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Sample records for conserved recombination patterns

  1. Resonances in dissociative recombination: Trends and patterns

    Energy Technology Data Exchange (ETDEWEB)

    Orel, A E; Ngassam, V; Royal, J [Department of Applied Science, University of California, Davis (United States); Roos, J B; Larson, A, E-mail: aeorel@ucdavis.ed [Department of Theoretical Chemistry, Royal Institute of Technology, Stockholm (Sweden)

    2009-11-15

    In dissociative recombination, the kinetic energy of the incident electron is transferred into excitation of the electrons of the target ion and then into kinetic energy of the fragments. In general, this proceeds via a resonance where the electron is temporarily trapped by the ion, leading to efficient energy transfer. The study of dissociative recombination is the study of these resonances, Rydberg states converging to the ground and excited states of the ion. For a number of systems, we have studied the electronic states involved in dissociative recombination, including the ground and excited states of the ion, the resonant states and the bound Rydberg states of the system, by combining electron scattering calculations with multi-reference configuration interaction quantum chemistry calculations. We will report on trends and patterns in these resonance states. We will discuss studies of dissociative recombination of the rare-gas ions, moving down the periodic table from He{sup +}{sub 2} to Ne{sup +}{sub 2} to Ar{sup +}{sub 2}, where the ground electronic state of the ion is constant, but its polarizability increases. We will also present results on isoelectronic polyatomic systems, such as HCO{sup +} and HCNH{sup +}, as well as the effects of changing the electronic structure slightly such as HCN{sup +}/HNC{sup +} and H{sub 2}CO{sup +}.

  2. Asy2/Mer2: an evolutionarily conserved mediator of meiotic recombination, pairing, and global chromosome compaction.

    Science.gov (United States)

    Tessé, Sophie; Bourbon, Henri-Marc; Debuchy, Robert; Budin, Karine; Dubois, Emeline; Liangran, Zhang; Antoine, Romain; Piolot, Tristan; Kleckner, Nancy; Zickler, Denise; Espagne, Eric

    2017-09-15

    Meiosis is the cellular program by which a diploid cell gives rise to haploid gametes for sexual reproduction. Meiotic progression depends on tight physical and functional coupling of recombination steps at the DNA level with specific organizational features of meiotic-prophase chromosomes. The present study reveals that every step of this coupling is mediated by a single molecule: Asy2/Mer2. We show that Mer2, identified so far only in budding and fission yeasts, is in fact evolutionarily conserved from fungi (Mer2/Rec15/Asy2/Bad42) to plants (PRD3/PAIR1) and mammals (IHO1). In yeasts, Mer2 mediates assembly of recombination-initiation complexes and double-strand breaks (DSBs). This role is conserved in the fungus Sordaria However, functional analysis of 13 mer2 mutants and successive localization of Mer2 to axis, synaptonemal complex (SC), and chromatin revealed, in addition, three further important functions. First, after DSB formation, Mer2 is required for pairing by mediating homolog spatial juxtaposition, with implications for crossover (CO) patterning/interference. Second, Mer2 participates in the transfer/maintenance and release of recombination complexes to/from the SC central region. Third, after completion of recombination, potentially dependent on SUMOylation, Mer2 mediates global chromosome compaction and post-recombination chiasma development. Thus, beyond its role as a recombinosome-axis/SC linker molecule, Mer2 has important functions in relation to basic chromosome structure. © 2017 Tessé et al.; Published by Cold Spring Harbor Laboratory Press.

  3. Estimating energy conservation patterns of Greek households

    International Nuclear Information System (INIS)

    Sardianou, Eleni

    2007-01-01

    This paper develops an empirical model to investigate the main determinants of household energy conservation patterns in Greece employing cross-section data. In the empirical analysis, household energy-conserving choices models are employed, using a discrete and a latent trait variable respectively as a dependent variable. The results show that socio-economic variables such as consumers' income and family size are suitable to explain differences towards energy conservation preferences. In addition, the results suggest that electricity expenditures and age of the respondent are negatively associated with the number of energy-conserving actions that a consumer is willing to adopt. Finally, other variables such as environmental information feedback and consciousness of energy problems are characteristics of the energy-saver consumer. By evaluating consumer's decision-making process with regards to energy conservation measures, we are able to formulate and propose an effective energy conservation framework for Greece. An energy policy framework is among the main prerequisites not only to achieve sustainable development but also to maintain consumers' quality of life

  4. Detecting Recombination Hotspots from Patterns of Linkage Disequilibrium.

    Science.gov (United States)

    Wall, Jeffrey D; Stevison, Laurie S

    2016-08-09

    With recent advances in DNA sequencing technologies, it has become increasingly easy to use whole-genome sequencing of unrelated individuals to assay patterns of linkage disequilibrium (LD) across the genome. One type of analysis that is commonly performed is to estimate local recombination rates and identify recombination hotspots from patterns of LD. One method for detecting recombination hotspots, LDhot, has been used in a handful of species to further our understanding of the basic biology of recombination. For the most part, the effectiveness of this method (e.g., power and false positive rate) is unknown. In this study, we run extensive simulations to compare the effectiveness of three different implementations of LDhot. We find large differences in the power and false positive rates of these different approaches, as well as a strong sensitivity to the window size used (with smaller window sizes leading to more accurate estimation of hotspot locations). We also compared our LDhot simulation results with comparable simulation results obtained from a Bayesian maximum-likelihood approach for identifying hotspots. Surprisingly, we found that the latter computationally intensive approach had substantially lower power over the parameter values considered in our simulations. Copyright © 2016 Wall and Stevison.

  5. Recombination pattern reanalysis of some HIV-1 circulating recombination forms suggest the necessity and difficulty of revision.

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    Lei Jia

    Full Text Available Recombination is one of the major mechanisms underlying the generation of HIV-1 variability. Currently 61 circulating recombinant forms of HIV-1 have been identified. With the development of recombination detection techniques and accumulation of HIV-1 reference stains, more accurate mosaic structures of circulating recombinant forms (CRFs, like CRF04 and CRF06, have undergone repeated analysis and upgrades. Such revisions may also be necessary for other CRFs. Unlike previous studies, whose results are based primarily on a single recombination detection program, the current study was based on multiple recombination analysis, which may have produced more impartial results.Representative references of 3 categories of intersubtype recombinants were selected, including BC recombinants (CRF07 and CRF08, BG recombinants (CRF23 and CRF24, and BF recombinants (CRF38 and CRF44. They were reanalyzed in detail using both the jumping profile hidden Markov model and RDP3.The results indicate that revisions and upgrades are very necessary and the entire re-analysis suggested 2 types of revision: (i length of inserted fragments; and (ii number of inserted fragments. The reanalysis also indicated that determination of small regions of about 200 bases or fewer should be performed with more caution.Results indicated that the involvement of multiple recombination detection programs is very necessary. Additionally, results suggested two major challenges, one involving the difficulty of accurately determining the locations of breakpoints and the second involving identification of small regions of about 200 bases or fewer with greater caution. Both indicate the complexity of HIV-1 recombination. The resolution would depend critically on development of a recombination analysis algorithm, accumulation of HIV-1 stains, and a higher sequencing quality. With the changes in recombination pattern, phylogenetic relationships of some CRFs may also change. All these results may

  6. Broad-scale recombination patterns underlying proper disjunction in humans.

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    Adi Fledel-Alon

    2009-09-01

    Full Text Available Although recombination is essential to the successful completion of human meiosis, it remains unclear how tightly the process is regulated and over what scale. To assess the nature and stringency of constraints on human recombination, we examined crossover patterns in transmissions to viable, non-trisomic offspring, using dense genotyping data collected in a large set of pedigrees. Our analysis supports a requirement for one chiasma per chromosome rather than per arm to ensure proper disjunction, with additional chiasmata occurring in proportion to physical length. The requirement is not absolute, however, as chromosome 21 seems to be frequently transmitted properly in the absence of a chiasma in females, a finding that raises the possibility of a back-up mechanism aiding in its correct segregation. We also found a set of double crossovers in surprisingly close proximity, as expected from a second pathway that is not subject to crossover interference. These findings point to multiple mechanisms that shape the distribution of crossovers, influencing proper disjunction in humans.

  7. Whole-genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine-scale recombination rate variation in birds.

    Science.gov (United States)

    Kawakami, Takeshi; Mugal, Carina F; Suh, Alexander; Nater, Alexander; Burri, Reto; Smeds, Linnéa; Ellegren, Hans

    2017-08-01

    Recombination rate is heterogeneous across the genome of various species and so are genetic diversity and differentiation as a consequence of linked selection. However, we still lack a clear picture of the underlying mechanisms for regulating recombination. Here we estimated fine-scale population recombination rate based on the patterns of linkage disequilibrium across the genomes of multiple populations of two closely related flycatcher species (Ficedula albicollis and F. hypoleuca). This revealed an overall conservation of the recombination landscape between these species at the scale of 200 kb, but we also identified differences in the local rate of recombination despite their recent divergence (recombination rate in a lineage-specific manner, indicating differences in the extent of linked selection between species. We detected 400-3,085 recombination hotspots per population. Location of hotspots was conserved between species, but the intensity of hotspot activity varied between species. Recombination hotspots were primarily associated with CpG islands (CGIs), regardless of whether CGIs were at promoter regions or away from genes. Recombination hotspots were also associated with specific transposable elements (TEs), but this association appears indirect due to shared preferences of the transposition machinery and the recombination machinery for accessible open chromatin regions. Our results suggest that CGIs are a major determinant of the localization of recombination hotspots, and we propose that both the distribution of TEs and fine-scale variation in recombination rate may be associated with the evolution of the epigenetic landscape. © 2017 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

  8. Variation in recombination frequency and distribution across eukaryotes: patterns and processes

    Science.gov (United States)

    Feulner, Philine G. D.; Johnston, Susan E.; Santure, Anna W.; Smadja, Carole M.

    2017-01-01

    Recombination, the exchange of DNA between maternal and paternal chromosomes during meiosis, is an essential feature of sexual reproduction in nearly all multicellular organisms. While the role of recombination in the evolution of sex has received theoretical and empirical attention, less is known about how recombination rate itself evolves and what influence this has on evolutionary processes within sexually reproducing organisms. Here, we explore the patterns of, and processes governing recombination in eukaryotes. We summarize patterns of variation, integrating current knowledge with an analysis of linkage map data in 353 organisms. We then discuss proximate and ultimate processes governing recombination rate variation and consider how these influence evolutionary processes. Genome-wide recombination rates (cM/Mb) can vary more than tenfold across eukaryotes, and there is large variation in the distribution of recombination events across closely related taxa, populations and individuals. We discuss how variation in rate and distribution relates to genome architecture, genetic and epigenetic mechanisms, sex, environmental perturbations and variable selective pressures. There has been great progress in determining the molecular mechanisms governing recombination, and with the continued development of new modelling and empirical approaches, there is now also great opportunity to further our understanding of how and why recombination rate varies. This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’. PMID:29109219

  9. High-Resolution Patterns of Meiotic Recombination across the Human Major Histocompatibility Complex

    Science.gov (United States)

    Cullen, Michael; Perfetto, Stephen P.; Klitz, William; Nelson, George; Carrington, Mary

    2002-01-01

    Definitive characteristics of meiotic recombination events over large (i.e., >1 Mb) segments of the human genome remain obscure, yet they are essential for establishing the haplotypic structure of the genome and for efficient mapping of complex traits. We present a high-resolution map of recombination at the kilobase level across a 3.3-Mb interval encompassing the major histocompatibility complex (MHC). Genotyping of 20,031 single sperm from 12 individuals resulted in the identification and fine mapping of 325 recombinant chromosomes within genomic intervals as small as 7 kb. Several principal characteristics of recombination in this region were observed: (1) rates of recombination can differ significantly between individuals; (2) intense hot spots of recombination occur at least every 0.8 Mb but are not necessarily evenly spaced; (3) distribution in the location of recombination events can differ significantly among individuals; (4) between hot spots, low levels of recombination occur fairly evenly across 100-kb segments, suggesting the presence of warm spots of recombination; and (5) specific sequence motifs associate significantly with recombination distribution. These data provide a plausible model for recombination patterns of the human genome overall. PMID:12297984

  10. Subdominant Outer Membrane Antigens in Anaplasma marginale: Conservation, Antigenicity, and Protective Capacity Using Recombinant Protein.

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    Deirdre R Ducken

    Full Text Available Anaplasma marginale is a tick-borne rickettsial pathogen of cattle with a worldwide distribution. Currently a safe and efficacious vaccine is unavailable. Outer membrane protein (OMP extracts or a defined surface protein complex reproducibly induce protective immunity. However, there are several knowledge gaps limiting progress in vaccine development. First, are these OMPs conserved among the diversity of A. marginale strains circulating in endemic regions? Second, are the most highly conserved outer membrane proteins in the immunogens recognized by immunized and protected animals? Lastly, can this subset of OMPs recognized by antibody from protected vaccinates and conserved among strains recapitulate the protection of outer membrane vaccines? To address the first goal, genes encoding OMPs AM202, AM368, AM854, AM936, AM1041, and AM1096, major subdominant components of the outer membrane, were cloned and sequenced from geographically diverse strains and isolates. AM202, AM936, AM854, and AM1096 share 99.9 to 100% amino acid identity. AM1041 has 97.1 to 100% and AM368 has 98.3 to 99.9% amino acid identity. While all four of the most highly conserved OMPs were recognized by IgG from animals immunized with outer membranes, linked surface protein complexes, or unlinked surface protein complexes and shown to be protected from challenge, the highest titers and consistent recognition among vaccinates were to AM854 and AM936. Consequently, animals were immunized with recombinant AM854 and AM936 and challenged. Recombinant vaccinates and purified outer membrane vaccinates had similar IgG and IgG2 responses to both proteins. However, the recombinant vaccinates developed higher bacteremia after challenge as compared to adjuvant-only controls and outer membrane vaccinates. These results provide the first evidence that vaccination with specific antigens may exacerbate disease. Progressing from the protective capacity of outer membrane formulations to

  11. Gene evolutionary trajectories and GC patterns driven by recombination in Zea mays

    Science.gov (United States)

    Recombination occurring during meiosis is critical for creating genetic variation and plays an essential role in plant evolution. In addition to creating novel gene combinations, recombination can affect genome structure through altering GC patterns. In maize (Zea mays) and other grasses, another in...

  12. Recombiner

    International Nuclear Information System (INIS)

    Kikuchi, Nobuo.

    1983-01-01

    Purpose: To shorten the pre-heating time for a recombiner and obtain a uniform temperature distribution for the charged catalyst layer in a BWR type reactor. Constitution: A pre-heating heater is disposed to the outer periphery of a vessel for a recombiner packed with catalysts for recombining hydrogen and oxygen in gases flowing through a radioactive gaseous wastes processing system. Heat pipes for transmitting the heat applied to said container to the catalyst are disposed vertically and horizontally within the container. Different length of the heat pipes are combined. In this way, pre-heating time for the recombiner before the operation start and before the system switching can be shortened and the uniform pre-heating for the inside of the recombiner is also made possible. Further, heater control in the pre-heating can be carried out effectively and with ease. (Moriyama, K.)

  13. Water use patterns and conservation in households of Wei River Basin, China

    NARCIS (Netherlands)

    Fan, L.; Liu, G.; Wang, F.; Geissen, V.; Ritsema, C.J.

    2013-01-01

    Fully understanding patterns of water use and water conservation among different consumer groups will help in implementing more effective water conservation programs worldwide. Consequently, we investigated water use patterns, water conservation practices, attitudes, and hindrances to water

  14. Recombination patterns reveal information about centromere location on linkage maps

    DEFF Research Database (Denmark)

    Limborg, Morten T.; McKinney, Garrett J.; Seeb, Lisa W.

    2016-01-01

    . mykiss) characterized by low and unevenly distributed recombination – a general feature of male meiosis in many species. Further, a high frequency of double crossovers along chromosome arms in barley reduced resolution for locating centromeric regions on most linkage groups. Despite these limitations...

  15. Recombiner

    International Nuclear Information System (INIS)

    Osumi, Morimichi.

    1979-01-01

    Purpose: To provide a recombiner which is capable of converting hydrogen gas into water by use of high-frequency heating at comparatively low temperatures and is safe and cheap in cost. Constitution: Hydrogen gas is introduced from an outer pipeline to the main structure of a recombiner, and when it passes through the vicinity of the central part of the recombiner, it is reacted with copper oxide (CuO 2 ) heated to a temperature more than 300 0 C by a high-frequency heater, and converted gently into water by reduction operation (2H 2 + CuO 2 → Cu + 2H 2 O). The thus prepared water is exhausted through the outer pipeline to a suppression pool. A part of hydrogen gas which has not been converted completely into water by the reaction and is remaining as hydrogen is recovered through exhaust nozzles and again introduced into the main structure of the recombiner. (Yoshino, Y.)

  16. Recombiner

    International Nuclear Information System (INIS)

    Saalfrank, H.

    1985-01-01

    Air containing hydrogen can be oxidized by heating in a container called a recombiner, in order to avoid the collection of hydrogen. The container is long and a large number of straight heating bars are arranged in parallel in it and they are flanged to a lid. The heating bars are surrounded by tubes, in order to obtain good heat transfer by a narrow annular gap. (orig.) [de

  17. Conservation patterns in different functional sequence categoriesof divergent Drosophila species

    Energy Technology Data Exchange (ETDEWEB)

    Papatsenko, Dmitri; Kislyuk, Andrey; Levine, Michael; Dubchak, Inna

    2005-10-01

    We have explored the distributions of fully conservedungapped blocks in genome-wide pairwise alignments of recently completedspecies of Drosophila: D.yakuba, D.ananassae, D.pseudoobscura, D.virilisand D.mojavensis. Based on these distributions we have found that nearlyevery functional sequence category possesses its own distinctiveconservation pattern, sometimes independent of the overall sequenceconservation level. In the coding and regulatory regions, the ungappedblocks were longer than in introns, UTRs and non-functional sequences. Atthe same time, the blocks in the coding regions carried 3N+2 signaturecharacteristic to synonymic substitutions in the 3rd codon positions.Larger block sizes in transcription regulatory regions can be explainedby the presence of conserved arrays of binding sites for transcriptionfactors. We also have shown that the longest ungapped blocks, or'ultraconserved' sequences, are associated with specific gene groups,including those encoding ion channels and components of the cytoskeleton.We discussed how restrained conservation patterns may help in mappingfunctional sequence categories and improving genomeannotation.

  18. High-resolution recombination patterns in a region of human chromosome 21 measured by sperm typing.

    Directory of Open Access Journals (Sweden)

    Irene Tiemann-Boege

    2006-05-01

    Full Text Available For decades, classical crossover studies and linkage disequilibrium (LD analysis of genomic regions suggested that human meiotic crossovers may not be randomly distributed along chromosomes but are focused instead in "hot spots." Recent sperm typing studies provided data at very high resolution and accuracy that defined the physical limits of a number of hot spots. The data were also used to test whether patterns of LD can predict hot spot locations. These sperm typing studies focused on several small regions of the genome already known or suspected of containing a hot spot based on the presence of LD breakdown or previous experimental evidence of hot spot activity. Comparable data on target regions not specifically chosen using these two criteria is lacking but is needed to make an unbiased test of whether LD data alone can accurately predict active hot spots. We used sperm typing to estimate recombination in 17 almost contiguous ~5 kb intervals spanning 103 kb of human Chromosome 21. We found two intervals that contained new hot spots. The comparison of our data with recombination rates predicted by statistical analyses of LD showed that, overall, the two datasets corresponded well, except for one predicted hot spot that showed little crossing over. This study doubles the experimental data on recombination in men at the highest resolution and accuracy and supports the emerging genome-wide picture that recombination is localized in small regions separated by cold areas. Detailed study of one of the new hot spots revealed a sperm donor with a decrease in recombination intensity at the canonical recombination site but an increase in crossover activity nearby. This unique finding suggests that the position and intensity of hot spots may evolve by means of a concerted mechanism that maintains the overall recombination intensity in the region.

  19. The Relation between Recombination Rate and Patterns of Molecular Evolution and Variation in Drosophila melanogaster

    Science.gov (United States)

    Campos, José L.; Halligan, Daniel L.; Haddrill, Penelope R.; Charlesworth, Brian

    2014-01-01

    Genetic recombination associated with sexual reproduction increases the efficiency of natural selection by reducing the strength of Hill–Robertson interference. Such interference can be caused either by selective sweeps of positively selected alleles or by background selection (BGS) against deleterious mutations. Its consequences can be studied by comparing patterns of molecular evolution and variation in genomic regions with different rates of crossing over. We carried out a comprehensive study of the benefits of recombination in Drosophila melanogaster, both by contrasting five independent genomic regions that lack crossing over with the rest of the genome and by comparing regions with different rates of crossing over, using data on DNA sequence polymorphisms from an African population that is geographically close to the putatively ancestral population for the species, and on sequence divergence from a related species. We observed reductions in sequence diversity in noncrossover (NC) regions that are inconsistent with the effects of hard selective sweeps in the absence of recombination. Overall, the observed patterns suggest that the recombination rate experienced by a gene is positively related to an increase in the efficiency of both positive and purifying selection. The results are consistent with a BGS model with interference among selected sites in NC regions, and joint effects of BGS, selective sweeps, and a past population expansion on variability in regions of the genome that experience crossing over. In such crossover regions, the X chromosome exhibits a higher rate of adaptive protein sequence evolution than the autosomes, implying a Faster-X effect. PMID:24489114

  20. Fish assemblage patterns as a tool to aid conservation in the ...

    African Journals Online (AJOL)

    Fish assemblage patterns as a tool to aid conservation in the Olifants River catchment ... Water SA. Journal Home · ABOUT THIS JOURNAL · Advanced Search · Current ... South Africa has committed to address freshwater conservation at the ...

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

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    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

  2. 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

  3. CRISPR-Cas and Contact-Dependent Secretion Systems Present on Excisable Pathogenicity Islands with Conserved Recombination Modules.

    Science.gov (United States)

    Carpenter, Megan R; Kalburge, Sai S; Borowski, Joseph D; Peters, Molly C; Colwell, Rita R; Boyd, E Fidelma

    2017-05-15

    Pathogenicity islands (PAIs) are mobile integrated genetic elements that contain a diverse range of virulence factors. PAIs integrate into the host chromosome at a tRNA locus that contains their specific bacterial attachment site, attB , via integrase-mediated site-specific recombination generating attL and attR sites. We identified conserved recombination modules (integrases and att sites) previously described in choleragenic Vibrio cholerae PAIs but with novel cargo genes. Clustered regularly interspaced short palindromic repeat (CRISPR)-associated proteins (Cas proteins) and a type VI secretion system (T6SS) gene cluster were identified at the Vibrio pathogenicity island 1 (VPI-1) insertion site in 19 V. cholerae strains and contained the same recombination module. Two divergent type I-F CRISPR-Cas systems were identified, which differed in Cas protein homology and content. The CRISPR repeat sequence was identical among all V. cholerae strains, but the CRISPR spacer sequences and the number of spacers varied. In silico analysis suggests that the CRISPR-Cas systems were active against phages and plasmids. A type III secretion system (T3SS) was present in 12 V. cholerae strains on a 68-kb island inserted at the same tRNA-serine insertion site as VPI-2 and contained the same recombination module. Bioinformatics analysis showed that two divergent T3SSs exist among the strains examined. Both the CRISPR and T3SS islands excised site specifically from the bacterial chromosome as complete units, and the cognate integrases were essential for this excision. These data demonstrated that identical recombination modules that catalyze integration and excision from the chromosome can acquire diverse cargo genes, signifying a novel method of acquisition for both CRISPR-Cas systems and T3SSs. IMPORTANCE This work demonstrated the presence of CRISPR-Cas systems and T3SSs on PAIs. Our work showed that similar recombination modules can associate with different cargo genes and

  4. Patterns of distribution and conservation status of freshwater fishes ...

    African Journals Online (AJOL)

    Hotspots of fish species richness occur in the north-eastern lowveld sectors of South Africa and along the ecotone between the tropical/ subtropical and temperate ... of conservation concern for freshwater fishes is emphasized, and highlights the importance of well-preserved voucher specimens for biodiversity conservation.

  5. Sequence recombination and conservation of Varroa destructor virus-1 and deformed wing virus in field collected honey bees (Apis mellifera.

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    Hui Wang

    Full Text Available We sequenced small (s RNAs from field collected honeybees (Apis mellifera and bumblebees (Bombuspascuorum using the Illumina technology. The sRNA reads were assembled and resulting contigs were used to search for virus homologues in GenBank. Matches with Varroadestructor virus-1 (VDV1 and Deformed wing virus (DWV genomic sequences were obtained for A. mellifera but not B. pascuorum. Further analyses suggested that the prevalent virus population was composed of VDV-1 and a chimera of 5'-DWV-VDV1-DWV-3'. The recombination junctions in the chimera genomes were confirmed by using RT-PCR, cDNA cloning and Sanger sequencing. We then focused on conserved short fragments (CSF, size > 25 nt in the virus genomes by using GenBank sequences and the deep sequencing data obtained in this study. The majority of CSF sites confirmed conservation at both between-species (GenBank sequences and within-population (dataset of this study levels. However, conserved nucleotide positions in the GenBank sequences might be variable at the within-population level. High mutation rates (Pi>10% were observed at a number of sites using the deep sequencing data, suggesting that sequence conservation might not always be maintained at the population level. Virus-host interactions and strategies for developing RNAi treatments against VDV1/DWV infections are discussed.

  6. Global patterns of terrestrial vertebrate diversity and conservation

    Science.gov (United States)

    Jenkins, Clinton N.; Pimm, Stuart L.; Joppa, Lucas N.

    2013-01-01

    Identifying priority areas for biodiversity is essential for directing conservation resources. Fundamentally, we must know where individual species live, which ones are vulnerable, where human actions threaten them, and their levels of protection. As conservation knowledge and threats change, we must reevaluate priorities. We mapped priority areas for vertebrates using newly updated data on >21,000 species of mammals, amphibians, and birds. For each taxon, we identified centers of richness for all species, small-ranged species, and threatened species listed with the International Union for the Conservation of Nature. Importantly, all analyses were at a spatial grain of 10 × 10 km, 100 times finer than previous assessments. This fine scale is a significant methodological improvement, because it brings mapping to scales comparable with regional decisions on where to place protected areas. We also mapped recent species discoveries, because they suggest where as-yet-unknown species might be living. To assess the protection of the priority areas, we calculated the percentage of priority areas within protected areas using the latest data from the World Database of Protected Areas, providing a snapshot of how well the planet’s protected area system encompasses vertebrate biodiversity. Although the priority areas do have more protection than the global average, the level of protection still is insufficient given the importance of these areas for preventing vertebrate extinctions. We also found substantial differences between our identified vertebrate priorities and the leading map of global conservation priorities, the biodiversity hotspots. Our findings suggest a need to reassess the global allocation of conservation resources to reflect today’s improved knowledge of biodiversity and conservation. PMID:23803854

  7. A conserved pattern in plant-mediated interactions between herbivores

    OpenAIRE

    Lu Jing; Robert Christelle A. M.; Lou Yonggen; Erb Matthias

    2016-01-01

    Abstract Plant?mediated interactions between herbivores are important determinants of community structure and plant performance in natural and agricultural systems. Current research suggests that the outcome of the interactions is determined by herbivore and plant identity, which may result in stochastic patterns that impede adaptive evolution and agricultural exploitation. However, few studies have systemically investigated specificity versus general patterns in a given plant system by varyi...

  8. 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

  9. Fine-Scale Recombination Maps of Fungal Plant Pathogens Reveal Dynamic Recombination Landscapes and Intragenic Hotspots.

    Science.gov (United States)

    Stukenbrock, Eva H; Dutheil, Julien Y

    2018-03-01

    Meiotic recombination is an important driver of evolution. Variability in the intensity of recombination across chromosomes can affect sequence composition, nucleotide variation, and rates of adaptation. In many organisms, recombination events are concentrated within short segments termed recombination hotspots. The variation in recombination rate and positions of recombination hotspot can be studied using population genomics data and statistical methods. In this study, we conducted population genomics analyses to address the evolution of recombination in two closely related fungal plant pathogens: the prominent wheat pathogen Zymoseptoria tritici and a sister species infecting wild grasses Z. ardabiliae We specifically addressed whether recombination landscapes, including hotspot positions, are conserved in the two recently diverged species and if recombination contributes to rapid evolution of pathogenicity traits. We conducted a detailed simulation analysis to assess the performance of methods of recombination rate estimation based on patterns of linkage disequilibrium, in particular in the context of high nucleotide diversity. Our analyses reveal overall high recombination rates, a lack of suppressed recombination in centromeres, and significantly lower recombination rates on chromosomes that are known to be accessory. The comparison of the recombination landscapes of the two species reveals a strong correlation of recombination rate at the megabase scale, but little correlation at smaller scales. The recombination landscapes in both pathogen species are dominated by frequent recombination hotspots across the genome including coding regions, suggesting a strong impact of recombination on gene evolution. A significant but small fraction of these hotspots colocalize between the two species, suggesting that hotspot dynamics contribute to the overall pattern of fast evolving recombination in these species. Copyright © 2018 Stukenbrock and Dutheil.

  10. Recombinant Envelope-Proteins with Mutations in the Conserved Fusion Loop Allow Specific Serological Diagnosis of Dengue-Infections.

    Directory of Open Access Journals (Sweden)

    Alexandra Rockstroh

    2015-11-01

    Full Text Available Dengue virus (DENV is a mosquito-borne flavivirus and a major international public health concern in many tropical and sub-tropical areas worldwide. DENV is divided into four major serotypes, and infection with one serotype leads to immunity against the same, but not the other serotypes. The specific diagnosis of DENV-infections via antibody-detection is problematic due to the high degree of cross-reactivity displayed by antibodies against related flaviviruses, such as West Nile virus (WNV, Yellow Fever virus (YFV or Tick-borne encephalitis virus (TBEV. Especially in areas where several flaviviruses co-circulate or in the context of vaccination e.g. against YFV or TBEV, this severely complicates diagnosis and surveillance. Most flavivirus cross-reactive antibodies are produced against the highly conserved fusion loop (FL domain in the viral envelope (E protein. We generated insect-cell derived recombinant E-proteins of the four DENV-serotypes which contain point mutations in the FL domain. By using specific mixtures of these mutant antigens, cross-reactivity against heterologous flaviviruses was strongly reduced, enabling sensitive and specific diagnosis of the DENV-infected serum samples in IgG and IgM-measurements. These results have indications for the development of serological DENV-tests with improved specificity.

  11. Effect of intradermal human recombinant copper-zinc superoxide dismutase on random pattern flaps in rats.

    Science.gov (United States)

    Schein, Ophir; Westreich, Melvyn; Shalom, Avshalom

    2013-09-01

    Studies have focused on enhancing flap viability using superoxide dismutase (SOD), but only a few used SOD from human origin, and most gave the compound systemically. We evaluated the ability of SOD to improve random skin flap survival using human recombinant copper-zinc superoxide dismutase (Hr-CuZnSOD) in variable doses, injected intradermally into the flap. Seventy male Sprague Dawley rats were randomly assigned into 4 groups. Cephalic random pattern flaps were elevated on their backs and intradermal injections of different dosages of Hr-CuZnSOD were given 15 minutes before surgery. Flap survival was evaluated by fluorescein fluorescence. Analysis of variance (ANOVA) and t test statistical analyses were performed. Flap survival in all treated groups was significantly better than in the controls. The beneficial effect of HR-CuZnSOD on flap survival is attained when it is given intradermally into the flap tissue. Theoretically, Hr-CuZnSOD delivered with local anesthetics used in flap elevation may be a valuable clinical tool. Copyright © 2012 Wiley Periodicals, Inc.

  12. Conservation genetics and geographic patterns of genetic variation of the vulnerable officinal herb Fritillaria walujewii (Liliaceae)

    Science.gov (United States)

    Zhihao Su; Borong Pan; Stewart C. Sanderson; Xiaojun Shi; Xiaolong Jiang

    2015-01-01

    The Chinese herb Fritillaria walujewii Regel is an important officinal species that is vulnerable because of over-harvesting. Here, we examined the geographic pattern of genetic variation across the species entire range, to study its evolution process and give implication needed for the conservation. Nine haplotypes were detected on the basis of three chloroplast...

  13. Recombining without Hotspots: A Comprehensive Evolutionary Portrait of Recombination in Two Closely Related Species of Drosophila

    Science.gov (United States)

    Smukowski Heil, Caiti S.; Ellison, Chris; Dubin, Matthew; Noor, Mohamed A.F.

    2015-01-01

    Meiotic recombination rate varies across the genome within and between individuals, populations, and species in virtually all taxa studied. In almost every species, this variation takes the form of discrete recombination hotspots, determined in some mammals by a protein called PRDM9. Hotspots and their determinants have a profound effect on the genomic landscape, and share certain features that extend across the tree of life. Drosophila, in contrast, are anomalous in their absence of hotspots, PRDM9, and other species-specific differences in the determination of recombination. To better understand the evolution of meiosis and general patterns of recombination across diverse taxa, we present a truly comprehensive portrait of recombination across time, combining recently published cross-based contemporary recombination estimates from each of two sister species with newly obtained linkage-disequilibrium-based historic estimates of recombination from both of these species. Using Drosophila pseudoobscura and Drosophila miranda as a model system, we compare recombination rate between species at multiple scales, and we suggest that Drosophila replicate the pattern seen in human–chimpanzee in which recombination rate is conserved at broad scales. We also find evidence of a species-wide recombination modifier(s), resulting in both a present and historic genome-wide elevation of recombination rates in D. miranda, and identify broad scale effects on recombination from the presence of an inversion. Finally, we reveal an unprecedented view of the distribution of recombination in D. pseudoobscura, illustrating patterns of linked selection and where recombination is taking place. Overall, by combining these estimation approaches, we highlight key similarities and differences in recombination between Drosophila and other organisms. PMID:26430062

  14. Recombining without Hotspots: A Comprehensive Evolutionary Portrait of Recombination in Two Closely Related Species of Drosophila.

    Science.gov (United States)

    Smukowski Heil, Caiti S; Ellison, Chris; Dubin, Matthew; Noor, Mohamed A F

    2015-10-01

    Meiotic recombination rate varies across the genome within and between individuals, populations, and species in virtually all taxa studied. In almost every species, this variation takes the form of discrete recombination hotspots, determined in some mammals by a protein called PRDM9. Hotspots and their determinants have a profound effect on the genomic landscape, and share certain features that extend across the tree of life. Drosophila, in contrast, are anomalous in their absence of hotspots, PRDM9, and other species-specific differences in the determination of recombination. To better understand the evolution of meiosis and general patterns of recombination across diverse taxa, we present a truly comprehensive portrait of recombination across time, combining recently published cross-based contemporary recombination estimates from each of two sister species with newly obtained linkage-disequilibrium-based historic estimates of recombination from both of these species. Using Drosophila pseudoobscura and Drosophila miranda as a model system, we compare recombination rate between species at multiple scales, and we suggest that Drosophila replicate the pattern seen in human-chimpanzee in which recombination rate is conserved at broad scales. We also find evidence of a species-wide recombination modifier(s), resulting in both a present and historic genome-wide elevation of recombination rates in D. miranda, and identify broad scale effects on recombination from the presence of an inversion. Finally, we reveal an unprecedented view of the distribution of recombination in D. pseudoobscura, illustrating patterns of linked selection and where recombination is taking place. Overall, by combining these estimation approaches, we highlight key similarities and differences in recombination between Drosophila and other organisms. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  15. Closely related glycosylation patterns of recombinant human IL-2 expressed in a CHO cell line and natural IL-2

    International Nuclear Information System (INIS)

    Vita, N.; Magazin, M.; Marchese, E.; Lupker, J.; Ferrara, P.

    1990-01-01

    We report here the study of the glycosylation pattern of human recombinant (r) IL2 expressed in a Chinese hamster ovary (CHO) cell line. The human rIL2 secreted by this high-producing recombinant CHO cell line was metabolically radiolabelled with [35S]-methionine, or with [3H]-glucosamine and [3H]-galactose, purified to homogeneity, and then characterized. The electrophoretic analysis of the [35S]-methionine-labelled proteins present in the culture medium of the CHO cell line showed that the rIL2 represents approximately 12% of the total secreted proteins. Furthermore, pulse-chase experiments showed that the glycosylated rIL2 is synthesized and secreted within 30 min. The point of attachment and the structure of the carbohydrate moiety of the rIL2 was determined by: amino-terminal sequencing and fingerprint analysis of the 3H-labelled rIL2, mass spectroscopy of the amino-terminal tryptic octapeptide, and carbohydrate analysis after enzymatic (Vibrio cholerae neuraminidase and Aspergillus oryzae beta-galactosidase) or sulfuric acid hydrolysis. The results indicate that the recombinant protein possesses a sugar moiety O-linked to the threonine residue at position 3 of the polypeptide chain, and that sialic acid, galactose and N-acetyl galactosamine are components of this carbohydrate moiety. Taken together these results suggest that the recombinant molecule is identical to natural IL2

  16. 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;

  17. 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,…

  18. Energy pattern and conservations of condiment produced from soybean (Glycine max)

    OpenAIRE

    Ismaila B. Anjorin; Rahman Akinoso; Mayowa S. Sanusi

    2018-01-01

    Energy being one of the largest operating expenses in most organizations especially manufacturing and processing industries leading to considerable scope for energy conservation and hence cost. Information on energy utilization and conservation pattern were obtained based on time taken, number of person involved and sources of energy using standard energy equations. A total of 445.40 ± 17.32MJkg-1 where thermal energy (420MJ ≈ 94%) and manual energy (25.40MJ ≈ 6%) were the only forms of energ...

