines with agonists of the PKC and PKA signal transduction systems demonstrates that this remote enhancer is influenced by PKA but not PKC dependent gene regulatory systems. These studies demonstrate the efficacy of combining comparative genomics and transgenic analyses and provide a platform for the study of the possible roles of Msx gene mis-regulation in the aetiology of congenital heart malformation.

  1. Reconciling Biodiversity Conservation and Timber Production in Mixed Uneven-Aged Mountain Forests: Identification of Ecological Intensification Pathways.

    Science.gov (United States)

    Lafond, Valentine; Cordonnier, Thomas; Courbaud, Benoît

    2015-11-01

    Mixed uneven-aged forests are considered favorable to the provision of multiple ecosystem services and to the conciliation of timber production and biodiversity conservation. However, some forest managers now plan to increase the intensity of thinning and harvesting operations in these forests. Retention measures or gap creation are considered to compensate potential negative impacts on biodiversity. Our objectives were to assess the effect of these management practices on timber production and biodiversity conservation and identify potential compensating effects between these practices, using the concept of ecological intensification as a framework. We performed a simulation study coupling Samsara2, a simulation model designed for spruce-fir uneven-aged mountain forests, an uneven-aged silviculture algorithm, and biodiversity models. We analyzed the effect of parameters related to uneven-aged management practices on timber production, biodiversity, and sustainability indicators. Our study confirmed that the indicators responded differently to management practices, leading to trade-offs situations. Increasing management intensity had negative impacts on several biodiversity indicators, which could be partly compensated by the positive effect of retention measures targeting large trees, non-dominant species, and deadwood. The impact of gap creation was more mitigated, with a positive effect on the diversity of tree sizes and deadwood but a negative impact on the spruce-fir mixing balance and on the diversity of the understory layer. Through the analysis of compensating effects, we finally revealed the existence of possible ecological intensification pathways, i.e., the possibility to increase management intensity while maintaining biodiversity through the promotion of nature-based management principles (gap creation and retention measures).

  2. Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition

    Directory of Open Access Journals (Sweden)

    O'Brien Kimberly

    2008-06-01

    Full Text Available Abstract Background The Solanaceae family contains a number of important crop species including potato (Solanum tuberosum which is grown for its underground storage organ known as a tuber. Albeit the 4th most important food crop in the world, other than a collection of ~220,000 Expressed Sequence Tags, limited genomic sequence information is currently available for potato and advances in potato yield and nutrition content would be greatly assisted through access to a complete genome sequence. While morphologically diverse, Solanaceae species such as potato, tomato, pepper, and eggplant share not only genes but also gene order thereby permitting highly informative comparative genomic analyses. Results In this study, we report on analysis 89.9 Mb of potato genomic sequence representing 10.2% of the genome generated through end sequencing of a potato bacterial artificial chromosome (BAC clone library (87 Mb and sequencing of 22 potato BAC clones (2.9 Mb. The GC content of potato is very similar to Solanum lycopersicon (tomato and other dicotyledonous species yet distinct from the monocotyledonous grass species, Oryza sativa. Parallel analyses of repetitive sequences in potato and tomato revealed substantial differences in their abundance, 34.2% in potato versus 46.3% in tomato, which is consistent with the increased genome size per haploid genome of these two Solanum species. Specific classes and types of repetitive sequences were also differentially represented between these two species including a telomeric-related repetitive sequence, ribosomal DNA, and a number of unclassified repetitive sequences. Comparative analyses between tomato and potato at the gene level revealed a high level of conservation of gene content, genic feature, and gene order although discordances in synteny were observed. Conclusion Genomic level analyses of potato and tomato confirm that gene sequence and gene order are conserved between these solanaceous species and that

  3. Alfalfa interseeded into silage corn can enhance productivity and soil and water conservation

    Science.gov (United States)

    Alfalfa and corn silage are widely planted for dairy forage production systems throughout the northern regions of the USA, accounting for about 0.8 and 1.9 million hectares per year, respectively. Much of this area could benefit from strategies to reduce soil erosion and nutrient losses. Because the...

  4. 77 FR 7547 - Energy Conservation Standards for Wine Chillers and Miscellaneous Refrigeration Products: Public...

    Science.gov (United States)

    2012-02-13

    ... Energy. ACTION: Notice of public meeting and availability of the framework document. SUMMARY: The U.S... of this notice. To inform stakeholders and facilitate this process, DOE has prepared a framework... set at ENERGY STAR levels effective in 2005 for the two most popular product classes of refrigerators...

  5. 75 FR 34726 - Energy Conservation Program for Consumer Products: Notice of Petition for Waiver of LG...

    Science.gov (United States)

    2010-06-18

    ..., and Whirlpool. LG is a manufacturer of digital appliances, as well as mobile communications, digital displays, and digital media products. Its appliances include refrigerators, refrigerator-freezers, air.... Furthermore, continued employment creation and ongoing investments in its marketing, sales and servicing...

  6. Use, production and conservation of palm fiber in South America: A review

    NARCIS (Netherlands)

    Isaza, C.; Bernal, R.; Howard, P.L.

    2013-01-01

    South American ethnic groups traditionally use palm fiber, which provides materials for domestic, commercial, and ceremonial purposes. A literature review of 185 references was carried out in order to identify and understand the extent of palm fiber production and the sustainability of harvesting

  7. 76 FR 51281 - Energy Conservation Program for Consumer Products and Certain Commercial and Industrial Equipment...

    Science.gov (United States)

    2011-08-18

    ... standards, DOE divides covered products into classes based on the type of energy used, their size or... often receive considerable attention when they are introduced, over time, public comments tend to focus... methodologies and results of fuel switching more explicit in all rulemakings in which fuel switching might occur...

  8. Long-term effects of conservation systems on productivity for the old rotation

    Science.gov (United States)

    Winter legumes in cotton (Gossypium hirsutum L.) production is not new to the Southeast. In 1896, the Old Rotation experiment at Auburn University was established to study the feasibility of producing cotton in crop rotations with winter legumes managed as a green manure crop. Throughout the experim...

  9. 78 FR 21215 - Energy Conservation Program for Consumer Products: Association of Home Appliance Manufacturers...

    Science.gov (United States)

    2013-04-10

    ... rule remains unchanged. AHAM argued that DOE has not explained what it considers to be de minimis, and... because the proposed amendments change what energy will be measured (i.e., the end of cycle energy... off of the ``Energy Star'' list, which may result in discontinuing production of the impacted models...

  10. 78 FR 79643 - Energy Conservation Program for Consumer Products: Landmark Legal Foundation; Petition for...

    Science.gov (United States)

    2013-12-31

    ... consumer behavior; and questions about why comments on the Draft National Climate Assessment were not... Program for Consumer Products: Landmark Legal Foundation; Petition for Reconsideration AGENCY: Office of... Energy Consumers of America (IECA), American Gas Association (AGA), Cato Institute Center for Study of...

  11. Rebalancing food production and nature conservation; the need for design-oriented research

    NARCIS (Netherlands)

    Rossing, W.A.H.; Sabatier, R.; Teillard, F.; Groot, J.C.J.; Tittonell, P.A.

    2016-01-01

    The unprecedented impacts of humans on the Earth (e.g. Rockström et al., 2009; Sachs et al., 2010; Foley, 2011) have prompted a debate on the future of land use and, with agriculture as the major anthropogenic use, on new models of agricultural production. In addition to concerns about the eects of

  12. 75 FR 29823 - Energy Conservation Program for Consumer Products: Test Procedures for Refrigerators...

    Science.gov (United States)

    2010-05-27

    .... This NOPR also discusses the proposed treatment of combination wine storage-freezer products that were.... Combination Wine Storage-Freezer Units C. Establishing New Appendices A and B, and Compliance Date for the... rule published in the Federal Register on September 14, 1977. 42 FR 46140. Industry representatives...

  13. 78 FR 41609 - Energy Conservation Program for Consumer Products: Test Procedures for Refrigerators...

    Science.gov (United States)

    2013-07-10

    ... September 14, 1977. 42 FR 46140. Industry representatives viewed these test procedures as too complex and... Freezers'' (HRF-1- 1979). Using this industry-created test procedure, DOE revised its test procedures on... compartment of such a product to be at a level that would effectively exclude the coverage of combination wine...

  14. RD & D priorities for energy production and resource conservation from municipal solid waste

    Energy Technology Data Exchange (ETDEWEB)

    1992-08-01

    This report identifies research, development, and demonstration (RD&D) needs and priorities associated with municipal solid waste (MSW) management technologies that conserve or produce energy or resources. The changing character of MSW waste management and the public`s heightened awareness of its real and perceived benefits and costs creates opportunities for RD&D in MSW technologies. Increased recycling, for example, creates new opportunities for energy, chemicals, and materials recovery. New technologies to control and monitor emissions from MSW combustion facilities are available for further improvement or application. Furthermore, emerging waste-to-energy technologies may offer environmental, economic, and other advantages. Given these developments, DOE identified a need to assess the RD&D needs and pdodties and carefully target RD&D efforts to help solve the carbon`s waste management problem and further the National Energy Strategy. This report presents such an assessment. It identifies and Documents RD&D needs and priorities in the broad area of MSW resource . recovery, focusing on efforts to make MSW management technologies commercially viable or to improve their commercial deployment over a 5 to l0 year period. Panels of technical experts identifies 279 RD&D needs in 12 technology areas, ranking about one-fifth of these needs as priorities. A ``Peer Review Group`` identified mass-burn combustion, ``systems studies,`` landfill gas, and ash utilization and disposal as high priority areas for RD&D based on cost and the impacts of further RD&D. The results of this assessment are intended to provide guidance to DOE concerning possible future RD&D projects.

  15. Vasopressin Gene-Related Products in the Management of Breast Cancer

    National Research Council Canada - National Science Library

    North, William

    1999-01-01

    ...), and this information coupled with an absence of vasopressin gene-related products from fibrocystic disease potentially provides us with a new screening test for distinguishing both breast cancer...

  16. Escherichia coli yjjPB genes encode a succinate transporter important for succinate production.

    Science.gov (United States)

    Fukui, Keita; Nanatani, Kei; Hara, Yoshihiko; Yamakami, Suguru; Yahagi, Daiki; Chinen, Akito; Tokura, Mitsunori; Abe, Keietsu

    2017-09-01

    Under anaerobic conditions, Escherichia coli produces succinate from glucose via the reductive tricarboxylic acid cycle. To date, however, no genes encoding succinate exporters have been established in E. coli. Therefore, we attempted to identify genes encoding succinate exporters by screening an E. coli MG1655 genome library. We identified the yjjPB genes as candidates encoding a succinate transporter, which enhanced succinate production in Pantoea ananatis under aerobic conditions. A complementation assay conducted in Corynebacterium glutamicum strain AJ110655ΔsucE1 demonstrated that both YjjP and YjjB are required for the restoration of succinate production. Furthermore, deletion of yjjPB decreased succinate production in E. coli by 70% under anaerobic conditions. Taken together, these results suggest that YjjPB constitutes a succinate transporter in E. coli and that the products of both genes are required for succinate export.

  17. Conservation and divergence of gene expression plasticity following c. 140 million years of evolution in lodgepole pine (Pinus contorta) and interior spruce (Picea glauca×Picea engelmannii).

    Science.gov (United States)

    Yeaman, Sam; Hodgins, Kathryn A; Suren, Haktan; Nurkowski, Kristin A; Rieseberg, Loren H; Holliday, Jason A; Aitken, Sally N

    2014-07-01

    Species respond to environmental stress through a combination of genetic adaptation and phenotypic plasticity, both of which may be important for survival in the face of climatic change. By characterizing the molecular basis of plastic responses and comparing patterns among species, it is possible to identify how such traits evolve. Here, we used de novo transcriptome assembly and RNAseq to explore how patterns of gene expression differ in response to temperature, moisture, and light regime treatments in lodgepole pine (Pinus contorta) and interior spruce (a natural hybrid population of Picea glauca and Picea engelmannii). We found wide evidence for an effect of treatment on expression within each species, with 6413 and 11,658 differentially expressed genes identified in spruce and pine, respectively. Comparing patterns of expression among these species, we found that 74% of all orthologs with differential expression had a pattern that was conserved in both species, despite 140 million yr of evolution. We also found that the specific treatments driving expression patterns differed between genes with conserved versus diverged patterns of expression. We conclude that natural selection has probably played a role in shaping plastic responses to environment in these species. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

  18. The response of early neural genes to FGF signaling or inhibition of BMP indicate the absence of a conserved neural induction module

    Directory of Open Access Journals (Sweden)

    Rogers Crystal D

    2011-12-01

    Full Text Available Abstract Background The molecular mechanism that initiates the formation of the vertebrate central nervous system has long been debated. Studies in Xenopus and mouse demonstrate that inhibition of BMP signaling is sufficient to induce neural tissue in explants or ES cells respectively, whereas studies in chick argue that instructive FGF signaling is also required for the expression of neural genes. Although additional signals may be involved in neural induction and patterning, here we focus on the roles of BMP inhibition and FGF8a. Results To address the question of necessity and sufficiency of BMP inhibition and FGF signaling, we compared the temporal expression of the five earliest genes expressed in the neuroectoderm and determined their requirements for induction at the onset of neural plate formation in Xenopus. Our results demonstrate that the onset and peak of expression of the genes vary and that they have different regulatory requirements and are therefore unlikely to share a conserved neural induction regulatory module. Even though all require inhibition of BMP for expression, some also require FGF signaling; expression of the early-onset pan-neural genes sox2 and foxd5α requires FGF signaling while other early genes, sox3, geminin and zicr1 are induced by BMP inhibition alone. Conclusions We demonstrate that BMP inhibition and FGF signaling induce neural genes independently of each other. Together our data indicate that although the spatiotemporal expression patterns of early neural genes are similar, the mechanisms involved in their expression are distinct and there are different signaling requirements for the expression of each gene.

  19. Multi-species comparative analysis of the equine ACE gene identifies a highly conserved potential transcription factor binding site in intron 16.

    Science.gov (United States)

    Hamilton, Natasha A; Tammen, Imke; Raadsma, Herman W

    2013-01-01

    Angiotensin converting enzyme (ACE) is essential for control of blood pressure. The human ACE gene contains an intronic Alu indel (I/D) polymorphism that has been associated with variation in serum enzyme levels, although the functional mechanism has not been identified. The polymorphism has also been associated with cardiovascular disease, type II diabetes, renal disease and elite athleticism. We have characterized the ACE gene in horses of breeds selected for differing physical abilities. The equine gene has a similar structure to that of all known mammalian ACE genes. Nine common single nucleotide polymorphisms (SNPs) discovered in pooled DNA were found to be inherited in nine haplotypes. Three of these SNPs were located in intron 16, homologous to that containing the Alu polymorphism in the human. A highly conserved 18 bp sequence, also within that intron, was identified as being a potential binding site for the transcription factors Oct-1, HFH-1 and HNF-3β, and lies within a larger area of higher than normal homology. This putative regulatory element may contribute to regulation of the documented inter-individual variation in human circulating enzyme levels, for which a functional mechanism is yet to be defined. Two equine SNPs occurred within the conserved area in intron 16, although neither of them disrupted the putative binding site. We propose a possible regulatory mechanism of the ACE gene in mammalian species which was previously unknown. This advance will allow further analysis leading to a better understanding of the mechanisms underpinning the associations seen between the human Alu polymorphism and enzyme levels, cardiovascular disease states and elite athleticism.

  20. Conserved intron positions in FGFR genes reflect the modular structure of FGFR and reveal stepwise addition of domains to an already complex ancestral FGFR.

    Science.gov (United States)

    Rebscher, Nicole; Deichmann, Christina; Sudhop, Stefanie; Fritzenwanker, Jens Holger; Green, Stephen; Hassel, Monika

    2009-10-01

    We have analyzed the evolution of fibroblast growth factor receptor (FGFR) tyrosine kinase genes throughout a wide range of animal phyla. No evidence for an FGFR gene was found in Porifera, but we tentatively identified an FGFR gene in the placozoan Trichoplax adhaerens. The gene encodes a protein with three immunoglobulin-like domains, a single-pass transmembrane, and a split tyrosine kinase domain. By superimposing intron positions of 20 FGFR genes from Placozoa, Cnidaria, Protostomia, and Deuterostomia over the respective protein domain structure, we identified ten ancestral introns and three conserved intron groups. Our analysis shows (1) that the position of ancestral introns correlates to the modular structure of FGFRs, (2) that the acidic domain very likely evolved in the last common ancestor of triploblasts, (3) that splicing of IgIII was enabled by a triploblast-specific insertion, and (4) that IgI is subject to substantial loss or duplication particularly in quickly evolving genomes. Moreover, intron positions in the catalytic domain of FGFRs map to the borders of protein subdomains highly conserved in other serine/threonine kinases. Nevertheless, these introns were introduced in metazoan receptor tyrosine kinases exclusively. Our data support the view that protein evolution dating back to the Cambrian explosion took place in such a short time window that only subtle changes in the domain structure are detectable in extant representatives of animal phyla. We propose that the first multidomain FGFR originated in the last common ancestor of Placozoa, Cnidaria, and Bilateria. Additional domains were introduced mainly in the ancestor of triploblasts and in the Ecdysozoa.