  19. Pressure for Pattern-Specific Intertypic Recombination between Sabin Polioviruses: Evolutionary Implications.

    Science.gov (United States)

    Korotkova, Ekaterina; Laassri, Majid; Zagorodnyaya, Tatiana; Petrovskaya, Svetlana; Rodionova, Elvira; Cherkasova, Elena; Gmyl, Anatoly; Ivanova, Olga E; Eremeeva, Tatyana P; Lipskaya, Galina Y; Agol, Vadim I; Chumakov, Konstantin

    2017-11-22

    Complete genomic sequences of a non-redundant set of 70 recombinants between three serotypes of attenuated Sabin polioviruses as well as location (based on partial sequencing) of crossover sites of 28 additional recombinants were determined and compared with the previously published data. It is demonstrated that the genomes of Sabin viruses contain distinct strain-specific segments that are eliminated by recombination. The presumed low fitness of these segments could be linked to mutations acquired upon derivation of the vaccine strains and/or may have been present in wild-type parents of Sabin viruses. These "weak" segments contribute to the propensity of these viruses to recombine with each other and with other enteroviruses as well as determine the choice of crossover sites. The knowledge of location of such segments opens additional possibilities for the design of more genetically stable and/or more attenuated variants, i.e., candidates for new oral polio vaccines. The results also suggest that the genome of wild polioviruses, and, by generalization, of other RNA viruses, may harbor hidden low-fitness segments that can be readily eliminated only by recombination.

  20. Pressure for Pattern-Specific Intertypic Recombination between Sabin Polioviruses: Evolutionary Implications

    Directory of Open Access Journals (Sweden)

    Ekaterina Korotkova

    2017-11-01

    Full Text Available Complete genomic sequences of a non-redundant set of 70 recombinants between three serotypes of attenuated Sabin polioviruses as well as location (based on partial sequencing of crossover sites of 28 additional recombinants were determined and compared with the previously published data. It is demonstrated that the genomes of Sabin viruses contain distinct strain-specific segments that are eliminated by recombination. The presumed low fitness of these segments could be linked to mutations acquired upon derivation of the vaccine strains and/or may have been present in wild-type parents of Sabin viruses. These “weak” segments contribute to the propensity of these viruses to recombine with each other and with other enteroviruses as well as determine the choice of crossover sites. The knowledge of location of such segments opens additional possibilities for the design of more genetically stable and/or more attenuated variants, i.e., candidates for new oral polio vaccines. The results also suggest that the genome of wild polioviruses, and, by generalization, of other RNA viruses, may harbor hidden low-fitness segments that can be readily eliminated only by recombination.

  1. Turing patterns in parabolic systems of conservation laws and numerically observed stability of periodic waves

    Science.gov (United States)

    Barker, Blake; Jung, Soyeun; Zumbrun, Kevin

    2018-03-01

    Turing patterns on unbounded domains have been widely studied in systems of reaction-diffusion equations. However, up to now, they have not been studied for systems of conservation laws. Here, we (i) derive conditions for Turing instability in conservation laws and (ii) use these conditions to find families of periodic solutions bifurcating from uniform states, numerically continuing these families into the large-amplitude regime. For the examples studied, numerical stability analysis suggests that stable periodic waves can emerge either from supercritical Turing bifurcations or, via secondary bifurcation as amplitude is increased, from subcritical Turing bifurcations. This answers in the affirmative a question of Oh-Zumbrun whether stable periodic solutions of conservation laws can occur. Determination of a full small-amplitude stability diagram - specifically, determination of rigorous Eckhaus-type stability conditions - remains an interesting open problem.

  2. Conserved Genetic Architecture Underlying Individual Recombination Rate Variation in a Wild Population of Soay Sheep (Ovis aries).

    Science.gov (United States)

    Johnston, Susan E; Bérénos, Camillo; Slate, Jon; Pemberton, Josephine M

    2016-05-01

    Meiotic recombination breaks down linkage disequilibrium (LD) and forms new haplotypes, meaning that it is an important driver of diversity in eukaryotic genomes. Understanding the causes of variation in recombination rate is important in interpreting and predicting evolutionary phenomena and in understanding the potential of a population to respond to selection. However, despite attention in model systems, there remains little data on how recombination rate varies at the individual level in natural populations. Here we used extensive pedigree and high-density SNP information in a wild population of Soay sheep (Ovis aries) to investigate the genetic architecture of individual autosomal recombination rates. Individual rates were high relative to other mammal systems and were higher in males than in females (autosomal map lengths of 3748 and 2860 cM, respectively). The heritability of autosomal recombination rate was low but significant in both sexes (h(2) = 0.16 and 0.12 in females and males, respectively). In females, 46.7% of the heritable variation was explained by a subtelomeric region on chromosome 6; a genome-wide association study showed the strongest associations at locus RNF212, with further associations observed at a nearby ∼374-kb region of complete LD containing three additional candidate loci, CPLX1, GAK, and PCGF3 A second region on chromosome 7 containing REC8 and RNF212B explained 26.2% of the heritable variation in recombination rate in both sexes. Comparative analyses with 40 other sheep breeds showed that haplotypes associated with recombination rates are both old and globally distributed. Both regions have been implicated in rate variation in mice, cattle, and humans, suggesting a common genetic architecture of recombination rate variation in mammals. Copyright © 2016 by the Genetics Society of America.

  3. Patterns of Assemblage Structure Indicate a Broader Conservation Potential of Focal Amphibians for Pond Management.

    Directory of Open Access Journals (Sweden)

    Elin Soomets

    Full Text Available Small freshwater ponds host diverse and vulnerable biotic assemblages but relatively few conspicuous, specially protected taxa. In Europe, the amphibians Triturus cristatus and Pelobates fuscus are among a few species whose populations have been successfully restored using pond restoration and management activities at the landscape scale. In this study, we explored whether the ponds constructed for those two target species have wider conservation significance, particularly for other species of conservation concern. We recorded the occurrence of amphibians and selected aquatic macro-invertebrates (dragonflies; damselflies; diving beetles; water scavenger beetles in 66 ponds specially constructed for amphibians (up to 8 years post construction and, for comparison, in 100 man-made ponds (created by local people for cattle or garden watering, peat excavation, etc. and 65 natural ponds in Estonia. We analysed nestedness of the species assemblages and its dependence on the environment, and described the co-occurrence patterns between the target amphibians and other aquatic species. The assemblages in all ponds were significantly nested, but the environmental determinants of nestedness and co-occurrence of particular species differed among pond types. Constructed ponds were most species-rich irrespective of the presence of the target species; however, T. cristatus was frequent in those ponds and rare elsewhere, and it showed nested patterns in every type of pond. We thus conclude that pond construction for the protected amphibians can serve broader habitat conservation aims in the short term. However, the heterogeneity and inconsistent presence of species of conservation concern observed in other types of ponds implies that long-term perspectives on pond management require more explicit consideration of different habitat and biodiversity values. We also highlight nestedness analysis as a tool that can be used for the practical task of selecting focal

  4. Contrasted patterns of crossover and non-crossover at Arabidopsis thaliana meiotic recombination hotspots.

    Directory of Open Access Journals (Sweden)

    Jan Drouaud

    2013-11-01

    Full Text Available The vast majority of meiotic recombination events (crossovers (COs and non-crossovers (NCOs cluster in narrow hotspots surrounded by large regions devoid of recombinational activity. Here, using a new molecular approach in plants, called "pollen-typing", we detected and characterized hundreds of CO and NCO molecules in two different hotspot regions in Arabidopsis thaliana. This analysis revealed that COs are concentrated in regions of a few kilobases where their rates reach up to 50 times the genome average. The hotspots themselves tend to cluster in regions less than 8 kilobases in size with overlapping CO distribution. Non-crossover (NCO events also occurred in the two hotspots but at very different levels (local CO/NCO ratios of 1/1 and 30/1 and their track lengths were quite small (a few hundred base pairs. We also showed that the ZMM protein MSH4 plays a role in CO formation and somewhat unexpectedly we also found that it is involved in the generation of NCOs but with a different level of effect. Finally, factors acting in cis and in trans appear to shape the rate and distribution of COs at meiotic recombination hotspots.

  5. Regulation of Meiotic Recombination

    Energy Technology Data Exchange (ETDEWEB)

    Gregory p. Copenhaver

    2011-11-09

    Meiotic recombination results in the heritable rearrangement of DNA, primarily through reciprocal exchange between homologous chromosome or gene conversion. In plants these events are critical for ensuring proper chromosome segregation, facilitating DNA repair and providing a basis for genetic diversity. Understanding this fundamental biological mechanism will directly facilitate trait mapping, conventional plant breeding, and development of genetic engineering techniques that will help support the responsible production and conversion of renewable resources for fuels, chemicals, and the conservation of energy (1-3). Substantial progress has been made in understanding the basal recombination machinery, much of which is conserved in organisms as diverse as yeast, plants and mammals (4, 5). Significantly less is known about the factors that regulate how often and where that basal machinery acts on higher eukaryotic chromosomes. One important mechanism for regulating the frequency and distribution of meiotic recombination is crossover interference - or the ability of one recombination event to influence nearby events. The MUS81 gene is thought to play an important role in regulating the influence of interference on crossing over. The immediate goals of this project are to use reverse genetics to identify mutants in two putative MUS81 homologs in the model plant Arabidopsis thaliana, characterize those mutants and initiate a novel forward genetic screen for additional regulators of meiotic recombination. The long-term goal of the project is to understand how meiotic recombination is regulated in higher eukaryotes with an emphasis on the molecular basis of crossover interference. The ability to monitor recombination in all four meiotic products (tetrad analysis) has been a powerful tool in the arsenal of yeast geneticists. Previously, the qrt mutant of Arabidopsis, which causes the four pollen products of male meiosis to remain attached, was developed as a facile system

  6. 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

  7. 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

  8. A Simple Predictive Enhancer Syntax for Hindbrain Patterning Is Conserved in Vertebrate Genomes.

    Directory of Open Access Journals (Sweden)

    Joseph Grice

    Full Text Available Determining the function of regulatory elements is fundamental for our understanding of development, disease and evolution. However, the sequence features that mediate these functions are often unclear and the prediction of tissue-specific expression patterns from sequence alone is non-trivial. Previous functional studies have demonstrated a link between PBX-HOX and MEIS/PREP binding interactions and hindbrain enhancer activity, but the defining grammar of these sites, if any exists, has remained elusive.Here, we identify a shared sequence signature (syntax within a heterogeneous set of conserved vertebrate hindbrain enhancers composed of spatially co-occurring PBX-HOX and MEIS/PREP transcription factor binding motifs. We use this syntax to accurately predict hindbrain enhancers in 89% of cases (67/75 predicted elements from a set of conserved non-coding elements (CNEs. Furthermore, mutagenesis of the sites abolishes activity or generates ectopic expression, demonstrating their requirement for segmentally restricted enhancer activity in the hindbrain. We refine and use our syntax to predict over 3,000 hindbrain enhancers across the human genome. These sequences tend to be located near developmental transcription factors and are enriched in known hindbrain activating elements, demonstrating the predictive power of this simple model.Our findings support the theory that hundreds of CNEs, and perhaps thousands of regions across the human genome, function to coordinate gene expression in the developing hindbrain. We speculate that deeply conserved sequences of this kind contributed to the co-option of new genes into the hindbrain gene regulatory network during early vertebrate evolution by linking patterns of hox expression to downstream genes involved in segmentation and patterning, and evolutionarily newer instances may have continued to contribute to lineage-specific elaboration of the hindbrain.

  9. IMPLICATIONS OF MATING PATTERNS FOR CONSERVATION OF THE ENDANGERED PLANT ERIOGONUM OVALIFOLIUM VAR. VINEUM (POLYGONACEAE). (R826102)

    Science.gov (United States)

    Mating patterns have direct application to: conservation because of their influence on structuring genetic diversity within and among populations and on maintaining that diversity over time. We measured population and family outcrossing rates, biparental inbreeding correlation of...

  10. Making Drosophila lineage-restricted drivers via patterned recombination in neuroblasts.

    Science.gov (United States)

    Awasaki, Takeshi; Kao, Chih-Fei; Lee, Ying-Jou; Yang, Ching-Po; Huang, Yaling; Pfeiffer, Barret D; Luan, Haojiang; Jing, Xiaotang; Huang, Yu-Fen; He, Yisheng; Schroeder, Mark David; Kuzin, Alexander; Brody, Thomas; Zugates, Christopher T; Odenwald, Ward F; Lee, Tzumin

    2014-04-01

    The Drosophila cerebrum originates from about 100 neuroblasts per hemisphere, with each neuroblast producing a characteristic set of neurons. Neurons from a neuroblast are often so diverse that many neuron types remain unexplored. We developed new genetic tools that target neuroblasts and their diverse descendants, increasing our ability to study fly brain structure and development. Common enhancer-based drivers label neurons on the basis of terminal identities rather than origins, which provides limited labeling in the heterogeneous neuronal lineages. We successfully converted conventional drivers that are temporarily expressed in neuroblasts, into drivers expressed in all subsequent neuroblast progeny. One technique involves immortalizing GAL4 expression in neuroblasts and their descendants. Another depends on loss of the GAL4 repressor, GAL80, from neuroblasts during early neurogenesis. Furthermore, we expanded the diversity of MARCM-based reagents and established another site-specific mitotic recombination system. Our transgenic tools can be combined to map individual neurons in specific lineages of various genotypes.

  11. The land use patterns for soil organic carbon conservation at Endanga watershed Southeast Sulawesi Indonesia

    Science.gov (United States)

    Leomo, S.; Ginting, S.; Sabaruddin, L.; Tufaila, M.; Muhidin

    2018-02-01

    The Endanga basin is one part of the Konaweeha watershed located in South Konawe, Southeast Sulawesi Province, covering an area of 1,353.67 hectares. The land use patterns in Endanga Watershed contained forests, shrubs, oil palm plantations, pepper fields, and cultivated fields of field rice, corn monoculture and intercropping of peanuts and corn. This watershed needs serious attention because most of its territory is on slope of 15-40%, with erosion hazard levels (EHL) varying from mild erosion to severe erosion. The loss of organic carbon (C-organic) soil is measured from the soil carried along with the surface stream and into the reservoir on various land uses. The result measurement of C-organic soil loss on forest land use is 14.02 kg ha-1, shrubs land 22.71 kg ha-1, oil palm 151.32 kg ha-1, pepper garden 93.69 kg ha-1, field rice 313.80 kg.ha-1, monoculture of maize 142.44 kg ha-1, intercropped maize and corn 51.10 kg ha-1 and open land 1,909.16 kg ha-1. The forest land and shrubs is best in conserving soil C-organic, but economically unfavorable for the community, so land use pattern for intercropping and pepper plantation can be used for soil C-organic conservation

  12. Diversity distribution patterns of Chinese endemic seed plant species and their implications for conservation planning

    Science.gov (United States)

    Huang, Jihong; Huang, Jianhua; Lu, Xinghui; Ma, Keping

    2016-01-01

    Endemism is an important concept in biogeography and biodiversity conservation. China is one of the richest countries in biodiversity, with very high levels of plant endemism. In this study, we analysed the distribution patterns of diversity, the degree of differentiation, and the endemicity of Chinese endemic seed plants using the floristic unit as a basic spatial analysis unit and 11 indices. The analysis was based on distribution data of 24,951 native seed plant species (excluding subspecies and varieties) and 12,980 Chinese endemic seed plant species, which were sourced from both specimen records and published references. The distribution patterns of Chinese endemic flora were generally consistent but disproportionate across China for diversity, degree of differentiation and endemicity. The South Hengduan Mountains Subregion had the highest values for all indices. At the regional level, both the Hengduan Mountains and the Central China regions were highest in diversity and degrees of differentiation. However, both the rate of local endemic to native species and the rate of local to Chinese endemic species were highest in the Taiwan Region and the South Taiwan Region. The Hengduan Mountains Region and the Central China Region are two key conservation priority areas for Chinese endemic seed plants. PMID:27658845

  13. Reconsidering residency: Characterization and conservation implications of complex migratory patterns of shortnose sturgeon (Acispenser brevirostrum)

    Science.gov (United States)

    Dionne, Phillip E.; Zydlewski, Gayle B.; Kinnison, Michael T.; Zydlewski, Joseph D.; Wippelhauser, Gail S.

    2013-01-01

    Efforts to conserve endangered species usually involve attempts to define and manage threats at the appropriate scale of population processes. In some species that scale is localized; in others, dispersal and migration link demic units within larger metapopulations. Current conservation strategies for endangered shortnose sturgeon (Acipenser brevirostrum) assume the species is river resident, with little to no movement between rivers. However we have found that shortnose sturgeon travel more than 130 km through coastal waters between the largest rivers in Maine. Indeed, acoustic telemetry shows that shortnose sturgeon enter six out of the seven acoustically monitored rivers we have monitored, with over 70% of tagged individuals undertaking coastal migrations between river systems. Four migration patterns were identified for shortnose sturgeon inhabiting the Penobscot River, Maine: river resident (28%), spring coastal emigrant (24%), fall coastal emigrant (33%), and summer coastal emigrant (15%). No shortnose sturgeon classified as maturing female exhibited a resident pattern, indicating differential migration. Traditional river-specific assessment and management of shortnose sturgeon could be better characterized using a broader metapopulation scale, at least in the Gulf of Maine, that accounts for diverse migratory strategies and the importance of migratory corridors as critical habitat.

  14. The first “lost year” of Mediterranean sea turtles: dispersal patterns indicate subregional management units for conservation

    DEFF Research Database (Denmark)

    Casale, Paolo; Mariani, Patrizio

    2014-01-01

    Identifying highly frequented areas is a priority for sea turtle conservation, and the distribution of young individuals in open waters represents a major knowledge gap due to methodological biases. The drift of hatchlings from 38 loggerhead and 10 green turtle nesting sites in the Mediterranean......-scale international approach. In-water studies in specific zones are identified as a research priority for improving the current knowledge and inform conservation plans....... The Levantine zone may be particularly key for the conservation of the Mediterranean populations of both species, since it may host the highest concentration of individuals. Subregional management units identified by dispersal patterns may facilitate turtle conservation through a relatively small...

  15. Multilocus sequence analysis of nectar pseudomonads reveals high genetic diversity and contrasting recombination patterns.

    Science.gov (United States)

    Alvarez-Pérez, Sergio; de Vega, Clara; Herrera, Carlos M

    2013-01-01

    The genetic and evolutionary relationships among floral nectar-dwelling Pseudomonas 'sensu stricto' isolates associated to South African and Mediterranean plants were investigated by multilocus sequence analysis (MLSA) of four core housekeeping genes (rrs, gyrB, rpoB and rpoD). A total of 35 different sequence types were found for the 38 nectar bacterial isolates characterised. Phylogenetic analyses resulted in the identification of three main clades [nectar groups (NGs) 1, 2 and 3] of nectar pseudomonads, which were closely related to five intrageneric groups: Pseudomonas oryzihabitans (NG 1); P. fluorescens, P. lutea and P. syringae (NG 2); and P. rhizosphaerae (NG 3). Linkage disequilibrium analysis pointed to a mostly clonal population structure, even when the analysis was restricted to isolates from the same floristic region or belonging to the same NG. Nevertheless, signatures of recombination were observed for NG 3, which exclusively included isolates retrieved from the floral nectar of insect-pollinated Mediterranean plants. In contrast, the other two NGs comprised both South African and Mediterranean isolates. Analyses relating diversification to floristic region and pollinator type revealed that there has been more unique evolution of the nectar pseudomonads within the Mediterranean region than would be expected by chance. This is the first work analysing the sequence of multiple loci to reveal geno- and ecotypes of nectar bacteria.

  16. Multilocus Sequence Analysis of Nectar Pseudomonads Reveals High Genetic Diversity and Contrasting Recombination Patterns

    Science.gov (United States)

    Álvarez-Pérez, Sergio; de Vega, Clara; Herrera, Carlos M.

    2013-01-01

    The genetic and evolutionary relationships among floral nectar-dwelling Pseudomonas ‘sensu stricto’ isolates associated to South African and Mediterranean plants were investigated by multilocus sequence analysis (MLSA) of four core housekeeping genes (rrs, gyrB, rpoB and rpoD). A total of 35 different sequence types were found for the 38 nectar bacterial isolates characterised. Phylogenetic analyses resulted in the identification of three main clades [nectar groups (NGs) 1, 2 and 3] of nectar pseudomonads, which were closely related to five intrageneric groups: Pseudomonas oryzihabitans (NG 1); P. fluorescens, P. lutea and P. syringae (NG 2); and P. rhizosphaerae (NG 3). Linkage disequilibrium analysis pointed to a mostly clonal population structure, even when the analysis was restricted to isolates from the same floristic region or belonging to the same NG. Nevertheless, signatures of recombination were observed for NG 3, which exclusively included isolates retrieved from the floral nectar of insect-pollinated Mediterranean plants. In contrast, the other two NGs comprised both South African and Mediterranean isolates. Analyses relating diversification to floristic region and pollinator type revealed that there has been more unique evolution of the nectar pseudomonads within the Mediterranean region than would be expected by chance. This is the first work analysing the sequence of multiple loci to reveal geno- and ecotypes of nectar bacteria. PMID:24116076

  17. Molecular Evolution at a Meiosis Gene Mediates Species Differences in the Rate and Patterning of Recombination.

    Science.gov (United States)

    Brand, Cara L; Cattani, M Victoria; Kingan, Sarah B; Landeen, Emily L; Presgraves, Daven C

    2018-04-23

    Crossing over between homologous chromosomes during meiosis repairs programmed DNA double-strand breaks, ensures proper segregation at meiosis I [1], shapes the genomic distribution of nucleotide variability in populations, and enhances the efficacy of natural selection among genetically linked sites [2]. Between closely related Drosophila species, large differences exist in the rate and chromosomal distribution of crossing over. Little, however, is known about the molecular genetic changes or population genetic forces that mediate evolved differences in recombination between species [3, 4]. Here, we show that a meiosis gene with a history of rapid evolution acts as a trans-acting modifier of species differences in crossing over. In transgenic flies, the dicistronic gene, mei-217/mei-218, recapitulates a large part of the species differences in the rate and chromosomal distribution of crossing over. These phenotypic differences appear to result from changes in protein sequence not gene expression. Our population genetics analyses show that the protein-coding sequence of mei-218, but not mei-217, has a history of recurrent positive natural selection. By modulating the intensity of centromeric and telomeric suppression of crossing over, evolution at mei-217/-218 has incidentally shaped gross differences in the chromosomal distribution of nucleotide variability between species. We speculate that recurrent bouts of adaptive evolution at mei-217/-218 might reflect a history of coevolution with selfish genetic elements. Copyright © 2018 Elsevier Ltd. All rights reserved.

  18. Energy consumption and conservation patterns in Canadian households. Summary report. Habitudes de consommation et de conservation de l'energie dans les foyers Canadiens. Resume

    Energy Technology Data Exchange (ETDEWEB)

    McDougall, G.H.G.; Ritchie, J.R.B.; Claxton, J.D.

    1978-01-01

    To examine the consumer behavior sector of energy demand patterns in Canada, this report undertook to identify major groupings of households based on energy consumption profiles and energy values, to relate these groupings to situational and demographic factors, and to initiate a comparative analysis of the receptivity of the major groupings to alternative energy conservation policy proposals. Data were collected from household surveys and energy suppliers. Householders were asked about their attitudes to energy conservation and energy policy, and profiles of energy consumption patterns of typical households were identified. To aid in evaluating the research, households were classified according to their levels of in-home energy consumption and automobile gasoline consumption. The findings indicated a range of lifestyles highly interrelated in terms of levels of energy consumption, ownership of energy-consuming products, knowledge and concern for energy issues, willingness to cut back energy consumption, and preferences for alternative conservation policies. The study has shown that most consumers are not very aware of the energy problem, do not see conservation as a serious need, and are unlikely to accept major policy interventions that result in major changes in energy supplies and current lifestyles. A number of recommendations are made as to policies, and their possible impact, to conserve household energy. 8 refs. 11 tabs.

  19. Energy consumption and conservation patterns in Canadian households. Summary report. Habitudes de consommation et de conservation de l'energie dans les foyers Canadiens. Resume

    Energy Technology Data Exchange (ETDEWEB)

    McDougall, G H.G.; Ritchie, J R.B.; Claxton, J D

    1978-01-01

    To examine the consumer behavior sector of energy demand patterns in Canada, this report undertook to identify major groupings of households based on energy consumption profiles and energy values, to relate these groupings to situational and demographic factors, and to initiate a comparative analysis of the receptivity of the major groupings to alternative energy conservation policy proposals. Data were collected from household surveys and energy suppliers. Householders were asked about their attitudes to energy conservation and energy policy, and profiles of energy consumption patterns of typical households were identified. To aid in evaluating the research, households were classified according to their levels of in-home energy consumption and automobile gasoline consumption. The findings indicated a range of lifestyles highly interrelated in terms of levels of energy consumption, ownership of energy-consuming products, knowledge and concern for energy issues, willingness to cut back energy consumption, and preferences for alternative conservation policies. The study has shown that most consumers are not very aware of the energy problem, do not see conservation as a serious need, and are unlikely to accept major policy interventions that result in major changes in energy supplies and current lifestyles. A number of recommendations are made as to policies, and their possible impact, to conserve household energy. 8 refs. 11 tabs.

  20. A recombination point is conserved in the mitochondrial genome of higher plant species and located downstream from the cox2 pseudogene in Solanum tuberosum L.

    Directory of Open Access Journals (Sweden)

    Susely F.S. Tada

    2006-01-01

    Full Text Available The potato (Solanum tuberosum L. mitochondrial cox3/sdh4/pseudo-cox2 gene cluster has previously been identified by heterologous hybridization using a Marchantia polymorpha sdh4 probe. In our present study we used Southern blotting using sdh4 and cox2 probes to show that the sdh4 and cox2 genes are clustered in the mitochondria of potato, soybean and pea. Northern blotting revealed cotranscription of sdh4 and cox2 in potato but not in cauliflower, indicating that these genes are not clustered in cauliflower. A putative recombination point was detected downstream of the cox2 pseudogene (pseudo-cox2 in potato mitochondrial DNA (mtDNA. This sequence corresponds to a 32 bp sequence which appears to be well-conserved and is adjacent to the terminals of some mitochondrial genes in Citrullus lanatus, Beta vulgaris and Arabidopsis thaliana and is probably involved in the genic rearrangements. It is possible the potato mtDNA pseudo-cox2 gene was generated by recombination during evolution in the same way as that of several other mitochondrial genes and remains as an inactive partial copy of the functional cox2 which was also detected in potato mtDNA.

  1. Identification and conservation application of signal, noise, and taxonomic effects in diversity patterns

    Directory of Open Access Journals (Sweden)

    Fleishman, E.

    2005-01-01

    Full Text Available Ongoing research on butterflies and birds in the Great Basin has identified biogeographic patterns while elucidating how dynamic measures of diversity (species richness and turnover affect inferences for conservation planning and adaptive management. Nested subsets analyses suggested that processes influencing predictability of assemblage composition differ among taxonomic groups, and the relative importance of those processes may vary spatially within a taxonomic group. There may be a time lag between deterministic environmental changes and a detectable faunal response, even for taxonomic groups that are known to be sensitive to changes in climate and land cover. Measures of beta diversity were sensitive to correlations between sampling resolution and local environmental heterogeneity. Temporal and spatial variation in species composition indicated that spatially extensive sampling is more effective for drawing inferences about biodiversity responses to environmental change than intensive sampling at relatively few, smaller sites.

  2. Geographic patterns of vertebrate diversity and identification of relevant areas for conservation in Europe

    Directory of Open Access Journals (Sweden)

    Assunção–Albuquerque, M. J. T.

    2012-06-01

    Full Text Available The ‘EU Council conclusions on biodiversity post–2010′ re–enforced Europe’s commitment to halt biodiversity loss by 2020. Identifying areas of high–value for biodiversity conservation is an important issue to meet this target. We investigated the geographic pattern of terrestrial vertebrate diversity status in Europe by assessing the species richness, rarity, vulnerability (according to IUCN criteria, and a combined index of the three former for the amphibians, reptiles, bird and mammals of this region. We also correlated the value of all indices with climate and human influence variables. Overall, clear geographic gradients of species diversity were found. The combined biodiversity index indicated that high–value biodiversity areas were mostly located in the Mediterranean basin and the highest vulnerability was found in the Iberian peninsula for most taxa. Across all indexes, the proportion of variance explained by climate and human influence factors was moderate to low. The results obtained in this study have the potential to provide valuable support for nature conservation policies in Europe and, consequently, might contribute to mitigate biodiversity decline in this region.

  3. 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.

  4. Recombinant immunoblot assay reaction patterns and hepatitis C virus RNA in blood donors and non-A, non-B hepatitis patients

    NARCIS (Netherlands)

    Bresters, D.; Zaaijer, H. L.; Cuypers, H. T.; Reesink, H. W.; Winkel, I. N.; van Exel-Oehlers, P. J.; van Drimmelen, A. A.; Jansen, P. L.; van der Poel, C. L.; Lelie, P. N.

    1993-01-01

    To establish the value of the second-generation recombinant immunoblot assay (RIBA-2) and cDNA polymerase chain reaction (cDNA PCR) for confirmation of hepatitis C virus (HCV) infection, anti-HCV reaction patterns and the presence of HCV RNA were examined in 610 blood donors and 255 non-A, non-B

  5. Application of Multio-bjective Fuzzy Goal Programming to Optimize Cropping Pattern with Emphasis on Using Conservation Tillage Methods

    Directory of Open Access Journals (Sweden)

    samad erfanifar

    2014-10-01

    Full Text Available In this study, the optimal cropping patterns based on individual aims are presented and followed by a multi-objective cropping pattern with emphasize on the use of conservation tillage methods in Darab region presented. Individual goals consisted of maximizing gross margin and food secIn this study, the optimal cropping patterns based on individual aims were presented and followed by using a multi-objective fuzzy goal programming with emphasize on the use of conservation tillage methods in the Darab region. Individual goals consisted of maximizing gross margin and food security and minimizing water consumption and urea fertilizer use. The results showed that in the multi-objective cropping pattern, gross margin and food security increased by 23.5% and 6.1% , while water and energy consumption decreased by 4% and 5.1%, respectively as compared to the current cropping pattern. The fuzzy composite distance improved by %36, as compared to the current condition. Moreover, having replaced the conventional tillage methods with conservation tillage methods in the cropping pattern, the diesel fuel consumption reduced by 27%. Therefore, replacing multi-objective cropping pattern ,on which the conservation tillage methods are emphasized, with the conventional cropping patterns improves economic and environmental conditions. urity index and minimizing water and urea fertilizer.The results showed that in the multi-objective cropping pattern, gross margin and food security index respectively increase by 23.5% and 6.1% and water and energy consumption decrease by 4% and 5.1% respectively as compared to current cropping pattern. The fuzzy composite distance improves by %36 compares to current condition and represents better cropping pattern than the others. Morever in this cropping pattern, conventional tillage method will be replaced by conservation tillage practices, therefore the amount of diesel fuel consumption reduces by 27% that is equivalent to an

  6. Documenting biogeographical patterns of African timber species using herbarium records: a conservation perspective based on native trees from Angola.

    Directory of Open Access Journals (Sweden)

    Maria M Romeiras

    Full Text Available In many tropical regions the development of informed conservation strategies is hindered by a dearth of biodiversity information. Biological collections can help to overcome this problem, by providing baseline information to guide research and conservation efforts. This study focuses on the timber trees of Angola, combining herbarium (2670 records and bibliographic data to identify the main timber species, document biogeographic patterns and identify conservation priorities. The study recognized 18 key species, most of which are threatened or near-threatened globally, or lack formal conservation assessments. Biogeographical analysis reveals three groups of species associated with the enclave of Cabinda and northwest Angola, which occur primarily in Guineo-Congolian rainforests, and evergreen forests and woodlands. The fourth group is widespread across the country, and is mostly associated with dry forests. There is little correspondence between the spatial pattern of species groups and the ecoregions adopted by WWF, suggesting that these may not provide an adequate basis for conservation planning for Angolan timber trees. Eight of the species evaluated should be given high conservation priority since they are of global conservation concern, they have very restricted distributions in Angola, their historical collection localities are largely outside protected areas and they may be under increasing logging pressure. High conservation priority was also attributed to another three species that have a large proportion of their global range concentrated in Angola and that occur in dry forests where deforestation rates are high. Our results suggest that timber tree species in Angola may be under increasing risk, thus calling for efforts to promote their conservation and sustainable exploitation. The study also highlights the importance of studying historic herbarium collections in poorly explored regions of the tropics, though new field surveys remain

  7. Documenting biogeographical patterns of African timber species using herbarium records: a conservation perspective based on native trees from Angola.

    Science.gov (United States)

    Romeiras, Maria M; Figueira, Rui; Duarte, Maria Cristina; Beja, Pedro; Darbyshire, Iain

    2014-01-01

    In many tropical regions the development of informed conservation strategies is hindered by a dearth of biodiversity information. Biological collections can help to overcome this problem, by providing baseline information to guide research and conservation efforts. This study focuses on the timber trees of Angola, combining herbarium (2670 records) and bibliographic data to identify the main timber species, document biogeographic patterns and identify conservation priorities. The study recognized 18 key species, most of which are threatened or near-threatened globally, or lack formal conservation assessments. Biogeographical analysis reveals three groups of species associated with the enclave of Cabinda and northwest Angola, which occur primarily in Guineo-Congolian rainforests, and evergreen forests and woodlands. The fourth group is widespread across the country, and is mostly associated with dry forests. There is little correspondence between the spatial pattern of species groups and the ecoregions adopted by WWF, suggesting that these may not provide an adequate basis for conservation planning for Angolan timber trees. Eight of the species evaluated should be given high conservation priority since they are of global conservation concern, they have very restricted distributions in Angola, their historical collection localities are largely outside protected areas and they may be under increasing logging pressure. High conservation priority was also attributed to another three species that have a large proportion of their global range concentrated in Angola and that occur in dry forests where deforestation rates are high. Our results suggest that timber tree species in Angola may be under increasing risk, thus calling for efforts to promote their conservation and sustainable exploitation. The study also highlights the importance of studying historic herbarium collections in poorly explored regions of the tropics, though new field surveys remain a priority to

  8. Historical collections reveal patterns of diffusion of sweet potato in Oceania obscured by modern plant movements and recombination.

    Science.gov (United States)

    Roullier, Caroline; Benoit, Laure; McKey, Doyle B; Lebot, Vincent

    2013-02-05

    The history of sweet potato in the Pacific has long been an enigma. Archaeological, linguistic, and ethnobotanical data suggest that prehistoric human-mediated dispersal events contributed to the distribution in Oceania of this American domesticate. According to the "tripartite hypothesis," sweet potato was introduced into Oceania from South America in pre-Columbian times and was then later newly introduced, and diffused widely across the Pacific, by Europeans via two historically documented routes from Mexico and the Caribbean. Although sweet potato is the most convincing example of putative pre-Columbian connections between human occupants of Polynesia and South America, the search for genetic evidence of pre-Columbian dispersal of sweet potato into Oceania has been inconclusive. Our study attempts to fill this gap. Using complementary sets of markers (chloroplast and nuclear microsatellites) and both modern and herbarium samples, we test the tripartite hypothesis. Our results provide strong support for prehistoric transfer(s) of sweet potato from South America (Peru-Ecuador region) into Polynesia. Our results also document a temporal shift in the pattern of distribution of genetic variation in sweet potato in Oceania. Later reintroductions, accompanied by recombination between distinct sweet potato gene pools, have reshuffled the crop's initial genetic base, obscuring primary patterns of diffusion and, at the same time, giving rise to an impressive number of local variants. Moreover, our study shows that phenotypes, names, and neutral genes do not necessarily share completely parallel evolutionary histories. Multidisciplinary approaches, thus, appear necessary for accurate reconstruction of the intertwined histories of plants and humans.

  9. Reprimo tissue-specific expression pattern is conserved between zebrafish and human.

    Directory of Open Access Journals (Sweden)

    Ricardo J Figueroa

    Full Text Available Reprimo (RPRM, a member of the RPRM gene family, is a tumor-suppressor gene involved in the regulation of the p53-mediated cell cycle arrest at G2/M. RPRM has been associated with malignant tumor progression and proposed as a potential biomarker for early cancer detection. However, the expression and role of RPRM, as well as its family, are poorly understood and their physiology is as yet unstudied. In this scenario, a model system like the zebrafish could serve to dissect the role of the RPRM family members in vivo. Phylogenetic analysis reveals that RPRM and RPRML have been differentially retained by most species throughout vertebrate evolution, yet RPRM3 has been retained only in a small group of distantly related species, including zebrafish. Herein, we characterized the spatiotemporal expression of RPRM (present in zebrafish as an infraclass duplication rprma/rprmb, RPRML and RPRM3 in the zebrafish. By whole-mount in situ hybridization (WISH and fluorescent in situ hybridization (FISH, we demonstrate that rprm (rprma/rprmb and rprml show a similar spatiotemporal expression profile during zebrafish development. At early developmental stages rprmb is expressed in somites. After one day post-fertilization, rprm (rprma/rprmb and rprml are expressed in the notochord, brain, blood vessels and digestive tube. On the other hand, rprm3 shows the most unique expression profile, being expressed only in the central nervous system (CNS. We assessed the expression patterns of RPRM gene transcripts in adult zebrafish and human RPRM protein product in tissue samples by RT-qPCR and immunohistochemistry (IHC staining, respectively. Strikingly, tissue-specific expression patterns of the RPRM transcripts and protein are conserved between zebrafish and humans. We propose the zebrafish as a powerful tool to elucidate the both physiological and pathological roles of the RPRM gene family.