  1. Multi-species comparative analysis of the equine ACE gene identifies a highly conserved potential transcription factor binding site in intron 16.

    Directory of Open Access Journals (Sweden)

    Natasha A Hamilton

    Full Text Available Angiotensin converting enzyme (ACE is essential for control of blood pressure. The human ACE gene contains an intronic Alu indel (I/D polymorphism that has been associated with variation in serum enzyme levels, although the functional mechanism has not been identified. The polymorphism has also been associated with cardiovascular disease, type II diabetes, renal disease and elite athleticism. We have characterized the ACE gene in horses of breeds selected for differing physical abilities. The equine gene has a similar structure to that of all known mammalian ACE genes. Nine common single nucleotide polymorphisms (SNPs discovered in pooled DNA were found to be inherited in nine haplotypes. Three of these SNPs were located in intron 16, homologous to that containing the Alu polymorphism in the human. A highly conserved 18 bp sequence, also within that intron, was identified as being a potential binding site for the transcription factors Oct-1, HFH-1 and HNF-3β, and lies within a larger area of higher than normal homology. This putative regulatory element may contribute to regulation of the documented inter-individual variation in human circulating enzyme levels, for which a functional mechanism is yet to be defined. Two equine SNPs occurred within the conserved area in intron 16, although neither of them disrupted the putative binding site. We propose a possible regulatory mechanism of the ACE gene in mammalian species which was previously unknown. This advance will allow further analysis leading to a better understanding of the mechanisms underpinning the associations seen between the human Alu polymorphism and enzyme levels, cardiovascular disease states and elite athleticism.

  2. Analysis of tomato plasma membrane H(+)-ATPase gene family suggests a mycorrhiza-mediated regulatory mechanism conserved in diverse plant species.

    Science.gov (United States)

    Liu, Junli; Liu, Jianjian; Chen, Aiqun; Ji, Minjie; Chen, Jiadong; Yang, Xiaofeng; Gu, Mian; Qu, Hongye; Xu, Guohua

    2016-10-01

    In plants, the plasma membrane H(+)-ATPase (HA) is considered to play a crucial role in regulating plant growth and respoding to environment stresses. Multiple paralogous genes encoding different isozymes of HA have been identified and characterized in several model plants, while limited information of the HA gene family is available to date for tomato. Here, we describe the molecular and expression features of eight HA-encoding genes (SlHA1-8) from tomato. All these genes are interrupted by multiple introns with conserved positions. SlHA1, 2, and 4 were widely expressed in all tissues, while SlHA5, 6, and 7 were almost only expressed in flowers. SlHA8, the transcripts of which were barely detectable under normal or nutrient-/salt-stress growth conditions, was strongly activated in arbuscular mycorrhizal (AM) fungal-colonized roots. Extreme lack of SlHA8 expression in M161, a mutant defective to AM fungal colonization, provided genetic evidence towards the dependence of its expression on AM symbiosis. A 1521-bp SlHA8 promoter could direct the GUS reporter expression specifically in colonized cells of transgenic tobacco, soybean, and rice mycorrhizal roots. Promoter deletion assay revealed a 223-bp promoter fragment of SlHA8 containing a variant of AM-specific cis-element MYCS (vMYCS) sufficient to confer the AM-induced activity. Targeted deletion of this motif in the corresponding promoter region causes complete abolishment of GUS staining in mycorrhizal roots. Together, these results lend cogent evidence towards the evolutionary conservation of a potential regulatory mechanism mediating the activation of AM-responsive HA genes in diverse mycorrhizal plant species.

  3. Synergies for Improving Oil Palm Production and Forest Conservation in Floodplain Landscapes

    Science.gov (United States)

    Abram, Nicola K.; Xofis, Panteleimon; Tzanopoulos, Joseph; MacMillan, Douglas C.; Ancrenaz, Marc; Chung, Robin; Peter, Lucy; Ong, Robert; Lackman, Isabelle; Goossens, Benoit; Ambu, Laurentius; Knight, Andrew T.

    2014-01-01

    these into policy and practice, may provide conservation and economic opportunities within these seemingly high opportunity cost landscapes. PMID:24887555

  4. Conservation of a microRNA cluster in parasitic nematodes and profiling of miRNAs in excretory-secretory products and microvesicles of Haemonchus contortus.

    Directory of Open Access Journals (Sweden)

    Henry Y Gu

    2017-11-01

    Full Text Available microRNAs are small non-coding RNAs that are important regulators of gene expression in a range of animals, including nematodes. We have analysed a cluster of four miRNAs from the pathogenic nematode species Haemonchus contortus that are closely linked in the genome. We find that the cluster is conserved only in clade V parasitic nematodes and in some ascarids, but not in other clade III species nor in clade V free-living nematodes. Members of the cluster are present in parasite excretory-secretory products and can be detected in the abomasum and draining lymph nodes of infected sheep, indicating their release in vitro and in vivo. As observed for other parasitic nematodes, H. contortus adult worms release extracellular vesicles (EV. Small RNA libraries were prepared from vesicle-enriched and vesicle-depleted supernatants from both adult worms and L4 stage larvae. Comparison of the miRNA species in the different fractions indicated that specific miRNAs are packaged within vesicles, while others are more abundant in vesicle-depleted supernatant. Hierarchical clustering analysis indicated that the gut is the likely source of vesicle-associated miRNAs in the L4 stage, but not in the adult worm. These findings add to the growing body of work demonstrating that miRNAs released from parasitic helminths may play an important role in host-parasite interactions.

  5. Decision analysis for conservation breeding: Maximizing production for reintroduction of whooping cranes

    Science.gov (United States)

    Smith, Des H.V.; Converse, Sarah J.; Gibson, Keith; Moehrenschlager, Axel; Link, William A.; Olsen, Glenn H.; Maguire, Kelly

    2011-01-01

    Captive breeding is key to management of severely endangered species, but maximizing captive production can be challenging because of poor knowledge of species breeding biology and the complexity of evaluating different management options. In the face of uncertainty and complexity, decision-analytic approaches can be used to identify optimal management options for maximizing captive production. Building decision-analytic models requires iterations of model conception, data analysis, model building and evaluation, identification of remaining uncertainty, further research and monitoring to reduce uncertainty, and integration of new data into the model. We initiated such a process to maximize captive production of the whooping crane (Grus americana), the world's most endangered crane, which is managed through captive breeding and reintroduction. We collected 15 years of captive breeding data from 3 institutions and used Bayesian analysis and model selection to identify predictors of whooping crane hatching success. The strongest predictor, and that with clear management relevance, was incubation environment. The incubation period of whooping crane eggs is split across two environments: crane nests and artificial incubators. Although artificial incubators are useful for allowing breeding pairs to produce multiple clutches, our results indicate that crane incubation is most effective at promoting hatching success. Hatching probability increased the longer an egg spent in a crane nest, from 40% hatching probability for eggs receiving 1 day of crane incubation to 95% for those receiving 30 days (time incubated in each environment varied independently of total incubation period). Because birds will lay fewer eggs when they are incubating longer, a tradeoff exists between the number of clutches produced and egg hatching probability. We developed a decision-analytic model that estimated 16 to be the optimal number of days of crane incubation needed to maximize the number of

  6. Coregulation of terpenoid pathway genes and prediction of isoprene production in Bacillus subtilis using transcriptomics

    Energy Technology Data Exchange (ETDEWEB)

    Hess, Becky M.; Xue, Junfeng; Markillie, Lye Meng; Taylor, Ronald C.; Wiley, H. S.; Ahring, Birgitte K.; Linggi, Bryan E.

    2013-06-19

    The isoprenoid pathway converts pyruvate to isoprene and related isoprenoid compounds in plants and some bacteria. Currently, this pathway is of great interest because of the critical role that isoprenoids play in basic cellular processes as well as the industrial value of metabolites such as isoprene. Although the regulation of several pathway genes has been described, there is a paucity of information regarding the system level regulation and control of the pathway. To address this limitation, we examined Bacillus subtilis grown under multiple conditions and then determined the relationship between altered isoprene production and the pattern of gene expression. We found that terpenoid genes appeared to fall into two distinct subsets with opposing correlations with respect to the amount of isoprene produced. The group whose expression levels positively correlated with isoprene production included dxs, the gene responsible for the commitment step in the pathway, as well as ispD, and two genes that participate in the mevalonate pathway, yhfS and pksG. The subset of terpenoid genes that inversely correlated with isoprene production included ispH, ispF, hepS, uppS, ispE, and dxr. A genome wide partial least squares regression model was created to identify other genes or pathways that contribute to isoprene production. This analysis showed that a subset of 213 regulated genes was sufficient to create a predictive model of isoprene production under different conditions and showed correlations at the transcriptional level. We conclude that gene expression levels alone are sufficiently informative about the metabolic state of a cell that produces increased isoprene and can be used to build a model which accurately predicts production of this secondary metabolite across many simulated environmental conditions.

  7. Lactobacillus plantarum gene clusters encoding putative cell-surface protein complexes for carbohydrate utilization are conserved in specific gram-positive bacteria

    Directory of Open Access Journals (Sweden)

    Muscariello Lidia

    2006-05-01

    Full Text Available Abstract Background Genomes of gram-positive bacteria encode many putative cell-surface proteins, of which the majority has no known function. From the rapidly increasing number of available genome sequences it has become apparent that many cell-surface proteins are conserved, and frequently encoded in gene clusters or operons, suggesting common functions, and interactions of multiple components. Results A novel gene cluster encoding exclusively cell-surface proteins was identified, which is conserved in a subgroup of gram-positive bacteria. Each gene cluster generally has one copy of four new gene families called cscA, cscB, cscC and cscD. Clusters encoding these cell-surface proteins were found only in complete genomes of Lactobacillus plantarum, Lactobacillus sakei, Enterococcus faecalis, Listeria innocua, Listeria monocytogenes, Lactococcus lactis ssp lactis and Bacillus cereus and in incomplete genomes of L. lactis ssp cremoris, Lactobacillus casei, Enterococcus faecium, Pediococcus pentosaceus, Lactobacillius brevis, Oenococcus oeni, Leuconostoc mesenteroides, and Bacillus thuringiensis. These genes are neither present in the genomes of streptococci, staphylococci and clostridia, nor in the Lactobacillus acidophilus group, suggesting a niche-specific distribution, possibly relating to association with plants. All encoded proteins have a signal peptide for secretion by the Sec-dependent pathway, while some have cell-surface anchors, novel WxL domains, and putative domains for sugar binding and degradation. Transcriptome analysis in L. plantarum shows that the cscA-D genes are co-expressed, supporting their operon organization. Many gene clusters are significantly up-regulated in a glucose-grown, ccpA-mutant derivative of L. plantarum, suggesting catabolite control. This is supported by the presence of predicted CRE-sites upstream or inside the up-regulated cscA-D gene clusters. Conclusion We propose that the CscA, CscB, CscC and Csc

  8. Stakeholder engagement in scenario development process - bioenergy production and biodiversity conservation in eastern Finland.

    Science.gov (United States)

    Haatanen, Anniina; den Herder, Michael; Leskinen, Pekka; Lindner, Marcus; Kurttila, Mikko; Salminen, Olli

    2014-03-15

    In this study participatory approaches were used to develop alternative forest resource management scenarios with particular respect to the effects on increased use of forest bioenergy and its effect on biodiversity in Eastern Finland. As technical planning tools, we utilized a forest management planning system (MELA) and the Tool for Sustainability Impact Assessment (ToSIA) to visualize the impacts of the scenarios. We organized a stakeholder workshop where group discussions were used as a participatory method to get the stakeholder preferences and insights concerning forest resource use in the year 2030. Feedback from the workshop was then complemented with a questionnaire. Based on the results of the workshop and a questionnaire we developed three alternative forest resource scenarios: (1) bioenergy 2030 - in which energy production is more centralized and efficient; (2) biodiversity 2030 - in which harvesting methods are more nature friendly and protected forests make up 10% of the total forest area; and (3) mixed bioenergy + biodiversity 2030 scenario - in which wood production, recreation and nature protection are assigned to the most suitable areas. The study showed that stakeholder engagement combined with the MELA and ToSIA tools can be a useful approach in scenario development. Copyright © 2014 Elsevier Ltd. All rights reserved.

  9. Analysing biodiversity and conservation knowledge products to support regional environmental assessments.

    Science.gov (United States)

    Brooks, Thomas M; Akçakaya, H Resit; Burgess, Neil D; Butchart, Stuart H M; Hilton-Taylor, Craig; Hoffmann, Michael; Juffe-Bignoli, Diego; Kingston, Naomi; MacSharry, Brian; Parr, Mike; Perianin, Laurence; Regan, Eugenie C; Rodrigues, Ana S L; Rondinini, Carlo; Shennan-Farpon, Yara; Young, Bruce E

    2016-02-16

    Two processes for regional environmental assessment are currently underway: the Global Environment Outlook (GEO) and Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES). Both face constraints of data, time, capacity, and resources. To support these assessments, we disaggregate three global knowledge products according to their regions and subregions. These products are: The IUCN Red List of Threatened Species, Key Biodiversity Areas (specifically Important Bird &Biodiversity Areas [IBAs], and Alliance for Zero Extinction [AZE] sites), and Protected Planet. We present fourteen Data citations: numbers of species occurring and percentages threatened; numbers of endemics and percentages threatened; downscaled Red List Indices for mammals, birds, and amphibians; numbers, mean sizes, and percentage coverages of IBAs and AZE sites; percentage coverage of land and sea by protected areas; and trends in percentages of IBAs and AZE sites wholly covered by protected areas. These data will inform the regional/subregional assessment chapters on the status of biodiversity, drivers of its decline, and institutional responses, and greatly facilitate comparability and consistency between the different regional/subregional assessments.

  10. Analysing biodiversity and conservation knowledge products to support regional environmental assessments

    Science.gov (United States)

    Brooks, Thomas M.; Akçakaya, H. Resit; Burgess, Neil D.; Butchart, Stuart H.M.; Hilton-Taylor, Craig; Hoffmann, Michael; Juffe-Bignoli, Diego; Kingston, Naomi; MacSharry, Brian; Parr, Mike; Perianin, Laurence; Regan, Eugenie C.; Rodrigues, Ana S.L.; Rondinini, Carlo; Shennan-Farpon, Yara; Young, Bruce E.

    2016-01-01

    Two processes for regional environmental assessment are currently underway: the Global Environment Outlook (GEO) and Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES). Both face constraints of data, time, capacity, and resources. To support these assessments, we disaggregate three global knowledge products according to their regions and subregions. These products are: The IUCN Red List of Threatened Species, Key Biodiversity Areas (specifically Important Bird & Biodiversity Areas [IBAs], and Alliance for Zero Extinction [AZE] sites), and Protected Planet. We present fourteen Data citations: numbers of species occurring and percentages threatened; numbers of endemics and percentages threatened; downscaled Red List Indices for mammals, birds, and amphibians; numbers, mean sizes, and percentage coverages of IBAs and AZE sites; percentage coverage of land and sea by protected areas; and trends in percentages of IBAs and AZE sites wholly covered by protected areas. These data will inform the regional/subregional assessment chapters on the status of biodiversity, drivers of its decline, and institutional responses, and greatly facilitate comparability and consistency between the different regional/subregional assessments. PMID:26881749

  11. Analysing biodiversity and conservation knowledge products to support regional environmental assessments

    Science.gov (United States)

    Brooks, Thomas M.; Akçakaya, H. Resit; Burgess, Neil D.; Butchart, Stuart H. M.; Hilton-Taylor, Craig; Hoffmann, Michael; Juffe-Bignoli, Diego; Kingston, Naomi; Macsharry, Brian; Parr, Mike; Perianin, Laurence; Regan, Eugenie C.; Rodrigues, Ana S. L.; Rondinini, Carlo; Shennan-Farpon, Yara; Young, Bruce E.

    2016-02-01

    Two processes for regional environmental assessment are currently underway: the Global Environment Outlook (GEO) and Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES). Both face constraints of data, time, capacity, and resources. To support these assessments, we disaggregate three global knowledge products according to their regions and subregions. These products are: The IUCN Red List of Threatened Species, Key Biodiversity Areas (specifically Important Bird & Biodiversity Areas [IBAs], and Alliance for Zero Extinction [AZE] sites), and Protected Planet. We present fourteen Data citations: numbers of species occurring and percentages threatened; numbers of endemics and percentages threatened; downscaled Red List Indices for mammals, birds, and amphibians; numbers, mean sizes, and percentage coverages of IBAs and AZE sites; percentage coverage of land and sea by protected areas; and trends in percentages of IBAs and AZE sites wholly covered by protected areas. These data will inform the regional/subregional assessment chapters on the status of biodiversity, drivers of its decline, and institutional responses, and greatly facilitate comparability and consistency between the different regional/subregional assessments.

  12. Analysis of MADS-Box Gene Family Reveals Conservation in Floral Organ ABCDE Model of Moso Bamboo (Phyllostachys edulis

    Directory of Open Access Journals (Sweden)

    Zhanchao Cheng

    2017-05-01

    Full Text Available Mini chromosome maintenance 1, agamous, deficiens, and serum response factor (MADS-box genes are transcription factors which play fundamental roles in flower development and regulation of floral organ identity. However, till date, identification and functions of MADS-box genes remain largely unclear in Phyllostachys edulis. In view of this, we performed a whole-genome survey and identified 34 MADS-box genes in P. edulis, and based on phylogeny, they were classified as MIKCC, MIKC∗, Mα, and Mβ. The detailed analysis about gene structure and motifs, phylogenetic classification, comparison of gene divergence and duplication are provided. Interestingly, expression patterns for most genes were found similar to those of Arabidopsis and rice, indicating that the well-established ABCDE model can be applied to P. edulis. Moreover, we overexpressed PheMADS15, an AP1-like gene, in Arabidopsis, and found that the transgenic plants have early flowering phenotype, suggesting that PheMADS15 might be a regulator of flowering transition in P. edulis. Taken together, this study provides not only insightful comprehension but also useful information for understanding the functions of MADS-box genes in P. edulis.

  13. Ex Situ gene conservation in high elevation white pine species in the United States-a beginning

    Science.gov (United States)

    Richard A. Sniezko; Anna Schoettle; Joan Dunlap; Detlev Vogler; David Conklin; Andrew Bower; Chris Jensen; Rob Mangold; Doug Daoust; Gary Man

    2011-01-01

    The eight white pine species native to the western United States face an array of biotic and abiotic challenges that impact the viability of populations or the species themselves. Well-established programs are already in place to conserve and restore Pinus monticola Dougl. ex D. Don and P. lambertiana Dougl. throughout significant portions of their geographic ranges....

  14. Id-1 and Id-2 genes and products as markers of epithelial cancer

    Science.gov (United States)

    Desprez, Pierre-Yves [El Cerrito, CA; Campisi, Judith [Berkeley, CA

    2008-09-30

    A method for detection and prognosis of breast cancer and other types of cancer. The method comprises detecting expression, if any, for both an Id-1 and an Id-2 genes, or the ratio thereof, of gene products in samples of breast tissue obtained from a patient. When expressed, Id-1 gene is a prognostic indicator that breast cancer cells are invasive and metastatic, whereas Id-2 gene is a prognostic indicator that breast cancer cells are localized and noninvasive in the breast tissue.

  15. Major genes and QTL influencing wool production and quality: a review

    Directory of Open Access Journals (Sweden)

    Purvis Ian

    2005-12-01

    Full Text Available Abstract The opportunity exists to utilise our knowledge of major genes that influence the economically important traits in wool sheep. Genes with Mendelian inheritance have been identified for many important traits in wool sheep. Of particular importance are genes influencing pigmentation, wool quality and the keratin proteins, the latter of which are important for the morphology of the wool fibre. Gene mapping studies have identified some chromosomal regions associated with variation in wool quality and production traits. The challenge now is to build on this knowledge base in a cost-effective way to deliver molecular tools that facilitate enhanced genetic improvement programs for wool sheep.

  16. Production of cloned pigs with targeted attenuation of gene expression.

    Directory of Open Access Journals (Sweden)

    Vilceu Bordignon

    Full Text Available The objective of this study was to demonstrate that RNA interference (RNAi and somatic cell nuclear transfer (SCNT technologies can be used to attenuate the expression of specific genes in tissues of swine, a large animal species. Apolipoprotein E (apoE, a secreted glycoprotein known for its major role in lipid and lipoprotein metabolism and transport, was selected as the target gene for this study. Three synthetic small interfering RNAs (siRNA targeting the porcine apoE mRNA were tested in porcine granulosa cells in primary culture and reduced apoE mRNA abundance ranging from 45-82% compared to control cells. The most effective sequence was selected for cloning into a short hairpin RNA (shRNA expression vector under the control of RNA polymerase III (U6 promoter. Stably transfected fetal porcine fibroblast cells were generated and used to produce embryos with in vitro matured porcine oocytes, which were then transferred into the uterus of surrogate gilts. Seven live and one stillborn piglet were born from three gilts that became pregnant. Integration of the shRNA expression vector into the genome of clone piglets was confirmed by PCR and expression of the GFP transgene linked to the expression vector. Analysis showed that apoE protein levels in the liver and plasma of the clone pigs bearing the shRNA expression vector targeting the apoE mRNA was significantly reduced compared to control pigs cloned from non-transfected fibroblasts of the same cell line. These results demonstrate the feasibility of applying RNAi and SCNT technologies for introducing stable genetic modifications in somatic cells for eventual attenuation of gene expression in vivo in large animal species.

  17. Identification and localization of a gene that specifies production of Escherichia coli DNA topoisomerase I

    International Nuclear Information System (INIS)

    Trucksis, M.; Depew, R.E.

    1981-01-01

    A gene that specifies production of Escherichia coli DNA topoisomerase I (ω protein) was identified with the aid of a radioimmunoassay for this protein. E. coli DNA topoisomerase I was produced by Salmonella typhimurium merodiploids that harbored E. coli plasmid F' 123, but not by strains that lost this plasmid. Analysis of strains with spontaneous deletions of F' 123 showed that the gene, topA, required for production of the E. coli ω protein was between the trp operon and the cysB gene. Deletions that eliminated topA also eliminated the supX gene. We suggest that topA is the structural gene of E. coli DNA topoisomerase I and that topA is identical to supX

  18. R-parity-violating production of single top squarks with R-parity-conserving decays

    International Nuclear Information System (INIS)

    Berger, E.L.; Harris, B.W.; Sullivan, Z.

    1999-01-01

    Single-top-squark production probes R-parity-violating extensions of the minimal supersymmetric standard model though the λ 3ij double p rime coupling. For top-squark masses in the range 180-325 GeV, and λ 3ij double p rime > 0.02-0.06, we show that discovery of the top squark is possible with 2 fb -1 of integrated luminosity at run II of the Fermilab Tevatron. The bound on λ 3ij double p rime can be reduced by up to an order of magnitude with existing data from run I, and by two orders of magnitude at run II if the top squark is not found

  19. Energy saving industrial products in Italy (marketing research, conservation program planning)

    Energy Technology Data Exchange (ETDEWEB)

    Agostini, M.; Clo' , A.; Goldoni, G. (Bologna Univ. (Italy))

    1989-09-01

    This article gathers the essential results of research, carried out by Nomisma for ENEA (Italian Commission for Nuclear and Alternative Energy Sources) about the market and industry structure of 7 different products for energy saving, i.e. high performance boilers, cogeneration plants, thermal insulation, organic residual combustors, heat pumps, heat recovery equipment and measuring and control instruments. The singling out of the operating firms and the collection of numerous, even if incomplete, economic and technical data, permit a first evaluation of the trend of the Italian energy saving market during the period 1983-87. This will be a useful tool in order to appraise the efficiency of past policies and direct future ones.

  20. Conservation of ParaHox genes' function in patterning of the digestive tract of the marine gastropod Gibbula varia

    Directory of Open Access Journals (Sweden)

    Steiner Gerhard

    2010-07-01

    Full Text Available Abstract Background Presence of all three ParaHox genes has been described in deuterostomes and lophotrochozoans, but to date one of these three genes, Xlox has not been reported from any ecdysozoan taxa and both Xlox and Gsx are absent in nematodes. There is evidence that the ParaHox genes were ancestrally a single chromosomal cluster. Colinear expression of the ParaHox genes in anterior, middle, and posterior tissues of several species studied so far suggest that these genes may be responsible for axial patterning of the digestive tract. So far, there are no data on expression of these genes in molluscs. Results We isolated the complete coding sequences of the three Gibbula varia ParaHox genes, and then tested their expression in larval and postlarval development. In Gibbula varia, the ParaHox genes participate in patterning of the digestive tract and are expressed in some cells of the neuroectoderm. The expression of these genes coincides with the gradual formation of the gut in the larva. Gva-Gsx patterns potential neural precursors of cerebral ganglia as well as of the apical sensory organ. During larval development this gene is involved in the formation of the mouth and during postlarval development it is expressed in the precursor cells involved in secretion of the radula, the odontoblasts. Gva-Xolx and Gva-Cdx are involved in gut patterning in the middle and posterior parts of digestive tract, respectively. Both genes are expressed in some ventral neuroectodermal cells; however the expression of Gva-Cdx fades in later larval stages while the expression of Gva-Xolx in these cells persists. Conclusions In Gibbula varia the ParaHox genes are expressed during anterior-posterior patterning of the digestive system. This colinearity is not easy to spot during early larval stages because the differentiated endothelial cells within the yolk permanently migrate to their destinations in the gut. After torsion, Gsx patterns the mouth and foregut

  1. Annotation Of Novel And Conserved MicroRNA Genes In The Build 10 Sus scrofa Reference Genome And Determination Of Their Expression Levels In Ten Different Tissues

    DEFF Research Database (Denmark)

    Thomsen, Bo; Nielsen, Mathilde; Hedegaard, Jakob

    The DNA template used in the pig genome sequencing project was provided by a Duroc pig named TJ Tabasco. In an effort to annotate microRNA (miRNA) genes in the reference genome we have conducted deep sequencing to determine the miRNA transcriptomes in ten different tissues isolated from Pinky......, a genetically identical clone of TJ Tabasco. The purpose was to generate miRNA sequences that are highly homologous to the reference genome sequence, which along with computational prediction will improve confidence in the genomic annotation of miRNA genes. Based on homology searches of the sequence data...... against miRBase, we identified more than 600 conserved known miRNA/miRNA*, which is a significant increase relative to the 211 porcine miRNA/miRNA* deposited in the current version of miRBase. Furthermore, the genome-wide transcript profiles provided important information on the relative abundance...

  2. Gene deletion of cytosolic ATP: citrate lyase leads to altered organic acid production in Aspergillus niger

    DEFF Research Database (Denmark)

    Meijer, Susan Lisette; Nielsen, Michael Lynge; Olsson, Lisbeth

    2009-01-01

    With the availability of the genome sequence of the filamentous fungus Aspergillus niger, the use of targeted genetic modifications has become feasible. This, together with the fact that A. niger is well established industrially, makes this fungus an attractive micro-organism for creating a cell...... factory platform for production of chemicals. Using molecular biology techniques, this study focused on metabolic engineering of A. niger to manipulate its organic acid production in the direction of succinic acid. The gene target for complete gene deletion was cytosolic ATP: citrate lyase (acl), which...... the acl gene. Additionally, the total amount of organic acids produced in the deletion strain was significantly increased. Genome-scale stoichiometric metabolic model predictions can be used for identifying gene targets. Deletion of the acl led to increased succinic acid production by A. niger....

  3. Identification and manipulation of the pleuromutilin gene cluster from Clitopilus passeckerianus for increased rapid antibiotic production

    Science.gov (United States)

    Bailey, Andy M.; Alberti, Fabrizio; Kilaru, Sreedhar; Collins, Catherine M.; de Mattos-Shipley, Kate; Hartley, Amanda J.; Hayes, Patrick; Griffin, Alison; Lazarus, Colin M.; Cox, Russell J.; Willis, Christine L.; O'Dwyer, Karen; Spence, David W.; Foster, Gary D.

    2016-05-01

    Semi-synthetic derivatives of the tricyclic diterpene antibiotic pleuromutilin from the basidiomycete Clitopilus passeckerianus are important in combatting bacterial infections in human and veterinary medicine. These compounds belong to the only new class of antibiotics for human applications, with novel mode of action and lack of cross-resistance, representing a class with great potential. Basidiomycete fungi, being dikaryotic, are not generally amenable to strain improvement. We report identification of the seven-gene pleuromutilin gene cluster and verify that using various targeted approaches aimed at increasing antibiotic production in C. passeckerianus, no improvement in yield was achieved. The seven-gene pleuromutilin cluster was reconstructed within Aspergillus oryzae giving production of pleuromutilin in an ascomycete, with a significant increase (2106%) in production. This is the first gene cluster from a basidiomycete to be successfully expressed in an ascomycete, and paves the way for the exploitation of a metabolically rich but traditionally overlooked group of fungi.

  4. Regulation of gene expression by tobacco product preparations in cultured human dermal fibroblasts

    International Nuclear Information System (INIS)

    Malpass, Gloria E.; Arimilli, Subhashini; Prasad, G.L.; Howlett, Allyn C.

    2014-01-01

    Skin fibroblasts comprise the first barrier of defense against wounds, and tobacco products directly contact the oral cavity. Cultured human dermal fibroblasts were exposed to smokeless tobacco extract (STE), total particulate matter (TPM) from tobacco smoke, or nicotine at concentrations comparable to those found in these extracts for 1 h or 5 h. Differences were identified in pathway-specific genes between treatments and vehicle using qRT-PCR. At 1 h, IL1α was suppressed significantly by TPM and less significantly by STE. Neither FOS nor JUN was suppressed at 1 h by tobacco products. IL8, TNFα, VCAM1, and NFκB1 were suppressed after 5 h with STE, whereas only TNFα and NFκB1 were suppressed by TPM. At 1 h with TPM, secreted levels of IL10 and TNFα were increased. Potentially confounding effects of nicotine were exemplified by genes such as ATF3 (5 h), which was increased by nicotine but suppressed by other components of STE. Within 2 h, TPM stimulated nitric oxide production, and both STE and TPM increased reactive oxygen species. The biological significance of these findings and utilization of the gene expression changes reported herein regarding effects of the tobacco product preparations on dermal fibroblasts will require additional research. - Highlights: • Tobacco product preparations (TPPs) alter gene expression in dermal fibroblasts. • Some immediate early genes critical to the inflammatory process are affected. • Different TPPs produce differential responses in certain pro-inflammatory genes

  5. Regulation of gene expression by tobacco product preparations in cultured human dermal fibroblasts

    Energy Technology Data Exchange (ETDEWEB)

    Malpass, Gloria E., E-mail: gloria.malpass@gmail.com [Department of Physiology and Pharmacology, Wake Forest University Health Sciences, Winston-Salem, NC 27157 (United States); Arimilli, Subhashini, E-mail: sarimill@wakehealth.edu [Department of Microbiology and Immunology, Wake Forest University Health Sciences, Winston-Salem, NC 27157 (United States); Prasad, G.L., E-mail: prasadg@rjrt.com [R and D Department, R.J. Reynolds Tobacco Company, Winston-Salem, NC 27102 (United States); Howlett, Allyn C., E-mail: ahowlett@wakehealth.edu [Department of Physiology and Pharmacology, Wake Forest University Health Sciences, Winston-Salem, NC 27157 (United States)

    2014-09-01

    Skin fibroblasts comprise the first barrier of defense against wounds, and tobacco products directly contact the oral cavity. Cultured human dermal fibroblasts were exposed to smokeless tobacco extract (STE), total particulate matter (TPM) from tobacco smoke, or nicotine at concentrations comparable to those found in these extracts for 1 h or 5 h. Differences were identified in pathway-specific genes between treatments and vehicle using qRT-PCR. At 1 h, IL1α was suppressed significantly by TPM and less significantly by STE. Neither FOS nor JUN was suppressed at 1 h by tobacco products. IL8, TNFα, VCAM1, and NFκB1 were suppressed after 5 h with STE, whereas only TNFα and NFκB1 were suppressed by TPM. At 1 h with TPM, secreted levels of IL10 and TNFα were increased. Potentially confounding effects of nicotine were exemplified by genes such as ATF3 (5 h), which was increased by nicotine but suppressed by other components of STE. Within 2 h, TPM stimulated nitric oxide production, and both STE and TPM increased reactive oxygen species. The biological significance of these findings and utilization of the gene expression changes reported herein regarding effects of the tobacco product preparations on dermal fibroblasts will require additional research. - Highlights: • Tobacco product preparations (TPPs) alter gene expression in dermal fibroblasts. • Some immediate early genes critical to the inflammatory process are affected. • Different TPPs produce differential responses in certain pro-inflammatory genes.

  6. Phylogenetic analysis and protein structure modelling identifies distinct Ca(2+)/Cation antiporters and conservation of gene family structure within Arabidopsis and rice species.