  10. Conserved regional patterns of GABA-related transcript expression in the neocortex of subjects with schizophrenia.

    Science.gov (United States)

    Hashimoto, Takanori; Bazmi, H Holly; Mirnics, Karoly; Wu, Qiang; Sampson, Allan R; Lewis, David A

    2008-04-01

    Individuals with schizophrenia exhibit disturbances in a number of cognitive, affective, sensory, and motor functions that depend on the circuitry of different cortical areas. The cognitive deficits associated with dysfunction of the dorsolateral prefrontal cortex result, at least in part, from abnormalities in GABA neurotransmission, as reflected in a specific pattern of altered expression of GABA-related genes. Consequently, the authors sought to determine whether this pattern of altered gene expression is restricted to the dorsolateral prefrontal cortex or could also contribute to the dysfunction of other cortical areas in subjects with schizophrenia. Real-time quantitative polymerase chain reaction was used to assess the levels of eight GABA-related transcripts in four cortical areas (dorsolateral prefrontal cortex, anterior cingulate cortex, and primary motor and primary visual cortices) of subjects (N=12) with schizophrenia and matched normal comparison subjects. Expression levels of seven transcripts were lower in subjects with schizophrenia, with the magnitude of reduction for each transcript comparable across the four areas. The largest reductions were detected for mRNA encoding somatostatin and parvalbumin, followed by moderate decreases in mRNA expression for the 67-kilodalton isoform of glutamic acid decarboxylase, the GABA membrane transporter GAT-1, and the alpha 1 and delta subunits of GABA(A) receptors. In contrast, the expression of calretinin mRNA did not differ between the subject groups in any of the four areas. Because the areas examined represent the major functional domains (e.g., association, limbic, motor, and sensory) of the cerebral cortex, our findings suggest that a conserved set of molecular alterations affecting GABA neurotransmission contribute to the pathophysiology of different clinical features of schizophrenia.

  11. 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.

  12. Social and Structural Patterns of Drought-Related Water Conservation and Rebound

    Science.gov (United States)

    Gonzales, Patricia; Ajami, Newsha

    2017-12-01

    Water use practices and conservation are the result of complex sociotechnical interactions of political, economic, hydroclimatic, and social factors. While the drivers of water demand have been extensively studied, they have traditionally been applied to models that assume stationary relationships between these various factors, and usually do not account for potential societal changes in response to increased scarcity awareness. For example, following a period of sustained low demand such as during a drought, communities often increase water use during a hydrologically wet period, a phenomenon known as "rebounding" water use. Previous experiences show the extent of this rebound is not a straightforward function of policy and efficiency improvements, but may also reflect short-term or long-lasting change in community behavior, which are not easily captured by models that assume stationarity. In this work, we develop a system dynamics model to represent water demand as a function of both structural and social factors. We apply this model to the analysis of three diverse water utilities in the San Francisco Bay Area between 1980 and 2017, identifying drought response trends and drivers over time. Our model is consistent with empirical patterns and historical context of water use in California, and provides important insights on the rebound phenomenon that can be extended to other locations. This comparative assessment indicates that policies, public outreach, and better data availability have played a key role in raising public awareness of water scarcity, especially with the raise of the internet era in recent years.

  13. Patterns of morphological variation of extant sloth skulls and their implication for future conservation efforts.

    Science.gov (United States)

    Hautier, Lionel; Billet, Guillaume; Eastwood, Bethany; Lane, Jemima

    2014-06-01

    Several studies have shown an increased morphological variability of sloths from mammalian norms, affecting varied phenotypic traits from skeletal parts to soft tissues. We present here the first descriptive comparison of the whole skull morphology within the two extant sloth genera, combining geometric morphometric approaches with comparative anatomy. We used these methods to explore the patterns of the intra- and interspecific morphological variation of the skull with regard to several factors such as phylogeny, geography, allometry, or sexual dimorphism. Our study first revealed strong phylogenetic and geographical imprints on the cranial and mandibular morphological traits. This result demonstrates the importance of accurate knowledge of species and their geographical distributions; here we show from an example pertaining to Bradypus variegatus populations the implications this has on conservation management. Moreover, in order to control the amount of this detected variation, we tentatively compared sloths to a wide range of mammalian species. Our analysis found no significant increase in the average deviation of skull shape within each investigated sloth species compared to other mammals. This suggests that the intraspecific cranial variation in sloths does not depart significantly from the variation observed in other mammals. This result has positive implications for the demarcation of anatomical regions that maintain high levels of morphological variation in sloths. Copyright © 2014 Wiley Periodicals, Inc.

  14. Conserved patterns of integrated developmental plasticity in a group of polyphenic tropical butterflies.

    Science.gov (United States)

    van Bergen, Erik; Osbaldeston, Dave; Kodandaramaiah, Ullasa; Brattström, Oskar; Aduse-Poku, Kwaku; Brakefield, Paul M

    2017-02-27

    Developmental plasticity is thought to have profound macro-evolutionary effects, for example, by increasing the probability of establishment in new environments and subsequent divergence into independently evolving lineages. In contrast to plasticity optimized for individual traits, phenotypic integration, which enables a concerted response of plastic traits to environmental variability, may affect the rate of local adaptation by constraining independent responses of traits to selection. Using a comparative framework, this study explores the evolution of reaction norms for a variety of life history and morphological traits across five related species of mycalesine butterflies from the Old World tropics. Our data indicate that an integrated response of a suite of key traits is shared amongst these species. Interestingly, the traits that make up the functional suite are all known to be regulated by ecdysteroid signalling in Bicyclus anynana, one of the species included in this study, suggesting the same underlying hormonal regulator may be conserved within this group of polyphenic butterflies. We also detect developmental thresholds for the expression of alternative morphs. The phenotypic plasticity of a broad suite of morphological and life history traits is integrated and shared among species from three geographically independent lineages of mycalesine butterflies, despite considerable periods of independent evolution and exposure to disparate environments. At the same time, we have detected examples of evolutionary change where independent traits show different patterns of reaction norms. We argue that the expression of more robust phenotypes may occur by shifting developmental thresholds beyond the boundaries of the typical environmental variation.

  15. Breast conservation treatment of early stage breast cancer: patterns of failure

    Energy Technology Data Exchange (ETDEWEB)

    Leborgne, Felix; Leborgne, Jose H; Ortega, Bettys; Doldan, Raquel; Zubizarreta, Eduardo

    1995-02-15

    Purpose: This study retrospectively assesses the patterns of failure in conservatively treated early stage breast cancer patients by correlating various clinical, pathologic, and treatment-related factors with local, axillary, and distant relapse. Methods and Materials: Between 1973 and 1990, 796 patients (817 breasts) received breast conservation surgery followed by radiotherapy. Local recurrences were counted as events even if they occurred simultaneously or after the appearance of axillary or distant metastases. Results: The 10-year actuarial relative disease-free survival (DFS) rate for T1N0, T2N0, and T1-2N1 was 82%, 71%, and 54%, respectively. Stage N0 patients had a significant DFS advantage over N1 patients (p = 0.02). The 15-year actuarial local recurrence-free rate for T1 and T2 tumors was 82% and 87%, respectively (p = nonsignificant). Univariate analysis identified three significant risk factors for local relapse: (a) 48 breasts with tumors showing an extensive intraductal component had a crude local recurrence rate of 23% compared to 8% for 769 breasts without intraductal component (p 0.0016); (b) the actuarial 10-year local recurrence-free rate for patients under age 40 years was 64% compared to 88% for patients over 40 years (p < 0.0001); (c) the 10-year actuarial local recurrence-free rate for 416 postmenopausal women without adjuvant tamoxifen was 83% compared to 97% for 107 postmenopausal women with tamoxifen (p = 0.0479). Salvage therapy for operable local recurrent patients resulted in a 8-year actuarial DFS rate of 47%, significantly lower than that obtained with primary treatment. The incidence of axillary relapse as the first sign of recurrence was 2%, and could be correlated with the lack of axillary dissection (p < 0.0000005) and primary tumor size (p = 0.03). Radiotherapy to the axilla did not influence axillary relapse. Actuarial 5-year DFS rate after treatment of isolated axillary recurrence was 27%. Axillary failure was a marker for

  16. Breast conservation treatment of early stage breast cancer: patterns of failure

    International Nuclear Information System (INIS)

    Leborgne, Felix; Leborgne, Jose H.; Ortega, Bettys; Doldan, Raquel; Zubizarreta, Eduardo

    1995-01-01

    Purpose: This study retrospectively assesses the patterns of failure in conservatively treated early stage breast cancer patients by correlating various clinical, pathologic, and treatment-related factors with local, axillary, and distant relapse. Methods and Materials: Between 1973 and 1990, 796 patients (817 breasts) received breast conservation surgery followed by radiotherapy. Local recurrences were counted as events even if they occurred simultaneously or after the appearance of axillary or distant metastases. Results: The 10-year actuarial relative disease-free survival (DFS) rate for T1N0, T2N0, and T1-2N1 was 82%, 71%, and 54%, respectively. Stage N0 patients had a significant DFS advantage over N1 patients (p = 0.02). The 15-year actuarial local recurrence-free rate for T1 and T2 tumors was 82% and 87%, respectively (p = nonsignificant). Univariate analysis identified three significant risk factors for local relapse: (a) 48 breasts with tumors showing an extensive intraductal component had a crude local recurrence rate of 23% compared to 8% for 769 breasts without intraductal component (p 0.0016); (b) the actuarial 10-year local recurrence-free rate for patients under age 40 years was 64% compared to 88% for patients over 40 years (p < 0.0001); (c) the 10-year actuarial local recurrence-free rate for 416 postmenopausal women without adjuvant tamoxifen was 83% compared to 97% for 107 postmenopausal women with tamoxifen (p = 0.0479). Salvage therapy for operable local recurrent patients resulted in a 8-year actuarial DFS rate of 47%, significantly lower than that obtained with primary treatment. The incidence of axillary relapse as the first sign of recurrence was 2%, and could be correlated with the lack of axillary dissection (p < 0.0000005) and primary tumor size (p = 0.03). Radiotherapy to the axilla did not influence axillary relapse. Actuarial 5-year DFS rate after treatment of isolated axillary recurrence was 27%. Axillary failure was a marker for

  17. Pattern of Ipsilateral Breast Tumor Recurrence After Breast-Conserving Therapy

    International Nuclear Information System (INIS)

    Jobsen, Jan; Palen, Job van der; Riemersma, Sietske; Heijmans, Harald; Ong, Francisca; Struikmans, Henk

    2014-01-01

    Purpose: To analyze the incidence and prognostic factors of ipsilateral breast tumor recurrence (IBTR) after breast-conserving therapy (BCT) in a large, population-based, single-center study with long-term follow-up. Methods and Materials: We analyzed 3595 cases in which BCT was performed in 3824 women with stage I or II breast cancer. The incidence of IBTR was analyzed over time and was based on IBTR as first event. Results: The 15-year local relapse-free survival was 90.9%. The hazard estimates for IBTR showed a time course with 2 peaks, the first at approximately 5 years and the second, twice as high, at 12 years. Stratifying subjects by age and margin status showed that, for women ≤40 years old with negative margins, adjuvant systemic therapy led to a 5-fold reduced risk of recurrence compared to none, and the presence of lymph vascular space invasion (LVSI) had a 3-fold increased risk compared to its absence. For women >40 years old, the presence of LVSI (hazard ratio [HR] 2.5) and the presence of lobular carcinoma in situ in the lumpectomy specimen (HR 2.3) were the only 2 risk factors. Conclusions: We demonstrated a pattern in risk of IBTR over time, with 2 peaks, first at approximately 5 years and a second, much higher peak at approximately 12 years, especially for women ≤40 years old. For women ≤40 years old with tumor-free resection margins, we noted that the absence of adjuvant systemic therapy and the presence of LVSI were independent prognostic factors of IBTR. For women >40 years old, the presence of LVSI and the presence of lobular carcinoma in situ were independent risk factors

  18. Pattern of Ipsilateral Breast Tumor Recurrence After Breast-Conserving Therapy

    Energy Technology Data Exchange (ETDEWEB)

    Jobsen, Jan, E-mail: j.jobsen@mst.nl [Department of Radiation Oncology, Medisch Spectrum Twente, Enschede (Netherlands); Palen, Job van der [Department of Epidemiology, Medisch Spectrum Twente, Enschede (Netherlands); Department of Research Methodology, Measurement, and Data Analysis, Faculty of Behavioral Science, University of Twente, Enschede (Netherlands); Riemersma, Sietske [Laboratory for Pathology Oost Nederland, Hengelo (Netherlands); Heijmans, Harald [Department of Surgery, Ziekenhuis Groep Twente, Hengelo (Netherlands); Ong, Francisca [Department of Radiation Oncology, Medisch Spectrum Twente, Enschede (Netherlands); Struikmans, Henk [Department of Radiation Oncology, Leiden University Medical Centre, Leiden (Netherlands); Radiotherapy Centre West, Medical Centre Haaglanden, The Hague (Netherlands)

    2014-08-01

    Purpose: To analyze the incidence and prognostic factors of ipsilateral breast tumor recurrence (IBTR) after breast-conserving therapy (BCT) in a large, population-based, single-center study with long-term follow-up. Methods and Materials: We analyzed 3595 cases in which BCT was performed in 3824 women with stage I or II breast cancer. The incidence of IBTR was analyzed over time and was based on IBTR as first event. Results: The 15-year local relapse-free survival was 90.9%. The hazard estimates for IBTR showed a time course with 2 peaks, the first at approximately 5 years and the second, twice as high, at 12 years. Stratifying subjects by age and margin status showed that, for women ≤40 years old with negative margins, adjuvant systemic therapy led to a 5-fold reduced risk of recurrence compared to none, and the presence of lymph vascular space invasion (LVSI) had a 3-fold increased risk compared to its absence. For women >40 years old, the presence of LVSI (hazard ratio [HR] 2.5) and the presence of lobular carcinoma in situ in the lumpectomy specimen (HR 2.3) were the only 2 risk factors. Conclusions: We demonstrated a pattern in risk of IBTR over time, with 2 peaks, first at approximately 5 years and a second, much higher peak at approximately 12 years, especially for women ≤40 years old. For women ≤40 years old with tumor-free resection margins, we noted that the absence of adjuvant systemic therapy and the presence of LVSI were independent prognostic factors of IBTR. For women >40 years old, the presence of LVSI and the presence of lobular carcinoma in situ were independent risk factors.

  19. Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Hellsten, Uffe [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Wright, Kevin M. [Harvard Univ., Cambridge, MA (United States); Jenkins, Jerry [USDOE Joint Genome Inst., Walnut Creek, CA (United States); HudsonAlpha Inst. of Biotechnology, Huntsville, AL (United States); Shu, Shengqiang [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Yuan, Yao-Wu [Univ. of Connecticut, Storrs, CT (United States); Wessler, Susan R. [Univ. of California, Riverside, CA (United States); Schmutz, Jeremy [USDOE Joint Genome Inst., Walnut Creek, CA (United States); HudsonAlpha Inst. of Biotechnology, Huntsville, AL (United States); Willis, John H. [Duke Univ., Durham, NC (United States); Rokhsar, Daniel S. [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Univ. of California, Berkeley, CA (United States)

    2013-11-13

    Meiotic recombination rates can vary widely across genomes, with hotspots of intense activity interspersed among cold regions. In yeast, hotspots tend to occur in promoter regions of genes, whereas in humans and mice hotspots are largely defined by binding sites of the PRDM9 protein. To investigate the detailed recombination pattern in a flowering plant we use shotgun resequencing of a wild population of the monkeyflower Mimulus guttatus to precisely locate over 400,000 boundaries of historic crossovers or gene conversion tracts. Their distribution defines some 13,000 hotspots of varying strengths, interspersed with cold regions of undetectably low recombination. Average recombination rates peak near starts of genes and fall off sharply, exhibiting polarity. Within genes, recombination tracts are more likely to terminate in exons than in introns. The general pattern is similar to that observed in yeast, as well as in PRDM9-knockout mice, suggesting that recombination initiation described here in Mimulus may reflect ancient and conserved eukaryotic mechanisms

  20. Genetic mapping of centromeres in the nine Citrus clementina chromosomes using half-tetrad analysis and recombination patterns in unreduced and haploid gametes.

    Science.gov (United States)

    Aleza, Pablo; Cuenca, José; Hernández, María; Juárez, José; Navarro, Luis; Ollitrault, Patrick

    2015-03-08

    Mapping centromere locations in plant species provides essential information for the analysis of genetic structures and population dynamics. The centromere's position affects the distribution of crossovers along a chromosome and the parental heterozygosity restitution by 2n gametes is a direct function of the genetic distance to the centromere. Sexual polyploidisation is relatively frequent in Citrus species and is widely used to develop new seedless triploid cultivars. The study's objectives were to (i) map the positions of the centromeres of the nine Citrus clementina chromosomes; (ii) analyse the crossover interference in unreduced gametes; and (iii) establish the pattern of genetic recombination in haploid clementine gametes along each chromosome and its relationship with the centromere location and distribution of genic sequences. Triploid progenies were derived from unreduced megagametophytes produced by second-division restitution. Centromere positions were mapped genetically for all linkage groups using half-tetrad analysis. Inference of the physical locations of centromeres revealed one acrocentric, four metacentric and four submetacentric chromosomes. Crossover interference was observed in unreduced gametes, with variation seen between chromosome arms. For haploid gametes, a strong decrease in the recombination rate occurred in centromeric and pericentromeric regions, which contained a low density of genic sequences. In chromosomes VIII and IX, these low recombination rates extended beyond the pericentromeric regions. The genomic region corresponding to a genetic distance recombination pattern along each chromosome. However, regions with low recombination rates extended beyond the pericentromeric regions of some chromosomes into areas richer in genic sequences. The persistence of strong linkage disequilibrium between large numbers of genes promotes the stability of epistatic interactions and multilocus-controlled traits over successive generations but

  1. Fish assemblage patterns as a tool to aid conservation in the ...

    African Journals Online (AJOL)

    2008-12-22

    Dec 22, 2008 ... Within a catchment, fish conservation may consider the full suite of species ... mental conditions, a river ecosystem may be transformed to the extent that a new ...... ent characteristics that should be considered functional units.

  2. Seed plant features, distribution patterns, diversity hotspots, and conservation gaps in Xinjiang, China

    Directory of Open Access Journals (Sweden)

    Jihong Huang

    2018-06-01

    Full Text Available The flora in Xinjiang is unique. Decisions about biodiversity conservation and management based on seed plant diversity hotspots and conservation gaps in Xinjiang are essential to maintain this unique flora. Based on a species distribution dataset of seed plants, we measured seed plant diversity using species richness and phylogenetic diversity indices. Five percent of Xinjiang’s total land area with the highest biodiversity was used to identify hotspots for each index. In total, eight hotspots were identified. Most hotspots were located in mountainous areas, mainly in the Tianshan Mountains and Altai Mountains. Furthermore, we detected conservation gaps for Xinjiang’s seed flora hotspots by overlaying nature reserve maps on to maps of identified hotspots and we designated priority conservation gaps for hotspots by overlaying global biodiversity hotspot maps on to hotspot conservation gaps maps. Most of Xinjiang’s seed plant hotspots are poorly protected; only 10.45% of these hotspots were covered by nature reserves. We suggest that it is essential to promote network function of nature reserves within these hotspots in Xinjiang to conserve this unique flora.

  3. Effect of Conservation on Spatial Pattern of Dominant Trees in Beech (Fagus Orientalis Lipsky Communities, (Case Study: Masal, Guilan

    Directory of Open Access Journals (Sweden)

    S. S. Ebrahimi

    2013-12-01

    Full Text Available Spatial patterns are suitable tools for optimal management in many forested areas. In this research, the effect of conservation on spatial pattern of dominant trees has been studied. To achieving this purpose, protected and non- protected forests were selected in Masal region of Guilan province as the study area. Sampling methods including fixed- area plots and distance methods, such as T- square and compound sampling were used 25 circle sample plots, each with an area 1000 m2and 25 sampling points were taken. Then, tree species in plot samples and the distance of interest were identified and measured. Dispersion indices such as Green, Morisata, standardized Morisata, Hopkins, Eberhart, Johnson and Zimmer, Hines and C were used to analyze the spatial pattern in the areas. All indices related to plot samples indicated the clumped pattern for dominant species in protected and non- protected areas. The results of the distance indices have indicated that destruction changes the spatial pattern of dominant species and these species had different pattern in these areas. Among the distance indices, C and Hines indices revealed differences and they were suitable to describe the spatial pattern of both areas.

  4. Replication labeling patterns and chromosome territories typical of mammalian nuclei are conserved in the early metazoan Hydra.

    Science.gov (United States)

    Alexandrova, Olga; Solovei, Irina; Cremer, Thomas; David, Charles N

    2003-12-01

    To investigate the evolutionary conservation of higher order nuclear architecture previously described for mammalian cells we have analyzed the nuclear architecture of the simple polyp Hydra. These diploblastic organisms have large nuclei (8-10 microm) containing about 3x10(9) bp of DNA organized in 15 chromosome pairs. They belong to the earliest metazoan phylum and are separated from mammals by at least 600 million years. Single and double pulse labeling with halogenated nucleotides (bromodeoxyuridine, iododeoxyuridine and chlorodeoxyuridine) revealed striking similarities to the known sequence of replication labeling patterns in mammalian nuclei. These patterns reflect a persistent nuclear arrangement of early, mid-, and late replicating chromatin foci that could be identified during all stages of interphase over at least 5-10 cell generations. Segregation of labeled chromatids led after several cell divisions to nuclei with single or a few labeled chromosome territories. In such nuclei distinct clusters of labeled chromatin foci were separated by extended nuclear areas with non-labeled chromatin, which is typical of a territorial arrangement of interphase chromosomes. Our results indicate the conservation of fundamental features of higher order chromatin arrangements throughout the evolution of metazoan animals and suggest the existence of conserved mechanism(s) controlling this architecture.

  5. Exploring spatial patterns of vulnerability for diverse biodiversity descriptors in regional conservation planning.

    Science.gov (United States)

    Vimal, Ruppert; Pluvinet, Pascal; Sacca, Céline; Mazagol, Pierre-Olivier; Etlicher, Bernard; Thompson, John D

    2012-03-01

    In this study, we developed a multi-criteria assessment of spatial variability of the vulnerability of three different biodiversity descriptors: sites of high conservation interest by virtue of the presence of rare or remarkable species, extensive areas of high ecological integrity, and landscape diversity in grid cells across an entire region. We assessed vulnerability in relation to (a) direct threats in and around sites to a distance of 2 km associated with intensive agriculture, building and road infrastructure and (b) indirect effects of human population density on a wider scale (50 km). The different combinations of biodiversity and threat indicators allowed us to set differential priorities for biodiversity conservation and assess their spatial variation. For example, with this method we identified sites and grid cells which combined high biodiversity with either high threat values or low threat values for the three different biodiversity indicators. In these two classes the priorities for conservation planning will be different, reduce threat values in the former and restrain any increase in the latter. We also identified low priority sites (low biodiversity with either high or low threats). This procedure thus allows for the integration of a spatial ranking of vulnerability into priority setting for regional conservation planning. Copyright © 2011 Elsevier Ltd. All rights reserved.

  6. Aligning conservation goals: are patterns of species richness and endemism concordant at regional scales?

    Directory of Open Access Journals (Sweden)

    Ricketts, T. H.

    2001-01-01

    Full Text Available Biodiversity conservation strategies commonly target areas of high species richness and/or high endemism. However, the correlation between richness and endemism at scales relevant to conservation is unclear; these two common goals of conservation plans may therefore be in conflict. Here the spatial concordance between richness and endemism is tested using five taxa in North America: butterflies, birds, mammals, amphibians, and reptiles. This concordance is also tested using overall indices of richness and endemism (incorporating all five taxa. For all taxa except birds, richness and endemism were significantly correlated, with amphibians, reptiles, and the overall indices showing the highest correlations (rs = 0.527-0.676. However, 'priority sets' of ecoregions (i.e., the top 10% of ecoregions based on richness generally overlapped poorly with those based on endemism (< 50% overlap for all but reptiles. These results offer only limited support for the idea that richness and endemism are correlated at broad scales and indicate that land managers will need to balance these dual, and often conflicting, goals of biodiversity conservation.

  7. Large-scale patterns of plant diversity and conservation priorities in South East Asia

    NARCIS (Netherlands)

    Marsh, S.T.; Brummitt, N.A.; Kok, de R.P.J.; Utteridge, T.M.A.

    2009-01-01

    In the absence of a complete floristic inventory, conservation priorities within South East Asia must often be based on incomplete knowledge or a rough approximation of diversity such as habitat cover. To help overcome this, a database containing distribution data for all 3 523 known flowering plant

  8. JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures.

    Science.gov (United States)

    Muth, Thilo; García-Martín, Juan A; Rausell, Antonio; Juan, David; Valencia, Alfonso; Pazos, Florencio

    2012-02-15

    We have implemented in a single package all the features required for extracting, visualizing and manipulating fully conserved positions as well as those with a family-dependent conservation pattern in multiple sequence alignments. The program allows, among other things, to run different methods for extracting these positions, combine the results and visualize them in protein 3D structures and sequence spaces. JDet is a multiplatform application written in Java. It is freely available, including the source code, at http://csbg.cnb.csic.es/JDet. The package includes two of our recently developed programs for detecting functional positions in protein alignments (Xdet and S3Det), and support for other methods can be added as plug-ins. A help file and a guided tutorial for JDet are also available.

  9. Murine leukemia virus-derived retroviral vector has differential integration patterns in human cell lines used to produce recombinant factor VIII

    Directory of Open Access Journals (Sweden)

    Marcela Cristina Correa de Freitas

    2014-06-01

    Full Text Available OBJECTIVE: Nowadays recombinant factor VIII is produced in murine cells including in Chinese hamster ovary (CHO and baby hamster kidney cells (BHK. Previous studies, using the murine leukemia virus-derived retroviral vector pMFG-FVIII-P140K, modified two recombinant human cell lines, HepG2 and Hek293 to produce recombinant factor VIII. In order to characterize these cells, the present study aimed to analyze the integration pattern of retroviral vector pMFG-FVIII-P140K.METHODS: This study used ligation-mediated polymerase chain reaction to locate the site of viral vector integration by sequencing polymerase chain reaction products. The sequences were compared to genomic databases to characterize respective clones.RESULTS: The retroviral vector presented different and non-random profiles of integration between cells lines. A preference of integration for chromosomes 19, 17 and 11 was observed for HepG2FVIIIdB/P140K and chromosome 9 for Hek293FVIIIdB/P140K. In genomic regions such as CpG islands and transcription factor binding sites, there was no difference in the integration profiles for both cell lines. Integration in intronic regions of encoding protein genes (RefSeq genes was also observed in both cell lines. Twenty percent of integrations occurred at fragile sites in the genome of the HepG2 cell line and 17% in Hek293.CONCLUSION: The results suggest that the cell type can affect the profile of chromosomal integration of the retroviral vector used; these differences may interfere in the level of expression of recombinant proteins.

  10. Adaptation of the Pivotal-Differential Genome Pattern for the Induction of Intergenomic Chromosome Recombination in Hybrids of Synthetic Amphidiploids within Triticeae Tribe

    Directory of Open Access Journals (Sweden)

    Michal T. Kwiatek

    2017-07-01

    Full Text Available A pivotal-differential evolution pattern is when two allopolyploids share a common genome, which is called pivotal, and differ with respect to the other genome or genomes, called differential. This feature induces the intergenomic recombination between chromosomes of differential genomes, which can lead to speciation. Our study is a cytomolecular insight into this mechanism which was adapted for the induction of intergenomic chromosome recombination in hybrids of synthetic amphidiploids Aegilops biuncialis × S. cereale (UUMMRR and triticale (AABBRR where R-genome was pivotal. We observed chromosome recombination events which were induced by both: (1 random chromosome fragmentation and non-homologous chromosome end joining at mitosis of root meristem cells and (2 intergenomic chromosome associations at meiosis of pollen mother cells (PMCs of F1 hybrids. Reciprocal chromosome translocations were identified in six F1 plants and 15 plants of F2 generation using fluorescence in situ hybridization (FISH with DNA clones (pTa-86, pTa-k374, pTa-465, pTa-535, pTa-k566, and pTa-713. We observed signals of pTa-86, pTa-535, and pTa-k566 probes in several chromosome breakpoints. The comparison of the DNA clone sequences distinguished a number of common motifs, which can be considered as characteristics of chromosome breakpoint loci. Immunodetection of synaptonemal complex proteins and genomic in situ hybridization analysis at meiosis of PMCs of F1 hybrids showed, that the homologous pairing of pivotal R—genome chromosomes is crucial for the fertility of F1 hybrids, however, these chromosomes can be also involved in the intergeneric recombination.

  11. Genomic Investigation Reveals Highly Conserved, Mosaic, Recombination Events Associated with Capsular Switching among Invasive Neisseria meningitidis Serogroup W Sequence Type (ST)-11 Strains.

    Science.gov (United States)

    Mustapha, Mustapha M; Marsh, Jane W; Krauland, Mary G; Fernandez, Jorge O; de Lemos, Ana Paula S; Dunning Hotopp, Julie C; Wang, Xin; Mayer, Leonard W; Lawrence, Jeffrey G; Hiller, N Luisa; Harrison, Lee H

    2016-07-03

    Neisseria meningitidis is an important cause of meningococcal disease globally. Sequence type (ST)-11 clonal complex (cc11) is a hypervirulent meningococcal lineage historically associated with serogroup C capsule and is believed to have acquired the W capsule through a C to W capsular switching event. We studied the sequence of capsule gene cluster (cps) and adjoining genomic regions of 524 invasive W cc11 strains isolated globally. We identified recombination breakpoints corresponding to two distinct recombination events within W cc11: A 8.4-kb recombinant region likely acquired from W cc22 including the sialic acid/glycosyl-transferase gene, csw resulted in a C→W change in capsular phenotype and a 13.7-kb recombinant segment likely acquired from Y cc23 lineage includes 4.5 kb of cps genes and 8.2 kb downstream of the cps cluster resulting in allelic changes in capsule translocation genes. A vast majority of W cc11 strains (497/524, 94.8%) retain both recombination events as evidenced by sharing identical or very closely related capsular allelic profiles. These data suggest that the W cc11 capsular switch involved two separate recombination events and that current global W cc11 meningococcal disease is caused by strains bearing this mosaic capsular switch. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  12. Evolutionary plasticity of habenular asymmetry with a conserved efferent connectivity pattern.

    Directory of Open Access Journals (Sweden)

    Aldo Villalón

    Full Text Available The vertebrate habenulae (Hb is an evolutionary conserved dorsal diencephalic nuclear complex that relays information from limbic and striatal forebrain regions to the ventral midbrain. One key feature of this bilateral nucleus is the presence of left-right differences in size, cytoarchitecture, connectivity, neurochemistry and/or gene expression. In teleosts, habenular asymmetry has been associated with preferential innervation of left-right habenular efferents into dorso-ventral domains of the midbrain interpeduncular nucleus (IPN. However, the degree of conservation of this trait and its relation to the structural asymmetries of the Hb are currently unknown. To address these questions, we performed the first systematic comparative analysis of structural and connectional asymmetries of the Hb in teleosts. We found striking inter-species variability in the overall shape and cytoarchitecture of the Hb, and in the frequency, strength and to a lesser degree, laterality of habenular volume at the population level. Directional asymmetry of the Hb was either to the left in D. rerio, E. bicolor, O. latipes, P. reticulata, B. splendens, or to the right in F. gardneri females. In contrast, asymmetry was absent in P. scalare and F. gardneri males at the population level, although in these species the Hb displayed volumetric asymmetries at the individual level. Inter-species variability was more pronounced across orders than within a single order, and coexisted with an overall conserved laterotopic representation of left-right habenular efferents into dorso-ventral domains of the IPN. These results suggest that the circuit design involving the Hb of teleosts promotes structural flexibility depending on developmental, cognitive and/or behavioural pressures, without affecting the main midbrain connectivity output, thus unveiling a key conserved role of this connectivity trait in the function of the circuit. We propose that ontogenic plasticity in habenular

  13. Recombinant Programming

    OpenAIRE

    Pawlak , Renaud; Cuesta , Carlos; Younessi , Houman

    2004-01-01

    This research report presents a promising new approach to computation called Recombinant Programming. The novelty of our approach is that it separates the program into two layers of computation: the recombination and the interpretation layer. The recombination layer takes sequences as inputs and allows the programmer to recombine these sequences through the definition of cohesive code units called extensions. The output of such recombination is a mesh that can be used by the interpretation la...

  14. Coevolution Pattern and Functional Conservation or Divergence of miR167s and their targets across Diverse Plant Species.

    Science.gov (United States)

    Barik, Suvakanta; Kumar, Ashutosh; Sarkar Das, Shabari; Yadav, Sandeep; Gautam, Vibhav; Singh, Archita; Singh, Sharmila; Sarkar, Ananda K

    2015-10-13

    microRNAs (miRNAs), a class of endogenously produced small non-coding RNAs of 20-21 nt length, processed from precursor miRNAs, regulate many developmental processes by negatively regulating the target genes in both animals and plants. The coevolutionary pattern of a miRNA family and their targets underscores its functional conservation or diversification. The miR167 regulates various aspects of plant development in Arabidopsis by targeting ARF6 and ARF8. The evolutionary conservation or divergence of miR167s and their target genes are poorly understood till now. Here we show the evolutionary relationship among 153 MIR167 genes obtained from 33 diverse plant species. We found that out of the 153 of miR167 sequences retrieved from the "miRBase", 27 have been annotated to be processed from the 3' end, and have diverged distinctively from the other miR167s produced from 5' end. Our analysis reveals that gma-miR167h/i and mdm-miR167a are processed from 3' end and have evolved separately, diverged most resulting in novel targets other than their known ones, and thus led to functional diversification, especially in apple and soybean. We also show that mostly conserved miR167 sequences and their target AUXIN RESPONSE FACTORS (ARFs) have gone through parallel evolution leading to functional diversification among diverse plant species.

  15. Population Genetic Patterns of Threatened European Mudminnow (Umbra krameri Walbaum, 1792 in a Fragmented Landscape: Implications for Conservation Management.

    Directory of Open Access Journals (Sweden)

    Péter Takács

    Full Text Available The European mudminnow (Umbra krameri is a Middle Danubian endemic fish species, which is characterised by isolated populations living mainly in artificial habitats in the centre of its range, in the Carpathian Basin. For their long term preservation, reliable information is needed about the structure of stocks and the level of isolation. The recent distribution pattern, and the population genetic structure within and among regions were investigated to designate the Evolutionary Significant, Conservation and Management Units (ESUs, CUs, MUs and to explore the conservation biological value of the shrinking populations. In total, eight microsatellite loci were studied in 404 specimens originating from eight regions. The results revealed a pronounced population structure, where strictly limited gene flow was detected among regions, as well as various strengths of connections within regions. Following the results of hierarchical structure analyses, two ESUs were supposed in the Carpathian Basin, corresponding to the Danube and Tisza catchments. Our results recommend designating the borders of CUs in an 80-90km range and 16 clusters should be set up as MUs for the 33 investigated populations. How these genetic findings can be used to better allocate conservation resources for the long term maintenance of the metapopulation structure of this threathened endemic fish is discussed.

  16. Comparison of nest-site selection patterns of different sympatric raptor species as a tool for their conservation

    Directory of Open Access Journals (Sweden)

    Poirazidis, K.

    2007-12-01

    Full Text Available In this study the nest-site selection patterns of four tree-nesting sympatric raptor species in Dadia National Park (Greece were compared in order to provide a sound conservation tool for their long-term management in the area. The species studied were the Black vulture (Aegypius monachus, the Lesser-spotted eagle (Aquila pomarina, the Booted eagle (Hieraaetus pennatus and the Goshawk (Accipiter gentilis. Twenty-six variables illustrating the landscape context and vegetation structure of nesting sites were analysed. Multivariate-ANOVA and Discriminant Function Analysis were used to test for significant differentiations in nest-site characteristics among the species. The species studied were initially differentiated by geomorphology and distance to foraging areas. Once these were determined their nesting areas were established according to forest structure. Our results indicate that forest management should integrate the preservation of mature forest stands with sparse canopy and forest heterogeneity in order to conserve suitable nesting habitats for the raptors. Specific conservation measures such as restriction of road construction should be implemented in order to protect the active nests and provisions should be made for adequate nesting sites for the Black vulture, which is sensitive to human disturbance.

  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. Conservation and diversification of an ancestral chordate gene regulatory network for dorsoventral patterning

    Czech Academy of Sciences Publication Activity Database

    Kozmiková, Iryna; Smolíková, Jana; Vlček, Čestmír; Kozmik, Zbyněk

    2011-01-01

    Roč. 6, č. 2 (2011), e14650 E-ISSN 1932-6203 R&D Projects: GA AV ČR IAA500520604; GA AV ČR IAA500520908 Institutional research plan: CEZ:AV0Z50520514 Keywords : Wnt Bmp * amphioxus * axial patterning Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.092, year: 2011

  19. Spatial patterns of biodiversity conservation in a multiregional general equilibrium model

    NARCIS (Netherlands)

    Eppink, F.V.; Withagen, C.A.A.M.