    Science.gov (United States)

    Pittman, Jon K; Hirschi, Kendal D

    2016-12-01

    The Ca(2+)/Cation Antiporter (CaCA) superfamily is an ancient and widespread family of ion-coupled cation transporters found in nearly all kingdoms of life. In animals, K(+)-dependent and K(+)-indendent Na(+)/Ca(2+) exchangers (NCKX and NCX) are important CaCA members. Recently it was proposed that all rice and Arabidopsis CaCA proteins should be classified as NCX proteins. Here we performed phylogenetic analysis of CaCA genes and protein structure homology modelling to further characterise members of this transporter superfamily. Phylogenetic analysis of rice and Arabidopsis CaCAs in comparison with selected CaCA members from non-plant species demonstrated that these genes form clearly distinct families, with the H(+)/Cation exchanger (CAX) and cation/Ca(2+) exchanger (CCX) families dominant in higher plants but the NCKX and NCX families absent. NCX-related Mg(2+)/H(+) exchanger (MHX) and CAX-related Na(+)/Ca(2+) exchanger-like (NCL) proteins are instead present. Analysis of genomes of ten closely-related rice species and four Arabidopsis-related species found that CaCA gene family structures are highly conserved within related plants, apart from minor variation. Protein structures were modelled for OsCAX1a and OsMHX1. Despite exhibiting broad structural conservation, there are clear structural differences observed between the different CaCA types. Members of the CaCA superfamily form clearly distinct families with different phylogenetic, structural and functional characteristics, and therefore should not be simply classified as NCX proteins, which should remain as a separate gene family.

  7. Maximizing Conservation and Production with Intensive Forest Management: It's All About Location

    Science.gov (United States)

    Tittler, Rebecca; Filotas, Élise; Kroese, Jasmin; Messier, Christian

    2015-11-01

    Functional zoning has been suggested as a way to balance the needs of a viable forest industry with those of healthy ecosystems. Under this system, part of the forest is set aside for protected areas, counterbalanced by intensive and extensive management of the rest of the forest. Studies indicate this may provide adequate timber while minimizing road construction and favoring the development of large mature and old stands. However, it is unclear how the spatial arrangement of intensive management areas may affect the success of this zoning. Should these areas be agglomerated or dispersed throughout the forest landscape? Should managers prioritize (a) proximity to existing roads, (b) distance from protected areas, or (c) site-specific productivity? We use a spatially explicit landscape simulation model to examine the effects of different spatial scenarios on landscape structure, connectivity for native forest wildlife, stand diversity, harvest volume, and road construction: (1) random placement of intensive management areas, and (2-8) all possible combinations of rules (a)-(c). Results favor the agglomeration of intensive management areas. For most wildlife species, connectivity was the highest when intensive management was far from the protected areas. This scenario also resulted in relatively high harvest volumes. Maximizing distance of intensive management areas from protected areas may therefore be the best way to maximize the benefits of intensive management areas while minimizing their potentially negative effects on forest structure and biodiversity.

  8. Soil Biochemical Changes Induced by Poultry Litter Application and Conservation Tillage under Cotton Production Systems

    Directory of Open Access Journals (Sweden)

    Seshadri Sajjala

    2012-07-01

    Full Text Available Problems arising from conventional tillage (CT systems (such as soil erosion, decrease of organic matter, environmental damage etc. have led many farmers to the adoption of no-till (NT systems that are more effective in improving soil physical, chemical and microbial properties. Results from this study clearly indicated that NT, mulch tillage (MT, and winter rye cover cropping systems increased the activity of phosphatase, β-glucosidase and arylsulfatase at a 0–10 cm soil depth but decreased the activity of these enzymes at 10–20 cm. The increase in enzyme activity was a good indicator of intensive soil microbial activity in different soil management practices. Poultry litter (PL application under NT, MT, and rye cropping system could be considered as effective management practices due to the improvement in carbon (C content and the biochemical quality at the soil surface. The activities of the studied enzymes were highly correlated with soil total nitrogen (STN soil organic carbon (SOC at the 0–10 cm soil depth, except for acid phosphatase where no correlation was observed. This study revealed that agricultural practices such as tillage, PL, and cover crop cropping system have a noticeable positive effect on soil biochemical activities under cotton production.

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

    Science.gov (United States)

    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.

  10. A survey of the gene repertoire of Gigaspora rosea unravels conserved features among Glomeromycota for obligate biotrophy

    Directory of Open Access Journals (Sweden)

    Nianwu eTANG

    2016-03-01

    Full Text Available Arbuscular mycorrhizal (AM fungi are a diverse group of soil fungi (Glomeromycota that form the most ancient mutualistic association termed arbuscular mycorrhizal symbiosis with a majority of land plants, improving their nutrition uptake and resistance to stresses. In contrast to their great ecological implications, the knowledge of the molecular biological mechanisms involved is still scant, partly due to the limited genomic resources available. Here, we describe the gene repertoire of a new AM fungus Gigaspora rosea (Diversisporales. Among the 86332 nonredundant virtual transcripts assembled, 15346 presented similarities with proteins in the Refseq database and 10175 were assigned with GO terms. KOG and Interpro domain annotations clearly showed an enrichment of genes involved in signal transduction in G. rosea. KEGG pathway analysis indicates that most primary metabolic processes are active in G. rosea. However, as for R. irregularis, several metabolic genes were not found, including the fatty acid synthase gene. This finding supports the hypothesis that AM fungi depend on the lipids produced by their hosts. Furthermore, the presence of a large number of transporters and hundreds of secreted proteins, together with the reduced number of plant cell wall degrading enzymes could be interpreted as an evolutionary adaptation to its mutualistic obligate biotrophy. The detection of meiosis-related genes suggests that G. rosea might use a cryptic sexual process. Lastly, a phylogeny of basal fungi clearly shows Glomeromycota as a sister clade to Mucoromycotina, not only to the Mucorales or Mortierellales. The characterization of the gene repertoire from an AM fungal species belonging to the order of Diversisporales and its comparison with the gene sets of R. irregularis (Glomerales and Gigaspora margarita (Diversisporales, reveal that AM fungi share several features linked to mutualistic obligate biotrophy. This work contributes to lay the foundation

  11. In Silico Analysis of Gene Expression Network Components Underlying Pigmentation Phenotypes in the Python Identified Evolutionarily Conserved Clusters of Transcription Factor Binding Sites

    Directory of Open Access Journals (Sweden)

    Kristopher J. L. Irizarry

    2016-01-01

    Full Text Available Color variation provides the opportunity to investigate the genetic basis of evolution and selection. Reptiles are less studied than mammals. Comparative genomics approaches allow for knowledge gained in one species to be leveraged for use in another species. We describe a comparative vertebrate analysis of conserved regulatory modules in pythons aimed at assessing bioinformatics evidence that transcription factors important in mammalian pigmentation phenotypes may also be important in python pigmentation phenotypes. We identified 23 python orthologs of mammalian genes associated with variation in coat color phenotypes for which we assessed the extent of pairwise protein sequence identity between pythons and mouse, dog, horse, cow, chicken, anole lizard, and garter snake. We next identified a set of melanocyte/pigment associated transcription factors (CREB, FOXD3, LEF-1, MITF, POU3F2, and USF-1 that exhibit relatively conserved sequence similarity within their DNA binding regions across species based on orthologous alignments across multiple species. Finally, we identified 27 evolutionarily conserved clusters of transcription factor binding sites within ~200-nucleotide intervals of the 1500-nucleotide upstream regions of AIM1, DCT, MC1R, MITF, MLANA, OA1, PMEL, RAB27A, and TYR from Python bivittatus. Our results provide insight into pigment phenotypes in pythons.

  12. Climate-Driven Reshuffling of Species and Genes: Potential Conservation Roles for Species Translocations and Recombinant Hybrid Genotypes

    Directory of Open Access Journals (Sweden)

    Jon Mark Scriber

    2013-12-01

    Full Text Available Comprising 50%–75% of the world’s fauna, insects are a prominent part of biodiversity in communities and ecosystems globally. Biodiversity across all levels of biological classifications is fundamentally based on genetic diversity. However, the integration of genomics and phylogenetics into conservation management may not be as rapid as climate change. The genetics of hybrid introgression as a source of novel variation for ecological divergence and evolutionary speciation (and resilience may generate adaptive potential and diversity fast enough to respond to locally-altered environmental conditions. Major plant and herbivore hybrid zones with associated communities deserve conservation consideration. This review addresses functional genetics across multi-trophic-level interactions including “invasive species” in various ecosystems as they may become disrupted in different ways by rapid climate change. “Invasive genes” (into new species and populations need to be recognized for their positive creative potential and addressed in conservation programs. “Genetic rescue” via hybrid translocations may provide needed adaptive flexibility for rapid adaptation to environmental change. While concerns persist for some conservationists, this review emphasizes the positive aspects of hybrids and hybridization. Specific implications of natural genetic introgression are addressed with a few examples from butterflies, including transgressive phenotypes and climate-driven homoploid recombinant hybrid speciation. Some specific examples illustrate these points using the swallowtail butterflies (Papilionidae with their long-term historical data base (phylogeographical diversity changes and recent (3-decade climate-driven temporal and genetic divergence in recombinant homoploid hybrids and relatively recent hybrid speciation of Papilio appalachiensis in North America. Climate-induced “reshuffling” (recombinations of species composition, genotypes

  13. Conservation of the fourth gene among rotaviruses recovered from asymptomatic newborn infants and its possible role in attenuation

    International Nuclear Information System (INIS)

    Flores, J.; Midthun, K.; Hoshino, Y.; Green, K.; Gorziglia, M.; Kapikian, A.Z.; Chanock, R.M.

    1986-01-01

    RNA-RNA hybridization was performed to assess the extent of genetic relatedness among human rotaviruses isolated from children with gastroenteritis and from asymptomatic newborn infants. 32 P-labeled single-stranded RNAs produced by in vitro transcription from viral cores of the different strains tested were used as probes in two different hybridization assays: (1) undenatured genomic RNAs were resolved by polyacrylamide gel electrophoresis, denatured in situ, electrophoretically transferred to diazobenzyloxymethyl-paper (Northern blots), and then hybridized to the probes under two different conditions of stringency; and (ii) denatured genomic double-stranded RNAs were hybridized to the probes in solution and the hybrids which formed were identified by polyacrylamide gel electrophoresis. When analyzed by Northern blot hybridization at a low level of stringency, all genes from the strains tested cross-hybridized, providing evidence for some sequence homology in each of the corresponding genes. However, when hybridization stringency was increased, a difference in gene 4 sequence was detected between strains recovered from asymptomatic newborn infants (nursery strains) and strains recovered from infants and young children with diarrhea. Although the nursery strains exhibited serotypic diversity, the fourth gene appeared to be highly conversed. These results were confirmed and extended during experiments in which the RNA-RNA hybridization was carried out in solution and the resulting hybrids were analyzed by polyacrylamide gel electrophoresis. Full-length hybrids did not form between the fourth genes from the nursery strains and the corresponding genes from the strains recovered from symptomatic infants and young children

  14. The greenGain project - Biomass from landscape conservation and maintenance work for renewable energy production in the EU

    Science.gov (United States)

    Clalüna, Aline; Baumgarten, Wibke; García Galindo, Daniel; Lenz, Klaus; Doležal, Jan; De Filippi, Federico; Lorenzo, Joaquín; Montagnoli, Louis

    2017-04-01

    The project greenGain is looking for solutions to increase the energy production with regional and local biomass from landscape conservation and maintenance work, which is performed in the public interest. The relevant resources analysed in the greenGain model regions are, among others, biomass residues from clearing invasive vegetation in marginal agricultural lands in Spain, and residues from abandoned vineyards and olive groves in landscape protected areas in Italy. The main target groups are regional and local players who are responsible for maintenance and conservation work and for the biomass residue management in their regions. Moreover, the focus will be on service providers - including farmers and forest owners, their associations, NGOs, energy providers and consumers. Local companies, municipalities and public authorities are collaborating to identify the still underutilised non-food biomass resources and to discuss the way to integrate them into the local and regional biomass markets. Since the start of the three year project in January 2015, the partners from Italy, Spain, Czech Republic and Germany analysed, among other, the biomass feedstock potential coming from landscape maintenance work, and assessed various technological options to utilise this type of biomass. Further, political, legal and environmental aspects as well as awareness raising and public acceptance actions regarding the energetic use of biomass from public areas were assessed. greenGain also facilitates the exchange between model regions and other similar relevant players in the EU and shares examples of good practice. General guidelines will be prepared to guarantee a wide dissemination to other regions in the EU. Thus, the project shows how to build-up reliable knowledge on local availability of this feedstock and provides know-how concerning planning, harvesting, pre-treatment, storage and sustainable conversion pathways to a wide range of stakeholders in the EU.

  15. Functional comparison of the nematode Hox gene lin-39 in C. elegans and P. pacificus reveals evolutionary conservation of protein function despite divergence of primary sequences.

    Science.gov (United States)

    Grandien, K; Sommer, R J

    2001-08-15

    Hox transcription factors have been implicated in playing a central role in the evolution of animal morphology. Many studies indicate the evolutionary importance of regulatory changes in Hox genes, but little is known about the role of functional changes in Hox proteins. In the nematodes Pristionchus pacificus and Caenorhabditis elegans, developmental processes can be compared at the cellular, genetic, and molecular levels and differences in gene function can be identified. The Hox gene lin-39 is involved in the regulation of nematode vulva development. Comparison of known lin-39 mutations in P. pacificus and C. elegans revealed both conservation and changes of gene function. Here, we study evolutionary changes of lin-39 function using hybrid transgenes and site-directed mutagenesis in an in vivo assay using C. elegans lin-39 mutants. Our data show that despite the functional differences of LIN-39 between the two species, Ppa-LIN-39, when driven by Cel-lin-39 regulatory elements, can functionally replace Cel-lin-39. Furthermore, we show that the MAPK docking and phosphorylation motifs unique for Cel-LIN-39 are dispensable for Cel-lin-39 function. Therefore, the evolution of lin-39 function is driven by changes in regulatory elements rather than changes in the protein itself.

  16. Improvement of heterologous protein production in Aspergillus oryzae by RNA interference with alpha-amylase genes.

    Science.gov (United States)

    Nemoto, Takashi; Maruyama, Jun-ichi; Kitamoto, Katsuhiko

    2009-11-01

    Aspergillus oryzae RIB40 has three alpha-amylase genes (amyA, amyB, and amyC), and secretes alpha-amylase abundantly. However, large amounts of endogenous secretory proteins such as alpha-amylase can compete with heterologous protein in the secretory pathway and decrease its production yields. In this study, we examined the effects of suppression of alpha-amylase on heterologous protein production in A. oryzae, using the bovine chymosin (CHY) as a reporter heterologous protein. The three alpha-amylase genes in A. oryzae have nearly identical DNA sequences from those promoters to the coding regions. Hence we performed silencing of alpha-amylase genes by RNA interference (RNAi) in the A. oryzae CHY producing strain. The silenced strains exhibited a reduction in alpha-amylase activity and an increase in CHY production in the culture medium. This result suggests that suppression of alpha-amylase is effective in heterologous protein production in A. oryzae.

  17. Mouse Nkrp1-Clr gene cluster sequence and expression analyses reveal conservation of tissue-specific MHC-independent immunosurveillance.

    Directory of Open Access Journals (Sweden)

    Qiang Zhang

    Full Text Available The Nkrp1 (Klrb1-Clr (Clec2 genes encode a receptor-ligand system utilized by NK cells as an MHC-independent immunosurveillance strategy for innate immune responses. The related Ly49 family of MHC-I receptors displays extreme allelic polymorphism and haplotype plasticity. In contrast, previous BAC-mapping and aCGH studies in the mouse suggest the neighboring and related Nkrp1-Clr cluster is evolutionarily stable. To definitively compare the relative evolutionary rate of Nkrp1-Clr vs. Ly49 gene clusters, the Nkrp1-Clr gene clusters from two Ly49 haplotype-disparate inbred mouse strains, BALB/c and 129S6, were sequenced. Both Nkrp1-Clr gene cluster sequences are highly similar to the C57BL/6 reference sequence, displaying the same gene numbers and order, complete pseudogenes, and gene fragments. The Nkrp1-Clr clusters contain a strikingly dissimilar proportion of repetitive elements compared to the Ly49 clusters, suggesting that certain elements may be partly responsible for the highly disparate Ly49 vs. Nkrp1 evolutionary rate. Focused allelic polymorphisms were found within the Nkrp1b/d (Klrb1b, Nkrp1c (Klrb1c, and Clr-c (Clec2f genes, suggestive of possible immune selection. Cell-type specific transcription of Nkrp1-Clr genes in a large panel of tissues/organs was determined. Clr-b (Clec2d and Clr-g (Clec2i showed wide expression, while other Clr genes showed more tissue-specific expression patterns. In situ hybridization revealed specific expression of various members of the Clr family in leukocytes/hematopoietic cells of immune organs, various tissue-restricted epithelial cells (including intestinal, kidney tubular, lung, and corneal progenitor epithelial cells, as well as myocytes. In summary, the Nkrp1-Clr gene cluster appears to evolve more slowly relative to the related Ly49 cluster, and likely regulates innate immunosurveillance in a tissue-specific manner.

  18. Trans-activation function of a 3' truncated X gene-cell fusion product from integrated hepatitis B virus DNA in chronic hepatitis tissues

    International Nuclear Information System (INIS)

    Takada, Shinako; Koike, Katsuro

    1990-01-01

    To investigate the expression and transactivation function of the X gene in integrated hepatitis B virus (HBV) DNA from chronic hepatitis tissues, a series of transfectants containing cloned integrated HBV DNAs was made and analyzed for X mRNA expression and trans-activation activity by using a chloramphenicol acetyltransferase assay. Most of the integrated HBV DNAs expressed X mRNA and encoded a product with trans-activation activity in spite of the loss of the 3' end region of the X gene due to integration. From cDNA cloning and sequence analysis of X mRNA transcribed from native or integrated HBV DNA, the X protein was found to be translated from the X open reading frame without splicing. For integrated HBV DNA, transcription was extended to a cellular flanking DNA and an X gene-cell fusion transcript was terminated by using a cellular poly(A) signal. The amino acid sequence deduced from an X-cell fusion transcript indicated truncation of the carboxyl-terminal five amino acids, but the upstream region of seven amino acids conserved among hepadnaviruses was retained in the integrated HBV DNA, suggesting that this conserved region is essential for the transactivation function of the X protein. These findings support the following explanation for hepatocarcinogenesis by HBV DNA integration: the expression of a cellular oncogene(s) is transactivated at the time of chronic infection by the increasing amounts of the integrated HBV gene product(s), such as the X-cell fusion product

  19. Genes, language, cognition, and culture: towards productive inquiry.

    Science.gov (United States)

    Fitch, W Tecumseh

    2011-04-01

    The Queen Mary conference on “Integrating Genetic and Cultural Evolutionary Approaches to Language,” and the papers in this special issue, clearly illustrate the excitement and potential of trans-disciplinary approaches to language as an evolved biological capacity (phylogeny) and an evolving cultural entity (glossogeny). Excepting the present author, the presenters/authors are mostly young rising stars in their respective fields, and include scientists with backgrounds in linguistics, animal communication, neuroscience, evolutionary biology, anthropology, and computer science. On display was a clear willingness to engage with different approaches and terminology and a commitment to shared standards of scientific rigor, empirically driven theory, and logical argument. Because the papers assembled here, together with the introduction, speak for themselves, I will focus in this “extro-duction” on some of the terminological and conceptual difficulties which threaten to block this exciting wave of scientific progress in understanding language evolution, in both senses of that term. In particular I will first argue against the regrettably widespread practice of opposing cultural and genetic explanations of human cognition as if they were dichotomous. Second, I will unpack the debate concerning “general-purpose” and “domain-specific” mechanisms, which masquerades as a debate about nativism but is nothing of the sort. I believe that framing discussions of language in these terms has generated more heat than light, and that a modern molecular understanding of genes, development, behavior, and evolution renders many of the assumptions underlying this debate invalid.

  20. The FRIABLE1 gene product affects cell adhesion in Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Lutz Neumetzler

    Full Text Available Cell adhesion in plants is mediated predominantly by pectins, a group of complex cell wall associated polysaccharides. An Arabidopsis mutant, friable1 (frb1, was identified through a screen of T-DNA insertion lines that exhibited defective cell adhesion. Interestingly, the frb1 plants displayed both cell and organ dissociations and also ectopic defects in organ separation. The FRB1 gene encodes a Golgi-localized, plant specific protein with only weak sequence similarities to known proteins (DUF246. Unlike other cell adhesion deficient mutants, frb1 mutants do not have reduced levels of adhesion related cell wall polymers, such as pectins. Instead, FRB1 affects the abundance of galactose- and arabinose-containing oligosaccharides in the Golgi. Furthermore, frb1 mutants displayed alteration in pectin methylesterification, cell wall associated extensins and xyloglucan microstructure. We propose that abnormal FRB1 action has pleiotropic consequences on wall architecture, affecting both the extensin and pectin matrices, with consequent changes to the biomechanical properties of the wall and middle lamella, thereby influencing cell-cell adhesion.

  1. Associations between variants of the HAL gene and milk production traits in Chinese Holstein cows.

    Science.gov (United States)

    Wang, Haifei; Jiang, Li; Wang, Wenwen; Zhang, Shengli; Yin, Zongjun; Zhang, Qin; Liu, Jian-Feng

    2014-11-25

    The histidine ammonia-lyse gene (HAL) encodes the histidine ammonia-lyase, which catalyzes the first reaction of histidine catabolism. In our previous genome-wide association study in Chinese Holstein cows to identify genetic variants affecting milk production traits, a SNP (rs41647754) located 357 bp upstream of HAL, was found to be significantly associated with milk yield and milk protein yield. In addition, the HAL gene resides within the reported QTLs for milk production traits. The aims of this study were to identify genetic variants in HAL and to test the association between these variants and milk production traits. Fifteen SNPs were identified within the regions under study of the HAL gene, including three coding mutations, seven intronic mutations, one promoter region mutation, and four 3'UTR mutations. Nine of these identified SNPs were chosen for subsequent genotyping and association analyses. Our results showed that five SNP markers (ss974768522, ss974768525, ss974768531, ss974768533 and ss974768534) were significantly associated with one or more milk production traits. Haplotype analysis showed that two haplotype blocks were significantly associated with milk yield and milk protein yield, providing additional support for the association between HAL variants and milk production traits in dairy cows (P HAL gene and milk production traits in Chinese Holstein cows, indicating the potential role of HAL variants in these traits. These identified SNPs may serve as genetic markers used in genomic selection schemes to accelerate the genetic gains of milk production traits in dairy cattle.

  2. A gene-based radiation hybrid map of the gilthead sea bream Sparus aurata refines and exploits conserved synteny with Tetraodon nigroviridis

    Directory of Open Access Journals (Sweden)

    Tsalavouta Matina

    2007-02-01

    Full Text Available Abstract Background Comparative teleost studies are of great interest since they are important in aquaculture and in evolutionary issues. Comparing genomes of fully sequenced model fish species with those of farmed fish species through comparative mapping offers shortcuts for quantitative trait loci (QTL detections and for studying genome evolution through the identification of regions of conserved synteny in teleosts. Here a comparative mapping study is presented by radiation hybrid (RH mapping genes of the gilthead sea bream Sparus aurata, a non-model teleost fish of commercial and evolutionary interest, as it represents the worldwide distributed species-rich family of Sparidae. Results An additional 74 microsatellite markers and 428 gene-based markers appropriate for comparative mapping studies were mapped on the existing RH map of Sparus aurata. The anchoring of the RH map to the genetic linkage map resulted in 24 groups matching the karyotype of Sparus aurata. Homologous sequences to Tetraodon were identified for 301 of the gene-based markers positioned on the RH map of Sparus aurata. Comparison between Sparus aurata RH groups and Tetraodon chromosomes (karyotype of Tetraodon consists of 21 chromosomes in this study reveals an unambiguous one-to-one relationship suggesting that three Tetraodon chromosomes correspond to six Sparus aurata radiation hybrid groups. The exploitation of this conserved synteny relationship is furthermore demonstrated by in silico mapping of gilthead sea bream expressed sequence tags (EST that give a significant similarity hit to Tetraodon. Conclusion The addition of primarily gene-based markers increased substantially the density of the existing RH map and facilitated comparative analysis. The anchoring of this gene-based radiation hybrid map to the genome maps of model species broadened the pool of candidate genes that mainly control growth, disease resistance, sex determination and reversal, reproduction as well

  3. GeneViTo: Visualizing gene-product functional and structural features in genomic datasets

    Directory of Open Access Journals (Sweden)

    Promponas Vasilis J

    2003-10-01

    Full Text Available Abstract Background The availability of increasing amounts of sequence data from completely sequenced genomes boosts the development of new computational methods for automated genome annotation and comparative genomics. Therefore, there is a need for tools that facilitate the visualization of raw data and results produced by bioinformatics analysis, providing new means for interactive genome exploration. Visual inspection can be used as a basis to assess the quality of various analysis algorithms and to aid in-depth genomic studies. Results GeneViTo is a JAVA-based computer application that serves as a workbench for genome-wide analysis through visual interaction. The application deals with various experimental information concerning both DNA and protein sequences (derived from public sequence databases or proprietary data sources and meta-data obtained by various prediction algorithms, classification schemes or user-defined features. Interaction with a Graphical User Interface (GUI allows easy extraction of genomic and proteomic data referring to the sequence itself, sequence features, or general structural and functional features. Emphasis is laid on the potential comparison between annotation and prediction data in order to offer a supplement to the provided information, especially in cases of "poor" annotation, or an evaluation of available predictions. Moreover, desired information can be output in high quality JPEG image files for further elaboration and scientific use. A compilation of properly formatted GeneViTo input data for demonstration is available to interested readers for two completely sequenced prokaryotes, Chlamydia trachomatis and Methanococcus jannaschii. Conclusions GeneViTo offers an inspectional view of genomic functional elements, concerning data stemming both from database annotation and analysis tools for an overall analysis of existing genomes. The application is compatible with Linux or Windows ME-2000-XP operating

  4. Production of the 2400 kb Duchenne muscular dystrophy (DMD) gene transcript; transcription time and cotranscriptional splicing

    Energy Technology Data Exchange (ETDEWEB)

    Tennyson, C.N.; Worton, R.G. [Univ. of Toronto and the Hospital for Sick Children, Ontario (Canada)

    1994-09-01

    The largest known gene in any organism is the human DMD gene which has 79 exons that span 2400 kb. The extreme nature of the DMD gene raises questions concerning the time required for transcription and whether splicing begins before transcription is complete. DMD gene transcription is induced as cultured human myoblasts differentiate to form multinucleated myotubes, providing a system for studying the kinetics of transcription and splicing. Using quantitative RT-PCR, transcript accumulation was monitored from four different regions within the gene following induction of expression. By comparing the accumulation of transcripts from the 5{prime} and 3{prime} ends of the gene we have shown that approximately 12 hours are required to transcribe 1770 kb of the gene, extrapolating to a time of 16 hours for the transcription unit expressed in muscle. Comparison of accumulation profiles for spliced and total transcript demonstrated that transcripts are spliced at the 5{prime} end before transcription is complete, providing strong evidence for cotranscriptional splicing of DMD gene transcripts. Finally, the rate of transcript accumulation was reduced at the 3{prime} end of the gene relative to the 5{prime} end, perhaps due to premature termination of transcription complexes as they traverse this enormous transcription unit. The lag between transcription initiation and the appearance of complete transcripts could be important in limiting transcript production in dividing cells and to the timing of mRNA appearance in differentiating muscle.

  5. Identification and analysis of Eimeria nieschulzi gametocyte genes reveal splicing events of gam genes and conserved motifs in the wall-forming proteins within the genus Eimeria (Coccidia, Apicomplexa

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    Wiedmer Stefanie

    2017-01-01

    Full Text Available The genus Eimeria (Apicomplexa, Coccidia provides a wide range of different species with different hosts to study common and variable features within the genus and its species. A common characteristic of all known Eimeria species is the oocyst, the infectious stage where its life cycle starts and ends. In our study, we utilized Eimeria nieschulzi as a model organism. This rat-specific parasite has complex oocyst morphology and can be transfected and even cultivated in vitro up to the oocyst stage. We wanted to elucidate how the known oocyst wall-forming proteins are preserved in this rodent Eimeria species compared to other Eimeria. In newly obtained genomics data, we were able to identify different gametocyte genes that are orthologous to already known gam genes involved in the oocyst wall formation of avian Eimeria species. These genes appeared putatively as single exon genes, but cDNA analysis showed alternative splicing events in the transcripts. The analysis of the translated sequence revealed different conserved motifs but also dissimilar regions in GAM proteins, as well as polymorphic regions. The occurrence of an underrepresented gam56 gene version suggests the existence of a second distinct E. nieschulzi genotype within the E. nieschulzi Landers isolate that we maintain.

  6. Identification and analysis of Eimeria nieschulzi gametocyte genes reveal splicing events of gam genes and conserved motifs in the wall-forming proteins within the genus Eimeria (Coccidia, Apicomplexa)

    Science.gov (United States)

    Wiedmer, Stefanie; Erdbeer, Alexander; Volke, Beate; Randel, Stephanie; Kapplusch, Franz; Hanig, Sacha; Kurth, Michael

    2017-01-01

    The genus Eimeria (Apicomplexa, Coccidia) provides a wide range of different species with different hosts to study common and variable features within the genus and its species. A common characteristic of all known Eimeria species is the oocyst, the infectious stage where its life cycle starts and ends. In our study, we utilized Eimeria nieschulzi as a model organism. This rat-specific parasite has complex oocyst morphology and can be transfected and even cultivated in vitro up to the oocyst stage. We wanted to elucidate how the known oocyst wall-forming proteins are preserved in this rodent Eimeria species compared to other Eimeria. In newly obtained genomics data, we were able to identify different gametocyte genes that are orthologous to already known gam genes involved in the oocyst wall formation of avian Eimeria species. These genes appeared putatively as single exon genes, but cDNA analysis showed alternative splicing events in the transcripts. The analysis of the translated sequence revealed different conserved motifs but also dissimilar regions in GAM proteins, as well as polymorphic regions. The occurrence of an underrepresented gam56 gene version suggests the existence of a second distinct E. nieschulzi genotype within the E. nieschulzi Landers isolate that we maintain. PMID:29210668

  7. Split-gene system for hybrid wheat seed production.

    Science.gov (United States)

    Kempe, Katja; Rubtsova, Myroslava; Gils, Mario

    2014-06-24

    Hybrid wheat plants are superior in yield and growth characteristics compared with their homozygous parents. The commercial production of wheat hybrids is difficult because of the inbreeding nature of wheat and the lack of a practical fertility control that enforces outcrossing. We describe a hybrid wheat system that relies on the expression of a phytotoxic barnase and provides for male sterility. The barnase coding information is divided and distributed at two loci that are located on allelic positions of the host chromosome and are therefore "linked in repulsion." Functional complementation of the loci is achieved through coexpression of the barnase fragments and intein-mediated ligation of the barnase protein fragments. This system allows for growth and maintenance of male-sterile female crossing partners, whereas the hybrids are fertile. The technology does not require fertility restorers and is based solely on the genetic modification of the female crossing partner.

  8. Characterization and cloning of laccase gene from Hericium coralloides NBRC 7716 suitable for production of epitheaflagallin 3-O-gallate.

    Science.gov (United States)

    Itoh, Nobuya; Takagi, Shinya; Miki, Asami; Kurokawa, Junji

    2016-01-01

    Epitheaflagallin 3-O-gallate (ETFGg) is a minor polyphenol found in black tea extract, which has good physiological functions. It is synthesized from epigallocatechin gallate (EGCg) with gallic acid via laccase oxidation. Various basidiomycetes and fungi were screened to find a suitable laccase for the production of ETFGg. A basidiomycete, Hericium coralloides NBRC 7716, produced an appropriate extracellular laccase. The purified laccase produced twice the level of ETFGg compared with commercially available laccase from Trametes sp. The enzyme, termed Lcc2, is a monomeric protein with an apparent molecular mass of 67.2 kDa. The N-terminal amino acid sequence of Lcc2 is quite different from laccase isolated from the fruiting bodies of Hericium. Lcc2 showed similar substrate specificity to known laccases and could oxidize various phenolic substrates, including pyrogallol, gallic acid, and 2,6-dimethoxyphenol. The full-length lcc2 gene was obtained by PCR using degenerate primers, which were designed based on the N-terminal amino acid sequence of Lcc2 and conserved copper-binding sites of laccases, and 5'-, and 3'-RACE PCR with mRNA. The Lcc2 gene showed homology with Lentinula edodes laccase (sharing 77% amino acid identity with Lcc6). We successfully produced extracellular Lcc2 using a heterologous expression system with Saccharomyces cerevisiae. Moreover, it was confirmed that the recombinant laccase generates similar levels of ETFGg as the native enzyme. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. Genetic Resources for Advanced Biofuel Production Described with the Gene Ontology

    Directory of Open Access Journals (Sweden)

    Trudy eTorto-Alalibo

    2014-10-01

    Full Text Available Dramatic increases in research in the area of microbial biofuel production coupled with high-throughput data generation on bioenergy-related microbes has led to a deluge of information in the scientific literature and in databases. Consolidating this information and making it easily accessible requires a unified vocabulary. The Gene Ontology (GO fulfills that requirement, as it is a well-developed structured vocabulary that describes the activities and locations of gene products in a consistent manner across all kingdoms of life. The Microbial Energy Gene Ontology (MENGO: http://www.mengo.biochem.vt.edu project is extending the GO to include new terms to describe microbial processes of interest to bioenergy production. Our effort has added over 600 bioenergy related terms to the Gene Ontology. These terms will aid in the comprehensive annotation of gene products from diverse energy-related microbial genomes. An area of microbial energy research that has received a lot of attention is microbial production of advanced biofuels. These include alcohols such as butanol, isopropanol, isobutanol, and fuels derived from fatty acids, isoprenoids, and polyhydroxyalkanoates. These fuels are superior to first generation biofuels (ethanol and biodiesel esterified from vegetable oil or animal fat, can be generated from non-food feedstock sources, can be used as supplements or substitutes for gasoline, diesel and jet fuels, and can be stored and distributed using existing infrastructure. Here we review the roles of genes associated with synthesis of advanced biofuels, and at the same time introduce the use of the GO to describe the functions of these genes in a standardized way.