    2009-01-01

    Migration dynamics and local biodiversity are interrelated in a way that is likely to affect patterns of regional specialisation. We assess this relationship with a New Economic Geography model that has been extended with biodiversity. Biodiversity is heterogeneous, and responds to habitat

  20. Hummingbird conservation: discovering diversity patterns in southwest U.S.A.

    Science.gov (United States)

    Susan M. Wethington; George C. West; Barbara A. Carlson

    2005-01-01

    Using data obtained in 2002 and 2003 from sites in the Hummingbird Monitoring Network, we investigated the effect of geographic factors—latitude, longitude, and elevation—and year on hummingbird diversity patterns in Southwestern U.S.A. In California, none of these factors affected hummingbird richness but elevation significantly affected abundance. In southeastern...

  1. Plant diversity patterns in neotropical dry forests and their conservation implications.

    Science.gov (United States)

    Banda-R, Karina; Delgado-Salinas, Alfonso; Dexter, Kyle G; Linares-Palomino, Reynaldo; Oliveira-Filho, Ary; Prado, Darién; Pullan, Martin; Quintana, Catalina; Riina, Ricarda; Rodríguez M, Gina M; Weintritt, Julia; Acevedo-Rodríguez, Pedro; Adarve, Juan; Álvarez, Esteban; Aranguren B, Anairamiz; Arteaga, Julián Camilo; Aymard, Gerardo; Castaño, Alejandro; Ceballos-Mago, Natalia; Cogollo, Álvaro; Cuadros, Hermes; Delgado, Freddy; Devia, Wilson; Dueñas, Hilda; Fajardo, Laurie; Fernández, Ángel; Fernández, Miller Ángel; Franklin, Janet; Freid, Ethan H; Galetti, Luciano A; Gonto, Reina; González-M, Roy; Graveson, Roger; Helmer, Eileen H; Idárraga, Álvaro; López, René; Marcano-Vega, Humfredo; Martínez, Olga G; Maturo, Hernán M; McDonald, Morag; McLaren, Kurt; Melo, Omar; Mijares, Francisco; Mogni, Virginia; Molina, Diego; Moreno, Natalia Del Pilar; Nassar, Jafet M; Neves, Danilo M; Oakley, Luis J; Oatham, Michael; Olvera-Luna, Alma Rosa; Pezzini, Flávia F; Dominguez, Orlando Joel Reyes; Ríos, María Elvira; Rivera, Orlando; Rodríguez, Nelly; Rojas, Alicia; Särkinen, Tiina; Sánchez, Roberto; Smith, Melvin; Vargas, Carlos; Villanueva, Boris; Pennington, R Toby

    2016-09-23

    Seasonally dry tropical forests are distributed across Latin America and the Caribbean and are highly threatened, with less than 10% of their original extent remaining in many countries. Using 835 inventories covering 4660 species of woody plants, we show marked floristic turnover among inventories and regions, which may be higher than in other neotropical biomes, such as savanna. Such high floristic turnover indicates that numerous conservation areas across many countries will be needed to protect the full diversity of tropical dry forests. Our results provide a scientific framework within which national decision-makers can contextualize the floristic significance of their dry forest at a regional and continental scale. Copyright © 2016, American Association for the Advancement of Science.

  2. 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.

  3. Analysis of a Caenorhabditis elegans Twist homolog identifies conserved and divergent aspects of mesodermal patterning

    OpenAIRE

    Harfe, Brian D.; Gomes, Ana Vaz; Kenyon, Cynthia; Liu, Jun; Krause, Michael; Fire, Andrew

    1998-01-01

    Mesodermal development is a multistep process in which cells become increasingly specialized to form specific tissue types. In Drosophila and mammals, proper segregation and patterning of the mesoderm involves the bHLH factor Twist. We investigated the activity of a Twist-related factor, CeTwist, during Caenorhabditis elegans mesoderm development. Embryonic mesoderm in C. elegans derives from a number of distinct founder cells that are specified during the early lineages; in contrast, a singl...

  4. Pattern of local recurrence after conservative surgery and whole-breast irradiation

    International Nuclear Information System (INIS)

    Freedman, Gary M.; Anderson, Penny R.; Hanlon, Alexandra L.; Eisenberg, Debra F.; Nicolaou, Nicos

    2005-01-01

    Purpose: Most recurrences in the breast after conservative surgery and whole-breast irradiation have been reported to occur within the same quadrant as the initial primary tumor. We analyzed the long-term risk of recurrence by area of the breast after whole-breast irradiation. Materials and Methods: In all, 1,990 women with Stage 0-II breast cancer were treated with conservative surgery and whole-breast irradiation from 1970-1998. Stage was ductal carcinoma in situ in 237, T1 in 1273, and T2 in 480 patients. Of 120 local recurrences, 71 were classified as true local (confined to the original quadrant) and 49 as elsewhere (involving outside the original quadrant). Kaplan-Meier methodology was used to calculate 5-year, 10-year, and 15-year rates of recurrence (95% confidence intervals in parentheses). The median follow-up is 80 months. Results: There was no apparent difference in the 15-year rate of true local vs. elsewhere recurrence, but the time to recurrence was different. The rate of true local recurrence was 2%, 5%, and 7% (5-9%) at 5, 10, and 15 years, respectively. The recurrences elsewhere in the breast were rare at 5 (1%) and 10 (2%) years, but increased to 6 (3-9%) at 15 years. This 15-year rate of elsewhere recurrence was half the rate of contralateral breast cancers of 13% (10-16%). Conclusions: Recurrence elsewhere in the breast is rare for the first 10 years, but by 15 years is nearly equal to true local recurrence even after whole-breast irradiation. The 15-year rate of elsewhere recurrence was half the rate of contralateral breast cancers. This may indicate a therapeutic effect of whole-breast radiation for other areas of the breast. Very long follow-up will be needed for partial breast irradiation with or without tamoxifen to show that the risk of elsewhere recurrence is not significantly different than after whole-breast irradiation

  5. Neuronal patterning of the tubular collar cord is highly conserved among enteropneusts but dissimilar to the chordate neural tube.

    Science.gov (United States)

    Kaul-Strehlow, Sabrina; Urata, Makoto; Praher, Daniela; Wanninger, Andreas

    2017-08-01

    A tubular nervous system is present in the deuterostome groups Chordata (cephalochordates, tunicates, vertebrates) and in the non-chordate Enteropneusta. However, the worm-shaped enteropneusts possess a less complex nervous system featuring only a short hollow neural tube, whereby homology to its chordate counterpart remains elusive. Since the majority of data on enteropneusts stem from the harrimaniid Saccoglossus kowalevskii, putative interspecific variations remain undetected resulting in an unreliable ground pattern that impedes homology assessments. In order to complement the missing data from another enteropneust family, we investigated expression of key neuronal patterning genes in the ptychoderid Balanoglossus misakiensis. The collar cord of B. misakiensis shows anterior Six3/6 and posterior Otx + Engrailed expression, in a region corresponding to the chordate brain. Neuronal Nk2.1/Nk2.2 expression is absent. Interestingly, we found median Dlx and lateral Pax6 expression domains, i.e., a condition that is reversed compared to chordates. Comparative analyses reveal that adult nervous system patterning is highly conserved among the enteropneust families Harrimaniidae, Spengelidae and Ptychoderidae. BmiDlx and BmiPax6 have no corresponding expression domains in the chordate brain, which may be indicative of independent acquisition of a tubular nervous system in Enteropneusta and Chordata.

  6. Seasonal changes in plant-water relations influence patterns of leaf display in Miombo woodlands: evidence of water conservative strategies.

    Science.gov (United States)

    Vinya, Royd; Malhi, Yadvinder; Brown, Nick D; Fisher, Joshua B; Brodribb, Timothy; Aragão, Luiz E O C

    2018-06-15

    Water availability has frequently been linked to seasonal leaf display in seasonally dry ecosystems, but there have been few ecohydrological investigations of this link. Miombo woodland is a dominant seasonally dry tropical forest ecosystem type in southern Africa; however, there are few data on the relationship between seasonal dynamics in plant-water relations and patterns of leaf display for Miombo woodland. Here we investigate this relationship among nine key Miombo woodland tree species differing in drought tolerance ability and leaf phenology. Results of this study showed that seasonal patterns of leaf phenology varied significantly with seasonal changes in stem water relations among the nine species. Leaf shedding coincided with the attainment of seasonal minimum stem water potential. Leaf flush occurred following xylem rehydration at the peak of the dry season suggesting that endogenous plant factors play a pivotal role in seasonal leaf display in this forest type. Drought-tolerant deciduous species suffered significantly higher seasonal losses in xylem hydraulic conductivity than the drought-intolerant semi-evergreen tree species (P water stress in seasonally dry tropical forests selects for water conservative traits that protect the vulnerable xylem transport system. Therefore, seasonal rhythms in xylem transport dictate patterns of leaf display in seasonally dry tropical forests.

  7. The national survey of breast cancer treatment pattern in Korea (1998): the use of breast-conserving treatment

    International Nuclear Information System (INIS)

    Shin, Hyun Soo; Chang, Sei Kyung; Lee, Hyung Sik

    2004-01-01

    In order to improve the proper use of radiotherapy and breast-conserving treatment (BCT) in the management of breast cancer, current status of breast cancer treatment in Korea was surveyed nationwide and the use of BCT were evaluated. Patients characteristics and treatment pattern of 1048 breast cancer patients from 27 institutions diagnosed between January, 1998 and June, 1998 were analyzed. The incidence of receiving BCT was analyzed according to the stage, age, geography, type of hospital, and the availability of radiotherapy facility. Radical mastectomy was performed in 64.8% of total patients and 26% of patients received breast-conserving surgery (BCS). The proportions of patients receiving BCT were 47.5% in stage 0, 54.4% in stage I and 20.3% in stage II. Some of the patients (6.6% of stage I, 10.1% of stage II and 66.7% of stage III) not received radiotherapy after BCS. Only 45% of stage III patients received post-operative radiotherapy after radical mastectomy. The proportion of patients receiving BCT was different according to the geography and availability of radiotherapy facilities. Radiotherapy was not fully used in the management of breast cancer, even in the patients received breast-conserving surgery. The proportion of the patients who received BCT was lower than the report of western countries. To improve the application of proper management of breast cancer, every efforts such as a training of physicians, public education, and improving accessibility of radiotherapy facilities should be done. The factors predicting receipt of BCT were accessibility of radiotherapy facility and geography. Also, periodic survey like current research is warranted

  8. Conserved relative timing of cranial ossification patterns in early mammalian evolution.

    Science.gov (United States)

    Sánchez-Villagra, Marcelo R; Goswami, Anjali; Weisbecker, Vera; Mock, Orin; Kuratani, Shigeru

    2008-01-01

    We analyzed a comprehensive data set of ossification sequences including seven marsupial, 13 placental and seven sauropsid species. Data are provided for the first time for two major mammalian clades, Chiroptera and Soricidae, and for two rodent species; the published sequences of three species were improved with additional sampling. The relative timing of the onset of ossification in 17 cranial elements was recorded, resulting in 136 event pairs, which were treated as characters for each species. Half of these characters are constant across all taxa, 30% are variable but phylogenetically uninformative, and 19% potentially deliver diagnostic features for clades of two or more taxa. Using the conservative estimate of heterochronic changes provided by the program Parsimov, only a few heterochronies were found to diagnose mammals, marsupials, or placentals. A later onset of ossification of the pterygoid with respect to six other cranial bones characterizes therian mammals. This result may relate to the relatively small size of this bone in this clade. One change in relative onset of ossification is hypothesized as a potential human autapomorphy in the context of the sampling made: the earlier onset of the ossification of the periotic with respect to the lacrimal and to three basicranial bones. Using the standard error of scaled ranks across all species as a measure of each element's lability in developmental timing, we found that ossification of early, middle, and late events are similarly labile, with basicranial traits the most labile in timing of onset of ossification. Despite marsupials and placental mammals diverging at least 130 Ma, few heterochronic shifts in cranial ossification diagnose these clades.

  9. Movement patterns of Antillean manatees in Chetumal Bay (Mexico) and coastal Belize: A challenge for regional conservation

    Science.gov (United States)

    Castelblanco-Martínez, Delma Nataly; Padilla-Saldivar, J.; Hernández-Arana, Héctor Abuid; Slone, D.H.; Reid, J.P.; Morales-Vela, B.

    2013-01-01

    Information from 15 satellite-tracked Antillean manatees (Trichechus manatus manatus) was analyzed in order to assess individual movements, home ranges, and high-use areas for conservation decisions. Manatees were captured in Chetumal Bay, Mexico, and tagged with Argos-monitored satellite transmitters. Location of the manatees and physical characteristics were assessed to describe habitat properties. Most manatees traveled to freshwater sources. The Maximum Area Size (MAS) for each manatee was determined using the observation-area method. Additional kernel densities of 95% home range and 50% Center of Activity (COA) were also calculated, with manatees having 1–3 COAs. Manatees exhibited two different movement patterns: remaining in Chetumal Bay, and long-distance (up to 240 km in 89 d). The residence time in Chetumal Bay was higher for females (89.6% of time) than for males (72.0%), but the daily travel rate (0.4–0.5 km/d) was similar for both sexes. Most of the COAs fell within Natural Protected Areas (NPA). However, manatees also travel for long distances into unprotected areas, where they face uncontrolled boat traffic, fishing activities, and habitat loss. Conservation of movement corridors may promote long-distance movements and facilitate genetic exchange.

  10. Marine protected area design patterns in the Mediterranean Sea: Implications for conservation.

    Science.gov (United States)

    Rodríguez-Rodríguez, D; Rodríguez, J; Blanco, J M; Abdul Malak, D

    2016-09-15

    Mediterranean marine protected area (MPA) design patterns regarding geographic distribution, size, spacing and shape were analysed as a proxy of the region's MPA's ecological effectiveness and a first step towards an ecologically coherent MPA network. Results for legally designated MPAs and ecologically functional MPAs accounting for overlaps are presented. Geographically, Mediterranean MPA area is very unevenly distributed, with four-fifths concentrated in just three countries of the north-western part of the basin. Average distance between functional MPAs lies within recommended ecological thresholds, which suggests adequate potential connectivity of the Mediterranean MPA system. Mediterranean designated MPAs are larger than MPAs worldwide on average, although they are generally smaller than international guidance suggests at different levels: ecoregion, country and designation category. On average, Mediterranean designated and functional MPAs have relatively high compactness, which makes them prone to spillover and adequate viability, and less vulnerable to edge effects. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Geographic patterns of genetic variation and conservation consequences in three South American rodents.

    Science.gov (United States)

    Miranda, Gustavo B; Andrades-Miranda, Jaqueline; Oliveira, Luiz F B; Langguth, Alfredo; Mattevi, Margarete S

    2007-12-01

    In this study, the geographic patterns of genetic variation of three rodent species belonging to the tribe Oryzomyini were investigated using the mitochondrial cytochrome b and nuclear IRBP genes in biomes that are undergoing degradation processes to a greater or lesser degree. The samples are from 25 collecting localities distributed throughout the Amazon, Cerrado, Atlantic Forest, and Pampa biomes. The results show that the three species have a population and geographic structure, besides being in demographic equilibrium. The phylogenetic analyses performed on Euryoryzomys russatus and Hylaeamys megacephalus showed these specimens grouped in three distinct clades forming geographic gradients (North-South direction in H. megacephalus). Intraspecific genetic divergence was higher in H. megacephalus (4.53%), followed by E. russatus (1.79%), and lowest in Sooretamys angouya (0.88%). The results obtained indicate that, necessarily, the management strategies to preserve genetic diversity should be different for each species, since each of them presented specific population parameters.

  12. Assessment of fuel resource diversity and utilization patterns in Askot Wildlife Sanctuary in Kumaun Himalaya, India, for conservation and management

    Energy Technology Data Exchange (ETDEWEB)

    Samant, Sher S.; Dhar, Uppeandra; Rawal, Ranbeer S. [G.B. Pant Inst. of Himalayan Environment and Development, Uttar Pradesh (India)

    2000-07-01

    A general decrease in abundance of wood plant species used as sources of fuel suggests that more detailed information is urgently needed on species-level trends and their conservation. Such studies have not been carried out so far in India and elsewhere; we therefore quantified the species-wise extraction of fuel from a site (Gori Ganga Valley) in Askot Wildlife Sanctuary in the Kumaun Himalaya. In all, 31 species (26 trees and 5 shrubs) were used as fuel, of which 14 were native to the Himalaya. Utilisation patterns, distributions, probabilities of use (PU), resources use indices (RUI), preferences and availabilities in forest communities of these species were determined. Use pattern did not vary much amongst low altitude villages (Similarity: 52-74%), whereas along the vertical (elevational) gradient it varied considerably (Similarity: 15-31%). Woodfordia fruticosa (L.) Kurz, Pinus roxburghii Sarg., Quercus leucotrichophora A. Camus, Macaranga pustulata King ex Hk. F., Quercus lanuginosa Don, Engelhardtia spicata Bl. and Mallotus philippensis (Lamk.) Muell. contributed most to collections, while Pyracantha crenulata (Don) Roem., Syzygium cuminii (L.) Skeels, Alnus nepalensis Don and Bauhinia vahlii Wt. and Arn. were in lesser demand. W. fruticosa, P. roxburghii, M. pustulata, Casearia elliptica Willd., E. spicata, M. philippensis, Q. leucotrichophora and Phoebe lanceolata (Nees) Nees showed high values of PU and RUI, indicating high pressure. Higher density of P. roxburghii, Rhododendron arboreum Sm., Q. lanuginosa, Q. leucotrichophora, Lyonia ovalifolia (Wall.) Drude, C. elliptica and M. pustulata amongst trees and Maesa indica A.DC., P. crenulata and W. fruticosa amongst shrubs exhibited high density but the remaining species showed low density indicating the possible depletion. Intensive management of natural habitats of species highly-referred for fuel, diversification of choice of species from natives to non-natives, large scale propagation of highly

  13. Connectivity and Dispersal Patterns of Protected Biogenic Reefs: Implications for the Conservation of Modiolus modiolus (L. in the Irish Sea.

    Directory of Open Access Journals (Sweden)

    Kate Gormley

    Full Text Available Biogenic reefs created by Modiolus modiolus (Linnaeus, 1758 (horse mussel reefs are marine habitats which support high levels of species biodiversity and provide valuable ecosystem services. Currently, M. modiolus reefs are listed as a threatened and/or declining species and habitat in all OSPAR regions and thus are highlighted as a conservation priority under the EU Marine Strategy Framework Directive (MSFD. Determining patterns of larval dispersal and genetic connectivity of remaining horse mussel populations can inform management efforts and is a critical component of effective marine spatial planning (MSP. Larval dispersal patterns and genetic structure were determined for several M. modiolus bed populations in the Irish Sea including those in Wales (North Pen Llŷn, Isle of Man (Point of Ayre and Northern Ireland (Ards Peninsula and Strangford Lough. Simulations of larval dispersal suggested extant connectivity between populations within the Irish Sea. Results from the genetic analysis carried out using newly developed microsatellite DNA markers were consistent with those of the biophysical model. Results indicated moderately significant differentiation between the Northern Ireland populations and those in the Isle of Man and Wales. Simulations of larval dispersal over a 30 day pelagic larval duration (PLD suggest that connectivity over a spatial scale of 150km is possible between some source and sink populations. However, it appears unlikely that larvae from Northern Ireland will connect directly with sites on the Llŷn or Isle of Man. It also appears unlikely that larvae from the Llŷn connect directly to any of the other sites. Taken together the data establishes a baseline for underpinning management and conservation of these important and threatened marine habitats in the southern part of the known range.

  14. 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

  15. Influence of recombinant interferon alpha on nutritional status and growth pattern in children with chronic viral hepatitis.

    Science.gov (United States)

    Gottrand, F; Michaud, L; Guimber, D; Ategbo, S; Dubar, G; Turck, D; Farriaux, J P

    1996-12-01

    Anorexia and weight loss are frequently reported as adverse effects during recombinant interferon alpha (rIFN-alpha) treatment. The aim of the present study was to assess both nutritional status and growth of children and adolescents treated with rIFN-alpha for chronic viral hepatitis. Eleven patients aged 4-16 years with histologically proven chronic active hepatitis (hepatitis B, n = 9; hepatitis C, n = 2) receiving rIFN-alpha subcutaneously thrice a week for 6 months were studied. Weight and height increments were assessed during the 6 months before starting rIFN-alpha. Weight and height were measured every 3 months (M0, M3, M6) during the 6 months of rIFN-alpha treatment, then every 6 months during the follow up period (6-36 months). Weight decreased in every child during rIFN-alpha treatment (weight loss varies from 0.5 to 2.6 kg after 3 months of treatment). Weight/age Z-score decreased from 0.12 at M0 to -0.69 at M3 (P Nutritional status was significantly impaired during treatment (Z-score for weight/height decreased from 0.18 at M0 to -0.74 at M3, P nutritional status are encountered constantly at the beginning of rIFN-alpha therapy without any deleterious effect on growth. Information of the families and nutritional intervention during treatment should be required, in order to limit the importance of weight loss.

  16. Skull ontogeny: developmental patterns of fishes conserved across major tetrapod clades.

    Science.gov (United States)

    Schoch, Rainer R

    2006-01-01

    In vertebrates, the ontogeny of the bony skull forms a particularly complex part of embryonic development. Although this area used to be restricted to neontology, recent discoveries of fossil ontogenies provide an additional source of data. One of the most detailed ossification sequences is known from Permo-Carboniferous amphibians, the branchiosaurids. These temnospondyls form a near-perfect link between the piscine osteichthyans and the various clades of extant tetrapods, retaining a full complement of dermal bones in the skull. For the first time, the broader evolutionary significance of these event sequences is analyzed, focusing on the identification of sequence heterochronies. A set of 120 event pairs was analyzed by event pair cracking, which helped identify active movers. A cladistic analysis of the event pair data was also carried out, highlighting some shared patterns between widely divergent clades of tetrapods. The analyses revealed an unexpected degree of similarity between the widely divergent taxa. Most interesting is the apparently modular composition of the cranial sequence: five clusters of bones were discovered in each of which the elements form in the same time window: (1) jaw bones, (2) marginal palatal elements, (3) circumorbital bones, (4) skull roof elements, and (5) neurocranial ossifications. In the studied taxa, these "modules" have in most cases been shifted fore and back on the trajectory relative to the Amia sequence, but did not disintegrate. Such "modules" might indicate a high degree of evolutionary limitation (constraint).

  17. [Distribution pattern of rare plants along riparian zone and its implication for conservation in Shennongjia area].

    Science.gov (United States)

    Jiang, Mingxi; Deng, Hongbing; Cai, Qinghua

    2002-11-01

    Due to the importance of riparian zone in maintaining and protecting regional biodiversity, more and more ecologists paid their attentions to riparian zone, and had been aware of the important effects of riparian zone in basic study and practical management. In this study, forty sampling belts (10 m x 100 m) parallel to the bank of Xiangxi River at different elevations in Shennongjia area were selected to investigate the riparian vegetation and rare plants. Fourteen species of rare plants were found in riparian zone, accounting for 42.4% of total rare plant species in Shennongjia area. The main distribution range of the fourteen rare plant species was the mixed evergreen and deciduous broadleaved forest at elevation of 1200-1800 m, where species diversity of plant community was the maximum at the moderate elevation. Fourteen rare plant species could be divided into three groups against the elevation, namely low elevation species group, moderate elevation species group, and high elevation group. In the paper, the authors discussed the reasons forming the distribution pattern of rare plant species, and pointed out the important function of riparian zone on rare plant species protection.

  18. Fire patterns in the range of the greater sage-grouse, 1984-2013 — Implications for conservation and management

    Science.gov (United States)

    Brooks, Matthew L.; Matchett, John R.; Shinneman, Douglas J.; Coates, Peter S.

    2015-09-10

    Fire ranks among the top three threats to the greater sage-grouse (Centrocercus urophasianus) throughout its range, and among the top two threats in the western part of its range. The national research strategy for this species and the recent U.S. Department of the Interior Secretarial Order 3336 call for science-based threats assessment of fire to inform conservation planning and fire management efforts. The cornerstone of such assessments is a clear understanding of where fires are occurring and what aspects of fire regimes may be shifting outside of their historical range of variation. This report fulfills this need by describing patterns of fire area, fire size, fire rotation, and fire season length and timing from 1984 to 2013 across the range of the greater sage-grouse. This information need is further addressed by evaluating the ecological and management implications of these fire patterns. Analyses are stratified by major vegetation types and the seven greater sage-grouse management zones, delineated regionally as four western and three eastern management zones. Soil temperature and moisture indicators of resilience to fire and resistance to cheatgrass invasion, and the potential for establishment of a grass/fire cycle, are used as unifying concepts in developing fire threat assessments for each analysis strata.

  19. Sexual segregation in marine fish, reptiles, birds and mammals behaviour patterns, mechanisms and conservation implications.

    Science.gov (United States)

    Wearmouth, Victoria J; Sims, David W

    2008-01-01

    Sexual segregation occurs when members of a species separate such that the sexes live apart, either singly or in single-sex groups. It can be broadly categorised into two types: habitat segregation and social segregation. Sexual segregation is a behavioural phenomenon that is widespread in the animal kingdom yet the underlying causes remain poorly understood. Sexual segregation has been widely studied among terrestrial mammals such as ungulates, but it has been less well documented in the marine environment. This chapter clarifies terms and concepts which have emerged from the investigation of sexual segregation in terrestrial ecology and examines how a similar methodological approach may be complicated by differences of marine species. Here we discuss the behavioural patterns of sexual segregation among marine fish, reptile, bird and mammal species. Five hypotheses have been forwarded to account for sexual segregation, largely emerging from investigation of sexual segregation in terrestrial ungulates: the predation risk, forage selection, activity budget, thermal niche-fecundity and social factors hypotheses. These mechanisms are reviewed following careful assessment of their applicability to marine vertebrate species and case studies of marine vertebrates which support each mechanism recounted. Rigorous testing of all hypotheses is lacking from both the terrestrial and marine vertebrate literature and those analyses which have been attempted are often confounded by factors such as sexual body-size dimorphism. In this context, we indicate the value of studying model species which are monomorphic with respect to body size and discuss possible underlying causes for sexual segregation in this species. We also discuss why it is important to understand sexual segregation, for example, by illustrating how differential exploitation of the sexes by humans can lead to population decline.

  20. Conservation status and spatial patterns of AGRRA vitality indices in Southwestern Atlantic Reefs

    Directory of Open Access Journals (Sweden)

    Ruy K.P Kikuchi

    2010-05-01

    Full Text Available Coral reefs along the Eastern Brazilian coast extend for a distance of 800km from 12° to 18°S. They are the largest and the richest reefs of Brazil coasts, and represent the Southernmost coral reefs of the Southwestern Atlantic Ocean. Few reef surveys were performed in the 90’s in reef areas of Bahia State, particularly in the Abrolhos reef complex, in the Southernmost side of the state. A monitoring program applying the Atlantic and Gulf Rapid Reef Assessment (AGRRA protocol was initiated in 2000, in the Abrolhos National Marine Park, after the creation of the South Tropical America (STA Regional Node of the Global Coral Reef Monitoring Network (GCRMN by the end of 1999. From that time up to 2005, nine reef surveys were conducted along the coast of the State of Bahia, including 26 reefs, with 95 benthic sites, 280 benthic transects, 2025 quadrats and 3537 stony corals. Eighteen of the 26 investigated reefs were assessed once and eight reefs of Abrolhos were surveyed twice to four times. The MDS ordination, analysis of similarity (ANOSIM, one way and two-way nested layouts and similarity percentages (SIMPER tests were applied to investigate the spatial and temporal patterns of reef vitality. Four indicators of the coral vitality: live coral cover, the density of the larger corals (colonies >20cm per reef site and of the coral recruits (colonies<2cm per square meter, and the percentage of macroalgae indicate that the nearshore reefs, which are located less than 5km from the coast, are in poorer condition than the reefs located more than 5km off the coast. A higher density of coral colonies, lower macroalgal index, higher relative percent of turf algae and higher density of coral recruits in offshore reefs compared to the nearshore reefs are the conditions that contribute more than 80% to the dissimilarity between them. The offshore reefs are in better vital condition than the nearhore reefs and have a set of vitality indices more closely

  1. Conservation status and spatial patterns of AGRRA vitality indices in Southwestern Atlantic reefs.

    Science.gov (United States)

    Kikuchi, Ruy K P; Leão, Zelinda M A N; Oliveira, Marília D M

    2010-05-01

    Coral reefs along the Eastern Brazilian coast extend for a distance of 800 km from 12 degrees to 18 degrees S. They are the largest and the richest reefs of Brazil coasts, and represent the Southernmost coral reefs of the Southwestern Atlantic Ocean. Few reef surveys were performed in the 90's in reef areas of Bahia State, particularly in the Abrolhos reef complex, in the Southernmost side of the state. A monitoring program applying the Atlantic and Gulf Rapid Reef Assessment (AGRRA) protocol was initiated in 2000, in the Abrolhos National Marine Park, after the creation of the South Tropical America (STA) Regional Node of the Global Coral Reef Monitoring Network (GCRMN) by the end of 1999. From that time up to 2005, nine reef surveys were conducted along the coast of the State of Bahia, including 26 reefs, with 95 benthic sites, 280 benthic transects, 2025 quadrats and 3537 stony corals. Eighteen of the 26 investigated reefs were assessed once and eight reefs of Abrolhos were surveyed twice to four times. The MDS ordination, analysis of similarity (ANOSIM, one way and two-way nested layouts) and similarity percentages (SIMPER) tests were applied to investigate the spatial and temporal patterns of reef vitality. Four indicators of the coral vitality: live coral cover, the density of the larger corals (colonics > 20cm per reef site) and of the coral recruits (colonies coast, are in poorer condition than the reefs located more than 5 km off the coast. A higher density of coral colonies, lower macroalgal index, higher relative percent of turf algae and higher density of coral recruits in offshore reefs compared to the nearshore reefs are the conditions that contribute more than 80% to the dissimilarity between them. The offshore reefs are in better vital condition than the nearshore reefs and have a set of vitality indices more closely related to the Northwestern Atlantic reefs than the nearshore reef. These have been most severely impacted by the effects of direct

  2. Testing the effects of perimeter fencing and elephant exclosures on lion predation patterns in a Kenyan wildlife conservancy.

    Science.gov (United States)

    Dupuis-Desormeaux, Marc; Davidson, Zeke; Pratt, Laura; Mwololo, Mary; MacDonald, Suzanne E

    2016-01-01

    The use of fences to segregate wildlife can change predator and prey behaviour. Predators can learn to incorporate fencing into their hunting strategies and prey can learn to avoid foraging near fences. A twelve-strand electric predator-proof fence surrounds our study site. There are also porous one-strand electric fences used to create exclosures where elephant (and giraffe) cannot enter in order to protect blocs of browse vegetation for two critically endangered species, the black rhinoceros (Diceros bicornis) and the Grevy's zebra (Equus grevyi). The denser vegetation in these exclosures attracts both browsing prey and ambush predators. In this study we examined if lion predation patterns differed near the perimeter fencing and inside the elephant exclosures by mapping the location of kills. We used a spatial analysis to compare the predation patterns near the perimeter fencing and inside the exclosures to predation in the rest of the conservancy. Predation was not over-represented near the perimeter fence but the pattern of predation near the fence suggests that fences may be a contributing factor to predation success. Overall, we found that predation was over-represented inside and within 50 m of the exclosures. However, by examining individual exclosures in greater detail using a hot spot analysis, we found that only a few exclosures contained lion predation hot spots. Although some exclosures provide good hunting grounds for lions, we concluded that exclosures did not necessarily create prey-traps per se and that managers could continue to use this type of exclusionary fencing to protect stands of dense vegetation.

  3. Testing the effects of perimeter fencing and elephant exclosures on lion predation patterns in a Kenyan wildlife conservancy

    Directory of Open Access Journals (Sweden)

    Marc Dupuis-Desormeaux

    2016-02-01

    Full Text Available The use of fences to segregate wildlife can change predator and prey behaviour. Predators can learn to incorporate fencing into their hunting strategies and prey can learn to avoid foraging near fences. A twelve-strand electric predator-proof fence surrounds our study site. There are also porous one-strand electric fences used to create exclosures where elephant (and giraffe cannot enter in order to protect blocs of browse vegetation for two critically endangered species, the black rhinoceros (Diceros bicornis and the Grevy’s zebra (Equus grevyi. The denser vegetation in these exclosures attracts both browsing prey and ambush predators. In this study we examined if lion predation patterns differed near the perimeter fencing and inside the elephant exclosures by mapping the location of kills. We used a spatial analysis to compare the predation patterns near the perimeter fencing and inside the exclosures to predation in the rest of the conservancy. Predation was not over-represented near the perimeter fence but the pattern of predation near the fence suggests that fences may be a contributing factor to predation success. Overall, we found that predation was over-represented inside and within 50 m of the exclosures. However, by examining individual exclosures in greater detail using a hot spot analysis, we found that only a few exclosures contained lion predation hot spots. Although some exclosures provide good hunting grounds for lions, we concluded that exclosures did not necessarily create prey-traps per se and that managers could continue to use this type of exclusionary fencing to protect stands of dense vegetation.

  4. Conservation status and spatial patterns of AGRRA vitality indices in Southwestern Atlantic Reefs

    Directory of Open Access Journals (Sweden)

    Ruy K.P Kikuchi

    2010-05-01

    Full Text Available Coral reefs along the Eastern Brazilian coast extend for a distance of 800km from 12° to 18°S. They are the largest and the richest reefs of Brazil coasts, and represent the Southernmost coral reefs of the Southwestern Atlantic Ocean. Few reef surveys were performed in the 90’s in reef areas of Bahia State, particularly in the Abrolhos reef complex, in the Southernmost side of the state. A monitoring program applying the Atlantic and Gulf Rapid Reef Assessment (AGRRA protocol was initiated in 2000, in the Abrolhos National Marine Park, after the creation of the South Tropical America (STA Regional Node of the Global Coral Reef Monitoring Network (GCRMN by the end of 1999. From that time up to 2005, nine reef surveys were conducted along the coast of the State of Bahia, including 26 reefs, with 95 benthic sites, 280 benthic transects, 2025 quadrats and 3537 stony corals. Eighteen of the 26 investigated reefs were assessed once and eight reefs of Abrolhos were surveyed twice to four times. The MDS ordination, analysis of similarity (ANOSIM, one way and two-way nested layouts and similarity percentages (SIMPER tests were applied to investigate the spatial and temporal patterns of reef vitality. Four indicators of the coral vitality: live coral cover, the density of the larger corals (colonies >20cm per reef site and of the coral recruits (coloniesDesde el año 2000 se inició un programa de monitoreo utilizando el protocolo AGRRA en el Parque Nacional Marino de Abrolhos en el marco de la creación del Nodo STA de la GCRMN. Entre 2000 y 2005 se realizaron varias evaluaciones en 26 arrecifes. Los patrones espaciales y temporales de la vitalidad de los arrecifes fueron estudiados mediante análisis de ordenación (MDS, similaridad (ANOSIM y porcentajes de similaridad (SIMPER. La cobertura de coral vivo, la densidad de colonias grandes (>20cm y de reclutas (<2cm y la cobertura de macroalgas indicaron que los arrecifes ubicados a más de 5km de la

  5. Ectopic application of recombinant BMP-2 and BMP-4 can change patterning of developing chick facial primordia.

    Science.gov (United States)

    Barlow, A J; Francis-West, P H

    1997-01-01

    The facial primordia initially consist of buds of undifferentiated mesenchyme, which give rise to a variety of tissues including cartilage, muscle and nerve. These must be arranged in a precise spatial order for correct function. The signals that control facial outgrowth and patterning are largely unknown. The bone morphogenetic proteins Bmp-2 and Bmp-4 are expressed in discrete regions at the distal tips of the early facial primordia suggesting possible roles for BMP-2 and BMP-4 during chick facial development. We show that expression of Bmp-4 and Bmp-2 is correlated with the expression of Msx-1 and Msx-2 and that ectopic application of BMP-2 and BMP-4 can activate Msx-1 and Msx-2 gene expression in the developing facial primordia. We correlate this activation of gene expression with changes in skeletal development. For example, activation of Msx-1 gene expression across the distal tip of the mandibular primordium is associated with an extension of Fgf-4 expression in the epithelium and bifurcation of Meckel's cartilage. In the maxillary primordium, extension of the normal domain of Msx-1 gene expression is correlated with extended epithelial expression of shh and bifurcation of the palatine bone. We also show that application of BMP-2 can increase cell proliferation of the mandibular primordia. Our data suggest that BMP-2 and BMP-4 are part of a signalling cascade that controls outgrowth and patterning of the facial primordia.

  6. Meta-analysis of breast cancer microarray studies in conjunction with conserved cis-elements suggest patterns for coordinate regulation

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    Lundberg Cathryn

    2008-01-01

    Full Text Available Abstract Background Gene expression measurements from breast cancer (BrCa tumors are established clinical predictive tools to identify tumor subtypes, identify patients showing poor/good prognosis, and identify patients likely to have disease recurrence. However, diverse breast cancer datasets in conjunction with diagnostic clinical arrays show little overlap in the sets of genes identified. One approach to identify a set of consistently dysregulated candidate genes in these tumors is to employ meta-analysis of multiple independent microarray datasets. This allows one to compare expression data from a diverse collection of breast tumor array datasets generated on either cDNA or oligonucleotide arrays. Results We gathered expression data from 9 published microarray studies examining estrogen receptor positive (ER+ and estrogen receptor negative (ER- BrCa tumor cases from the Oncomine database. We performed a meta-analysis and identified genes that were universally up or down regulated with respect to ER+ versus ER- tumor status. We surveyed both the proximal promoter and 3' untranslated regions (3'UTR of our top-ranking genes in each expression group to test whether common sequence elements may contribute to the observed expression patterns. Utilizing a combination of known transcription factor binding sites (TFBS, evolutionarily conserved mammalian promoter and 3'UTR motifs, and microRNA (miRNA seed sequences, we identified numerous motifs that were disproportionately represented between the two gene classes suggesting a common regulatory network for the observed gene expression patterns. Conclusion Some of the genes we identified distinguish key transcripts previously seen in array studies, while others are newly defined. Many of the genes identified as overexpressed in ER- tumors were previously identified as expression markers for neoplastic transformation in multiple human cancers. Moreover, our motif analysis identified a collection of

  7. Genetic Recombination

    Science.gov (United States)

    Whitehouse, H. L. K.