  10. Haloalkane-utilizing Rhodococcus strains isolated from geographically distinct locations possess a highly conserved gene cluster encoding haloalkane catabolism

    NARCIS (Netherlands)

    Poelarends, GJ; Bosma, T; Kulakov, LA; Larkin, MJ; Marchesi, [No Value; Weightman, AJ; Janssen, DB; Kulakov, Leonid A.; Larkin, Michael J.; Marchesi, Julian R.; Weightman, Andrew J.

    The sequences of the 16S rRNA and haloalkane dehalogenase (dhaA) genes of five gram-positive haloalkane-utilizing bacteria isolated from contaminated sites in Europe, Japan, and the United States and of the archetypal haloalkane-degrading bacterium Rhodococcus sp. strain NCIMB13064 were compared.

  11. How developments in cryobiology, reproductive technologies and conservation genomics could shape gene banking strategies for (farm) animals

    NARCIS (Netherlands)

    Woelders, H.; Windig, J.J.; Hiemstra, S.J.

    2012-01-01

    Many local breeds are currently at risk because of replacement by a limited number of specialized commercial breeds. Concurrently, for many breeds, allelic diversity within breeds declines because of inbreeding. Gene banking of germplasm may serve to secure the breeds and the alleles for any future

  12. Conservation potential of agricultural water conservation subsidies

    Science.gov (United States)

    Huffaker, Ray

    2008-07-01

    A current policy subsidizes farmers to invest in improved on-farm irrigation efficiency, expecting water to be conserved off farm. Contrary to expectation, water has been increasingly depleted in some regions after such improvements. This paper investigates the policy's failure to conserve water consistently by (1) formulating an economic model of irrigated crop production to determine a profit-maximizing irrigator's range of responses to a subsidy and (2) embedding these responses into hypothetical streamflow diagrams to ascertain their potential to conserve water under various hydrologic regimes. Testable hypotheses are developed to predict the conservation potential of a subsidy in real-world application.

  13. Regulation of metabolic products and gene expression in Fusarium asiaticum by agmatine addition.

    Science.gov (United States)

    Suzuki, Tadahiro; Kim, Young-Kyung; Yoshioka, Hifumi; Iwahashi, Yumiko

    2013-05-01

    The metabolic products resulting from the cultivation of F. asiaticum in agmatine were identified using capillary electrophoresis-time of flight mass spectrometry. Glyoxylic acid was detected from fungal cultures grown in agmatine, while it was absent in control cells. The abundance of other metabolic products of the glycolytic pathway also increased because of agmatine; however, there was no increase in the amounts of pyruvic acid or metabolites from the tricarboxylic acid cycle. Moreover, gene expression levels within Fusarium asiaticum exposed to agmatine were analyzed by DNA microarray. Changes in gene expression levels directed the changes in metabolic products. Our results suggest that acetyl coenzyme A, which is a starting substrate for the biosynthesis of deoxynivalenol (DON), was simultaneously produced by activated β-oxidation. Furthermore, the content of 4-aminobutyrate (GABA) was increased in the agmatine addition culture medium. GABA can be synthesized from agmatine through putrescine and might influence the regulation of DON-related genes.

  14. MADS-box gene evolution - structure and transcription patterns

    DEFF Research Database (Denmark)

    Johansen, Bo; Pedersen, Louise Buchholt; Skipper, Martin

    2002-01-01

    Mads-box genes, ABC model, Evolution, Phylogeny, Transcription patterns, Gene structure, Conserved motifs......Mads-box genes, ABC model, Evolution, Phylogeny, Transcription patterns, Gene structure, Conserved motifs...

  15. A Common histone modification code on C4 genes in maize and its conservation in Sorghum and Setaria italica.

    Science.gov (United States)

    Heimann, Louisa; Horst, Ina; Perduns, Renke; Dreesen, Björn; Offermann, Sascha; Peterhansel, Christoph

    2013-05-01

    C4 photosynthesis evolved more than 60 times independently in different plant lineages. Each time, multiple genes were recruited into C4 metabolism. The corresponding promoters acquired new regulatory features such as high expression, light induction, or cell type-specific expression in mesophyll or bundle sheath cells. We have previously shown that histone modifications contribute to the regulation of the model C4 phosphoenolpyruvate carboxylase (C4-Pepc) promoter in maize (Zea mays). We here tested the light- and cell type-specific responses of three selected histone acetylations and two histone methylations on five additional C4 genes (C4-Ca, C4-Ppdk, C4-Me, C4-Pepck, and C4-RbcS2) in maize. Histone acetylation and nucleosome occupancy assays indicated extended promoter regions with regulatory upstream regions more than 1,000 bp from the transcription initiation site for most of these genes. Despite any detectable homology of the promoters on the primary sequence level, histone modification patterns were highly coregulated. Specifically, H3K9ac was regulated by illumination, whereas H3K4me3 was regulated in a cell type-specific manner. We further compared histone modifications on the C4-Pepc and C4-Me genes from maize and the homologous genes from sorghum (Sorghum bicolor) and Setaria italica. Whereas sorghum and maize share a common C4 origin, C4 metabolism evolved independently in S. italica. The distribution of histone modifications over the promoters differed between the species, but differential regulation of light-induced histone acetylation and cell type-specific histone methylation were evident in all three species. We propose that a preexisting histone code was recruited into C4 promoter control during the evolution of C4 metabolism.

  16. Wood products used in constructing conservation and development projects by the Corps of Engineers in the United States, 1962 and 1978

    Science.gov (United States)

    W. H. Reid; D. B. McKeever

    Estimates of the amounts of wood products used in constructing civil conservation and development projects by the Corps of Engineers in the United States are presented for the years 1962 and 1978. Amounts of lumber, laminated lumber, poles and piling, and plywood used in construction are stratified by five construction categories, and three types of uses. Estimates of...

  17. Balancing development and conservation? An assessment of livelihood and environmental outcomes of nontimber forest product trade in Asia, Africa, and Latin America

    NARCIS (Netherlands)

    Kusters, K.; Achdiawan, R.; Belcher, B.; Ruiz Pérez, M.; Hussain, A.

    2008-01-01

    This chapter addresses the question, to what extent and under which conditions nontimber forest product (NTFP) trade leads to both livelihood improvement and forest conservation. We based the analysis on a standardized expert-judgment assessment of the livelihood and environmental outcomes of 55

  18. Effect of soil and water conservation on rehabilitation of degraded lands and crop productivity in Maego watershed, North Ethiopia

    Directory of Open Access Journals (Sweden)

    Gebremariam Yaebiyo Dimtsu

    2018-04-01

    Full Text Available Many soil and water conservation (SWC measures were undertaken to decrease land degradation in Ethiopia. However, evaluation of their performance is essential to understand their success or failure and readjusting accordingly in the future planning.  Therefore, the objective of this study was to evaluate effectiveness of SWC measures in rehabilitation of degraded watershed and increase crop productivity in Maego watershed, Ethiopia. Seventy six sample plots were randomly taken from treated and untreated sub-watersheds for woody species and soil sampling. Crops yield was measured on top side, middle zone and below side of SWC structures. There were significantly higher woody species density and diversity, total nitrogen (TN, soil organic matter (SOM and soil moisture in the treated uncultivated land than the untreated one. The highest tree and sapling species density and diversity, TN and SOM were recorded on the exclosure part of the treated sub-watershed. Landscape position affected soil fertility, but has no effect on woody species density and diversity. The highest barley and wheat yield was measured on top side of SWC structures. Therefore, physical SWC structures should be integrated with exclosure to enhance rehabilitation of degraded watersheds/landscapes. Integration of biological SWC measures that improve soil fertility are essential on the cultivated land of the watershed. Most of the existing SWC structures, especially the old ones are filled with accumulated sediment, so maintenance is needed.

  19. Significance of Mangrove Biodiversity Conservation in Fishery Production and Living Conditions of Coastal Communities in Sri Lanka

    Directory of Open Access Journals (Sweden)

    Chaya Sarathchandra

    2018-03-01

    Full Text Available Sri Lanka is an island nation where ~59% of the population live in coastal regions. The main income source in these areas is fishing, which contributes to ~44% of the national GDP. Fishery resources depend on mangroves, especially in estuaries and lagoons, as mangroves provide the best nursery grounds for both brackish and marine species that are significant for the island’s fishing industry. However, growing pressures from an increasing population and development are causing substantial damage to mangroves resulting in loss of mangrove diversity. We analyzed whether variation in mangrove diversity within a lagoon system affects fishery production and livelihoods. Along the lagoon we selected three sites, which were 5 km apart from each other, for the survey. We used three 50 m long transects at each site for faunal and floral diversity assessments. The fishery catch was recorded from three crafts in each side. The socio-economic survey was conducted in 30 households per site using a standard questionnaire. In the site with the highest floral and faunal diversity, we also recorded the highest fish catch, but not the highest crab or shrimp catches. Our results confirm that higher mangrove diversity—and not just area—supports higher income generation. Thus, future development should prioritize biodiversity conservation in coastal regions.

  20. Development of Ecogenomic Sensors for Remote Detection of Marine Microbes, Their Genes and Gene Products

    Science.gov (United States)

    Scholin, C.; Preston, C.; Harris, A.; Birch, J.; Marin, R.; Jensen, S.; Roman, B.; Everlove, C.; Makarewicz, A.; Riot, V.; Hadley, D.; Benett, W.; Dzenitis, J.

    2008-12-01

    An internet search using the phrase "ecogenomic sensor" will return numerous references that speak broadly to the idea of detecting molecular markers indicative of specific organisms, genes or other biomarkers within an environmental context. However, a strict and unified definition of "ecogenomic sensor" is lacking and the phrase may be used for laboratory-based tools and techniques as well as semi or fully autonomous systems that can be deployed outside of laboratory. We are exploring development of an ecogenomic sensor from the perspective of a field-portable device applied towards oceanographic research and water quality monitoring. The device is known as the Environmental Sample Processor, or ESP. The ESP employs wet chemistry molecular analytical techniques to autonomously assess the presence and abundance of specific organisms, their genes and/or metabolites in near real-time. Current detection chemistries rely on low- density DNA probe and protein arrays. This presentation will emphasize results from 2007-8 field trials when the ESP was moored in Monterey Bay, CA, as well as current engineering activities for improving analytical capacity of the instrument. Changes in microbial community structure at the rRNA level were observed remotely in accordance with changing chemical and physical oceanographic conditions. Current developments include incorporation of a reusable solid phase extraction column for purifying nucleic acids and a 4-channel real-time PCR module. Users can configure this system to support a variety of PCR master mixes, primer/probe combinations and control templates. An update on progress towards fielding a PCR- enabled ESP will be given along with an outline of plans for its use in coastal and oligotrophic oceanic regimes.

  1. Trade-offs for food production, nature conservation and climate limit the terrestrial carbon dioxide removal potential.

    Science.gov (United States)

    Boysen, Lena R; Lucht, Wolfgang; Gerten, Dieter

    2017-10-01

    Large-scale biomass plantations (BPs) are a common factor in climate mitigation scenarios as they promise double benefits: extracting carbon from the atmosphere and providing a renewable energy source. However, their terrestrial carbon dioxide removal (tCDR) potentials depend on important factors such as land availability, efficiency of capturing biomass-derived carbon and the timing of operation. Land availability is restricted by the demands of future food production depending on yield increases and population growth, by requirements for nature conservation and, with respect to climate mitigation, avoiding unfavourable albedo changes. We integrate these factors in one spatially explicit biogeochemical simulation framework to explore the tCDR opportunity space on land available after these constraints are taken into account, starting either in 2020 or 2050, and lasting until 2100. We find that assumed future needs for nature protection and food production strongly limit tCDR potentials. BPs on abandoned crop and pasture areas (~1,300 Mha in scenarios of either 8.0 billion people and yield gap reductions of 25% until 2020 or 9.5 billion people and yield gap reductions of 50% until 2050) could, theoretically, sequester ~100 GtC in land carbon stocks and biomass harvest by 2100. However, this potential would be ~80% lower if only cropland was available or ~50% lower if albedo decreases were considered as a factor restricting land availability. Converting instead natural forest, shrubland or grassland into BPs could result in much larger tCDR potentials ̶ but at high environmental costs (e.g. biodiversity loss). The most promising avenue for effective tCDR seems to be improvement of efficient carbon utilization pathways, changes in dietary trends or the restoration of marginal lands for the implementation of tCDR. © 2017 John Wiley & Sons Ltd.

  2. Functional dissection of the promoter of the pollen-specific gene NTP303 reveals a novel pollen-specific, and conserved cis-regulatory element.

    Science.gov (United States)

    Weterings, K; Schrauwen, J; Wullems, G; Twell, D

    1995-07-01

    Regulatory elements within the promoter of the pollen-specific NTP303 gene from tobacco were analysed by transient and stable expression analyses. Analysis of precisely targeted mutations showed that the NTP303 promoter is not regulated by any of the previously described pollen-specific cis-regulatory elements. However, two adjacent regions from -103 to -86 bp and from -86 to -59 bp were shown to contain sequences which positively regulated the NTP303 promoter. Both of these regions were capable of driving pollen-specific expression from a heterologous promoter, independent of orientation and in an additive manner. The boundaries of the minimal, functional NTP303 promoter were determined to lie within the region -86 to -51 bp. The sequence AAATGA localized from -94 to -89 bp was identified as a novel cis-acting element, of which the TGA triplet was shown to comprise an active part. This element was shown to be completely conserved in the similarly regulated promoter of the Bp 10 gene from Brassica napus encoding a homologue of the NTP303 gene.

  3. Conservation of Tcrg-V5 and limited allelic sequence polymorphism of the other Tcrg-V genes used by mouse tissue-specific gd-T lymphocytes

    Energy Technology Data Exchange (ETDEWEB)

    Roger, T.; Morisset, J.; Seman, M. [Universite Denis Diderot, Paris (France)

    1996-12-31

    The mouse Tcrg locus comprises seven Tcrg-V, four Tcrg-J, and four Tcrg-C segments which generate only six major types of functional g chains, Vg7-, Vg4-, Vg6-, or Vg5-Jg1-Cg1, Vg2-Jg2-Cg2, and Vg1-Jg4-Cg4. A complete analysis of restriction fragment length polymorphism (RFLP) of the Tcrg locus in wild and inbred mice suggested its relative conservation compared to other loci of the immunoglobulin (Ig) gene family. Three haplotypes have been characterized in laboratory mice: gA, gB, and gC, represented by BALB/c, DBA/2, and AKR prototypes. Tcr-gA and -gC haplotypes are highly related. By contrast, Tcr-gB, likely inherited from Asian mouse subspecies, appeared very different by RFLP analysis. Yet only partial sequence data have been reported on gA and gB Tcrg-V genes. Here, the complete sequence of all Tcrg-V genes of the two haplotypes is described. 16 refs., 1 fig.

  4. DNA repair synthesis dependent on the uvrA,B gene products

    International Nuclear Information System (INIS)

    Moses, R.E.; Moody, E.E.M.

    1975-01-01

    Ultraviolet irradiation of toluene-treated Escherichia coli causes an inhibition of replicative DNA synthesis. This is followed by the appearance of nonconservative DNA repair synthesis which does not require either the polymerase or 5' → 3' exonucleolytic activities of DNA polymerase I. The repair synthesis may be catalyzed by DNA polymerase III activity but does not require a functional DNA polymerase II. The ultraviolet-induced synthesis requires ATP and is dependent on a functional uvrA and uvrB gene product. However, other uvr gene products are not required for the synthesis. The recB function is also not required

  5. Sequence Conservation and Sexually Dimorphic Expression of the Ftz-F1 Gene in the Crustacean Daphnia magna.

    Directory of Open Access Journals (Sweden)

    Nur Syafiqah Mohamad Ishak

    Full Text Available Identifying the genes required for environmental sex determination is important for understanding the evolution of diverse sex determination mechanisms in animals. Orthologs of Drosophila orphan receptor Fushi tarazu factor-1 (Ftz-F1 are known to function in genetic sex determination. In contrast, their roles in environmental sex determination remain unknown. In this study, we have cloned and characterized the Ftz-F1 ortholog in the branchiopod crustacean Daphnia magna, which produces males in response to environmental stimuli. Similar to that observed in Drosophila, D. magna Ftz-F1 (DapmaFtz-F1 produces two splicing variants, αFtz-F1 and βFtz-F1, which encode 699 and 777 amino acids, respectively. Both isoforms share a DNA-binding domain, a ligand-binding domain, and an AF-2 activation domain and differ only at the A/B domain. The phylogenetic position and genomic structure of DapmaFtz-F1 suggested that this gene has diverged from an ancestral gene common to branchiopod crustacean and insect Ftz-F1 genes. qRT-PCR showed that at the one cell and gastrulation stages, both DapmaFtz-F1 isoforms are two-fold more abundant in males than in females. In addition, in later stages, their sexual dimorphic expressions were maintained in spite of reduced expression. Time-lapse imaging of DapmaFtz-F1 RNAi embryos was performed in H2B-GFP expressing transgenic Daphnia, demonstrating that development of the RNAi embryos slowed down after the gastrulation stage and stopped at 30-48 h after ovulation. DapmaFtz-F1 shows high homology to insect Ftz-F1 orthologs based on its amino acid sequence and exon-intron organization. The sexually dimorphic expression of DapmaFtz-F1 suggests that it plays a role in environmental sex determination of D. magna.

  6. Improvement of oxytetracycline production mediated via cooperation of resistance genes in Streptomyces rimosus.

    Science.gov (United States)

    Yin, Shouliang; Wang, Xuefeng; Shi, Mingxin; Yuan, Fang; Wang, Huizhuan; Jia, Xiaole; Yuan, Fang; Sun, Jinliang; Liu, Tiejun; Yang, Keqian; Zhang, Yuxiu; Fan, Keqiang; Li, Zilong

    2017-09-01

    Increasing the self-resistance levels of Streptomyces is an effective strategy to improve the production of antibiotics. To increase the oxytetracycline (OTC) production in Streptomyces rimosus, we investigated the cooperative effect of three co-overexpressing OTC resistance genes: one gene encodes a ribosomal protection protein (otrA) and the other two express efflux proteins (otrB and otrC). Results indicated that combinational overexpression of otrA, otrB, and otrC (MKABC) exerted a synergetic effect. OTC production increased by 179% in the recombinant strain compared with that of the wild-type strain M4018. The resistance level to OTC was increased by approximately two-fold relative to the parental strain, thereby indicating that applying the cooperative effect of self-resistance genes is useful to improve OTC production. Furthermore, the previously identified cluster-situated activator OtcR was overexpressed in MKABC in constructing the recombinant strain MKRABC; such strain can produce OTC of approximately 7.49 g L -1 , which represents an increase of 19% in comparison with that of the OtcR-overexpressing strain alone. Our work showed that the cooperative overexpression of self-resistance genes is a promising strategy to enhance the antibiotics production in Streptomyces.

  7. The inflammatory bowel disease (IBD susceptibility genes NOD1 and NOD2 have conserved anti-bacterial roles in zebrafish

    Directory of Open Access Journals (Sweden)

    Stefan H. Oehlers

    2011-11-01

    Inflammatory bowel disease (IBD, in the form of Crohn’s disease (CD or ulcerative colitis (UC, is a debilitating chronic immune disorder of the intestine. A complex etiology resulting from dysfunctional interactions between the intestinal immune system and its microflora, influenced by host genetic susceptibility, makes disease modeling challenging. Mutations in NOD2 have the highest disease-specific risk association for CD, and a related gene, NOD1, is associated with UC. NOD1 and NOD2 encode intracellular bacterial sensor proteins acting as innate immune triggers, and represent promising therapeutic targets. The zebrafish has the potential to aid in modeling genetic and environmental aspects of IBD pathogenesis. Here, we report the characterization of the Nod signaling components in the zebrafish larval intestine. The nod1 and nod2 genes are expressed in intestinal epithelial cells and neutrophils together with the Nod signaling pathway genes ripk2, a20, aamp, cd147, centaurin b1, erbin and grim-19. Using a zebrafish embryo Salmonella infection model, morpholino-mediated depletion of Nod1 or Nod2 reduced the ability of embryos to control systemic infection. Depletion of Nod1 or Nod2 decreased expression of dual oxidase in the intestinal epithelium and impaired the ability of larvae to reduce intracellular bacterial burden. This work highlights the potential use of zebrafish larvae in the study of components of IBD pathogenesis.

  8. Applications of gene-based technologies for improving animal production and health in developing countries

    International Nuclear Information System (INIS)

    Makkar, H.P.S.; Viljoen, G.J.

    2005-01-01

    This book provides a compilation of peer-reviewed scientific contributions from authoritative researchers attending an international symposium convened by the Animal Production and Health Sub-programme of the Animal Production and Health (APH), Joint FAO/IAEA Programme in cooperation with the Animal Production and Health Division of the FAO. These Proceedings contain invaluable information on the role and future potential of gene-based technologies for improving animal production and health, possible applications and constraints in the use of this technology in developing countries and their specific research needs

  9. Genetic diversity within and between broodstocks of the white shrimp Litopenaeus vannamei (Boone, 1931 (Decapoda, Penaeidae and its implication for the gene pool conservation

    Directory of Open Access Journals (Sweden)

    PD. Freitas

    Full Text Available Genetic variation within and between fifteen closed broodstock lines of the Pacific white shrimp Litopenaeus vannamei, reared at different hatcheries in the Brazilian coast, was assessed by RAPD analysis. Fifty two polymorphic loci were identified when a set of five decamer primers was used in PCR. The genetic diversity analysis within lines evidenced genetic variation loss probably related to bottleneck effects and inbreeding. In addition, the genetic divergence values between the different samples appear to reflect the initial founder composition of such stocks, in some cases, sharing a common origin, suggesting a putative importance of interbreeding for the establishment of genetic improvement programs for these broodstocks. The genetic variation monitoring appears to be helpful to the gene pool conservation of this aquaculture species, mainly if considered its exotic status in Brazil and the current impossibility of new introduction of wild individuals.

  10. Increasing cocoa butter-like lipid production of Saccharomyces cerevisiae by expression of selected cocoa genes

    DEFF Research Database (Denmark)

    Wei, Yongjun; Gossing, Michael; Bergenholm, David

    2017-01-01

    for CB biosynthesis from the cocoa genome using a phylogenetic analysis approach. By expressing the selected cocoa genes in S. cerevisiae, we successfully increased total fatty acid production, TAG production and CBL production in some S. cerevisiae strains. The relative CBL content in three yeast...... higher level of CBL compared with the control strain. In summary, CBL production by S. cerevisiae were increased through expressing selected cocoa genes potentially involved in CB biosynthesis.......Cocoa butter (CB) extracted from cocoa beans mainly consists of three different kinds of triacylglycerols (TAGs), 1,3-dipalmitoyl-2-oleoyl-glycerol (POP, C16:0-C18:1-C16:0), 1-palmitoyl-3-stearoyl-2-oleoyl-glycerol(POS,C16:0C18:1-C18:0) and 1,3-distearoyl-2-oleoyl-glycerol (SOS, C18:0-C18:1-C18...

  11. Mutations that alter a conserved element upstream of the potato virus X triple block and coat protein genes affect subgenomic RNA accumulation.

    Science.gov (United States)

    Kim, K H; Hemenway, C

    1997-05-26

    The putative subgenomic RNA (sgRNA) promoter regions upstream of the potato virus X (PVX) triple block and coat protein (CP) genes contain sequences common to other potexviruses. The importance of these sequences to PVX sgRNA accumulation was determined by inoculation of Nicotiana tabacum NT1 cell suspension protoplasts with transcripts derived from wild-type and modified PVX cDNA clones. Analyses of RNA accumulation by S1 nuclease digestion and primer extension indicated that a conserved octanucleotide sequence element and the spacing between this element and the start-site for sgRNA synthesis are critical for accumulation of the two major sgRNA species. The impact of mutations on CP sgRNA levels was also reflected in the accumulation of CP. In contrast, genomic minus- and plus-strand RNA accumulation were not significantly affected by mutations in these regions. Studies involving inoculation of tobacco plants with the modified transcripts suggested that the conserved octanucleotide element functions in sgRNA accumulation and some other aspect of the infection process.

  12. A novel, highly conserved metallothionein family in basidiomycete fungi and characterization of two representative SlMTa and SlMTb genes in the ectomycorrhizal fungus Suillus luteus.

    Science.gov (United States)

    Nguyen, Hoai; Rineau, François; Vangronsveld, Jaco; Cuypers, Ann; Colpaert, Jan V; Ruytinx, Joske

    2017-07-01

    The basidiomycete Suillus luteus is an important member of the ectomycorrhizal community that thrives in heavy metal polluted soils covered with pioneer pine forests. This study aimed to identify potential heavy metal chelators in S. luteus. Two metallothionein (MT) coding genes, SlMTa and SlMTb, were identified. When heterologously expressed in yeast, both SlMTa and SlMTb can rescue the Cu sensitive mutant from Cu toxicity. In S. luteus, transcription of both SlMTa and SlMTb is induced by Cu but not Cd or Zn. Several putative Cu-sensing and metal-response elements are present in the promoter sequences. These results indicate that SlMTa and SlMTb function as Cu-thioneins. Homologs of the S. luteus MTs are present in 49 species belonging to 10 different orders of the subphylum Agaricomycotina and are remarkably conserved. The length of the proteins, number and distribution of cysteine residues indicate a novel family of fungal MTs. The ubiquitous and highly conserved features of these MTs suggest that they are important for basic cellular functions in species in the subphylum Agaricomycotina. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  13. Conserved Epigenetic Mechanisms Could Play a Key Role in Regulation of Photosynthesis and Development-Related Genes during Needle Development of Pinus radiata.

    Science.gov (United States)

    Valledor, Luis; Pascual, Jesús; Meijón, Mónica; Escandón, Mónica; Cañal, María Jesús

    2015-01-01

    Needle maturation is a complex process that involves cell growth, differentiation and tissue remodelling towards the acquisition of full physiological competence. Leaf induction mechanisms are well known; however, those underlying the acquisition of physiological competence are still poorly understood, especially in conifers. We studied the specific epigenetic regulation of genes defining organ function (PrRBCS and PrRBCA) and competence and stress response (PrCSDP2 and PrSHMT4) during three stages of needle development and one de-differentiated control. Gene-specific changes in DNA methylation and histone were analysed by bisulfite sequencing and chromatin immunoprecipitation (ChIP). The expression of PrRBCA and PrRBCS increased during needle maturation and was associated with the progressive loss of H3K9me3, H3K27me3 and the increase in AcH4. The maturation-related silencing of PrSHMT4 was correlated with increased H3K9me3 levels, and the repression of PrCSDP2, to the interplay between AcH4, H3K27me3, H3K9me3 and specific DNA methylation. The employ of HAT and HDAC inhibitors led to a further determination of the role of histone acetylation in the regulation of our target genes. The integration of these results with high-throughput analyses in Arabidopsis thaliana and Populus trichocarpa suggests that the specific epigenetic mechanisms that regulate photosynthetic genes are conserved between the analysed species.

  14. Conserved Epigenetic Mechanisms Could Play a Key Role in Regulation of Photosynthesis and Development-Related Genes during Needle Development of Pinus radiata.

    Directory of Open Access Journals (Sweden)

    Luis Valledor

    Full Text Available Needle maturation is a complex process that involves cell growth, differentiation and tissue remodelling towards the acquisition of full physiological competence. Leaf induction mechanisms are well known; however, those underlying the acquisition of physiological competence are still poorly understood, especially in conifers. We studied the specific epigenetic regulation of genes defining organ function (PrRBCS and PrRBCA and competence and stress response (PrCSDP2 and PrSHMT4 during three stages of needle development and one de-differentiated control. Gene-specific changes in DNA methylation and histone were analysed by bisulfite sequencing and chromatin immunoprecipitation (ChIP. The expression of PrRBCA and PrRBCS increased during needle maturation and was associated with the progressive loss of H3K9me3, H3K27me3 and the increase in AcH4. The maturation-related silencing of PrSHMT4 was correlated with increased H3K9me3 levels, and the repression of PrCSDP2, to the interplay between AcH4, H3K27me3, H3K9me3 and specific DNA methylation. The employ of HAT and HDAC inhibitors led to a further determination of the role of histone acetylation in the regulation of our target genes. The integration of these results with high-throughput analyses in Arabidopsis thaliana and Populus trichocarpa suggests that the specific epigenetic mechanisms that regulate photosynthetic genes are conserved between the analysed species.

  15. Regulatory structures for gene therapy medicinal products in the European Union.

    Science.gov (United States)

    Klug, Bettina; Celis, Patrick; Carr, Melanie; Reinhardt, Jens

    2012-01-01

    Taking into account the complexity and technical specificity of advanced therapy medicinal products: (gene and cell therapy medicinal products and tissue engineered products), a dedicated European regulatory framework was needed. Regulation (EC) No. 1394/2007, the "ATMP Regulation" provides tailored regulatory principles for the evaluation and authorization of these innovative medicines. The majority of gene or cell therapy product development is carried out by academia, hospitals, and small- and medium-sized enterprises (SMEs). Thus, acknowledging the particular needs of these types of sponsors, the legislation also provides incentives for product development tailored to them. The European Medicines Agency (EMA) and, in particular, its Committee for Advanced Therapies (CAT) provide a variety of opportunities for early interaction with developers of ATMPs to enable them to have early regulatory and scientific input. An important tool to promote innovation and the development of new medicinal products by micro-, small-, and medium-sized enterprises is the EMA's SME initiative launched in December 2005 to offer financial and administrative assistance to smaller companies. The European legislation also foresees the involvement of stakeholders, such as patient organizations, in the development of new medicines. Considering that gene therapy medicinal products are developed in many cases for treatment of rare diseases often of monogenic origin, the involvement of patient organizations, which focus on rare diseases and genetic and congenital disorders, is fruitful. Two such organizations are represented in the CAT. Research networks play another important role in the development of gene therapy medicinal products. The European Commission is funding such networks through the EU Sixth Framework Program. Copyright © 2012 Elsevier Inc. All rights reserved.

  16. Unusual evolutionary conservation and further species-specific adaptations of a large family of nonclassical MHC class Ib genes across different degrees of genome ploidy in the amphibian subfamily Xenopodinae.

    Science.gov (United States)

    Edholm, Eva-Stina; Goyos, Ana; Taran, Joseph; De Jesús Andino, Francisco; Ohta, Yuko; Robert, Jacques

    2014-06-01

    Nonclassical MHC class Ib (class Ib) genes are a family of highly diverse and rapidly evolving genes wherein gene numbers, organization, and expression markedly differ even among closely related species rendering class Ib phylogeny difficult to establish. Whereas among mammals there are few unambiguous class Ib gene orthologs, different amphibian species belonging to the anuran subfamily Xenopodinae exhibit an unusually high degree of conservation among multiple class Ib gene lineages. Comparative genomic analysis of class Ib gene loci of two divergent (~65 million years) Xenopodinae subfamily members Xenopus laevis (allotetraploid) and Xenopus tropicalis (diploid) shows that both species possess a large cluster of class Ib genes denoted as Xenopus/Silurana nonclassical (XNC/SNC). Our study reveals two distinct phylogenetic patterns among these genes: some gene lineages display a high degree of flexibility, as demonstrated by species-specific expansion and contractions, whereas other class Ib gene lineages have been maintained as monogenic subfamilies with very few changes in their nucleotide sequence across divergent species. In this second category, we further investigated the XNC/SNC10 gene lineage that in X. laevis is required for the development of a distinct semi-invariant T cell population. We report compelling evidence of the remarkable high degree of conservation of this gene lineage that is present in all 12 species of the Xenopodinae examined, including species with different degrees of ploidy ranging from 2, 4, 8 to 12 N. This suggests that the critical role of XNC10 during early T cell development is conserved in amphibians.

  17. Blood and Blood Product Conservation: Results of Strategies to Improve Clinical Outcomes in Open Heart Surgery Patients at a Tertiary Hospital.

    Science.gov (United States)

    Khan, Junaid H; Green, Emily A; Chang, Jimmin; Ayala, Alexandria M; Barkin, Marilyn S; Reinys, Emily E; Stanton, Jeffrey; Stanten, Russell D

    2017-12-01

    Blood product usage is a quality outcome for patients undergoing cardiac surgery. To address an increase in blood product usage since the discontinuation of aprotinin, blood conservation strategies were initiated at a tertiary hospital in Oakland, CA. Improving transfusion rates for open heart surgery patients requiring Cardiopulmonary bypass (CPB) involved multiple departments in coordination. Specific changes to conserve blood product usage included advanced CPB technology upgrades, and precise individualized heparin dose response titration assay for heparin and protamine management. Retrospective analysis of blood product usage pre-implementation, post-CPB changes and post-Hemostasis Management System (HMS) implementation was done to determine the effectiveness of the blood conservation strategies. Statistically significant decrease in packed red blood cells, fresh frozen plasma, cryoprecipitate, and platelet usage over the stepped implementation of both technologies was observed. New oxygenator and centrifugal pump technologies reduced active circuitry volume and caused less damage to blood cells. Individualizing heparin and protamine dosing to a patient using the HMS led to transfusion reductions as well. Overall trends toward reductions in hospital length of stay and intensive care unit stay, and as a result, blood product cost and total hospitalization cost are positive over the period of implementation of both CPB circuit changes and HMS implementation. Although they are multifactorial in nature, these trends provide positive enforcement to the changes implemented.