    1973-01-01

    Discusses the mechanisms of genetic recombination with particular emphasis on the study of the fungus Sordaria brevicollis. The study of recombination is facilitated by the use of mutants of this fungus in which the color of the ascospores is affected. (JR)

  8. Complex patterns of genetic and phenotypic divergence in an island bird and the consequences for delimiting conservation units.

    Science.gov (United States)

    Phillimore, A B; Owens, I P F; Black, R A; Chittock, J; Burke, T; Clegg, S M

    2008-06-01

    Substantial phenotypic and genetic variation is often found below the species level and this may be useful in quantifying biodiversity and predicting future diversification. However, relatively few studies have tested whether different aspects of intraspecific variation show congruent patterns across populations. Here, we quantify several aspects of divergence between 13 insular populations of an island endemic bird, the Vanuatu white-eye (Zosterops flavifrons). The components of divergence studied are mitochondrial DNA (mtDNA), nuclear DNA microsatellites and morphology. These different aspects of divergence present subtly different scenarios. For instance, an mtDNA phylogenetic tree reveals a potential cryptic species on the most southerly island in Vanuatu and considerable divergence between at least two other major phylogroups. Microsatellite loci suggest that population genetic divergence between insular populations, both between and within phylogroups, is substantial, a result that is consistent with a low level of interisland gene flow. Finally, most populations were found to be strongly morphologically divergent, but no single population was morphologically diagnosable from all others. Taken together, our results show that, although many measures of divergence are concordant in this system, the number of divergent units identified varies widely depending on the characters considered and approach used. A continuum of divergence and a degree of discordance between different characters are both to be expected under simple models of evolution, but they present problems in terms of delimiting conservation units.

  9. Species diversity, vegetation pattern and conservation of Gentiana macrophylla Pall. communities in Dongling mountain meadow, Beijing, China

    International Nuclear Information System (INIS)

    Sadia, S.; Zhang, J.T.; Bai, X.; Shedayi, A.A.; Tariq, A.

    2017-01-01

    Gentiana macrophylla, native to mountainous areas of Central and Southern Asia, is most popular remedy for rheumatism and pains in Traditional Chinese Medicine with an extensive demand in local market. Our study aimed to classify G. macrophylla communities and to find out the impact of topographic and soil factors on their diversity and distribution in Dongling mountain meadow, Beijing, China. Seventy five samples in 15 transects separated by 50m distance in altitude along an elevation gradient (1592-2298m) were established by quadrate method. TWINSAPN and CCA were used for classification and ordination, respectively. Six diversity indices (Species richness, Shannon-Weiner heterogeneity, Simpson’s index, Hill’s index, Pielou evenness and McIntosh evenness) were used to analyze the pattern of species diversity and polynomial regression analysis was used to establish their relationship with environmental variables. TWINSPAN classified G. macrophylla communities into 8 types and CCA indicated that soil pH, soil temperature, soil type, disturbance, total N, total K, Mg and Zn were significantly related to these communities. Elevation was the most significant factor that affecting the diversity and distribution of G. macrophylla communities. Significant effect of environment, topography and disturbance to meadow communities of G. macrophylla highly suggests some important measures such as uprooting restriction, tourism limitation in meadow area, monitoring of functional diversity, fertilization, irrigation, cloning and cultivation to protect and conserve it and its communities to be used in medicine industry. (author)

  10. An Assessment of Land Conservation Patterns in Maine Based on Spatial Analysis of Ecological and Socioeconomic Indicators

    Science.gov (United States)

    Cronan, Christopher S.; Lilieholm, Robert J.; Tremblay, Jill; Glidden, Timothy

    2010-05-01

    Given the nature of modern conservation acquisitions, which often result from gifts and opportunistic purchases of full or partial property rights, there is a risk that the resulting mosaic of conserved resources may not represent a coherent set of public values and benefits. With different public and private entities engaged in land conservation, one would further expect that each organization would apply separate goals and criteria to the selection and acquisition of its conservation portfolio. This set of circumstances raises an important question: what is the aggregate outcome of this land conservation process? Retrospective assessments provide a means of reviewing cumulative historical decisions and elucidating lessons for improving future conservation strategies. This study used GIS-based spatial analysis to examine the relationships of private and public conservation lands in Maine to a variety of landscape metrics in order to determine the degree to which these lands represent core ecological and socioeconomic values that are meaningful to a wide cross-section of citizens. Results revealed that the gains of past conservation efforts in Maine are counter-balanced to some extent by apparent gaps in the existing fabric of conservation holdings. Conservation lands capture a representative sample of diverse habitat, provide a large measure of protection for multiple conservation values and indicators, and offer an unusual mix of outdoor recreational opportunities for residents and visitors alike. Yet, the majority of parcels are relatively small and isolated, and thus do not provide contiguous habitat blocks that offset ongoing processes of landscape fragmentation. Furthermore, the majority of area associated with many of the ecological metrics examined in this report is located outside the boundaries of current conservation holdings. The under-represented metrics identified in this investigation can be viewed as potential targets for new strategic conservation

  11. Genome-Wide Fine-Scale Recombination Rate Variation in Drosophila melanogaster

    Science.gov (United States)

    Song, Yun S.

    2012-01-01

    Estimating fine-scale recombination maps of Drosophila from population genomic data is a challenging problem, in particular because of the high background recombination rate. In this paper, a new computational method is developed to address this challenge. Through an extensive simulation study, it is demonstrated that the method allows more accurate inference, and exhibits greater robustness to the effects of natural selection and noise, compared to a well-used previous method developed for studying fine-scale recombination rate variation in the human genome. As an application, a genome-wide analysis of genetic variation data is performed for two Drosophila melanogaster populations, one from North America (Raleigh, USA) and the other from Africa (Gikongoro, Rwanda). It is shown that fine-scale recombination rate variation is widespread throughout the D. melanogaster genome, across all chromosomes and in both populations. At the fine-scale, a conservative, systematic search for evidence of recombination hotspots suggests the existence of a handful of putative hotspots each with at least a tenfold increase in intensity over the background rate. A wavelet analysis is carried out to compare the estimated recombination maps in the two populations and to quantify the extent to which recombination rates are conserved. In general, similarity is observed at very broad scales, but substantial differences are seen at fine scales. The average recombination rate of the X chromosome appears to be higher than that of the autosomes in both populations, and this pattern is much more pronounced in the African population than the North American population. The correlation between various genomic features—including recombination rates, diversity, divergence, GC content, gene content, and sequence quality—is examined using the wavelet analysis, and it is shown that the most notable difference between D. melanogaster and humans is in the correlation between recombination and

  12. The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains

    Directory of Open Access Journals (Sweden)

    Wang Yiguo

    2008-10-01

    Full Text Available Abstract Background Many well-represented domains recognize primary sequences usually less than 10 amino acids in length, called Short Linear Motifs (SLiMs. Accurate prediction of SLiMs has been difficult because they are short (often Results Our combined approach revealed that SLiMs are highly conserved in proteins from functional classes that are known to interact with a specific domain, but that they are not conserved in most other protein groups. We found that SLiMs recognized by SH2 domains were highly conserved in receptor kinases/phosphatases, adaptor molecules, and tyrosine kinases/phosphatases, that SLiMs recognized by SH3 domains were highly conserved in cytoskeletal and cytoskeletal-associated proteins, that SLiMs recognized by PDZ domains were highly conserved in membrane proteins such as channels and receptors, and that SLiMs recognized by S/T kinase domains were highly conserved in adaptor molecules, S/T kinases/phosphatases, and proteins involved in transcription or cell cycle control. We studied Tyr-SLiMs recognized by SH2 domains in more detail, and found that SH2-recognized Tyr-SLiMs on the cytoplasmic side of membrane proteins are more highly conserved than those on the extra-cellular side. Also, we found that SH2-recognized Tyr-SLiMs that are associated with SH3 motifs and a tyrosine kinase phosphorylation motif are more highly conserved. Conclusion The interactome of protein domains is reflected by the evolutionary conservation of SLiMs recognized by these domains. Combining scoring matrixes derived from peptide libraries and conservation analysis, we would be able to find those protein groups that are more likely to interact with specific domains.

  13. Spectrum Recombination.

    Science.gov (United States)

    Greenslade, Thomas B., Jr.

    1984-01-01

    Describes several methods of executing lecture demonstrations involving the recombination of the spectrum. Groups the techniques into two general classes: bringing selected portions of the spectrum together using lenses or mirrors and blurring the colors by rapid movement or foreshortening. (JM)

  14. Review of Parton Recombination Models

    International Nuclear Information System (INIS)

    Bass, Steffen A

    2006-01-01

    Parton recombination models have been very successful in explaining data taken at RHIC on hadron spectra and emission patterns in Au+Au collisions at transverse momenta above 2 GeV/c, which have exhibited features which could not be understood in the framework of basic perturbative QCD. In this article I will review the current status on recombination models and outline which future challenges need to be addressed by this class of models

  15. Fish Assemblage Patterns as a Tool to Aid Conservation in the Olifants River Catchment (East), South Africa

    Science.gov (United States)

    South Africa has committed to address freshwater conservation at the catchment scale, using a combination of landscape-level and species-level features as surrogates of freshwater biodiversity. Here we examined fishes in the Olifants catchment, where multiple anthropogenic pressu...

  16. Conservation patterns of HIV-1 RT connection and RNase H domains: identification of new mutations in NRTI-treated patients.

    Directory of Open Access Journals (Sweden)

    André F A Santos

    Full Text Available BACKGROUND: Although extensive HIV drug resistance information is available for the first 400 amino acids of its reverse transcriptase, the impact of antiretroviral treatment in C-terminal domains of Pol (thumb, connection and RNase H is poorly understood. METHODS AND FINDINGS: We wanted to characterize conserved regions in RT C-terminal domains among HIV-1 group M subtypes and CRF. Additionally, we wished to identify NRTI-related mutations in HIV-1 RT C-terminal domains. We sequenced 118 RNase H domains from clinical viral isolates in Brazil, and analyzed 510 thumb and connection domain and 450 RNase H domain sequences collected from public HIV sequence databases, together with their treatment status and histories. Drug-naïve and NRTI-treated datasets were compared for intra- and inter-group conservation, and differences were determined using Fisher's exact tests. One third of RT C-terminal residues were found to be conserved among group M variants. Three mutations were found exclusively in NRTI-treated isolates. Nine mutations in the connection and 6 mutations in the RNase H were associated with NRTI treatment in subtype B. Some of them lay in or close to amino acid residues which contact nucleic acid or near the RNase H active site. Several of the residues pointed out herein have been recently associated to NRTI exposure or increase drug resistance to NRTI. CONCLUSIONS: This is the first comprehensive genotypic analysis of a large sequence dataset that describes NRTI-related mutations in HIV-1 RT C-terminal domains in vivo. The findings into the conservation of RT C-terminal domains may pave the way to more rational drug design initiatives targeting those regions.

  17. Use patterns, use values and management of Afzelia africana Sm. in Burkina Faso: implications for species domestication and sustainable conservation.

    Science.gov (United States)

    Balima, Larba Hubert; Nacoulma, Blandine Marie Ivette; Ekué, Marius Rodrigue Mensah; Kouamé, François N'Guessan; Thiombiano, Adjima

    2018-03-27

    The lack of literature on the interactions between indigenous people and the valuable agroforestry trees hinder the promotion of sustainable management of plant resources in West African Sahel. This study aimed at assessing local uses and management of Afzelia africana Sm. in Burkina Faso, as a prerequisite to address issues of domestication and sustainable conservation. One thousand forty-four peoples of seven dominant ethnic groups were questioned in 11 villages through 221 semi-structured focus group interviews. The surveys encompassed several rural communities living around six protected areas along the species distribution range. Questions refer mainly to vernacular names of A. africana, locals' motivations to conserve the species, the uses, management practices and local ecological knowledge on the species. Citation frequency was calculated for each response item of each questionnaire section to obtain quantitative data. The quantitative data were then submitted to comparison tests and multivariate statistics in R program. A. africana is a locally well-known tree described as a refuge of invisible spirits. Due to this mystery and its multipurpose uses, A. africana is conserved within the agroforestry systems. The species is widely and mostly used as fodder (87.55%), drugs (75.93%), fetish or sanctuary (70.95%), food (41.49%), and raw material for carpentry (36.19%) and construction (7.05%). While the uses as fodder, food and construction involved one organ, the leaves and wood respectively, the medicinal use was the most diversified. All tree organs were traditionally used in 10 medical prescriptions to cure about 20 diseases. The species use values differed between ethnic groups with lower values within the Dagara and Fulani. The findings reveal a total absence of specific management practices such as assisted natural regeneration, seeding, or transplantation of A. africana sapling. However, trees were permanently pruned and debarked by local people

  18. Distribution patterns of long-lived individuals of relict plants around Fanjingshan Mountain in China: Implications for in situ conservation

    Directory of Open Access Journals (Sweden)

    Liao, H. Y.

    2015-12-01

    Full Text Available The mountain areas in south-central China are widely recognized as refugia of relict plants during the late Neogene and Quaternary periods. In this paper, we try to explore the distribution patterns of natural habitats and to exactly locate the refugia of relict species around Fanjingshan Mountain using dendrological data of long-lived individuals (≥ 100 years old. Six typical relict plants were found around the mountain, i.e. Cyclocarya paliurus, Ginkgo biloba, Liriodendron chinense, Pinus massoniana, Podocarpus macrophyllus, and Taxus chinensis. The long-lived individuals were divided into three classes according to their ages: Class-I (≥ 500 years, Class-II (300–499 years, and Class-III (100–299 years. Our results showed that the south-west region to the mountain was the main distribution area of Class-I trees of G. biloba and T. chinensis, most of which occurring in the same small village (Yangliu Village of Yinjiang County. The north-east region harboured all the six relict species. Floristic analyses also indicated these two regions were very similar in tree growth as measured by DBH (diameter at breast height of 1.3 m. Thus, these two areas would have provided long-term suitable habitats for relict species. The south-west region, especially the small village Yangliu, should be given highest priority for in situ conservation of relict species and other rare and endangered plants. Attention should also be paid to the north-east region for its very high species diversity of relict species.Las áreas montañosas de la región centro-sur de China están ampliamente reconocidas por su papel como refugio de plantas relictas durante la última etapa del Neógeno y el Cuaternario. En el presente trabajo se intentan explorar los patrones de distribución de los hábitats naturales y la localización exacta de los refugios para especies vegetales relictas en los alrededores de la montaña Fanjinshan, mediante el empleo de datos dendrol

  19. Analysis of HIV-1 intersubtype recombination breakpoints suggests region with high pairing probability may be a more fundamental factor than sequence similarity affecting HIV-1 recombination.

    Science.gov (United States)

    Jia, Lei; Li, Lin; Gui, Tao; Liu, Siyang; Li, Hanping; Han, Jingwan; Guo, Wei; Liu, Yongjian; Li, Jingyun

    2016-09-21

    With increasing data on HIV-1, a more relevant molecular model describing mechanism details of HIV-1 genetic recombination usually requires upgrades. Currently an incomplete structural understanding of the copy choice mechanism along with several other issues in the field that lack elucidation led us to perform an analysis of the correlation between breakpoint distributions and (1) the probability of base pairing, and (2) intersubtype genetic similarity to further explore structural mechanisms. Near full length sequences of URFs from Asia, Europe, and Africa (one sequence/patient), and representative sequences of worldwide CRFs were retrieved from the Los Alamos HIV database. Their recombination patterns were analyzed by jpHMM in detail. Then the relationships between breakpoint distributions and (1) the probability of base pairing, and (2) intersubtype genetic similarities were investigated. Pearson correlation test showed that all URF groups and the CRF group exhibit the same breakpoint distribution pattern. Additionally, the Wilcoxon two-sample test indicated a significant and inexplicable limitation of recombination in regions with high pairing probability. These regions have been found to be strongly conserved across distinct biological states (i.e., strong intersubtype similarity), and genetic similarity has been determined to be a very important factor promoting recombination. Thus, the results revealed an unexpected disagreement between intersubtype similarity and breakpoint distribution, which were further confirmed by genetic similarity analysis. Our analysis reveals a critical conflict between results from natural HIV-1 isolates and those from HIV-1-based assay vectors in which genetic similarity has been shown to be a very critical factor promoting recombination. These results indicate the region with high-pairing probabilities may be a more fundamental factor affecting HIV-1 recombination than sequence similarity in natural HIV-1 infections. Our

  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. Spatial and temporal patterns in golden eagle diets in the western United States, with implications for conservation planning

    Science.gov (United States)

    Bedrosian, Geoffrey; Watson, James W.; Steenhof, Karen; Kochert, Michael N.; Preston, Charles R.; Woodbridge, Brian; Williams, Gary E.; Keller, Kent R.; Crandall, Ross H.

    2017-01-01

    Detailed information on diets and predatory ecology of Golden Eagles (Aquila chrysaetos) is essential to prioritize prey species management and to develop landscape-specific conservation strategies, including mitigation of the effects of energy development across the western United States. We compiled published and unpublished data on Golden Eagle diets to (1) summarize available information on Golden Eagle diets in the western U.S., (2) compare diets among biogeographic provinces, and (3) discuss implications for conservation planning and future research. We analyzed 35 studies conducted during the breeding season at 45 locations from 1940–2015. Golden Eagle diet differed among western ecosystems. Lower dietary breadth was associated with desert and shrub-steppe ecosystems and higher breadth with mountain ranges and the Columbia Plateau. Correlations suggest that percentage of leporids in the diet is the factor driving overall diversity of prey and percentage of other prey groups in the diet of Golden Eagles. Leporids were the primary prey of breeding Golden Eagles in 78% of study areas, with sciurids reported as primary prey in 18% of study areas. During the nonbreeding season, Golden Eagles were most frequently recorded feeding on leporids and carrion. Golden Eagles can be described as both generalist and opportunistic predators; they can feed on a wide range of prey species but most frequently feed on abundant medium-sized prey species in a given habitat. Spatial variations in Golden Eagle diet likely reflect regional differences in prey community, whereas temporal trends likely reflect responses to long-term change in prey populations. Evidence suggests dietary shifts from traditional (leporid) prey can have adverse effects on Golden Eagle reproductive rates. Land management practices that support or restore shrub-steppe ecosystem diversity should benefit Golden Eagles. More information is needed on nonbreeding-season diet to determine what food resources

  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. A dense SNP-based linkage map for Atlantic salmon (Salmo salar reveals extended chromosome homeologies and striking differences in sex-specific recombination patterns

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    Lien Sigbjørn

    2011-12-01

    Full Text Available Abstract Background The Atlantic salmon genome is in the process of returning to a diploid state after undergoing a whole genome duplication (WGD event between 25 and100 million years ago. Existing data on the proportion of paralogous sequence variants (PSVs, multisite variants (MSVs and other types of complex sequence variation suggest that the rediplodization phase is far from over. The aims of this study were to construct a high density linkage map for Atlantic salmon, to characterize the extent of rediploidization and to improve our understanding of genetic differences between sexes in this species. Results A linkage map for Atlantic salmon comprising 29 chromosomes and 5650 single nucleotide polymorphisms (SNPs was constructed using genotyping data from 3297 fish belonging to 143 families. Of these, 2696 SNPs were generated from ESTs or other gene associated sequences. Homeologous chromosomal regions were identified through the mapping of duplicated SNPs and through the investigation of syntenic relationships between Atlantic salmon and the reference genome sequence of the threespine stickleback (Gasterosteus aculeatus. The sex-specific linkage maps spanned a total of 2402.3 cM in females and 1746.2 cM in males, highlighting a difference in sex specific recombination rate (1.38:1 which is much lower than previously reported in Atlantic salmon. The sexes, however, displayed striking differences in the distribution of recombination sites within linkage groups, with males showing recombination strongly localized to telomeres. Conclusion The map presented here represents a valuable resource for addressing important questions of interest to evolution (the process of re-diploidization, aquaculture and salmonid life history biology and not least as a resource to aid the assembly of the forthcoming Atlantic salmon reference genome sequence.

  4. The patterns of care study for breast-conserving therapy in Japan: Analysis of process survey from 1995 to 1997

    International Nuclear Information System (INIS)

    Mitsumori, Michihide; Hiraoka, Masahiro; Negoro, Yoshiharu; Yamauchi, Chikako; Shikama, Naoto; Sasaki, Shigeru; Yamamoto, Tokihiro; Teshima, Teruki; Inoue, Toshihiko

    2005-01-01

    Purpose: To present the results of a process survey on breast-conserving therapy (BCT) in Japan from 1995 to 1997. Methods and Materials: From September 1998 to December 1999, data on the treatment process of 865 randomly selected BCT patients were collected by extramural audits. Results: For primary surgery, wide excision or tumorectomy was performed in 372 patients (43.0%), and quadrantectomy or segmental mastectomy was performed in 493 patients (57%). The extent of axillary dissection was equal or beyond Level II in 590 patients (68.2%). Systemic chemotherapy was administered to 103 of 160 node-positive patients (64.4%) and 180 of 569 node-negative patients (31.6%). Tamoxifen was administered to 234 of 323 hormone receptor-positive patients (72.5%) and 68 of 130 hormone receptor-negative patients (52.3%). Photon energy of 10 MV was administered for whole breast irradiation in 38 patients (4.4%) without bolus. Conclusions: The extent of surgical resection for BCT was large in Japan. Pathologic assessment and the technique of radiation therapy were apparently suboptimal in some cases. Information on prognostic/predictive factors was not fully utilized to individualize systemic adjuvant therapy. Establishment and widespread use of guidelines for BCT for in Japan are desirable. Repeated surveys will demonstrate how such guidelines affect clinical practices

  5. Patterns of Utilization of Adjuvant Radiotherapy and Outcomes in Black Women After Breast Conservation at a Large Multidisciplinary Cancer Center

    International Nuclear Information System (INIS)

    Edwards-Bennett, Sophia M.; Jacks, Lindsay M.; McCormick, Beryl; Zhang, Zhigang; Azu, Michelle; Ho, Alice; Powell, Simon; Brown, Carol

    2011-01-01

    Purpose: Population-based studies have reported that as many of 35% of black women do not undergo radiotherapy (RT) after breast conservation surgery (BCS). The objective of the present study was to determine whether this trend persisted at a large multidisciplinary cancer center, and to identify the factors that predict for noncompliance with RT and determine the outcomes for this subset of patients. Methods and Materials: Between January 2002 and December 2007, 83 black women underwent BCS at Memorial Sloan-Kettering Cancer Center and were therefore eligible for the present study. Of the 83 women, 38 (46%) had Stage I, 38 (46%) Stage II, and 7 (8%) Stage III disease. Of the study cohort, 31 (37%) had triple hormone receptor-negative tumors. RT was recommended for 81 (98%) of the 83 patients (median dose, 60 Gy). Results: Of the 81 women, 12 (15%) did not receive the recommended adjuvant breast RT. Nonreceipt of chemotherapy (p = .003) and older age (p = .009) were associated with nonreceipt of RT. With a median follow-up of 70 months, the 3-year local control, locoregional control, recurrence-free survival, disease-free survival, and overall survival rate was 99% (actuarial 5-year rate, 97%), 96% (actuarial 5-year rate, 93%), 95% (actuarial 5-year rate, 92%), 92% (actuarial 5-year rate, 89%), and 95% (actuarial 5-year rate, 91%), respectively. Conclusion: We found a greater rate of utilization adjuvant breast RT (85%) among black women after BCS than has been reported in recent studies, indicating that excellent outcomes are attainable for black women after BCS when care is administered in a multidisciplinary cancer center.

  6. Patterns of citations of open access and non-open access conservation biology journal papers and book chapters.

    Science.gov (United States)

    Calver, Michael C; Bradley, J Stuart

    2010-06-01

    Open access (OA) publishing, whereby authors, their institutions, or their granting bodies pay or provide a repository through which peer-reviewed work is available online for free, is championed as a model to increase the number of citations per paper and disseminate results widely, especially to researchers in developing countries. We compared the number of citations of OA and non-OA papers in six journals and four books published since 2000 to test whether OA increases number of citations overall and increases citations made by authors in developing countries. After controlling for type of paper (e.g., review or research paper), length of paper, authors' citation profiles, number of authors per paper, and whether the author or the publisher released the paper in OA, OA had no statistically significant influence on the overall number of citations per journal paper. Journal papers were cited more frequently if the authors had published highly cited papers previously, were members of large teams of authors, or published relatively long papers, but papers were not cited more frequently if they were published in an OA source. Nevertheless, author-archived OA book chapters accrued up to eight times more citations than chapters in the same book that were not available through OA, perhaps because there is no online abstracting service for book chapters. There was also little evidence that journal papers or book chapters published in OA received more citations from authors in developing countries relative to those journal papers or book chapters not published in OA. For scholarly publications in conservation biology, only book chapters had an OA citation advantage, and OA did not increase the number of citations papers or chapters received from authors in developing countries.

  7. Soft tissue sarcomas of the extremities: survival and patterns of failure with conservative surgery and postoperative irradiation compared to surgery alone

    International Nuclear Information System (INIS)

    Leibel, S.A.; Tranbaugh, R.F.; Wara, W.M.; Beckstead, J.H.; Bovill, E.G.; Phillips, T.L.

    1982-01-01

    Between 1960 and 1978, 81 patients received their primary treatment for localized soft tissue sarcomas of the extremities, buttock and shoulder at the University of California, San Francisco. Initial treatment consisted of surgery alone in 47 patients, planned conservative surgery followed by radiation therapy in 29 patients, and irradiation alone in five patients. The two- and five-year determinate survival for all cases was 86% and 73%, respectively. The local control rate achieved with surgery alone was related to the extent of surgery. Eighty-seven percent (14/16) of the patients undergoing amputation were locally controlled. Seventy-two percent (8/11) were treated with wide en bloc resection and had local tumor control while only 30% (6/20) having simple excision were controlled. The local control rate with surgery and postoperative irradiation was 90% (26/29). No patients treated with irradiation therapy alone were controlled. This review suggests that local tumor control achieved with limb preserving conservative surgery and postoperative irradiation is superior to limited surgery alone. The survival and patterns of failure of patients undergoing radical surgery is comparable to combined treatment with the risk-benefit ratio favoring the latter

  8. Conserved and divergent expression patterns of markers of axial development in reptilian embryos: Chinese soft-shell turtle and Madagascar ground gecko.

    Science.gov (United States)

    Yoshida, Michio; Kajikawa, Eriko; Kurokawa, Daisuke; Noro, Miyuki; Iwai, Tatsuhiro; Yonemura, Shigenobu; Kobayashi, Kensaku; Kiyonari, Hiroshi; Aizawa, Shinichi

    2016-07-01

    The processes of development leading up to gastrulation have been markedly altered during the evolution of amniotes, and it is uncertain how the mechanisms of axis formation are conserved and diverged between mouse and chick embryos. To assess the conservation and divergence of these mechanisms, this study examined gene expression patterns during the axis formation process in Chinese soft-shell turtle and Madagascar ground gecko preovipositional embryos. The data suggest that NODAL signaling, similarly to avian embryos but in contrast to eutherian embryos, does not have a role in epiblast and hypoblast development in reptilian embryos. The posterior marginal epiblast (PME) is the initial molecular landmark of axis formation in reptilian embryos prior to primitive plate development. Ontogenetically, PME may be the precursor of the primitive plate, and phylogenetically, Koller's sickle and posterior marginal zone in avian development may have been derived from the PME. Most of the genes expressed in the mouse anterior visceral endoderm (AVE genes), especially signaling antagonist genes, are not expressed in the hypoblast of turtle and gecko embryos, though they are expressed in the avian hypoblast. This study proposes that AVE gene expression in the hypoblast and the visceral endoderm could have been independently established in avian and eutherian lineages, similar to the primitive streak that has been independently acquired in these lineages. Copyright © 2016 Elsevier Inc. All rights reserved.

  9. Uneven large-scale movement patterns in wild and reintroduced pre-adult bearded vultures: conservation implications.

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    Antoni Margalida

    Full Text Available After the quasi-extinction of much of the European vertebrate megafauna during the last few centuries, many reintroduction projects seek to restore decimated populations. However, the future of numerous species depends on the management scenarios of metapopulations where the flow of individuals can be critical to ensure their viability. This is the case of the bearded vulture Gypaetus barbatus, an Old World, large body-sized and long-lived scavenger living in mountain ranges. Although persecution in Western Europe restrained it to the Pyrenees, the species is nowadays present in other mountains thanks to reintroduction projects. We examined the movement patterns of pre-adult non-breeding individuals born in the wild population of the Pyrenees (n = 9 and in the reintroduced populations of the Alps (n = 24 and Andalusia (n = 13. Most birds were equipped with GPS-GSM radio transmitters, which allowed accurate determination of individual dispersal patterns. Two estimators were considered: i step length (i.e., the distance travelled per day by each individual, calculated considering only successive days; and ii total dispersal distance (i.e., the distance travelled between each mean daily location and the point of release. Both dispersal estimators showed a positive relationship with age but were also highly dependent on the source population, birds in Andalusia and Alps moving farther than in Pyrenees. Future research should confirm if differences in dispersal distances are the rule, in which case the dynamics of future populations would be strongly influenced. In summary, our findings highlight that inter-population differences can affect the flow of individuals among patches (a key aspect to ensure the viability of the European metapopulation of the endangered bearded vulture, and thus should be taken into account when planning reintroduction programs. This result also raises questions about whether similar scenarios may occur in other

  10. Mitochondrial DNA haplotype distribution patterns in Pinus ponderosa (Pinaceae): range-wide evolutionary history and implications for conservation.

    Science.gov (United States)

    Potter, Kevin M; Hipkins, Valerie D; Mahalovich, Mary F; Means, Robert E

    2013-08-01

    Ponderosa pine (Pinus ponderosa Douglas ex P. Lawson & C. Lawson) exhibits complicated patterns of morphological and genetic variation across its range in western North America. This study aims to clarify P. ponderosa evolutionary history and phylogeography using a highly polymorphic mitochondrial DNA marker, with results offering insights into how geographical and climatological processes drove the modern evolutionary structure of tree species in the region. We amplified the mtDNA nad1 second intron minisatellite region for 3,100 trees representing 104 populations, and sequenced all length variants. We estimated population-level haplotypic diversity and determined diversity partitioning among varieties, races and populations. After aligning sequences of minisatellite repeat motifs, we evaluated evolutionary relationships among haplotypes. The geographical structuring of the 10 haplotypes corresponded with division between Pacific and Rocky Mountain varieties. Pacific haplotypes clustered with high bootstrap support, and appear to have descended from Rocky Mountain haplotypes. A greater proportion of diversity was partitioned between Rocky Mountain races than between Pacific races. Areas of highest haplotypic diversity were the southern Sierra Nevada mountain range in California, northwestern California, and southern Nevada. Pinus ponderosa haplotype distribution patterns suggest a complex phylogeographic history not revealed by other genetic and morphological data, or by the sparse paleoecological record. The results appear consistent with long-term divergence between the Pacific and Rocky Mountain varieties, along with more recent divergences not well-associated with race. Pleistocene refugia may have existed in areas of high haplotypic diversity, as well as the Great Basin, Southwestern United States/northern Mexico, and the High Plains.

  11. 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.

  12. Known from a handful of specimens: analyzing the worldwide patterns of occurrence and conservation of rodents and shrews recorded only from the type locality

    Directory of Open Access Journals (Sweden)

    Giovanni Amori

    2016-03-01

    Full Text Available Traditionally, conservation research has not focused on Rodentia and Soricomorpha, and many species are known from a handful of specimens and the type locality only (few and type locality species (FETP.  Here we studied the patterns of occurrence of FETP rodents and soricomorphs in relation to geographical area and vegetation zones and report some conservation considerations.  Overall, 91 species of Rodentia and 19 species of Soricomorpha were selected.  There was a positive correlation between number of species per genus and number of FETP species in each genus.  The majority of FETP rodents occur in the Neotropical, Afrotropical and Oriental regions, and soricomorphs in the Afrotropical and Oriental regions. Higher numbers of FETP rodent species occurred in Argentina and Indonesia.  There was a positive relationship between species richness of rodents per country and number of FETP species.  In terms of habitat type, FETP species of rodents and soricomorphs showed similar patterns, with most species being found in rainforest.  The great majority of selected species of both groups were Data Deficient (DD, with Critically Endangered (CR accounting for 16.5% of Rodentia and 5.3% of Soricomorpha.  Overall, IUCN threatened species mostly occur in the Neotropical region, followed by the Afrotropical region.  It is urged that IUCN authorities should promptly revise all FETP species and their precautionary CR status, at least when a reasonable timespan (i.e., >25 years has passed since the last records. 

  13. Padrões espaciais e conservação da diversidade de serpentes do bioma cerrado = Spatial patterns and biodiversity conservation of snakes from Cerrado biome

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    Larice de Fátima Couto

    2007-01-01

    Full Text Available Em geral, as tentativas para estabelecer áreas prioritárias para conservação no Cerrado têm sido baseadas em critérios subjetivos. No presente trabalho, foram utilizados dados macroecológicos de distribuição de 129 espécies de serpentes distribuídas em 181 células com 1o de latitude/longitude do Cerrado para analisar padrões espaciais na riqueza e propor uma estratégia de conservação para essas espécies. Verificou-se que as cinco variáveis ambientaisanalisadas explicaram apenas 34,65% da variação na riqueza de serpentes do Cerrado. Para seleção de áreas prioritárias utilizando-se procedimentos de otimização, estabeleceu-se que 14 células são necessárias para representar todas as espécies pelo menos uma vez. Também foram incorporados ao modelo os padrões de ocupação humana no Cerrado, visando minimizar conflitos entre desenvolvimento e conservação, e neste caso as células concentram-se principalmente nosudoeste do bioma. Em função da falta geral de conhecimento sobre os padrões mais locais de distribuição de espécies no Cerrado, esses resultados devem ser considerados preliminares. De qualquer modo, o presente estudo, em escala biogeográfica, é importante para estabelecer estratégias metodológicas e para fornecer uma visão ampla dos padrões de diversidade e de que regiões seriam mais importantes para sua conservação. Until recently, the conservation of Cerrado has been neglected andattempts to establish conservation priorities were usually based on subjective criteria. In this paper, macroecological data of distribution of 129 species of snakes in the Cerrado were used to evaluate spatial patterns in species richness and to establish a system of potential areas that preserves all snake species in the region. The five environment variables used as predictors explained only 34.65% of the variance in species richness. In order to establishconservation priorities, optimization procedures were used

  14. Origin of the vertebrate body plan via mechanically biased conservation of regular geometrical patterns in the structure of the blastula.

    Science.gov (United States)

    Edelman, David B; McMenamin, Mark; Sheesley, Peter; Pivar, Stuart

    2016-09-01

    We present a plausible account of the origin of the archetypal vertebrate bauplan. We offer a theoretical reconstruction of the geometrically regular structure of the blastula resulting from the sequential subdivision of the egg, followed by mechanical deformations of the blastula in subsequent stages of gastrulation. We suggest that the formation of the vertebrate bauplan during development, as well as fixation of its variants over the course of evolution, have been constrained and guided by global mechanical biases. Arguably, the role of such biases in directing morphology-though all but neglected in previous accounts of both development and macroevolution-is critical to any substantive explanation for the origin of the archetypal vertebrate bauplan. We surmise that the blastula inherently preserves the underlying geometry of the cuboidal array of eight cells produced by the first three cleavages that ultimately define the medial-lateral, dorsal-ventral, and anterior-posterior axes of the future body plan. Through graphical depictions, we demonstrate the formation of principal structures of the vertebrate body via mechanical deformation of predictable geometrical patterns during gastrulation. The descriptive rigor of our model is supported through comparisons with previous characterizations of the embryonic and adult vertebrate bauplane. Though speculative, the model addresses the poignant absence in the literature of any plausible account of the origin of vertebrate morphology. A robust solution to the problem of morphogenesis-currently an elusive goal-will only emerge from consideration of both top-down (e.g., the mechanical constraints and geometric properties considered here) and bottom-up (e.g., molecular and mechano-chemical) influences. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  15. Spatial patterns in occupancy and reproduction of Golden Eagles during drought: Prospects for conservation in changing environments

    Science.gov (United States)

    Wiens, David; Kolar, Patrick; Hunt, W. Grainger; Hunt, Teresa; Fuller, Mark R.; Bell, Douglas A.