  18. Regulation of the E. coli SOS response by the lexA gene product

    International Nuclear Information System (INIS)

    Brent, R.

    1983-01-01

    In an Escherichia coli that is growing normally, transcription of many genes is repressed by the product of the lexA gene. If cellular DNA is damaged, proteolytically competent recA protein (recA protease) inactivates lexA protein and these genes are induced. Many of the cellular phenomena observed during the cellular response to DNA damage (the SOS response) are the consequence of the expression of these lexA-prepressed genes. Since the SOS response of E. coli has recently been the subject of a comprehensive review, in this paper I would like to concentrate on some modifications to the picture based on new data. 12 references, 2 figures

  19. A positive feedback-based gene circuit to increase the production of a membrane protein

    Directory of Open Access Journals (Sweden)

    Gennis Robert B

    2010-05-01

    Full Text Available Abstract Background Membrane proteins are an important class of proteins, playing a key role in many biological processes, and are a promising target in pharmaceutical development. However, membrane proteins are often difficult to produce in large quantities for the purpose of crystallographic or biochemical analyses. Results In this paper, we demonstrate that synthetic gene circuits designed specifically to overexpress certain genes can be applied to manipulate the expression kinetics of a model membrane protein, cytochrome bd quinol oxidase in E. coli, resulting in increased expression rates. The synthetic circuit involved is an engineered, autoinducer-independent variant of the lux operon activator LuxR from V. fischeri in an autoregulatory, positive feedback configuration. Conclusions Our proof-of-concept experiments indicate a statistically significant increase in the rate of production of the bd oxidase membrane protein. Synthetic gene networks provide a feasible solution for the problem of membrane protein production.

  20. Improving the Safety of Cell Therapy Products by Suicide Gene Transfer

    Directory of Open Access Journals (Sweden)

    Antonio eDi Stasi

    2014-11-01

    Full Text Available Adoptive T-cell therapy can involve donor lymphocyte infusion (DLI after allogeneic hematopoietic stem cell transplantation, the administration of tumor infiltrating lymphocyte (TILs expanded ex-vivo, or more recently the use of T cell receptor (TCR or chimeric antigen receptor (CAR redirected T cells. However cellular therapies can pose significant risks, including graft-versus-host-disease and other on and off-target effects, and therefore strategies need to be implemented to permanently reverse any sign of toxicity. A suicide gene is a genetically encoded molecule that allows selective destruction of adoptively transferred cells. Suicide gene addition to cellular therapeutic products can lead to selective ablation of gene-modified cells, preventing collateral damage to contiguous cells and/or tissues. The ‘ideal’ suicide gene would ensure the safety of gene modified cellular applications by granting irreversible elimination of ‘all’ and ‘only’ the cells responsible for the unwanted toxicity. This review presents the suicide gene safety systems reported to date, with a focus on the state-of-the-art and potential applications regarding two of the most extensively validated suicide genes, including the clinical setting: herpes-simplex-thymidine-kinase (HSV-TK and inducible-caspase-9 (iCasp9.

  1. An allele of an ancestral transcription factor dependent on a horizontally acquired gene product.

    Science.gov (United States)

    Chen, H Deborah; Jewett, Mollie W; Groisman, Eduardo A

    2012-01-01

    Changes in gene regulatory circuits often give rise to phenotypic differences among closely related organisms. In bacteria, these changes can result from alterations in the ancestral genome and/or be brought about by genes acquired by horizontal transfer. Here, we identify an allele of the ancestral transcription factor PmrA that requires the horizontally acquired pmrD gene product to promote gene expression. We determined that a single amino acid difference between the PmrA proteins from the human adapted Salmonella enterica serovar Paratyphi B and the broad host range S. enterica serovar Typhimurium rendered transcription of PmrA-activated genes dependent on the PmrD protein in the former but not the latter serovar. Bacteria harboring the serovar Typhimurium allele exhibited polymyxin B resistance under PmrA- or under PmrA- and PmrD-inducing conditions. By contrast, isogenic strains with the serovar Paratyphi B allele displayed PmrA-regulated polymyxin B resistance only when experiencing activating conditions for both PmrA and PmrD. We establish that the two PmrA orthologs display quantitative differences in several biochemical properties. Strains harboring the serovar Paratyphi B allele showed enhanced biofilm formation, a property that might promote serovar Paratyphi B's chronic infection of the gallbladder. Our findings illustrate how subtle differences in ancestral genes can impact the ability of horizontally acquired genes to confer new properties.

  2. Assembly of Highly Standardized Gene Fragments for High-Level Production of Porphyrins in E. coli

    DEFF Research Database (Denmark)

    Nielsen, Morten Thrane; Madsen, Karina Marie; Seppala, Susanna

    2015-01-01

    to formulate a molecular cloning pipeline and iteratively assemble and optimize a six-gene pathway for protoporphyrin IX synthesis in Escherichia coli. State of the art production levels were achieved through two simple cycles of engineering and screening. The principles defined here are generally applicable...

  3. EpsA is an essential gene in exopolysaccharide production in Lactobacillus johnsonii FI9785.

    Science.gov (United States)

    Dertli, Enes; Mayer, Melinda J; Colquhoun, Ian J; Narbad, Arjan

    2016-07-01

    Lactobacillus johnsonii FI9785 has an eps gene cluster which is required for the biosynthesis of homopolymeric exopolysaccharides (EPS)-1 and heteropolymeric EPS-2 as a capsular layer. The first gene of the cluster, epsA, is the putative transcriptional regulator. In this study we showed the crucial role of epsA in EPS biosynthesis by demonstrating that deletion of epsA resulted in complete loss of both EPS-1 and EPS-2 on the cell surface. Plasmid complementation of the epsA gene fully restored EPS production, as confirmed by transmission electron microscopy and nuclear magnetic resonance (NMR) analysis. Furthermore, this complementation resulted in a twofold increase in the expression levels of this gene, which almost doubled amounts of EPS production in comparison with the wild-type strain. Analysis of EPS by NMR showed an increased ratio of the heteropolysaccharide to homopolysaccharide in the complemented strain and allowed identification of the acetylated residue in EPS-2 as the (1,4)-linked βGlcp unit, with the acetyl group located at O-6. These findings indicate that epsA is a positive regulator of EPS production and that EPS production can be manipulated by altering its expression. © 2015 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  4. Role of nitric oxide and flavohemoglobin homolog genes in Aspergillus nidulans sexual development and mycotoxin production

    Science.gov (United States)

    Flavohemoglobins are widely distributed proteins in both prokaryotic and eukaryotic organisms, conferring resistance against nitrosative stress. In the present study we investigated the role of two flavohemoglobin homologous genes, fhbA and fhbB, in morphogenesis and in the production of the mycotox...

  5. Functional Reconstitution of a Fungal Natural Product Gene Cluster by Advanced Genome Editing

    DEFF Research Database (Denmark)

    Weber, Jakob; Valiante, Vito; Nødvig, Christina Spuur

    2017-01-01

    is not produced among different isolates. Combining computational analysis with targeted gene editing, we could link a single nucleotide insertion in the polyketide synthase of the trypacidin biosynthetic pathway and reconstitute its production in a nonproducing strain. Thus, we present a CRISPR/Cas9-based tool...... for advanced molecular genetic studies in filamentous fungi, exploiting selectable markers separated from the edited locus....

  6. The effects of processing non-timber forest products and trade partnerships on people's well-being and forest conservation in Amazonian societies.

    Directory of Open Access Journals (Sweden)

    Carla Morsello

    Full Text Available This study evaluated whether processing non-timber forest products (NTFPs and establishing trade partnerships between forest communities and companies enhance the outcomes of NTFP commercialization. In particular, we evaluated whether product processing, partnerships, or their combination was associated with a number of outcomes related to the well-being of forest inhabitants and forest conservation. We based our analyses on ethnographic and quantitative data (i.e., survey and systematic observations gathered at seven communities from five societies of the Brazilian and Bolivian Amazon. Our results indicated that product processing and partnerships do not represent a silver bullet able to improve the results of NTFP commercialization in terms of well-being and conservation indicators. Compared with cases without interventions, households adopting partnerships but not product processing were most often associated with improved economic proxies of well-being (total income, NTFP income, food consumption and gender equality in income. In comparison, the combination of product processing and partnerships was associated with similar outcomes. Unexpectedly, product processing alone was associated with negative outcomes in the economic indicators of well-being. All of the investigated strategies were associated with less time spent in social and cultural activities. With respect to forest conservation, the strategies that included a partnership with or without processing produced similar results: while household deforestation tended to decrease, the hunting impact increased. Processing alone was also associated with higher levels of hunting, though it did not reduce deforestation. Our results indicate that establishing partnerships may enhance the outcomes of NTFP trade in terms of the financial outcomes of local communities, but practitioners need to use caution when adopting the processing strategy and they need to evaluate potential negative results

  7. The effects of processing non-timber forest products and trade partnerships on people's well-being and forest conservation in Amazonian societies.

    Science.gov (United States)

    Morsello, Carla; Ruiz-Mallén, Isabel; Diaz, Maria Dolores Montoya; Reyes-García, Victoria

    2012-01-01

    This study evaluated whether processing non-timber forest products (NTFPs) and establishing trade partnerships between forest communities and companies enhance the outcomes of NTFP commercialization. In particular, we evaluated whether product processing, partnerships, or their combination was associated with a number of outcomes related to the well-being of forest inhabitants and forest conservation. We based our analyses on ethnographic and quantitative data (i.e., survey and systematic observations) gathered at seven communities from five societies of the Brazilian and Bolivian Amazon. Our results indicated that product processing and partnerships do not represent a silver bullet able to improve the results of NTFP commercialization in terms of well-being and conservation indicators. Compared with cases without interventions, households adopting partnerships but not product processing were most often associated with improved economic proxies of well-being (total income, NTFP income, food consumption and gender equality in income). In comparison, the combination of product processing and partnerships was associated with similar outcomes. Unexpectedly, product processing alone was associated with negative outcomes in the economic indicators of well-being. All of the investigated strategies were associated with less time spent in social and cultural activities. With respect to forest conservation, the strategies that included a partnership with or without processing produced similar results: while household deforestation tended to decrease, the hunting impact increased. Processing alone was also associated with higher levels of hunting, though it did not reduce deforestation. Our results indicate that establishing partnerships may enhance the outcomes of NTFP trade in terms of the financial outcomes of local communities, but practitioners need to use caution when adopting the processing strategy and they need to evaluate potential negative results for indicators of

  8. The Effects of Processing Non-Timber Forest Products and Trade Partnerships on People's Well-Being and Forest Conservation in Amazonian Societies

    Science.gov (United States)

    Morsello, Carla; Ruiz-Mallén, Isabel; Diaz, Maria Dolores Montoya; Reyes-García, Victoria

    2012-01-01

    This study evaluated whether processing non-timber forest products (NTFPs) and establishing trade partnerships between forest communities and companies enhance the outcomes of NTFP commercialization. In particular, we evaluated whether product processing, partnerships, or their combination was associated with a number of outcomes related to the well-being of forest inhabitants and forest conservation. We based our analyses on ethnographic and quantitative data (i.e., survey and systematic observations) gathered at seven communities from five societies of the Brazilian and Bolivian Amazon. Our results indicated that product processing and partnerships do not represent a silver bullet able to improve the results of NTFP commercialization in terms of well-being and conservation indicators. Compared with cases without interventions, households adopting partnerships but not product processing were most often associated with improved economic proxies of well-being (total income, NTFP income, food consumption and gender equality in income). In comparison, the combination of product processing and partnerships was associated with similar outcomes. Unexpectedly, product processing alone was associated with negative outcomes in the economic indicators of well-being. All of the investigated strategies were associated with less time spent in social and cultural activities. With respect to forest conservation, the strategies that included a partnership with or without processing produced similar results: while household deforestation tended to decrease, the hunting impact increased. Processing alone was also associated with higher levels of hunting, though it did not reduce deforestation. Our results indicate that establishing partnerships may enhance the outcomes of NTFP trade in terms of the financial outcomes of local communities, but practitioners need to use caution when adopting the processing strategy and they need to evaluate potential negative results for indicators of

  9. Management and Area-wide Evaluation of Water Conservation Zones in Agricultural Catchments for Biomass Production, Water Quality and Food Security

    International Nuclear Information System (INIS)

    2016-04-01

    Global land and water resources are under threat from both the agricultural and urban development to meet increased demand for food and from the resulting degradation of the environment. Poor crop yields due to water stress is one of the main reasons for the prevailing hunger and rural poverty in parts of the world. The Green Revolution of the 1960s and 1970s particularly in Latin America and Asia resulted in increased agricultural production and depended partly on water management. In the future, most food will still need to come from rain-fed agriculture. Water conservation zones in agricultural catchments, particularly in rainfed areas, play an important role in the capture and storage of water and nutrients from farmlands and wider catchments, and help improve crop production in times of need in these areas. Water conservation zones are considered to be an important part of water resource management strategies that have been developed to prevent reservoir siltation, reduce water quality degradation, mitigate flooding, enhance groundwater recharge and provide water for farming. In addition to making crop production possible in dry areas, water conservation zones minimize soil erosion, improve soil moisture status through capillary rise and enhance soil fertility and quality. These water conservation zones include natural and constructed wetlands (including riparian wetlands), farm ponds and riparian buffer zones. The management of water conservation zones has been a challenge due to the poor understanding of the relationship between upstream land use and the functions of these zones and their internal dynamics. Knowledge of sources and sinks of water and redefining water and nutrient budgets for water conservation zones are important for optimizing the capture, storage and use of water and nutrients in agricultural landscapes. The overall objective of this coordinated research project (CRP) was to assess and enhance ecosystem services provided by wetlands, ponds

  10. Exploiting deterministic maintenance opportunity windows created by conservative engineering design rules that result in free time locked into large high-speed coupled production lines with finite buffers

    Directory of Open Access Journals (Sweden)

    Durandt, Casper

    2016-08-01

    Full Text Available Conservative engineering design rules for large serial coupled production processes result in machines having locked-in free time (also called ‘critical downtime’ or ‘maintenance opportunity windows’, which cause idle time if not used. Operators are not able to assess a large production process holistically, and so may not be aware that they form the current bottleneck – or that they have free time available due to interruptions elsewhere. A real-time method is developed to accurately calculate and display free time in location and magnitude, and efficiency improvements are demonstrated in large-scale production runs.

  11. The Bacillus subtilis yaaH Gene Is Transcribed by SigE RNA Polymerase during Sporulation, and Its Product Is Involved in Germination of Spores

    Science.gov (United States)

    Kodama, Takeko; Takamatsu, Hiromu; Asai, Kei; Kobayashi, Kazuo; Ogasawara, Naotake; Watabe, Kazuhito

    1999-01-01

    The expression of 21 novel genes located in the region from dnaA to abrB of the Bacillus subtilis chromosome was analyzed. One of the genes, yaaH, had a predicted promoter sequence conserved among SigE-dependent genes. Northern blot analysis revealed that yaaH mRNA was first detected from 2 h after the cessation of logarithmic growth (T2) of sporulation in wild-type cells and in spoIIIG (SigG−) and spoIVCB (SigK−) mutants but not in spoIIAC (SigF−) and spoIIGAB (SigE−) mutants. The transcription start point was determined by primer extension analysis; the −10 and −35 regions are very similar to the consensus sequences recognized by SigE-containing RNA polymerase. A YaaH-His tag fusion encoded by a plasmid with a predicted promoter for the yaaH gene was produced from T2 of sporulation in a B. subtilis transformant and extracted from mature spores, indicating that the yaaH gene product is a spore protein. Inactivation of the yaaH gene by insertion of an erythromycin resistance gene did not affect vegetative growth or spore resistance to heat, chloroform, and lysozyme. The germination of yaaH mutant spores in a mixture of l-asparagine, d-glucose, d-fructose, and potassium chloride was almost the same as that of wild-type spores, but the mutant spores were defective in l-alanine-stimulated germination. These results suggest that yaaH is a novel gene encoding a spore protein produced in the mother cell compartment from T2 of sporulation and that it is required for the l-alanine-stimulated germination pathway. PMID:10419957

  12. Scarless and sequential gene modification in Pseudomonas using PCR product flanked by short homology regions

    Directory of Open Access Journals (Sweden)

    Liang Rubing

    2010-08-01

    Full Text Available Abstract Background The lambda Red recombination system has been used to inactivate chromosomal genes in various bacteria and fungi. The procedure consists of electroporating a polymerase chain reaction (PCR fragment containing antibiotic cassette flanked by homology regions to the target locus into a strain that can express the lambda Red proteins (Gam, Bet, Exo. Results Here a scarless gene modification strategy based on the Red recombination system has been developed to modify Pseudomonas genome DNA via sequential deletion of multiple targets. This process