    2018-01-01

    We used a broad-scale sampling design to investigate spatial patterns in occupancy and breeding success of territorial pairs of Golden Eagles (Aquila chrysaetos) in the Diablo Range, California, USA, during a period of exceptional drought (2014–2016). We surveyed 138 randomly selected sample sites over 4 occasions each year and identified 199 pairs of eagles, 100 of which were detected in focal sample sites. We then used dynamic multistate modeling to identify relationships between site occupancy and reproduction of Golden Eagles relative to spatial variability in landscape composition and drought conditions. We observed little variability among years in site occupancy (3-yr mean = 0.74), but the estimated annual probability of successful reproduction was relatively low during the study period and declined from 0.39 (± 0.08 SE) to 0.18 (± 0.07 SE). Probabilities of site occupancy and reproduction were substantially greater at sample sites that were occupied by successful breeders in the previous year, indicating the presence of sites that were consistently used by successfully reproducing eagles. We found strong evidence for nonrandom spatial distribution in both occupancy and reproduction: Sites with the greatest potential for occupancy were characterized by rugged terrain conditions with intermediate amounts of grassland interspersed with patches of oak woodland and coniferous forest, whereas successful reproduction was most strongly associated with the amount of precipitation that a site received during the nesting period. Our findings highlight the contribution of consistently occupied and productive breeding sites to overall productivity of the local breeding population, and show that both occupancy and reproduction at these sites were maintained even during a period of exceptional drought. Our approach to quantifying and mapping site quality should be especially useful for the spatial prioritization of compensation measures intended to help offset the

  16. Recombination Modulates How Selection Affects Linked Sites in Drosophila

    Science.gov (United States)

    McGaugh, Suzanne E.; Heil, Caiti S. S.; Manzano-Winkler, Brenda; Loewe, Laurence; Goldstein, Steve; Himmel, Tiffany L.; Noor, Mohamed A. F.

    2012-01-01

    One of the most influential observations in molecular evolution has been a strong association between local recombination rate and nucleotide polymorphisms across the genome. This is interpreted as evidence for ubiquitous natural selection. The alternative explanation, that recombination is mutagenic, has been rejected by the absence of a similar association between local recombination rate and nucleotide divergence between species. However, many recent studies show that recombination rates are often very different even in closely related species, questioning whether an association between recombination rate and divergence between species has been tested satisfactorily. To circumvent this problem, we directly surveyed recombination across approximately 43% of the D. pseudoobscura physical genome in two separate recombination maps and 31% of the D. miranda physical genome, and we identified both global and local differences in recombination rate between these two closely related species. Using only regions with conserved recombination rates between and within species and accounting for multiple covariates, our data support the conclusion that recombination is positively related to diversity because recombination modulates Hill–Robertson effects in the genome and not because recombination is predominately mutagenic. Finally, we find evidence for dips in diversity around nonsynonymous substitutions. We infer that at least some of this reduction in diversity resulted from selective sweeps and examine these dips in the context of recombination rate. PMID:23152720

  17. Structural basis for new pattern of conserved amino acid residues related to chitin-binding in the antifungal peptide from the coconut rhinoceros beetle Oryctes rhinoceros.

    Science.gov (United States)

    Hemmi, Hikaru; Ishibashi, Jun; Tomie, Tetsuya; Yamakawa, Minoru

    2003-06-20

    Scarabaecin isolated from hemolymph of the coconut rhinoceros beetle Oryctes rhinoceros is a 36-residue polypeptide that has antifungal activity. The solution structure of scarabaecin has been determined from twodimensional 1H NMR spectroscopic data and hybrid distance geometry-simulated annealing protocol calculation. Based on 492 interproton and 10 hydrogen-bonding distance restraints and 36 dihedral angle restraints, we obtained 20 structures. The average backbone root-mean-square deviation for residues 4-35 is 0.728 +/- 0.217 A from the mean structure. The solution structure consists of a two-stranded antiparallel beta-sheet connected by a type-I beta-turn after a short helical turn. All secondary structures and a conserved disulfide bond are located in the C-terminal half of the peptide, residues 18-36. Overall folding is stabilized by a combination of a disulfide bond, seven hydrogen bonds, and numerous hydrophobic interactions. The structural motif of the C-terminal half shares a significant tertiary structural similarity with chitin-binding domains of plant and invertebrate chitin-binding proteins, even though scarabaecin has no overall sequence similarity to other peptide/polypeptides including chitin-binding proteins. The length of its primary structure, the number of disulfide bonds, and the pattern of conserved functional residues binding to chitin in scarabaecin differ from those of chitin-binding proteins in other invertebrates and plants, suggesting that scarabaecin does not share a common ancestor with them. These results are thought to provide further strong experimental evidence to the hypothesis that chitin-binding proteins of invertebrates and plants are correlated by a convergent evolution process.

  18. Meiotic recombination in human oocytes.

    Directory of Open Access Journals (Sweden)

    Edith Y Cheng

    2009-09-01

    Full Text Available Studies of human trisomies indicate a remarkable relationship between abnormal meiotic recombination and subsequent nondisjunction at maternal meiosis I or II. Specifically, failure to recombine or recombination events located either too near to or too far from the centromere have been linked to the origin of human trisomies. It should be possible to identify these abnormal crossover configurations by using immunofluorescence methodology to directly examine the meiotic recombination process in the human female. Accordingly, we initiated studies of crossover-associated proteins (e.g., MLH1 in human fetal oocytes to analyze their number and distribution on nondisjunction-prone human chromosomes and, more generally, to characterize genome-wide levels of recombination in the human female. Our analyses indicate that the number of MLH1 foci is lower than predicted from genetic linkage analysis, but its localization pattern conforms to that expected for a crossover-associated protein. In studies of individual chromosomes, our observations provide evidence for the presence of "vulnerable" crossover configurations in the fetal oocyte, consistent with the idea that these are subsequently translated into nondisjunctional events in the adult oocyte.

  19. Expression of recombinant Antibodies

    Directory of Open Access Journals (Sweden)

    André eFrenzel

    2013-07-01

    Full Text Available Recombinant antibodies are highly specific detection probes in research, diagnostics and have emerged over the last two decades as the fastest growing class of therapeutic proteins. Antibody generation has been dramatically accelerated by in vitro selection systems, particularly phage display. An increasing variety of recombinant production systems have been developed, ranging from Gram-negative and positive bacteria, yeasts and filamentous fungi, insect cell lines, mammalian cells to transgenic plants and animals. Currently, almost all therapeutic antibodies are still produced in mammalian cell lines in order to reduce the risk of immunogenicity due to altered, non-human glycosylation patterns. However, recent developments of glycosylation-engineered yeast, insect cell lines and transgenic plants are promising to obtain antibodies with human-like post-translational modifications. Furthermore, smaller antibody fragments including bispecific antibodies without any glycosylation are successfully produced in bacteria and have advanced to clinical testing. The first therapeutic antibody products from a non-mammalian source can be expected in coming next years. In this review, we focus on current antibody production systems including their usability for different applications.

  20. Mitochondrial recombination increases with age in Podospora anserina

    NARCIS (Netherlands)

    van Diepeningen, Anne D; Goedbloed, Daniël J; Slakhorst, S Marijke; Koopmanschap, A Bertha; Maas, Marc F P M; Hoekstra, Rolf F; Debets, Alfons J M

    With uniparental inheritance of mitochondria, there seems little reason for homologous recombination in mitochondria, but the machinery for mitochondrial recombination is quite well-conserved in many eukaryote species. In fungi and yeasts heteroplasmons may be formed when strains fuse and transfer

  1. Effects of Demographic History on the Detection of Recombination Hotspots from Linkage Disequilibrium.

    Science.gov (United States)

    Dapper, Amy L; Payseur, Bret A

    2018-02-01

    In some species, meiotic recombination is concentrated in small genomic regions. These "recombination hotspots" leave signatures in fine-scale patterns of linkage disequilibrium, raising the prospect that the genomic landscape of hotspots can be characterized from sequence variation. This approach has led to the inference that hotspots evolve rapidly in some species, but are conserved in others. Historic demographic events, such as population bottlenecks, are known to affect patterns of linkage disequilibrium across the genome, violating population genetic assumptions of this approach. Although such events are prevalent, demographic history is generally ignored when making inferences about the evolution of recombination hotspots. To determine the effect of demography on the detection of recombination hotspots, we use the coalescent to simulate haplotypes with a known recombination landscape. We measure the ability of popular linkage disequilibrium-based programs to detect hotspots across a range of demographic histories, including population bottlenecks, hidden population structure, population expansions, and population contractions. We find that demographic events have the potential to greatly reduce the power and increase the false positive rate of hotspot discovery. Neither the power nor the false positive rate of hotspot detection can be predicted without also knowing the demographic history of the sample. Our results suggest that ignoring demographic history likely overestimates the power to detect hotspots and therefore underestimates the degree of hotspot sharing between species. We suggest strategies for incorporating demographic history into population genetic inferences about recombination hotspots. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  2. Abundance and fragmentation patterns of the ecosystem engineer Lithophyllum byssoides (Lamarck) Foslie along the Iberian Peninsula Atlantic coast. Conservation and management implications

    Science.gov (United States)

    Veiga, Puri; Rubal, Marcos; Cacabelos, Eva; Moreira, Juan; Sousa-Pinto, Isabel

    2013-10-01

    The crustose calcareous red macroalgae Lithophyllum byssoides (Lamarck) Foslie is a common ecosystem engineer along the Atlantic and Mediterranean coast of the Iberian Peninsula. This species is threatened by several anthropogenic impacts acting at different spatial scales, such as pollution or global warming. The aim of this study is to identify scales of spatial variation in the abundance and fragmentation patterns of L. byssoides along the Atlantic coast of the Iberian Peninsula. For this aim we used a hierarchical sampling design considering four spatial scales (from metres to 100s of kilometres). Results of the present study indicated no significant variability among regions investigated whereas significant variability was found at the scales of shore and site in spatial patterns of abundance and fragmentation of L. byssoides. Variance components were higher at the spatial scale of shore for abundance and fragmentation of L. byssoides with the only exception of percentage cover and thus, processes acting at the scale of 10s of kilometres seem to be more relevant in shaping the spatial variability both in abundance and fragmentation of L. byssoides. These results provided quantitative estimates of abundance and fragmentation of L. byssoides at the Atlantic coast of the Iberian Peninsula establishing the observational basis for future assessment, monitoring and experimental investigations to identify the processes and anthropogenic impacts affecting L. byssoides populations. Finally we have also identified percentage cover and patch density as the best variables for long-term monitoring programs aimed to detect future anthropogenic impacts on L. byssoides. Therefore, our results have important implications for conservation and management of this valuable ecosystem engineer along the Atlantic coast of the Iberian Peninsula.

  3. Therapeutic Recombinant Monoclonal Antibodies

    Science.gov (United States)

    Bakhtiar, Ray

    2012-01-01

    During the last two decades, the rapid growth of biotechnology-derived techniques has led to a myriad of therapeutic recombinant monoclonal antibodies with significant clinical benefits. Recombinant monoclonal antibodies can be obtained from a number of natural sources such as animal cell cultures using recombinant DNA engineering. In contrast to…

  4. Photoionization and Recombination

    Science.gov (United States)

    Nahar, Sultana N.

    2000-01-01

    Theoretically self-consistent calculations for photoionization and (e + ion) recombination are described. The same eigenfunction expansion for the ion is employed in coupled channel calculations for both processes, thus ensuring consistency between cross sections and rates. The theoretical treatment of (e + ion) recombination subsumes both the non-resonant recombination ("radiative recombination"), and the resonant recombination ("di-electronic recombination") processes in a unified scheme. In addition to the total, unified recombination rates, level-specific recombination rates and photoionization cross sections are obtained for a large number of atomic levels. Both relativistic Breit-Pauli, and non-relativistic LS coupling, calculations are carried out in the close coupling approximation using the R-matrix method. Although the calculations are computationally intensive, they yield nearly all photoionization and recombination parameters needed for astrophysical photoionization models with higher precision than hitherto possible, estimated at about 10-20% from comparison with experimentally available data (including experimentally derived DR rates). Results are electronically available for over 40 atoms and ions. Photoionization and recombination of He-, and Li-like C and Fe are described for X-ray modeling. The unified method yields total and complete (e+ion) recombination rate coefficients, that can not otherwise be obtained theoretically or experimentally.

  5. A global RNA-seq-driven analysis of CHO host and production cell lines reveals distinct differential expression patterns of genes contributing to recombinant antibody glycosylation.

    Science.gov (United States)

    Könitzer, Jennifer D; Müller, Markus M; Leparc, Germán; Pauers, Martin; Bechmann, Jan; Schulz, Patrick; Schaub, Jochen; Enenkel, Barbara; Hildebrandt, Tobias; Hampel, Martin; Tolstrup, Anne B

    2015-09-01

    Boehringer Ingelheim uses two CHO-DG44 lines for manufacturing biotherapeutics, BI-HEX-1 and BI-HEX-2, which produce distinct cell type-specific antibody glycosylation patterns. A recently established CHO-K1 descended host, BI-HEX-K1, generates antibodies with glycosylation profiles differing from CHO-DG44. Manufacturing process development is significantly influenced by these unique profiles. To investigate the underlying glycosylation related gene expression, we leveraged our CHO host and production cell RNA-seqtranscriptomics and product quality database together with the CHO-K1 genome. We observed that each BI-HEX host and antibody producing cell line has a unique gene expression fingerprint. CHO-DG44 cells only transcribe Fut10, Gfpt2 and ST8Sia6 when expressing antibodies. BI-HEX-K1 cells express ST8Sia6 at host cell level. We detected a link between BI-HEX-1/BI-HEX-2 antibody galactosylation and mannosylation and the gene expression of the B4galt gene family and genes controlling mannose processing. Furthermore, we found major differences between the CHO-DG44 and CHO-K1 lineages in the expression of sialyl transferases and enzymes synthesizing sialic acid precursors, providing a rationale for the lack of immunogenic NeuGc/NGNA synthesis in CHO. Our study highlights the value of systems biotechnology to understand glycoprotein synthesis and product glycoprofiles. Such data improve future production clone selection and process development strategies for better steering of biotherapeutic product quality. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Recombination of cluster ions

    Science.gov (United States)

    Johnsen, Rainer

    1993-01-01

    Some of our recent work on molecular band emissions from recombination of molecular dimer ions (N4(+) and CO(+) CO) is discussed. Much of the experimental work was done by Y. S. Cao; the results on N4(+) recombination have been published. A brief progress report is given on our ongoing measurements of neutral products of recombination using the flowing-afterglow Langmuir-probe technique in conjunction with laser-induced fluorescence.

  7. The generation of recombinant influenza A viruses expressing a PB2 fusion protein requires the conservation of a packaging signal overlapping the coding and noncoding regions at the 5' end of the PB2 segment

    International Nuclear Information System (INIS)

    Dos Santos Afonso, Emmanuel; Escriou, Nicolas; Leclercq, India; Werf, Sylvie van der; Naffakh, Nadia

    2005-01-01

    We generated recombinant A/WSN/33 influenza A viruses expressing a PB2 protein fused to a Flag epitope at the N- (Flag-PB2) or C-terminus (PB2-Flag), which replicated efficiently and proved to be stable upon serial passage in vitro on MDCK cells. Rescue of PB2-Flag viruses required that the 5' end of the PB2 segment was kept identical to the wild-type beyond the 34 noncoding terminal nucleotides. This feature was achieved by a duplication of the 109 last nucleotides encoding PB2 between the Flag sequence and the 5'NCR. In PB2 minigenomes rescue experiments, both the 5' and 3' coding ends of the PB2 segment were found to promote the incorporation of minigenomes into virions. However, the presence of the Flag sequence at the junction between the 3'NCR and the coding sequence did not prevent the rescue of Flag-PB2 viruses. Our observations define requirements that may be useful for the purpose of engineering influenza RNAs

  8. Accumulation pattern of endogenous cytokinins and phenolics in different organs of 1-year-old cytokinin pre-incubated plants: implications for conservation

    Czech Academy of Sciences Publication Activity Database

    Aremu, A.O.; Plačková, Lenka; Grúz, Jiří; Bíba, Ondřej; Šubrtová, Michaela; Novák, Ondřej; Doležal, Karel; van Staden, J.

    2015-01-01

    Roč. 17, č. 6 (2015), s. 1146-1155 ISSN 1435-8603 R&D Projects: GA MŠk(CZ) LO1204; GA MŠk LK21306 Institutional support: RVO:61389030 Keywords : Acclimatisation * conservation * meta-topolins Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.216, year: 2015

  9. Interplay of recombination and selection in the genomes of Chlamydia trachomatis

    Directory of Open Access Journals (Sweden)

    Dean Deborah

    2011-05-01

    Full Text Available Abstract Background Chlamydia trachomatis is an obligate intracellular bacterial parasite, which causes several severe and debilitating diseases in humans. This study uses comparative genomic analyses of 12 complete published C. trachomatis genomes to assess the contribution of recombination and selection in this pathogen and to understand the major evolutionary forces acting on the genome of this bacterium. Results The conserved core genes of C. trachomatis are a large proportion of the pan-genome: we identified 836 core genes in C. trachomatis out of a range of 874-927 total genes in each genome. The ratio of recombination events compared to mutation (ρ/θ was 0.07 based on ancestral reconstructions using the ClonalFrame tool, but recombination had a significant effect on genetic diversification (r/m = 0.71. The distance-dependent decay of linkage disequilibrium also indicated that C. trachomatis populations behaved intermediately between sexual and clonal extremes. Fifty-five genes were identified as having a history of recombination and 92 were under positive selection based on statistical tests. Twenty-three genes showed evidence of being under both positive selection and recombination, which included genes with a known role in virulence and pathogencity (e.g., ompA, pmps, tarp. Analysis of inter-clade recombination flux indicated non-uniform currents of recombination between clades, which suggests the possibility of spatial population structure in C. trachomatis infections. Conclusions C. trachomatis is the archetype of a bacterial species where recombination is relatively frequent yet gene gains by horizontal gene transfer (HGT and losses (by deletion are rare. Gene conversion occurs at sites across the whole C. trachomatis genome but may be more often fixed in genes that are under diversifying selection. Furthermore, genome sequencing will reveal patterns of serotype specific gene exchange and selection that will generate important

  10. Poliovirus Polymerase Leu420 Facilitates RNA Recombination and Ribavirin Resistance

    Science.gov (United States)

    Kempf, Brian J.; Peersen, Olve B.

    2016-01-01

    ABSTRACT RNA recombination is important in the formation of picornavirus species groups and the ongoing evolution of viruses within species groups. In this study, we examined the structure and function of poliovirus polymerase, 3Dpol, as it relates to RNA recombination. Recombination occurs when nascent RNA products exchange one viral RNA template for another during RNA replication. Because recombination is a natural aspect of picornavirus replication, we hypothesized that some features of 3Dpol may exist, in part, to facilitate RNA recombination. Furthermore, we reasoned that alanine substitution mutations that disrupt 3Dpol-RNA interactions within the polymerase elongation complex might increase and/or decrease the magnitudes of recombination. We found that an L420A mutation in 3Dpol decreased the frequency of RNA recombination, whereas alanine substitutions at other sites in 3Dpol increased the frequency of recombination. The 3Dpol Leu420 side chain interacts with a ribose in the nascent RNA product 3 nucleotides from the active site of the polymerase. Notably, the L420A mutation that reduced recombination also rendered the virus more susceptible to inhibition by ribavirin, coincident with the accumulation of ribavirin-induced G→A and C→U mutations in viral RNA. We conclude that 3Dpol Leu420 is critically important for RNA recombination and that RNA recombination contributes to ribavirin resistance. IMPORTANCE Recombination contributes to the formation of picornavirus species groups and the emergence of circulating vaccine-derived polioviruses (cVDPVs). The recombinant viruses that arise in nature are occasionally more fit than either parental strain, especially when the two partners in recombination are closely related, i.e., members of characteristic species groups, such as enterovirus species groups A to H or rhinovirus species groups A to C. Our study shows that RNA recombination requires conserved features of the viral polymerase. Furthermore, a

  11. Conservation Value

    OpenAIRE

    Tisdell, Clement A.

    2010-01-01

    This paper outlines the significance of the concept of conservation value and discusses ways in which it is determined paying attention to views stemming from utilitarian ethics and from deontological ethics. The importance of user costs in relation to economic decisions about the conservation and use of natural resources is emphasised. Particular attention is given to competing views about the importance of conserving natural resources in order to achieve economic sustainability. This then l...

  12. Bayesian inference of shared recombination hotspots between humans and chimpanzees.

    Science.gov (United States)

    Wang, Ying; Rannala, Bruce

    2014-12-01

    Recombination generates variation and facilitates evolution. Recombination (or lack thereof) also contributes to human genetic disease. Methods for mapping genes influencing complex genetic diseases via association rely on linkage disequilibrium (LD) in human populations, which is influenced by rates of recombination across the genome. Comparative population genomic analyses of recombination using related primate species can identify factors influencing rates of recombination in humans. Such studies can indicate how variable hotspots for recombination may be both among individuals (or populations) and over evolutionary timescales. Previous studies have suggested that locations of recombination hotspots are not conserved between humans and chimpanzees. We made use of the data sets from recent resequencing projects and applied a Bayesian method for identifying hotspots and estimating recombination rates. We also reanalyzed SNP data sets for regions with known hotspots in humans using samples from the human and chimpanzee. The Bayes factors (BF) of shared recombination hotspots between human and chimpanzee across regions were obtained. Based on the analysis of the aligned regions of human chromosome 21, locations where the two species show evidence of shared recombination hotspots (with high BFs) were identified. Interestingly, previous comparative studies of human and chimpanzee that focused on the known human recombination hotspots within the β-globin and HLA regions did not find overlapping of hotspots. Our results show high BFs of shared hotspots at locations within both regions, and the estimated locations of shared hotspots overlap with the locations of human recombination hotspots obtained from sperm-typing studies. Copyright © 2014 by the Genetics Society of America.

  13. Small RNA analysis in Petunia hybrida identifies unusual tissue-specific expression patterns of conserved miRNAs and of a 24mer RNA

    Science.gov (United States)

    Tedder, Philip; Zubko, Elena; Westhead, David R.; Meyer, Peter

    2009-01-01

    Two pools of small RNAs were cloned from inflorescences of Petunia hybrida using a 5′-ligation dependent and a 5′-ligation independent approach. The two libraries were integrated into a public website that allows the screening of individual sequences against 359,769 unique clones. The library contains 15 clones with 100% identity and 53 clones with one mismatch to miRNAs described for other plant species. For two conserved miRNAs, miR159 and miR390, we find clear differences in tissue-specific distribution, compared with other species. This shows that evolutionary conservation of miRNA sequences does not necessarily include a conservation of the miRNA expression profile. Almost 60% of all clones in the database are 24-nucleotide clones. In accordance with the role of 24mers in marking repetitive regions, we find them distributed across retroviral and transposable element sequences but other 24mers map to promoter regions and to different transcript regions. For one target region we observe tissue-specific variation of matching 24mers, which demonstrates that, as for 21mers, 24mer concentrations are not necessarily identical in different tissues. Asymmetric distribution of a putative novel miRNA in the two libraries suggests that the cloning method can be selective for the representation of certain small RNAs in a collection. PMID:19369427

  14. Activated recombinant adenovirus proteinases

    Science.gov (United States)

    Anderson, Carl W.; Mangel, Walter F.

    1999-08-10

    This application describes methods and expression constructs for producing activatable recombinant adenovirus proteinases. Purified activatable recombinant adenovirus proteinases and methods of purification are described. Activated adenovirus proteinases and methods for obtaining activated adenovirus proteinases are further included. Isolated peptide cofactors of adenovirus proteinase activity, methods of purifying and identifying said peptide cofactors are also described. Antibodies immunoreactive with adenovirus proteinases, immunospecific antibodies, and methods for preparing them are also described. Other related methods and materials are also described.

  15. Hadron correlations from recombination

    Energy Technology Data Exchange (ETDEWEB)

    Fries, Rainer J [School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455 (United States)

    2005-01-01

    Quark recombination is a successful model to describe the hadronization of a deconfined quark gluon plasma. Jet-like dihadron correlations measured at RHIC provide a challenge for this picture. We discuss how correlations between hadrons can arise from correlations between partons before hadronization. An enhancement of correlations through the recombination process, similar to the enhancement of elliptic flow is found. Hot spots from completely or partially quenched jets are a likely source of such parton correlations.

  16. The Recombination Landscape in Wild House Mice Inferred Using Population Genomic Data.

    Science.gov (United States)

    Booker, Tom R; Ness, Rob W; Keightley, Peter D

    2017-09-01

    Characterizing variation in the rate of recombination across the genome is important for understanding several evolutionary processes. Previous analysis of the recombination landscape in laboratory mice has revealed that the different subspecies have different suites of recombination hotspots. It is unknown, however, whether hotspots identified in laboratory strains reflect the hotspot diversity of natural populations or whether broad-scale variation in the rate of recombination is conserved between subspecies. In this study, we constructed fine-scale recombination rate maps for a natural population of the Eastern house mouse, Mus musculus castaneus We performed simulations to assess the accuracy of recombination rate inference in the presence of phase errors, and we used a novel approach to quantify phase error. The spatial distribution of recombination events is strongly positively correlated between our castaneus map, and a map constructed using inbred lines derived predominantly from M. m. domesticus Recombination hotspots in wild castaneus show little overlap, however, with the locations of double-strand breaks in wild-derived house mouse strains. Finally, we also find that genetic diversity in M. m. castaneus is positively correlated with the rate of recombination, consistent with pervasive natural selection operating in the genome. Our study suggests that recombination rate variation is conserved at broad scales between house mouse subspecies, but it is not strongly conserved at fine scales. Copyright © 2017 by the Genetics Society of America.

  17. 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...

  18. Effect of Planting Patterns' and Plant Population on Some of Morphological Traits, Harvest Index and Conservable Grain Yield of Sweet Corn

    Directory of Open Access Journals (Sweden)

    M. Nasrolah Alhossini

    2012-04-01

    Full Text Available Sweet corn is one of the most important crops in Iran and due to its short period of growth, it has been an important position after wheat and barley in khorasane Razavi Province. In this study two methods of planting (one raised bed and furrow planting and 3 plant densities (65000, 75000 and 85000 plant/ha was evaluated on some of Morphological Traits, harvest index and conservable grain yield of sweet Corn(Chase and KSC403su Varieties in Torbat-e-Heidarie in saline (4.060ds/m condition on 2009. The experimental design was factorial based on RCBC with 4 replications. The result of ANOVA showed significant differences between Anthesis silking interval (ASI, tassel length, plant height, ear height, stem diameter, harvest index, and conservable grain yield of sweet corn varieties that effected by planting methods. the highest harvest index was belonged to Chase in 75000 Plant/ha on one raised bed planting method with 31.75% and the lowest mean was belonged to KSC403su in 85000 Plant/ha on furrow planting method with 14.93%. In addition the highest grain yield was belonged to chase variety at 75000 plant/ha and furrow planting method with 11.912 ton/ha, while the lowest grain yield was belonged to KSC403su variety at 85000 plant/ha and raised bed planting (3.610 ton/ha. The Chase variety was better than KSC403su Due to its canopy and photo period is shorter than KSC403su. The superiority of Chase variety can be related to better distribution of leaves, highest harvest index, conservable grain yield and plant arrangement in the row.

  19. Recombinational repair: workshop summary

    International Nuclear Information System (INIS)

    Howard-Flanders, P.

    1983-01-01

    Recombinational repair may or may not be synonymous with postreplication repair. Considerable progress has been made in the study of the relevant enzymes, particularly those from bacteria. In this workshop we focus on the recombination enzyme RecA protein. What structural changes take place in the protein and in DNA during repair. How does homologous pairing take place. How is ATP hydrolysis coupled to the stand exchange reaction and the formation of heteroduplx DNA. Turning to another enzyme needed for certain kinds of bacterial recombination, we will ask whether the purified recB protein and recC protein complement each other and are sufficient for exonuclease V activity. In higher cells, we would like to know whether sister exchanges, which occur in bacteria after uv irradiation, are also seen in animal cells

  20. Meiotic recombination hotspots - a comparative view.

    Science.gov (United States)

    Choi, Kyuha; Henderson, Ian R

    2015-07-01

    During meiosis homologous chromosomes pair and undergo reciprocal genetic exchange, termed crossover. Meiotic recombination has a profound effect on patterns of genetic variation and is an important tool during crop breeding. Crossovers initiate from programmed DNA double-stranded breaks that are processed to form single-stranded DNA, which can invade a homologous chromosome. Strand invasion events mature into double Holliday junctions that can be resolved as crossovers. Extensive variation in the frequency of meiotic recombination occurs along chromosomes and is typically focused in narrow hotspots, observed both at the level of DNA breaks and final crossovers. We review methodologies to profile hotspots at different steps of the meiotic recombination pathway that have been used in different eukaryote species. We then discuss what these studies have revealed concerning specification of hotspot locations and activity and the contributions of both genetic and epigenetic factors. Understanding hotspots is important for interpreting patterns of genetic variation in populations and how eukaryotic genomes evolve. In addition, manipulation of hotspots will allow us to accelerate crop breeding, where meiotic recombination distributions can be limiting. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

  1. Fundamental Studies of Recombinant Hydrogenases

    Energy Technology Data Exchange (ETDEWEB)

    Adams, Michael W. [Univ. of Georgia, Athens, GA (United States)

    2014-01-25

    This research addressed the long term goals of understanding the assembly and organization of hydrogenase enzymes, of reducing them in size and complexity, of determining structure/function relationships, including energy conservation via charge separation across membranes, and in screening for novel H2 catalysts. A key overall goal of the proposed research was to define and characterize minimal hydrogenases that are produced in high yields and are oxygen-resistant. Remarkably, in spite of decades of research carried out on hydrogenases, it is not possible to readily manipulate or design the enzyme using molecular biology approaches since a recombinant form produced in a suitable host is not available. Such resources are essential if we are to understand what constitutes a “minimal” hydrogenase and design such catalysts with certain properties, such as resistance to oxygen, extreme stability and specificity for a given electron donor. The model system for our studies is Pyrococcus furiosus, a hyperthermophile that grows optimally at 100°C, which contains three different nickel-iron [NiFe-] containing hydrogenases. Hydrogenases I and II are cytoplasmic while the other, MBH, is an integral membrane protein that functions to both evolve H2 and pump protons. Three important breakthroughs were made during the funding period with P. furiosus soluble hydrogenase I (SHI). First, we produced an active recombinant form of SHI in E. coli by the co-expression of sixteen genes using anaerobically-induced promoters. Second, we genetically-engineered P. furiosus to overexpress SHI by an order of magnitude compared to the wild type strain. Third, we generated the first ‘minimal’ form of SHI, one that contained two rather than four subunits. This dimeric form was stable and active, and directly interacted with a pyruvate-oxidizing enzyme with any intermediate electron carrier. The research resulted in five peer-reviewed publications.

  2. Padrões espaciais e conservação da diversidade de serpentes do bioma cerrado - DOI: 10.4025/actascibiolsci.v29i1.145 Spatial patterns and biodiversity conservation of snakes from Cerrado biome

    Directory of Open Access Journals (Sweden)

    Levi Carina Terribile

    2007-11-01

    Full Text Available Em geral, as tentativas para estabelecer áreas prioritárias para conservação no Cerrado têm sido baseadas em critérios subjetivos. No presente trabalho, foram utilizados dados macroecológicos de distribuição de 129 espécies de serpentes distribuídas em 181 células com 1o de latitude/longitude do Cerrado para analisar padrões espaciais na riqueza e propor uma estratégia de conservação para essas espécies. Verificou-se que as cinco variáveis ambientais analisadas explicaram apenas 34,65% da variação na riqueza de serpentes do Cerrado. Para seleção de áreas prioritárias utilizando-se procedimentos de otimização, estabeleceu-se que 14 células são necessárias para representar todas as espécies pelo menos uma vez. Também foram incorporados ao modelo os padrões de ocupação humana no Cerrado, visando minimizar conflitos entre desenvolvimento e conservação, e neste caso as células concentram-se principalmente no sudoeste do bioma. Em função da falta geral de conhecimento sobre os padrões mais locais de distribuição de espécies no Cerrado, esses resultados devem ser considerados preliminares. De qualquer modo, o presente estudo, em escala biogeográfica, importante para estabelecer estratégias metodológicas e para fornecer uma visão ampla dos padrões de diversidade e de que regiões seriam mais importantes para sua conservação.Until recently, the conservation of Cerrado has been neglected and attempts to establish conservation priorities were usually based on subjective criteria. In this paper, macroecological data of distribution of 129 species of snakes in the Cerrado were used to evaluate spatial patterns in species richness and to establish a system of potential areas that preserves all snake species in the region. The five environment variables used as predictors explained only 34.65% of the variance in species richness. In order to establish conservation priorities, optimization procedures were used

  3. Parton recombination model

    International Nuclear Information System (INIS)

    Hwa, R.C.

    1978-08-01

    Low P/sub T/ meson production in hadronic collisions is described in the framework of the parton model. The recombination of quark and antiquark is suggested as the dominant mechanism in the large x region. Phenomenological evidences for the mechanism are given. The application to meson initiated reactions yields the quark distribution in mesons. 21 references

  4. Conservation endocrinology

    Science.gov (United States)

    McCormick, Stephen; Romero, L. Michael

    2017-01-01

    Endocrinologists can make significant contributions to conservation biology by helping to understand the mechanisms by which organisms cope with changing environments. Field endocrine techniques have advanced rapidly in recent years and can provide substantial information on the growth, stress, and reproductive status of individual animals, thereby providing insight into current and future responses of populations to changes in the environment. Environmental stressors and reproductive status can be detected nonlethally by measuring a number of endocrine-related endpoints, including steroids in plasma, living and nonliving tissue, urine, and feces. Information on the environmental or endocrine requirements of individual species for normal growth, development, and reproduction will provide critical information for species and ecosystem conservation. For many taxa, basic information on endocrinology is lacking, and advances in conservation endocrinology will require approaches that are both “basic” and “applied” and include integration of laboratory and field approaches.

  5. Conserved Patterns of Microbial Immune Escape: Pathogenic Microbes of Diverse Origin Target the Human Terminal Complement Inhibitor Vitronectin via a Single Common Motif.

    Directory of Open Access Journals (Sweden)

    Teresia Hallström

    Full Text Available Pathogenicity of many microbes relies on their capacity to resist innate immunity, and to survive and persist in an immunocompetent human host microbes have developed highly efficient and sophisticated complement evasion strategies. Here we show that different human pathogens including Gram-negative and Gram-positive bacteria, as well as the fungal pathogen Candida albicans, acquire the human terminal complement regulator vitronectin to their surface. By using truncated vitronectin fragments we found that all analyzed microbial pathogens (n = 13 bound human vitronectin via the same C-terminal heparin-binding domain (amino acids 352-374. This specific interaction leaves the terminal complement complex (TCC regulatory region of vitronectin accessible, allowing inhibition of C5b-7 membrane insertion and C9 polymerization. Vitronectin complexed with the various microbes and corresponding proteins was thus functionally active and inhibited complement-mediated C5b-9 deposition. Taken together, diverse microbial pathogens expressing different structurally unrelated vitronectin-binding molecules interact with host vitronectin via the same conserved region to allow versatile control of the host innate immune response.

  6. Scrambling Eggs: Meiotic Drive and the Evolution of Female Recombination Rates

    Science.gov (United States)

    Brandvain, Yaniv; Coop, Graham

    2012-01-01

    Theories to explain the prevalence of sex and recombination have long been a central theme of evolutionary biology. Yet despite decades of attention dedicated to the evolution of sex and recombination, the widespread pattern of sex differences in the recombination rate is not well understood and has received relatively little theoretical attention. Here, we argue that female meiotic drivers—alleles that increase in frequency by exploiting the asymmetric cell division of oogenesis—present a potent selective pressure favoring the modification of the female recombination rate. Because recombination plays a central role in shaping patterns of variation within and among dyads, modifiers of the female recombination rate can function as potent suppressors or enhancers of female meiotic drive. We show that when female recombination modifiers are unlinked to female drivers, recombination modifiers that suppress harmful female drive can spread. By contrast, a recombination modifier tightly linked to a driver can increase in frequency by enhancing female drive. Our results predict that rapidly evolving female recombination rates, particularly around centromeres, should be a common outcome of meiotic drive. We discuss how selection to modify the efficacy of meiotic drive may contribute to commonly observed patterns of sex differences in recombination. PMID:22143919

  7. [Conservation Units.

    Science.gov (United States)

    Texas Education Agency, Austin.

    Each of the six instructional units deals with one aspect of conservation: forests, water, rangeland, minerals (petroleum), and soil. The area of the elementary school curriculum with which each correlates is indicated. Lists of general and specific objectives are followed by suggested teaching procedures, including ideas for introducing the…

  8. Creative conservation

    NARCIS (Netherlands)

    Bentham, Roelof J.

    1968-01-01

    The increasing exploitation of our natural resources, the unlimited occupation of ever more new areas, and the intensification of land-use, make it necessary for us to expand the concept of conservation. But we also need to reconsider that concept itself. For the changing conditions in the

  9. Reshaping conservation

    DEFF Research Database (Denmark)

    Funder, Mikkel; Danielsen, Finn; Ngaga, Yonika

    2013-01-01

    members strengthen the monitoring practices to their advantage, and to some extent move them beyond the reach of government agencies and conservation and development practitioners. This has led to outcomes that are of greater social and strategic value to communities than the original 'planned' benefits...

  10. Pattern and polarity in the development and evolution of the gnathostome jaw: both conservation and heterotopy in the branchial arches of the shark, Scyliorhinus canicula.

    Science.gov (United States)

    Compagnucci, Claudia; Debiais-Thibaud, Melanie; Coolen, Marion; Fish, Jennifer; Griffin, John N; Bertocchini, Federica; Minoux, Maryline; Rijli, Filippo M; Borday-Birraux, Véronique; Casane, Didier; Mazan, Sylvie; Depew, Michael J

    2013-05-15

    The acquisition of jaws constitutes a landmark event in vertebrate evolution, one that in large part potentiated their success and diversification. Jaw development and patterning involves an intricate spatiotemporal series of reciprocal inductive and responsive interactions between the cephalic epithelia and the cranial neural crest (CNC) and cephalic mesodermal mesenchyme. The coordinated regulation of these interactions is critical for both the ontogenetic registration of the jaws and the evolutionary elaboration of variable jaw morphologies and designs. Current models of jaw development and evolution have been built on molecular and cellular evidence gathered mostly in amniotes such as mice, chicks and humans, and augmented by a much smaller body of work on the zebrafish. These have been partnered by essential work attempting to understand the origins of jaws that has focused on the jawless lamprey. Chondrichthyans (cartilaginous fish) are the most distant group to amniotes within extant gnathostomes, and comprise the crucial clade uniting amniotes and agnathans; yet despite their critical phylogenetic position, evidence of the molecular and cellular underpinnings of jaw development in chondrichthyans is still lacking. Recent advances in genome and molecular developmental biology of the lesser spotted dogfish shark, Scyliorhinus canicula, make it ideal for the molecular study of chondrichthyan jaw development. Here, following the 'Hinge and Caps' model of jaw development, we have investigated evidence of heterotopic (relative changes in position) and heterochronic (relative changes in timing) shifts in gene expression, relative to amniotes, in the jaw primordia of S. canicula embryos. We demonstrate the presence of clear proximo-distal polarity in gene expression patterns in the shark embryo, thus establishing a baseline molecular baüplan for branchial arch-derived jaw development and further validating the utility of the 'Hinge and Caps' model in comparative

  11. Variation in Recombination Rate and Its Genetic Determinism in Sheep Populations.

    Science.gov (United States)

    Petit, Morgane; Astruc, Jean-Michel; Sarry, Julien; Drouilhet, Laurence; Fabre, Stéphane; Moreno, Carole R; Servin, Bertrand

    2017-10-01

    Recombination is a complex biological process that results from a cascade of multiple events during meiosis. Understanding the genetic determinism of recombination can help to understand if and how these events are interacting. To tackle this question, we studied the patterns of recombination in sheep, using multiple approaches and data sets. We constructed male recombination maps in a dairy breed from the south of France (the Lacaune breed) at a fine scale by combining meiotic recombination rates from a large pedigree genotyped with a 50K SNP array and historical recombination rates from a sample of unrelated individuals genotyped with a 600K SNP array. This analysis revealed recombination patterns in sheep similar to other mammals but also genome regions that have likely been affected by directional and diversifying selection. We estimated the average recombination rate of Lacaune sheep at 1.5 cM/Mb, identified ∼50,000 crossover hotspots on the genome, and found a high correlation between historical and meiotic recombination rate estimates. A genome-wide association study revealed two major loci affecting interindividual variation in recombination rate in Lacaune, including the RNF212 and HEI10 genes and possibly two other loci of smaller effects including the KCNJ15 and FSHR genes. The comparison of these new results to those obtained previously in a distantly related population of domestic sheep (the Soay) revealed that Soay and Lacaune males have a very similar distribution of recombination along the genome. The two data sets were thus combined to create more precise male meiotic recombination maps in Sheep. However, despite their similar recombination maps, Soay and Lacaune males were found to exhibit different heritabilities and QTL effects for interindividual variation in genome-wide recombination rates. This highlights the robustness of recombination patterns to underlying variation in their genetic determinism. Copyright © 2017 by the Genetics Society

  12. Recombination among multiple mitochondrial pseudogenes from a passerine genus

    DEFF Research Database (Denmark)

    Nielsen, Kirstine Klitgaard; Arctander, P.

    2001-01-01

    to the observed differences in substitution patterns 58% of the cloned sequences were identified as pseudogenes. Recombination could be traced in 19% of the inferred nuclear pseudogenes, but this figure probably represents a Significant underestimation of the factual recombination events. The nonrecombined...... pseudogenes consisted of multiple haplotypes found to diverge from 1 to 16% from the mitochondrial gene. The number of mitochondrial nuclear copies and their apparent frequent recombination suggest that pseudogenes constitute a serious potential risk in confounding phylogenetic studies and population genetic...

  13. Recombination rate variation in mice from an isolated island.

    Science.gov (United States)

    Wang, Richard J; Gray, Melissa M; Parmenter, Michelle D; Broman, Karl W; Payseur, Bret A

    2017-01-01

    Recombination rate is a heritable trait that varies among individuals. Despite the major impact of recombination rate on patterns of genetic diversity and the efficacy of selection, natural variation in this phenotype remains poorly characterized. We present a comparison of genetic maps, sampling 1212 meioses, from a unique population of wild house mice (Mus musculus domesticus) that recently colonized remote Gough Island. Crosses to a mainland reference strain (WSB/EiJ) reveal pervasive variation in recombination rate among Gough Island mice, including subchromosomal intervals spanning up to 28% of the genome. In spite of this high level of polymorphism, the genomewide recombination rate does not significantly vary. In general, we find that recombination rate varies more when measured in smaller genomic intervals. Using the current standard genetic map of the laboratory mouse to polarize intervals with divergent recombination rates, we infer that the majority of evolutionary change occurred in one of the two tested lines of Gough Island mice. Our results confirm that natural populations harbour a high level of recombination rate polymorphism and highlight the disparities in recombination rate evolution across genomic scales. © 2016 John Wiley & Sons Ltd.

  14. Site directed recombination

    Science.gov (United States)

    Jurka, Jerzy W.

    1997-01-01

    Enhanced homologous recombination is obtained by employing a consensus sequence which has been found to be associated with integration of repeat sequences, such as Alu and ID. The consensus sequence or sequence having a single transition mutation determines one site of a double break which allows for high efficiency of integration at the site. By introducing single or double stranded DNA having the consensus sequence flanking region joined to a sequence of interest, one can reproducibly direct integration of the sequence of interest at one or a limited number of sites. In this way, specific sites can be identified and homologous recombination achieved at the site by employing a second flanking sequence associated with a sequence proximal to the 3'-nick.

  15. Nonradiative recombination in semiconductors

    CERN Document Server

    Abakumov, VN; Yassievich, IN

    1991-01-01

    In recent years, great progress has been made in the understandingof recombination processes controlling the number of excessfree carriers in semiconductors under nonequilibrium conditions. As a result, it is now possible to give a comprehensivetheoretical description of these processes. The authors haveselected a number of experimental results which elucidate theunderlying physical problems and enable a test of theoreticalmodels. The following topics are dealt with: phenomenological theory ofrecombination, theoretical models of shallow and deep localizedstates, cascade model of carrier captu

  16. Failure pattern and survival after breast conserving therapy. Long-term results of the Danish Breast Cancer Group (DBCG) 89 TM cohort

    DEFF Research Database (Denmark)

    Lyngholm, C D; Laurberg, T; Alsner, J

    2016-01-01

    -year overall survival (OS) and recurrence-free survival were 63.7% and 43.1%, respectively. Subdivided by age groups cumulative incidences at 20 years were LR: 18.9%, 10.5% and 12.4%, and DSM: 28.9%, 18.9% and 28.4% in young (≤45 years), middle-aged (46–55 years) and older (≥56 years) women, respectively....... Data from the DBCG database were completed via search through the Danish Pathology Data Bank and medical records. Results: Median follow-up time was 17 years. At 20 years the cumulative incidences of local recurrence (LR) and disease-specific mortality (DSM) were 15.3% and 25.8%, respectively. Twenty....... In an adjusted analysis age maintained a significant and independent effect on both LR and DSM. Conclusion: The DBCG 82 TM program was successfully implemented. The women treated with BCT in the DBCG 89 program displayed equal failure pattern and improved survival in comparison with women from the DBCG 82 TM...

  17. Recombination epoch revisited

    International Nuclear Information System (INIS)

    Krolik, J.H.

    1989-01-01

    Previous studies of cosmological recombination have shown that this process produces as a by-product a highly superthermal population of Ly-alpha photons which retard completion of recombination. Cosmological redshifting was thought to determine the frequency distribution of the photons, while two-photon decay of hydrogen's 2s state was thought to control their numbers. It is shown here that frequency diffusion due to photon scattering dominate the cosmological redshift in the frequency range near line center which fixes the ratio of ground state to excited state population, while incoherent scattering into the far-red damping wing effectively destroys Ly-alpha photons as a rate which is competitive with two-photon decay. The former effect tends to hold back recombination, while the latter tends to accelerate it; the net results depends on cosmological parameters, particularly the combination Omega(b) h/sq rt (2q0), where Omega(b) is the fraction of the critical density provided by baryons. 18 references

  18. Dielectronic recombination theory

    International Nuclear Information System (INIS)

    LaGattuta, K.J.

    1991-01-01

    A theory now in wide use for the calculation of dielectronic recombination cross sections (σ DR ) and rate coefficients (α DR ) was one introduced originally by Feshbach for nuclear physics applications, and then later adapted for atomic scattering problems by Hahn. In the following, we briefly review this theory in a very general form, which allows one to account for the effects of overlapping and interacting resonances, as well as continuum-continuum coupling. An extension of our notation will then also allow for the inclusion of the effects of direct radiative recombination, along with a treatment of the interference between radiative and dielectronic recombination. Other approaches to the calculation of σ DR have been described by Fano and by Seaton. We will not consider those theories here. Calculations of α DR have progressed considerably over the last 25 years, since the early work of Burgess. Advances in the reliability of theoretical predictions have also been promoted recently b a variety of direct laboratory measurements of σ DR . While the measurements of σ DR for δn ≠ 0 excitations have tended to agree very well with calculations, the case of δn = 0 has been much problematic. However, by invoking a mechanism originally proposed by Jacobs, which takes into account the effect of stray electric fields on high Rydberg states (HRS) participating in the DR process, new calculations have improved the agreement between theory and experiment for these cases. Nevertheless, certain discrepancies still remain

  19. Conservation of Charge and Conservation of Current

    OpenAIRE

    Eisenberg, Bob

    2016-01-01

    Conservation of current and conservation of charge are nearly the same thing: when enough is known about charge movement, conservation of current can be derived from conservation of charge, in ideal dielectrics, for example. Conservation of current is enforced implicitly in ideal dielectrics by theories that conserve charge. But charge movement in real materials like semiconductors or ionic solutions is never ideal. We present an apparently universal derivation of conservation of current and ...

  20. Conserved and divergent patterns of expression of DAZL, VASA and OCT4 in the germ cells of the human fetal ovary and testis

    Directory of Open Access Journals (Sweden)

    Coutts Shona

    2007-12-01

    patterns of expression are temporally and spatially distinct. In the 1st trimester OCT4 was detected in most germ cells. In the 2nd trimester the onset of expression of VASA was associated with the formation of oocytes and spermatogonia both of which were OCT-4 negative. Relocation of DAZL from nucleus to cytoplasm paralleled the down regulation of OCT4 and the onset of expression of VASA. These data reveal similarities between the expression of key regulatory proteins within germ cells as they mature in male and female fetal human gonads suggesting that in the female these maturational changes are not determined by entry into meiosis.

  1. RPA homologs and ssDNA processing during meiotic recombination.

    Science.gov (United States)

    Ribeiro, Jonathan; Abby, Emilie; Livera, Gabriel; Martini, Emmanuelle

    2016-06-01

    Meiotic homologous recombination is a specialized process that involves homologous chromosome pairing and strand exchange to guarantee proper chromosome segregation and genetic diversity. The formation and repair of DNA double-strand breaks (DSBs) during meiotic recombination differs from those during mitotic recombination in that the homologous chromosome rather than the sister chromatid is the preferred repair template. The processing of single-stranded DNA (ssDNA) formed on intermediate recombination structures is central to driving the specific outcomes of DSB repair during meiosis. Replication protein A (RPA) is the main ssDNA-binding protein complex involved in DNA metabolism. However, the existence of RPA orthologs in plants and the recent discovery of meiosis specific with OB domains (MEIOB), a widely conserved meiosis-specific RPA1 paralog, strongly suggest that multiple RPA complexes evolved and specialized to subdivide their roles during DNA metabolism. Here we review ssDNA formation and maturation during mitotic and meiotic recombination underlying the meiotic specific features. We describe and discuss the existence and properties of MEIOB and multiple RPA subunits in plants and highlight how they can provide meiosis-specific fates to ssDNA processing during homologous recombination. Understanding the functions of these RPA homologs and how they interact with the canonical RPA subunits is of major interest in the fields of meiosis and DNA repair.

  2. Insights into the Functions of a Prophage Recombination Directionality Factor

    Directory of Open Access Journals (Sweden)

    Mireille Ansaldi

    2012-10-01

    Full Text Available Recombination directionality factors (RDFs, or excisionases, are essential players of prophage excisive recombination. Despite the essentially catalytic role of the integrase in both integrative and excisive recombination, RDFs are required to direct the reaction towards excision and to prevent re-integration of the prophage genome when entering a lytic cycle. KplE1, HK620 and numerous (prophages that integrate at the same site in enterobacteria genomes (such as the argW tRNA gene all share a highly conserved recombination module. This module comprises the attL and attR recombination sites and the RDF and integrase genes. The KplE1 RDF was named TorI after its initial identification as a negative regulator of the tor operon. However, it was characterized as an essential factor of excisive recombination. In this study, we designed an extensive random mutagenesis protocol of the torI gene and identified key residues involved in both functions of the TorI protein. We show that, in addition to TorI-TorR protein-protein interaction, TorI interacts in solution with the IntS integrase. Moreover, in vitro, TorR and IntS appear to compete for TorI binding. Finally, our mutagenesis results suggest that the C-terminal part of the TorI protein is dedicated to protein-protein interactions with both proteins TorR and IntS.

  3. Recombinant Collagenlike Proteins

    Science.gov (United States)

    Fertala, Andzej

    2007-01-01

    A group of collagenlike recombinant proteins containing high densities of biologically active sites has been invented. The method used to express these proteins is similar to a method of expressing recombinant procollagens and collagens described in U. S. Patent 5,593,859, "Synthesis of human procollagens and collagens in recombinant DNA systems." Customized collagenous proteins are needed for biomedical applications. In particular, fibrillar collagens are attractive for production of matrices needed for tissue engineering and drug delivery. Prior to this invention, there was no way of producing customized collagenous proteins for these and other applications. Heretofore, collagenous proteins have been produced by use of such biological systems as yeasts, bacteria, and transgenic animals and plants. These products are normal collagens that can also be extracted from such sources as tendons, bones, and hides. These products cannot be made to consist only of biologically active, specific amino acid sequences that may be needed for specific applications. Prior to this invention, it had been established that fibrillar collagens consist of domains that are responsible for such processes as interaction with cells, binding of growth factors, and interaction with a number of structural proteins present in the extracellular matrix. A normal collagen consists of a sequence of domains that can be represented by a corresponding sequence of labels, e.g., D1D2D3D4. A collagenlike protein of the present invention contains regions of collagen II that contain multiples of a single domain (e.g., D1D1D1D1 or D4D4D4D4) chosen for its specific biological activity. By virtue of the multiplicity of the chosen domain, the density of sites having that specific biological activity is greater than it is in a normal collagen. A collagenlike protein according to this invention can thus be made to have properties that are necessary for tissue engineering.

  4. Retroviral Vectors for Analysis of Viral Mutagenesis and Recombination

    Directory of Open Access Journals (Sweden)

    Jonathan M.O. Rawson

    2014-09-01

    Full Text Available Retrovirus population diversity within infected hosts is commonly high due in part to elevated rates of replication, mutation, and recombination. This high genetic diversity often complicates the development of effective diagnostics, vaccines, and antiviral drugs. This review highlights the diverse vectors and approaches that have been used to examine mutation and recombination in retroviruses. Retroviral vectors for these purposes can broadly be divided into two categories: those that utilize reporter genes as mutation or recombination targets and those that utilize viral genes as targets of mutation or recombination. Reporter gene vectors greatly facilitate the detection, quantification, and characterization of mutants and/or recombinants, but may not fully recapitulate the patterns of mutagenesis or recombination observed in native viral gene sequences. In contrast, the detection of mutations or recombination events directly in viral genes is more biologically relevant but also typically more challenging and inefficient. We will highlight the advantages and disadvantages of the various vectors and approaches used as well as propose ways in which they could be improved.

  5. The influence of recombination on human genetic diversity.

    Directory of Open Access Journals (Sweden)

    Chris C A Spencer

    2006-09-01

    Full Text Available In humans, the rate of recombination, as measured on the megabase scale, is positively associated with the level of genetic variation, as measured at the genic scale. Despite considerable debate, it is not clear whether these factors are causally linked or, if they are, whether this is driven by the repeated action of adaptive evolution or molecular processes such as double-strand break formation and mismatch repair. We introduce three innovations to the analysis of recombination and diversity: fine-scale genetic maps estimated from genotype experiments that identify recombination hotspots at the kilobase scale, analysis of an entire human chromosome, and the use of wavelet techniques to identify correlations acting at different scales. We show that recombination influences genetic diversity only at the level of recombination hotspots. Hotspots are also associated with local increases in GC content and the relative frequency of GC-increasing mutations but have no effect on substitution rates. Broad-scale association between recombination and diversity is explained through covariance of both factors with base composition. To our knowledge, these results are the first evidence of a direct and local influence of recombination hotspots on genetic variation and the fate of individual mutations. However, that hotspots have no influence on substitution rates suggests that they are too ephemeral on an evolutionary time scale to have a strong influence on broader scale patterns of base composition and long-term molecular evolution.

  6. Recombinant Innovation and Endogenous Transitions

    OpenAIRE

    Koen Frenken; Luis R. Izquierdo; Paolo Zeppini

    2012-01-01

    We propose a model of technological transitions based on two different types of innovations. Branching innovations refer to technological improvements along a particular path, while recombinant innovations represent fusions of multiple paths. Recombinant innovations create “short-cuts” which reduce switching costs allowing agents to escape a technological lock-in. As a result, recombinant innovations speed up technological progress allowing transitions that are impossible with only branching ...

  7. A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors

    Directory of Open Access Journals (Sweden)

    Huixuan Liang

    2012-09-01

    Nestin-cre transgenic mice have been widely used to direct recombination to neural stem cells (NSCs and intermediate neural progenitor cells (NPCs. Here we report that a readily utilized, and the only commercially available, Nestin-cre line is insufficient for directing recombination in early embryonic NSCs and NPCs. Analysis of recombination efficiency in multiple cre-dependent reporters and a genetic mosaic line revealed consistent temporal and spatial patterns of recombination in NSCs and NPCs. For comparison we utilized a knock-in Emx1cre line and found robust recombination in NSCs and NPCs in ventricular and subventricular zones of the cerebral cortices as early as embryonic day 12.5. In addition we found that the rate of Nestin-cre driven recombination only reaches sufficiently high levels in NSCs and NPCs during late embryonic and early postnatal periods. These findings are important when commercially available cre lines are considered for directing recombination to embryonic NSCs and NPCs.

  8. Measuring the Edge Recombination Velocity of Monolayer Semiconductors.

    Science.gov (United States)

    Zhao, Peida; Amani, Matin; Lien, Der-Hsien; Ahn, Geun Ho; Kiriya, Daisuke; Mastandrea, James P; Ager, Joel W; Yablonovitch, Eli; Chrzan, Daryl C; Javey, Ali

    2017-09-13

    Understanding edge effects and quantifying their impact on the carrier properties of two-dimensional (2D) semiconductors is an essential step toward utilizing this material for high performance electronic and optoelectronic devices. WS 2 monolayers patterned into disks of varying diameters are used to experimentally explore the influence of edges on the material's optical properties. Carrier lifetime measurements show a decrease in the effective lifetime, τ effective , as a function of decreasing diameter, suggesting that the edges are active sites for carrier recombination. Accordingly, we introduce a metric called edge recombination velocity (ERV) to characterize the impact of 2D material edges on nonradiative carrier recombination. The unpassivated WS 2 monolayer disks yield an ERV ∼ 4 × 10 4 cm/s. This work quantifies the nonradiative recombination edge effects in monolayer semiconductors, while simultaneously establishing a practical characterization approach that can be used to experimentally explore edge passivation methods for 2D materials.

  9. On the relict recombination lines

    International Nuclear Information System (INIS)

    Bershtejn, I.N.; Bernshtejn, D.N.; Dubrovich, V.K.

    1977-01-01

    Accurate numerical calculation of intensities and profiles of hydrogen recombination lines of cosmological origin is made. Relie radiation distortions stipulated by recombination quantum release at the irrevocable recombination are investigated. Mean number calculation is given for guantums educing for one irrevocably-lost electron. The account is taken of the educed quantums interraction with matter. The main quantum-matter interrraction mechanisms are considered: electronic blow broadening; free-free, free-bound, bound-bound absorptions Recombination dynamics is investigated depending on hydrogen density and total density of all the matter kinds in the Universe

  10. Two novel porcine epidemic diarrhea virus (PEDV) recombinants from a natural recombinant and distinct subtypes of PEDV variants.

    Science.gov (United States)

    Chen, Nanhua; Li, Shuangjie; Zhou, Rongyun; Zhu, Meiqin; He, Shan; Ye, Mengxue; Huang, Yucheng; Li, Shuai; Zhu, Cong; Xia, Pengpeng; Zhu, Jianzhong

    2017-10-15

    Porcine epidemic diarrhea virus (PEDV) causes devastating impact on global pig-breeding industry and current vaccines have become not effective against the circulating PEDV variants since 2011. During the up-to-date investigation of PEDV prevalence in Fujian China 2016, PEDV was identified in vaccinated pig farms suffering severe diarrhea while other common diarrhea-associated pathogens were not detected. Complete genomes of two PEDV representatives (XM1-2 and XM2-4) were determined. Genomic comparison showed that these two viruses share the highest nucleotide identities (99.10% and 98.79%) with the 2011 ZMDZY strain, but only 96.65% and 96.50% nucleotide identities with the attenuated CV777 strain. Amino acid alignment of spike (S) proteins indicated that they have the similar mutation, insertion and deletion pattern as other Chinese PEDV variants but also contain several unique substitutions. Phylogenetic analysis showed that 2016 PEDV variants belong to the cluster of recombination strains but form a new branch. Recombination detection suggested that both XM1-2 and XM2-4 are inter-subgroup recombinants with breakpoints within ORF1b. Remarkably, the natural recombinant HNQX-3 isolate serves as a parental virus for both natural recombinants identified in this study. This up-to-date investigation provides the direct evidence that natural recombinants may serve as parental viruses to generate recombined PEDV progenies that are probably associated with the vaccination failure. Copyright © 2017. Published by Elsevier B.V.

  11. Mutations in the RNA-binding domains of tombusvirus replicase proteins affect RNA recombination in vivo

    International Nuclear Information System (INIS)

    Panaviene, Zivile; Nagy, Peter D.

    2003-01-01

    RNA recombination, which is thought to occur due to replicase errors during viral replication, is one of the major driving forces of virus evolution. In this article, we show evidence that the replicase proteins of Cucumber necrosis virus, a tombusvirus, are directly involved in RNA recombination in vivo. Mutations within the RNA-binding domains of the replicase proteins affected the frequency of recombination observed with a prototypical defective-interfering (DI) RNA, a model template for recombination studies. Five of the 17 replicase mutants tested showed delay in the formation of recombinants when compared to the wild-type helper virus. Interestingly, two replicase mutants accelerated recombinant formation and, in addition, these mutants also increased the level of subgenomic RNA synthesis (Virology 308 (2003), 191-205). A trans-complementation system was used to demonstrate that mutation in the p33 replicase protein resulted in altered recombination rate. Isolated recombinants were mostly imprecise (nonhomologous), with the recombination sites clustered around a replication enhancer region and a putative cis-acting element, respectively. These RNA elements might facilitate the proposed template switching events by the tombusvirus replicase. Together with data in the article cited above, results presented here firmly establish that the conserved RNA-binding motif of the replicase proteins is involved in RNA replication, subgenomic RNA synthesis, and RNA recombination

  12. Characterization of recombination features and the genetic basis in multiple cattle breeds.

    Science.gov (United States)

    Shen, Botong; Jiang, Jicai; Seroussi, Eyal; Liu, George E; Ma, Li

    2018-04-27

    Crossover generated by meiotic recombination is a fundamental event that facilitates meiosis and sexual reproduction. Comparative studies have shown wide variation in recombination rate among species, but the characterization of recombination features between cattle breeds has not yet been performed. Cattle populations in North America count millions, and the dairy industry has genotyped millions of individuals with pedigree information that provide a unique opportunity to study breed-level variations in recombination. Based on large pedigrees of Jersey, Ayrshire and Brown Swiss cattle with genotype data, we identified over 3.4 million maternal and paternal crossover events from 161,309 three-generation families. We constructed six breed- and sex-specific genome-wide recombination maps using 58,982 autosomal SNPs for two sexes in the three dairy cattle breeds. A comparative analysis of the six recombination maps revealed similar global recombination patterns between cattle breeds but with significant differences between sexes. We confirmed that male recombination map is 10% longer than the female map in all three cattle breeds, consistent with previously reported results in Holstein cattle. When comparing recombination hotspot regions between cattle breeds, we found that 30% and 10% of the hotspots were shared between breeds in males and females, respectively, with each breed exhibiting some breed-specific hotspots. Finally, our multiple-breed GWAS found that SNPs in eight loci affected recombination rate and that the PRDM9 gene associated with hotspot usage in multiple cattle breeds, indicating a shared genetic basis for recombination across dairy cattle breeds. Collectively, our results generated breed- and sex-specific recombination maps for multiple cattle breeds, provided a comprehensive characterization and comparison of recombination patterns between breeds, and expanded our understanding of the breed-level variations in recombination features within an

  13. Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning

    Directory of Open Access Journals (Sweden)

    Martin Darren P

    2009-04-01

    Full Text Available Abstract Background Recombination has a profound impact on the evolution of viruses, but characterizing recombination patterns in molecular sequences remains a challenging endeavor. Despite its importance in molecular evolutionary studies, identifying the sequences that exhibit such patterns has received comparatively less attention in the recombination detection framework. Here, we extend a quartet-mapping based recombination detection method to enable identification of recombinant sequences without prior specifications of either query and reference sequences. Through simulations we evaluate different recombinant identification statistics and significance tests. We compare the quartet approach with triplet-based methods that employ additional heuristic tests to identify parental and recombinant sequences. Results Analysis of phylogenetic simulations reveal that identifying the descendents of relatively old recombination events is a challenging task for all methods available, and that quartet scanning performs relatively well compared to the triplet based methods. The use of quartet scanning is further demonstrated by analyzing both well-established and putative HIV-1 recombinant strains. In agreement with recent findings, we provide evidence that the presumed circulating recombinant CRF02_AG is a 'pure' lineage, whereas the presumed parental lineage subtype G has a recombinant origin. We also demonstrate HIV-1 intrasubtype recombination, confirm the hybrid origin of SIV in chimpanzees and further disentangle the recombinant history of SIV lineages in a primate immunodeficiency virus data set. Conclusion Quartet scanning makes a valuable addition to triplet-based methods for identifying recombinant sequences without prior specifications of either query and reference sequences. The new method is available in the VisRD v.3.0 package http://www.cmp.uea.ac.uk/~vlm/visrd.

  14. Mechanisms and Regulation of Mitotic Recombination in Saccharomyces cerevisiae

    Science.gov (United States)

    Symington, Lorraine S.; Rothstein, Rodney; Lisby, Michael

    2014-01-01

    Homology-dependent exchange of genetic information between DNA molecules has a profound impact on the maintenance of genome integrity by facilitating error-free DNA repair, replication, and chromosome segregation during cell division as well as programmed cell developmental events. This chapter will focus on homologous mitotic recombination in budding yeast Saccharomyces cerevisiae. However, there is an important link between mitotic and meiotic recombination (covered in the forthcoming chapter by Hunter et al. 2015) and many of the functions are evolutionarily conserved. Here we will discuss several models that have been proposed to explain the mechanism of mitotic recombination, the genes and proteins involved in various pathways, the genetic and physical assays used to discover and study these genes, and the roles of many of these proteins inside the cell. PMID:25381364

  15. RTEL1 maintains genomic stability by suppressing homologous recombination.

    Science.gov (United States)

    Barber, Louise J; Youds, Jillian L; Ward, Jordan D; McIlwraith, Michael J; O'Neil, Nigel J; Petalcorin, Mark I R; Martin, Julie S; Collis, Spencer J; Cantor, Sharon B; Auclair, Melissa; Tissenbaum, Heidi; West, Stephen C; Rose, Ann M; Boulton, Simon J

    2008-10-17

    Homologous recombination (HR) is an important conserved process for DNA repair and ensures maintenance of genome integrity. Inappropriate HR causes gross chromosomal rearrangements and tumorigenesis in mammals. In yeast, the Srs2 helicase eliminates inappropriate recombination events, but the functional equivalent of Srs2 in higher eukaryotes has been elusive. Here, we identify C. elegans RTEL-1 as a functional analog of Srs2 and describe its vertebrate counterpart, RTEL1, which is required for genome stability and tumor avoidance. We find that rtel-1 mutant worms and RTEL1-depleted human cells share characteristic phenotypes with yeast srs2 mutants: lethality upon deletion of the sgs1/BLM homolog, hyperrecombination, and DNA damage sensitivity. In vitro, purified human RTEL1 antagonizes HR by promoting the disassembly of D loop recombination intermediates in a reaction dependent upon ATP hydrolysis. We propose that loss of HR control after deregulation of RTEL1 may be a critical event that drives genome instability and cancer.

  16. Multispecies genetic objectives in spatial conservation planning.

    Science.gov (United States)

    Nielsen, Erica S; Beger, Maria; Henriques, Romina; Selkoe, Kimberly A; von der Heyden, Sophie

    2017-08-01

    Growing threats to biodiversity and global alteration of habitats and species distributions make it increasingly necessary to consider evolutionary patterns in conservation decision making. Yet, there is no clear-cut guidance on how genetic features can be incorporated into conservation-planning processes, despite multiple molecular markers and several genetic metrics for each marker type to choose from. Genetic patterns differ between species, but the potential tradeoffs among genetic objectives for multiple species in conservation planning are currently understudied. We compared spatial conservation prioritizations derived from 2 metrics of genetic diversity (nucleotide and haplotype diversity) and 2 metrics of genetic isolation (private haplotypes and local genetic differentiation) in mitochondrial DNA of 5 marine species. We compared outcomes of conservation plans based only on habitat representation with plans based on genetic data and habitat representation. Fewer priority areas were selected for conservation plans based solely on habitat representation than on plans that included habitat and genetic data. All 4 genetic metrics selected approximately similar conservation-priority areas, which is likely a result of prioritizing genetic patterns across a genetically diverse array of species. Largely, our results suggest that multispecies genetic conservation objectives are vital to creating protected-area networks that appropriately preserve community-level evolutionary patterns. © 2016 Society for Conservation Biology.

  17. Evidence of animal mtDNA recombination between divergent populations of the potato cyst nematode Globodera pallida.

    Science.gov (United States)

    Hoolahan, Angelique H; Blok, Vivian C; Gibson, Tracey; Dowton, Mark

    2012-03-01

    Recombination is typically assumed to be absent in animal mitochondrial genomes (mtDNA). However, the maternal mode of inheritance means that recombinant products are indistinguishable from their progenitor molecules. The majority of studies of mtDNA recombination assess past recombination events, where patterns of recombination are inferred by comparing the mtDNA of different individuals. Few studies assess contemporary mtDNA recombination, where recombinant molecules are observed as direct mosaics of known progenitor molecules. Here we use the potato cyst nematode, Globodera pallida, to investigate past and contemporary recombination. Past recombination was assessed within and between populations of G. pallida, and contemporary recombination was assessed in the progeny of experimental crosses of these populations. Breeding of genetically divergent organisms may cause paternal mtDNA leakage, resulting in heteroplasmy and facilitating the detection of recombination. To assess contemporary recombination we looked for evidence of recombination between the mtDNA of the parental populations within the mtDNA of progeny. Past recombination was detected between a South American population and several UK populations of G. pallida, as well as between two South American populations. This suggests that these populations may have interbred, paternal mtDNA leakage occurred, and the mtDNA of these populations subsequently recombined. This evidence challenges two dogmas of animal mtDNA evolution; no recombination and maternal inheritance. No contemporary recombination between the parental populations was detected in the progeny of the experimental crosses. This supports current arguments that mtDNA recombination events are rare. More sensitive detection methods may be required to adequately assess contemporary mtDNA recombination in animals.

  18. Genome-wide variation in recombination rate in Eucalyptus.

    Science.gov (United States)

    Gion, Jean-Marc; Hudson, Corey J; Lesur, Isabelle; Vaillancourt, René E; Potts, Brad M; Freeman, Jules S

    2016-08-09

    chromosomes in recombination rates appear stable across Eucalyptus species. Together with the strong correlations between recombination rate and features of the Eucalyptus reference genome, we maintain these findings provide further evidence for a broad conservation of genome architecture across the globally significant lineages of Eucalyptus.

  19. Dissociative recombination of dications

    International Nuclear Information System (INIS)

    Seiersen, K.; Heber, O.; Jensen, M.J.; Safvan, C.P.; Andersen, L. H.

    2003-01-01

    Dissociative recombination (DR) of doubly-charged positive ions has been studied at the heavy ion storage ring ASTRID. Low-energy electrons were scattered on the dication of the N 2 molecule, and the absolute cross section was measured in the energy range of 10 -4 -50 eV. From the measured cross section, a thermal rate coefficient of 5.8x10 -7 cm 3 s -1 at 300 K was extracted. Furthermore, we present new results on the CO 2+ DR rate, and a summary and comparison of measured DR rate coefficients for both the singly and doubly-charged ions of CO, CO 2 , and N 2 is presented

  20. The role of recombination in the emergence of a complex and dynamic HIV epidemic

    Directory of Open Access Journals (Sweden)

    Morgenstern Burkhard

    2010-03-01

    Full Text Available Abstract Background Inter-subtype recombinants dominate the HIV epidemics in three geographical regions. To better understand the role of HIV recombinants in shaping the current HIV epidemic, we here present the results of a large-scale subtyping analysis of 9435 HIV-1 sequences that involve subtypes A, B, C, G, F and the epidemiologically important recombinants derived from three continents. Results The circulating recombinant form CRF02_AG, common in West Central Africa, appears to result from recombination events that occurred early in the divergence between subtypes A and G, followed by additional recent recombination events that contribute to the breakpoint pattern defining the current recombinant lineage. This finding also corrects a recent claim that G is a recombinant and a descendant of CRF02, which was suggested to be a pure subtype. The BC and BF recombinants in China and South America, respectively, are derived from recent recombination between contemporary parental lineages. Shared breakpoints in South America BF recombinants indicate that the HIV-1 epidemics in Argentina and Brazil are not independent. Therefore, the contemporary HIV-1 epidemic has recombinant lineages of both ancient and more recent origins. Conclusions Taken together, we show that these recombinant lineages, which are highly prevalent in the current HIV epidemic, are a mixture of ancient and recent recombination. The HIV pandemic is moving towards having increasing complexity and higher prevalence of recombinant forms, sometimes existing as "families" of related forms. We find that the classification of some CRF designations need to be revised as a consequence of (1 an estimated > 5% error in the original subtype assignments deposited in the Los Alamos sequence database; (2 an increasing number of CRFs are defined while they do not readily fit into groupings for molecular epidemiology and vaccine design; and (3 a dynamic HIV epidemic context.

  1. Cell biology of mitotic recombination

    DEFF Research Database (Denmark)

    Lisby, Michael; Rothstein, Rodney

    2015-01-01

    Homologous recombination provides high-fidelity DNA repair throughout all domains of life. Live cell fluorescence microscopy offers the opportunity to image individual recombination events in real time providing insight into the in vivo biochemistry of the involved proteins and DNA molecules as w...

  2. Hadron Correlations and Parton Recombination

    Energy Technology Data Exchange (ETDEWEB)

    Fries, R.J. [School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455 (United States)]. E-mail: rjfries@comp.tamu.edu

    2007-02-15

    Parton recombination has been found to be an extremely useful model to understand hadron production at the Relativistic Heavy Ion Collider. It is particularly important to explore its connections with hard processes. This article reviews some of the aspects of the quark recombination model and places particular emphasis on hadron correlations.

  3. Tailoring Charge Recombination in Photoelectrodes Using Oxide Nanostructures

    DEFF Research Database (Denmark)

    Iandolo, Beniamino; Wickman, Björn; Svensson, Elin

    2016-01-01

    Optimizing semiconductor devices for solar energy conversion requires an explicit control of the recombination of photogenerated electron−hole pairs. Here we show how the recombination of charge carriers can be controlled in semiconductor thin films by surface patterning with oxide nanodisks....... The control mechanism relies on the formation of dipole-like electric fields at the interface that, depending on the field direction, attract or repel minority carriers from underneath the disks. The charge recombination rate can be controlled through the choice of oxide material and the surface coverage...... of nanodisks. We provide proof-of-principle demonstration of this approach by patterning the surface of Fe2O3, one of the most studied semiconductors for light-driven water splitting, with TiO2 and Cu2O nanodisks. We expect this method to be generally applicable to a range of semiconductor-based solar energy...

  4. SPECIES RICHNESS AND BIODIVERSITY CONSERVATION PRIORITIES IN BRITISH COLUMBIA

    Science.gov (United States)

    Patterns in the geographic distribution of seven species groups were used to identify important areas for conservation in British Columbia, Canada. Potential priority sites for conservation were determined using an integer programming algorithm that maximized the number of speci...

  5. Auger recombination in sodium iodide

    Science.gov (United States)

    McAllister, Andrew; Kioupakis, Emmanouil; Åberg, Daniel; Schleife, André

    2014-03-01

    Scintillators are an important tool used to detect high energy radiation - both in the interest of national security and in medicine. However, scintillator detectors currently suffer from lower energy resolutions than expected from basic counting statistics. This has been attributed to non-proportional light yield compared to incoming radiation, but the specific mechanism for this non-proportionality has not been identified. Auger recombination is a non-radiative process that could be contributing to the non-proportionality of scintillating materials. Auger recombination comes in two types - direct and phonon-assisted. We have used first-principles calculations to study Auger recombination in sodium iodide, a well characterized scintillating material. Our findings indicate that phonon-assisted Auger recombination is stronger in sodium iodide than direct Auger recombination. Computational resources provided by LLNL and NERSC. Funding provided by NA-22.

  6. Within-host dynamics of the emergence of Tomato yellow leaf curl virus recombinants.

    Directory of Open Access Journals (Sweden)

    Cica Urbino

    Full Text Available Tomato yellow leaf curl virus (TYLCV is a highly damaging begomovirus native to the Middle East. TYLCV has recently spread worldwide, recombining with other begomoviruses. Recent analysis of mixed infections between TYLCV and Tomato leaf curl Comoros begomovirus (ToLCKMV has shown that, although natural selection preserves certain co-evolved intra-genomic interactions, numerous and diverse recombinants are produced at 120 days post-inoculation (dpi, and recombinant populations from different tomato plants are very divergent. Here, we investigate the population dynamics that lead to such patterns in tomato plants co-infected with TYLCV and ToLCKMV either by agro-inoculation or using the natural whitefly vector Bemisia tabaci. We monitored the frequency of parental and recombinant genotypes independently in 35 plants between 18 and 330 dpi and identified 177 recombinants isolated at different times. Recombinants were detected from 18 dpi and their frequency increased over time to reach about 50% at 150 dpi regardless of the inoculation method. The distribution of breakpoints detected on 96 fully sequenced recombinants was consistent with a continuous generation of new recombinants as well as random and deterministic effects in their maintenance. A severe population bottleneck of around 10 genomes was estimated during early systemic infection-a phenomenon that could account partially for the heterogeneity in recombinant patterns observed among plants. The detection of the same recombinant genome in six of the thirteen plants analysed beyond 30 dpi supported the influence of selection on observed recombination patterns. Moreover, a highly virulent recombinant genotype dominating virus populations within one plant has, apparently, the potential to be maintained in the natural population according to its infectivity, within-host accumulation, and transmission efficiency - all of which were similar or intermediate to those of the parent genotypes. Our

  7. Correlation between pairing initiation sites, recombination nodules and meiotic recombination in Sordaria macrospora.

    Science.gov (United States)

    Zickler, D; Moreau, P J; Huynh, A D; Slezec, A M

    1992-09-01

    The decrease of meiotic exchanges (crossing over and conversion) in two mutants of Sordaria macrospora correlated strongly with a reduction of chiasmata and of both types of "recombination nodules." Serial section reconstruction electron microscopy was used to compare the synapsis pattern of meiotic prophase I in wild type and mutants. First, synapsis occurred but the number of synaptonemal complex initiation sites was reduced in both mutants. Second, this reduction was accompanied by, or resulted in, modifications of the pattern of synapsis. Genetic and synaptonemal complex maps were compared in three regions along one chromosome arm divided into well marked intervals. Reciprocal exchange frequencies and number of recombination nodules correlated in wild type in the three analyzed intervals, but disparity was found between the location of recombination nodules and exchanges in the mutants. Despite the twofold exchange decrease, sections of the genome such as the short arm of chromosome 2 and telomere regions were sheltered from nodule decrease and from pairing modifications. This indicated a certain amount of diversity in the control of these features and suggested that exchange frequency was dependent not only on the amount of effective pairing but also on the localization of the pairing sites, as revealed by the synaptonemal complex progression in the mutants.

  8. Genetic recombination is targeted towards gene promoter regions in dogs.

    Science.gov (United States)

    Auton, Adam; Rui Li, Ying; Kidd, Jeffrey; Oliveira, Kyle; Nadel, Julie; Holloway, J Kim; Hayward, Jessica J; Cohen, Paula E; Greally, John M; Wang, Jun; Bustamante, Carlos D; Boyko, Adam R

    2013-01-01

    The identification of the H3K4 trimethylase, PRDM9, as the gene responsible for recombination hotspot localization has provided considerable insight into the mechanisms by which recombination is initiated in mammals. However, uniquely amongst mammals, canids appear to lack a functional version of PRDM9 and may therefore provide a model for understanding recombination that occurs in the absence of PRDM9, and thus how PRDM9 functions to shape the recombination landscape. We have constructed a fine-scale genetic map from patterns of linkage disequilibrium assessed using high-throughput sequence data from 51 free-ranging dogs, Canis lupus familiaris. While broad-scale properties of recombination appear similar to other mammalian species, our fine-scale estimates indicate that canine highly elevated recombination rates are observed in the vicinity of CpG rich regions including gene promoter regions, but show little association with H3K4 trimethylation marks identified in spermatocytes. By comparison to genomic data from the Andean fox, Lycalopex culpaeus, we show that biased gene conversion is a plausible mechanism by which the high CpG content of the dog genome could have occurred.

  9. Population Demographic History Can Cause the Appearance of Recombination Hotspots

    Science.gov (United States)

    Johnston, Henry R.; Cutler, David J.

    2012-01-01

    Although the prevailing view among geneticists suggests that recombination hotspots exist ubiquitously across the human genome, there is only limited experimental evidence from a few genomic regions to support the generality of this claim. A small number of true recombination hotspots are well supported experimentally, but the vast majority of hotspots have been identified on the basis of population genetic inferences from the patterns of linkage disequilibrium (LD) seen in the human population. These inferences are made assuming a particular model of human history, and one of the assumptions of that model is that the effective population size of humans has remained constant throughout our history. Our results show that relaxation of the constant population size assumption can create LD and variation patterns that are qualitatively and quantitatively similar to human populations without any need to invoke localized hotspots of recombination. In other words, apparent recombination hotspots could be an artifact of variable population size over time. Several lines of evidence suggest that the vast majority of hotspots identified on the basis of LD information are unlikely to have elevated recombination rates. PMID:22560089

  10. Identification and utilization of inter-species conserved (ISC probesets on Affymetrix human GeneChip® platforms for the optimization of the assessment of expression patterns in non human primate (NHP samples

    Directory of Open Access Journals (Sweden)

    Arnold Alma

    2004-10-01

    Full Text Available Abstract Background While researchers have utilized versions of the Affymetrix human GeneChip® for the assessment of expression patterns in non human primate (NHP samples, there has been no comprehensive sequence analysis study undertaken to demonstrate that the probe sequences designed to detect human transcripts are reliably hybridizing with their orthologs in NHP. By aligning probe sequences with expressed sequence tags (ESTs in NHP, inter-species conserved (ISC probesets, which have two or more probes complementary to ESTs in NHP, were identified on human GeneChip® platforms. The utility of human GeneChips® for the assessment of NHP expression patterns can be effectively evaluated by analyzing the hybridization behaviour of ISC probesets. Appropriate normalization methods were identified that further improve the reliability of human GeneChips® for interspecies (human vs NHP comparisons. Results ISC probesets in each of the seven Affymetrix GeneChip® platforms (U133Plus2.0, U133A, U133B, U95Av2, U95B, Focus and HuGeneFL were identified for both monkey and chimpanzee. Expression data was generated from peripheral blood mononuclear cells (PBMCs of 12 human and 8 monkey (Indian origin Rhesus macaque samples using the Focus GeneChip®. Analysis of both qualitative detection calls and quantitative signal intensities showed that intra-species reproducibility (human vs. human or monkey vs. monkey was much higher than interspecies reproducibility (human vs. monkey. ISC probesets exhibited higher interspecies reproducibility than the overall expressed probesets. Importantly, appropriate normalization methods could be leveraged to greatly improve interspecies correlations. The correlation coefficients between human (average of 12 samples and monkey (average of 8 Rhesus macaque samples are 0.725, 0.821 and 0.893 for MAS5.0 (Microarray Suite version 5.0, dChip and RMA (Robust Multi-chip Average normalization method, respectively. Conclusion It is

  11. High-throughput measurement of recombination rates and genetic interference in Saccharomyces cerevisiae.

    Science.gov (United States)

    Raffoux, Xavier; Bourge, Mickael; Dumas, Fabrice; Martin, Olivier C; Falque, Matthieu

    2018-06-01

    Allelic recombination owing to meiotic crossovers is a major driver of genome evolution, as well as a key player for the selection of high-performing genotypes in economically important species. Therefore, we developed a high-throughput and low-cost method to measure recombination rates and crossover patterning (including interference) in large populations of the budding yeast Saccharomyces cerevisiae. Recombination and interference were analysed by flow cytometry, which allows time-consuming steps such as tetrad microdissection or spore growth to be avoided. Moreover, our method can also be used to compare recombination in wild-type vs. mutant individuals or in different environmental conditions, even if the changes in recombination rates are small. Furthermore, meiotic mutants often present recombination and/or pairing defects affecting spore viability but our method does not involve growth steps and thus avoids filtering out non-viable spores. Copyright © 2018 John Wiley & Sons, Ltd.

  12. Oxygen-hydrogen recombination system

    International Nuclear Information System (INIS)

    Sato, Shuichiro; Takejima, Masaki.

    1981-01-01

    Purpose: To avoid reduction in the performance of catalyst used for an oxygen-hydrogen recombiner in the off gas processing system of a nuclear reactor. Constitution: A thermometer is provided for the detection of temperature in an oxygen-hydrogen recombiner. A cooling pipe is provided in the recombiner and cooling medium is introduced externally. The cooling medium may be water or air. In accordance with the detection value from the thermometer, ON-OFF control is carried out for a valve to control the flow rate of the cooling medium thereby rendering the temperature in the recombiner to a predetermined value. This can prevent the catalyst from being exposed to high temperature and avoid the reduction in the performance of the catalyst. (Ikeda, J.)

  13. Controlled Release from Recombinant Polymers

    Science.gov (United States)

    Price, Robert; Poursaid, Azadeh; Ghandehari, Hamidreza

    2014-01-01

    Recombinant polymers provide a high degree of molecular definition for correlating structure with function in controlled release. The wide array of amino acids available as building blocks for these materials lend many advantages including biorecognition, biodegradability, potential biocompatibility, and control over mechanical properties among other attributes. Genetic engineering and DNA manipulation techniques enable the optimization of structure for precise control over spatial and temporal release. Unlike the majority of chemical synthetic strategies used, recombinant DNA technology has allowed for the production of monodisperse polymers with specifically defined sequences. Several classes of recombinant polymers have been used for controlled drug delivery. These include, but are not limited to, elastin-like, silk-like, and silk-elastinlike proteins, as well as emerging cationic polymers for gene delivery. In this article, progress and prospects of recombinant polymers used in controlled release will be reviewed. PMID:24956486

  14. Hydrogen recombiner development at AECL

    International Nuclear Information System (INIS)

    Dewit, W.A.; Koroll, G.W.; Loesel Sitar, J.; Graham, W.R.C.

    1997-01-01

    Catalytic recombiners have been developed at AECL for the purpose of hydrogen removal in post-accident nuclear containment buildings. The recombiners are based on a particular catalyst designed by AECL which has extraordinary resistance to fouling from water and water vapour and a large thermodynamic range of operation. The catalysts were developed, originally, for the purpose of heavy water manufacturing by way of a catalytic exchange process. Application of these catalyst materials in recombiners for containment applications began in the late 1980's. The first application was a passive recombiner, qualified for use in control of radiolytic hydrogen in the headspace of a pool-type experimental reactor of AECL design in 1988. The passive, or natural convection recombiner concept has continued development to commercial stage for application in power reactor containments. This paper reviews the AECL recombiner development, describes the current model and shows results from tests of full-scale recombiners in the Large Scale Vented Combustion Test Facility at AECL-WL. The AECL recombiner is designed for compactness and ease of engineering into containment. The design is a simple, open-ended rectangular enclosure with catalyst elements arranged inside to promote optimum convective flow driven by heat of recombination at the catalyst surface. Self start, as evidenced by catalyst heating and initiation of flow, is achieved in less than 1% hydrogen, with available oxygen, at room temperature and 100% relative humidity. This low temperature start-up in condensing atmospheres is viewed as the most challenging condition for wet-proofing effectiveness. Cold start-up is a vital performance requirement in containments, such as CANDU, where engineered air-cooling systems are operating and where long-term hydrogen control is required, after containment atmospheres have cooled. Once started, the removal capacity scales linearly with the inlet cross-section area and the partial

  15. Recombinant snake venom prothrombin activators

    OpenAIRE

    L?vgren, Ann

    2012-01-01

    Three prothrombin activators; ecarin, which was originally isolated from the venom of the saw-scaled viper Echis carinatus, trocarin from the rough-scaled snake Tropidechis carinatus, and oscutarin from the Taipan snake Oxyuranus scutellatus, were expressed in mammalian cells with the purpose to obtain recombinant prothrombin activators that could be used to convert prothrombin to thrombin. We have previously reported that recombinant ecarin can efficiently generate thrombin without the need ...

  16. Delayed recombination and cosmic parameters

    International Nuclear Information System (INIS)

    Galli, Silvia; Melchiorri, Alessandro; Bean, Rachel; Silk, Joseph

    2008-01-01

    Current cosmological constraints from cosmic microwave background anisotropies are typically derived assuming a standard recombination scheme, however additional resonance and ionizing radiation sources can delay recombination, altering the cosmic ionization history and the cosmological inferences drawn from the cosmic microwave background data. We show that for recent observations of the cosmic microwave background anisotropy, from the Wilkinson microwave anisotropy probe satellite mission (WMAP) 5-year survey and from the arcminute cosmology bolometer array receiver experiment, additional resonance radiation is nearly degenerate with variations in the spectral index, n s , and has a marked effect on uncertainties in constraints on the Hubble constant, age of the universe, curvature and the upper bound on the neutrino mass. When a modified recombination scheme is considered, the redshift of recombination is constrained to z * =1078±11, with uncertainties in the measurement weaker by 1 order of magnitude than those obtained under the assumption of standard recombination while constraints on the shift parameter are shifted by 1σ to R=1.734±0.028. From the WMAP5 data we obtain the following constraints on the resonance and ionization sources parameters: ε α i <0.058 at 95% c.l.. Although delayed recombination limits the precision of parameter estimation from the WMAP satellite, we demonstrate that this should not be the case for future, smaller angular scales measurements, such as those by the Planck satellite mission.

  17. Fast Dissemination of New HIV-1 CRF02/A1 Recombinants in Pakistan.

    Directory of Open Access Journals (Sweden)

    Yue Chen

    Full Text Available A number of HIV-1 subtypes are identified in Pakistan by characterization of partial viral gene sequences. Little is known whether new recombinants are generated and how they disseminate since whole genome sequences for these viruses have not been characterized. Near full-length genome (NFLG sequences were obtained by amplifying two overlapping half genomes or next generation sequencing from 34 HIV-1-infected individuals in Pakistan. Phylogenetic tree analysis showed that the newly characterized sequences were 16 subtype As, one subtype C, and 17 A/G recombinants. Further analysis showed that all 16 subtype A1 sequences (47%, together with the vast majority of sequences from Pakistan from other studies, formed a tight subcluster (A1a within the subtype A1 clade, suggesting that they were derived from a single introduction. More in-depth analysis of 17 A/G NFLG sequences showed that five shared similar recombination breakpoints as in CRF02 (15% but were phylogenetically distinct from the prototype CRF02 by forming a tight subcluster (CRF02a while 12 (38% were new recombinants between CRF02a and A1a or a divergent A1b viruses. Unique recombination patterns among the majority of the newly characterized recombinants indicated ongoing recombination. Interestingly, recombination breakpoints in these CRF02/A1 recombinants were similar to those in prototype CRF02 viruses, indicating that recombination at these sites more likely generate variable recombinant viruses. The dominance and fast dissemination of new CRF02a/A1 recombinants over prototype CRF02 suggest that these recombinant have more adapted and may become major epidemic strains in Pakistan.

  18. Fast Dissemination of New HIV-1 CRF02/A1 Recombinants in Pakistan

    Science.gov (United States)

    Chen, Yue; Hora, Bhavna; DeMarco, Todd; Shah, Sharaf Ali; Ahmed, Manzoor; Sanchez, Ana M.; Su, Chang; Carter, Meredith; Stone, Mars; Hasan, Rumina; Hasan, Zahra; Busch, Michael P.; Denny, Thomas N.; Gao, Feng

    2016-01-01

    A number of HIV-1 subtypes are identified in Pakistan by characterization of partial viral gene sequences. Little is known whether new recombinants are generated and how they disseminate since whole genome sequences for these viruses have not been characterized. Near full-length genome (NFLG) sequences were obtained by amplifying two overlapping half genomes or next generation sequencing from 34 HIV-1-infected individuals in Pakistan. Phylogenetic tree analysis showed that the newly characterized sequences were 16 subtype As, one subtype C, and 17 A/G recombinants. Further analysis showed that all 16 subtype A1 sequences (47%), together with the vast majority of sequences from Pakistan from other studies, formed a tight subcluster (A1a) within the subtype A1 clade, suggesting that they were derived from a single introduction. More in-depth analysis of 17 A/G NFLG sequences showed that five shared similar recombination breakpoints as in CRF02 (15%) but were phylogenetically distinct from the prototype CRF02 by forming a tight subcluster (CRF02a) while 12 (38%) were new recombinants between CRF02a and A1a or a divergent A1b viruses. Unique recombination patterns among the majority of the newly characterized recombinants indicated ongoing recombination. Interestingly, recombination breakpoints in these CRF02/A1 recombinants were similar to those in prototype CRF02 viruses, indicating that recombination at these sites more likely generate variable recombinant viruses. The dominance and fast dissemination of new CRF02a/A1 recombinants over prototype CRF02 suggest that these recombinant have more adapted and may become major epidemic strains in Pakistan. PMID:27973597

  19. Blood-conservation techniques in craniofacial surgery.

    Science.gov (United States)

    Meara, John G; Smith, Ebonie M; Harshbarger, Raymond J; Farlo, Joe N; Matar, Marla M; Levy, Mike L

    2005-05-01

    Attempts at reducing exposure to allogeneic transfusions, using blood conservation techniques such as controlled hypotension and normovolemic hemodilution, have met with mixed results and are not always practical in small infants. Recombinant human erythropoietin (RHE), a hormone that stimulates RBC production, increases the hematocrit when administered to infants. A retrospective chart review of all patients undergoing fronto-orbital advancement for craniosynostosis by the same plastic surgeon between January 2002 and December 2002 was conducted. A subgroup of patients (10/19) received RHE as a blood-conservation strategy. Transfusion requirements were lower in the RHE group (5/10) versus the control group (9/9). Total volume of blood products transfused was statistically lower in the RHE group (154 mL RHE group versus 421 mL control) (P conservation techniques was associated with a decreased need for blood transfusion, thus exposing the patient to fewer risks associated with allogeneic transfusion.

  20. Assembly and dynamics of the bacteriophage T4 homologous recombination machinery

    Directory of Open Access Journals (Sweden)

    Morrical Scott W

    2010-12-01

    Full Text Available Abstract Homologous recombination (HR, a process involving the physical exchange of strands between homologous or nearly homologous DNA molecules, is critical for maintaining the genetic diversity and genome stability of species. Bacteriophage T4 is one of the classic systems for studies of homologous recombination. T4 uses HR for high-frequency genetic exchanges, for homology-directed DNA repair (HDR processes including DNA double-strand break repair, and for the initiation of DNA replication (RDR. T4 recombination proteins are expressed at high levels during T4 infection in E. coli, and share strong sequence, structural, and/or functional conservation with their counterparts in cellular organisms. Biochemical studies of T4 recombination have provided key insights on DNA strand exchange mechanisms, on the structure and function of recombination proteins, and on the coordination of recombination and DNA synthesis activities during RDR and HDR. Recent years have seen the development of detailed biochemical models for the assembly and dynamics of presynaptic filaments in the T4 recombination system, for the atomic structure of T4 UvsX recombinase, and for the roles of DNA helicases in T4 recombination. The goal of this chapter is to review these recent advances and their implications for HR and HDR mechanisms in all organisms.

  1. Recombinational DSBs-intersected genes converge on specific disease- and adaptability-related pathways.

    Science.gov (United States)

    Yang, Zhi-Kai; Luo, Hao; Zhang, Yanming; Wang, Baijing; Gao, Feng

    2018-05-03

    The budding yeast Saccharomyces cerevisiae is a model species powerful for studying the recombination of eukaryotes. Although many recombination studies have been performed for this species by experimental methods, the population genomic study based on bioinformatics analyses is urgently needed to greatly increase the range and accuracy of recombination detection. Here, we carry out the population genomic analysis of recombination in S. cerevisiae to reveal the potential rules between recombination and evolution in eukaryotes. By population genomic analysis, we discover significantly more and longer recombination events in clinical strains, which indicates that adverse environmental conditions create an obviously wider range of genetic combination in response to the selective pressure. Based on the analysis of recombinational DSBs-intersected genes (RDIGs), we find that RDIGs significantly converge on specific disease- and adaptability-related pathways, indicating that recombination plays a biologically key role in the repair of DSBs related to diseases and environmental adaptability, especially the human neurological disorders (NDs). By evolutionary analysis of RDIGs, we find that the RDIGs highly prevailing in populations of yeast tend to be more evolutionarily conserved, indicating the accurate repair of DSBs in these RDIGs is critical to ensure the eukaryotic survival or fitness. fgao@tju.edu.cn. Supplementary data are available at Bioinformatics online.

  2. The Impact of Recombination Hotspots on Genome Evolution of a Fungal Plant Pathogen.

    Science.gov (United States)

    Croll, Daniel; Lendenmann, Mark H; Stewart, Ethan; McDonald, Bruce A

    2015-11-01

    Recombination has an impact on genome evolution by maintaining chromosomal integrity, affecting the efficacy of selection, and increasing genetic variability in populations. Recombination rates are a key determinant of the coevolutionary dynamics between hosts and their pathogens. Historic recombination events created devastating new pathogens, but the impact of ongoing recombination in sexual pathogens is poorly understood. Many fungal pathogens of plants undergo regular sexual cycles, and sex is considered to be a major factor contributing to virulence. We generated a recombination map at kilobase-scale resolution for the haploid plant pathogenic fungus Zymoseptoria tritici. To account for intraspecific variation in recombination rates, we constructed genetic maps from two independent crosses. We localized a total of 10,287 crossover events in 441 progeny and found that recombination rates were highly heterogeneous within and among chromosomes. Recombination rates on large chromosomes were inversely correlated with chromosome length. Short accessory chromosomes often lacked evidence for crossovers between parental chromosomes. Recombination was concentrated in narrow hotspots that were preferentially located close to telomeres. Hotspots were only partially conserved between the two crosses, suggesting that hotspots are short-lived and may vary according to genomic background. Genes located in hotspot regions were enriched in genes encoding secreted proteins. Population resequencing showed that chromosomal regions with high recombination rates were strongly correlated with regions of low linkage disequilibrium. Hence, genes in pathogen recombination hotspots are likely to evolve faster in natural populations and may represent a greater threat to the host. Copyright © 2015 by the Genetics Society of America.

  3. PROGENITORS OF RECOMBINING SUPERNOVA REMNANTS

    Energy Technology Data Exchange (ETDEWEB)

    Moriya, Takashi J., E-mail: takashi.moriya@ipmu.jp [Kavli Institute for the Physics and Mathematics of the Universe, Todai Institutes for Advanced Study, University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba 277-8583 (Japan)

    2012-05-01

    Usual supernova remnants have either ionizing plasma or plasma in collisional ionization equilibrium, i.e., the ionization temperature is lower than or equal to the electron temperature. However, the existence of recombining supernova remnants, i.e., supernova remnants with ionization temperature higher than the electron temperature, has been recently confirmed. One suggested way to have recombining plasma in a supernova remnant is to have a dense circumstellar medium at the time of the supernova explosion. If the circumstellar medium is dense enough, collisional ionization equilibrium can be established in the early stage of the evolution of the supernova remnant and subsequent adiabatic cooling, which occurs after the shock wave gets out of the dense circumstellar medium, makes the electron temperature lower than the ionization temperature. We study the circumstellar medium around several supernova progenitors and show which supernova progenitors can have a circumstellar medium dense enough to establish collisional ionization equilibrium soon after the explosion. We find that the circumstellar medium around red supergiants (especially massive ones) and the circumstellar medium dense enough to make Type IIn supernovae can establish collisional ionization equilibrium soon after the explosion and can evolve to become recombining supernova remnants. Wolf-Rayet stars and white dwarfs have the possibility to be recombining supernova remnants but the fraction is expected to be very small. As the occurrence rate of the explosions of red supergiants is much higher than that of Type IIn supernovae, the major progenitors of recombining supernova remnants are likely to be red supergiants.

  4. Recombination in diverse maize is stable, predictable, and associated with genetic load.

    Science.gov (United States)

    Rodgers-Melnick, Eli; Bradbury, Peter J; Elshire, Robert J; Glaubitz, Jeffrey C; Acharya, Charlotte B; Mitchell, Sharon E; Li, Chunhui; Li, Yongxiang; Buckler, Edward S

    2015-03-24

    Among the fundamental evolutionary forces, recombination arguably has the largest impact on the practical work of plant breeders. Varying over 1,000-fold across the maize genome, the local meiotic recombination rate limits the resolving power of quantitative trait mapping and the precision of favorable allele introgression. The consequences of low recombination also theoretically extend to the species-wide scale by decreasing the power of selection relative to genetic drift, and thereby hindering the purging of deleterious mutations. In this study, we used genotyping-by-sequencing (GBS) to identify 136,000 recombination breakpoints at high resolution within US and Chinese maize nested association mapping populations. We find that the pattern of cross-overs is highly predictable on the broad scale, following the distribution of gene density and CpG methylation. Several large inversions also suppress recombination in distinct regions of several families. We also identify recombination hotspots ranging in size from 1 kb to 30 kb. We find these hotspots to be historically stable and, compared with similar regions with low recombination, to have strongly differentiated patterns of DNA methylation and GC content. We also provide evidence for the historical action of GC-biased gene conversion in recombination hotspots. Finally, using genomic evolutionary rate profiling (GERP) to identify putative deleterious polymorphisms, we find evidence for reduced genetic load in hotspot regions, a phenomenon that may have considerable practical importance for breeding programs worldwide.

  5. Serendipitous identification of natural intergenotypic recombinants of hepatitis C in Ireland.

    LENUS (Irish Health Repository)

    Moreau, Isabelle

    2006-01-01

    BACKGROUND: Recombination between hepatitis C single stranded RNA viruses is a rare event. Natural viable intragenotypic and intergenotypic recombinants between 1b-1a, 1a-1c and 2k-1b, 2i-6p, respectively, have been reported. Diagnostically recombinants represent an intriguing challenge. Hepatitis C genotype is defined by interrogation of the sequence composition of the 5\\' untranslated region [5\\'UTR]. Occasionally, ambiguous specimens require further investigation of the genome, usually by interrogation of the NS5B region. The original purpose of this study was to confirm the existence of a suspected mixed genotype infection of genotypes 2 and 4 by clonal analysis at the NS5B region of the genome in two specimens from two separate individuals. This initial identification of genotype was based on analysis of the 5\\'UTR of the genome by reverse line probe hybridisation [RLPH]. RESULTS: The original diagnosis of a mixed genotype infection was not confirmed by clonal analysis of the NS5B region of the genome. The phylogenetic analysis indicated that both specimens were natural intergenotypic recombinant forms of HCV. The recombination was between genotypes 2k and 1b for both specimens. The recombination break point was identified as occurring within the NS2 region of the genome. CONCLUSION: The viral recombinants identified here resemble the recombinant form originally identified in Russia. The RLPH pattern observed in this study may be a signature indicative of this particular type of intergenotype recombinant of hepatitis C meriting clonal analysis of NS2.

  6. 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.

  7. Electric hydrogen recombiner special tests

    International Nuclear Information System (INIS)

    Wilson, J.F.

    1975-12-01

    Westinghouse has produced an electric hydrogen recombiner to control hydrogen levels in reactor containments following a postulated loss-of-coolant accident. The recombiner underwent extensive testing for NRC qualification (see WCAP 7709-L and Supplements 1, 2, 3, 4). As a result, WCAP 7709-L and Supplements 1, 2, 3, and 4 have been accepted by the NRC for reference in applications not committed to IEEE-323-1974. Supplement 5 and the next supplement will demonstrate conformance to IEEE-323-1974. This supplement describes additional tests, beyond those necessary to qualify the system, which will be referenced in supplement 6. Each test has demonstrated a considerable margin of safety over required performance. Concurrently, the test results increased the fund of technical information on the electric hydrogen recombiner

  8. Efficient preparation of shuffled DNA libraries through recombination (Gateway) cloning.

    Science.gov (United States)

    Lehtonen, Soili I; Taskinen, Barbara; Ojala, Elina; Kukkurainen, Sampo; Rahikainen, Rolle; Riihimäki, Tiina A; Laitinen, Olli H; Kulomaa, Markku S; Hytönen, Vesa P

    2015-01-01

    Efficient and robust subcloning is essential for the construction of high-diversity DNA libraries in the field of directed evolution. We have developed a more efficient method for the subcloning of DNA-shuffled libraries by employing recombination cloning (Gateway). The Gateway cloning procedure was performed directly after the gene reassembly reaction, without additional purification and amplification steps, thus simplifying the conventional DNA shuffling protocols. Recombination-based cloning, directly from the heterologous reassembly reaction, conserved the high quality of the library and reduced the time required for the library construction. The described method is generally compatible for the construction of DNA-shuffled gene libraries. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  9. Recombinant Plasmodium falciparum glutamate rich protein; purification and use in enzyme-linked immunosorbent assay

    DEFF Research Database (Denmark)

    Dziegiel, Morten Hanefeld; Borre, M B; Jepsen, S

    1991-01-01

    New Guinea (MAD20) and Honduras (HB3) completely absorbed specific antibodies, indicating the presence of conserved epitopes produced by all isolates of P. falciparum. Recombinant GLURP489-1271 ELISA is sensitive and rapid, and therefore well-suited for sero-epidemiological studies, and for control...

  10. Disruption of mouse RAD54 reduces ionizing radiation resistance and homologous recombination.

    NARCIS (Netherlands)

    J. Essers (Jeroen); R.W. Hendriks (Rudi); S.M.A. Swagemakers (Sigrid); C. Troelstra (Christine); J. de Wit (Jan); D. Bootsma (Dirk); J.H.J. Hoeijmakers (Jan); R. Kanaar (Roland)

    1997-01-01

    textabstractDouble-strand DNA break (DSB) repair by homologous recombination occurs through the RAD52 pathway in Saccharomyces cerevisiae. Its biological importance is underscored by the conservation of many RAD52 pathway genes, including RAD54, from fungi to humans. We have analyzed the phenotype

  11. Enhancement of exciton radiative recombination for In-doped ZnO nanowires with aluminum cylindrical micropillars

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Jen-Cheng; Liang, Yu-Ting; Cheng, Fang-Ching; Fang, Chia-Hui; Chen, Hung-Ing; Tsai, Chung-Yuan [Graduate Institute of Electro-Optical Engineering and Department of Electronic Engineering, Chang Gung University, 259 Wen-Hwa 1st Road, Kwei-Shan, Tao-Yuan 333, Taiwan, ROC (China); Jiang, Joe-Air [Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei 106, Taiwan, ROC (China); Nee, Tzer-En, E-mail: neete@mail.cgu.edu.tw [Graduate Institute of Electro-Optical Engineering and Department of Electronic Engineering, Chang Gung University, 259 Wen-Hwa 1st Road, Kwei-Shan, Tao-Yuan 333, Taiwan, ROC (China)

    2013-04-15

    Zinc oxide (ZnO) has attracted intensive research effort in recent years, due to its unique properties and versatile applications. Recent work on the conservation of surface plasmon (SP) and light through period metal arrays has elucidated the propagation of SP resonance behavior. In this paper, we discuss the enhancement of exciton radiative recombination of the ZnO nanowires with Al cylindrical micropillars. Optical characterization of exciton interacted with SP resonance for indium-doped ZnO nanowires with Al cylindrical micropillars has been also investigated. From photoluminescence spectra of In-doped ZnO nanowires, it is found that the In-doped ZnO nanowires have a blue emission at 425 nm, which resulted from the ZnO band-to-band transition. Prior to the arrays of samples were annealed, a broad green emission centered at 500 nm was observed, which is attributed to ZnO native point defects. The relatively strong green band emission results from the radiative recombination that arises from the ionized oxygen vacancy and surface-defect related luminescence. Compare the In-doped ZnO on Si substrate, the enhancement of PL intensity for In-doped ZnO with deposited Al pattern film can be attributed to strong interaction with SP resonance and exciton over a broad temperature range. These experimental results indicate that Al cylindrical micropillars can significantly enhance carrier confinement and increase the quantum efficiency of In-doped ZnO/Al heterostructures due to the interaction of SP resonance between the In-doped ZnO nanowires and Al cylindrical micropillar structures, the surface-defect related luminescence, and the auxiliary test structures with variable micropillar parameters. -- Highlights: ► We examine the exciton radiative recombination of the ZnO nanowires. ► Al cylindrical micropillars affect the carrier recombination of ZnO/Al structures. ► The interaction of SP resonance between In-doped ZnO nanowire and Al pattern film. ► The carrier

  12. Emergence of recombinant forms in geographic regions with co-circulating HIV subtypes in the dynamic HIV-1 epidemic

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Ming [Los Alamos National Laboratory; Letiner, Thomas K [Los Alamos National Laboratory; Korber, Bette T [Los Alamos National Laboratory; Foley, Brian [Los Alamos National Laboratory

    2009-01-01

    We have reexamined the subtype designations of {approx}10,000 subtype A, B, C, G, and AG, BC, BF recombinant sequences, and compared the results of the new analysis with their published designations. Intersubtype recombinants dominate HIV epidemics in three different geographical regions. The circulating recombinant from (CRF) CRF02-AG, common in West Central Africa, appears to result from a recombination event that occurred early in the divergence between subtypes A and G, although additional more recent recombination events may have contributed to the breakpoint pattern in this recombinant lineage as well. The Chinese recombinant epidemic strains CRF07 and CRF08, in contrast, result from recent recombinations between more contemporary strains. Nevertheless, CRF07 and CRF08 contributed to many subsequent recombination events. The BF recombinant epidemics in two HIV-1 epicenters in South America are not independent and BF epidemics in South America have an unusually high fraction of unique recombinant forms (URFs) that have each been found only once and carry distinctive breakpoints. Taken together, these analyses reveal a complex and dynamic picture of the current HIV-1 epidemic, and suggest a means of grouping and tracking relationships between viruses through preservation of shared breakpints.

  13. Production and recombination of gluons

    International Nuclear Information System (INIS)

    Temiraliev, A.T.

    2006-01-01

    Full text: Nonlinear Markov process of parton production has been considered. The Kolmogorov equation is applied for the evolution equation based on the approximation of independent gluons production in every decay act. We introduced a 'crossing' parameter and used the combination relations to obtain nonlinear recombination equation for the evolution of gluon structure function. (author)

  14. Recombinator of hydrogen and oxygen

    International Nuclear Information System (INIS)

    Stejskal, J.; Klein, O.; Scholtz, G.; Schmidt, P.; Olaussson, A.

    1976-01-01

    Improvements are proposed for the well known reactors for the catalytic recombination of hydrogen and oxygen, which should permit this being used in contiuous operation in nuclear reactors (BWRs). The improvements concern the geometric arrangement of gas-inlet and -outlet pipes, the inclination of the axis of the catalyst container and the introduction of remote operation. (UWI) [de

  15. Improving recombinant protein purification yield

    Science.gov (United States)

    Production of adequate amounts of recombinant proteins is essential for antibody production, biochemical activity study, and structural determination during the post-genomic era. It’s technologically challenging and a limiting factor for tung oil research because analytical reagents such as high qua...

  16. Recombination in hepatitis C virus.

    Science.gov (United States)

    González-Candelas, Fernando; López-Labrador, F Xavier; Bracho, María Alma

    2011-10-01

    Hepatitis C virus (HCV) is a Flavivirus with a positive-sense, single-stranded RNA genome of about 9,600 nucleotides. It is a major cause of liver disease, infecting almost 200 million people all over the world. Similarly to most RNA viruses, HCV displays very high levels of genetic diversity which have been used to differentiate six major genotypes and about 80 subtypes. Although the different genotypes and subtypes share basic biological and pathogenic features they differ in clinical outcomes, response to treatment and epidemiology. The first HCV recombinant strain, in which different genome segments derived from parentals of different genotypes, was described in St. Petersburg (Russia) in 2002. Since then, there have been only a few more than a dozen reports including descriptions of HCV recombinants at all levels: between genotypes, between subtypes of the same genotype and even between strains of the same subtype. Here, we review the literature considering the reasons underlying the difficulties for unequivocally establishing recombination in this virus along with the analytical methods necessary to do it. Finally, we analyze the potential consequences, especially in clinical practice, of HCV recombination in light of the coming new therapeutic approaches against this virus.

  17. Mechanism of Homologous Recombination and Implications for Aging-Related Deletions in Mitochondrial DNA

    Science.gov (United States)

    2013-01-01

    SUMMARY Homologous recombination is a universal process, conserved from bacteriophage to human, which is important for the repair of double-strand DNA breaks. Recombination in mitochondrial DNA (mtDNA) was documented more than 4 decades ago, but the underlying molecular mechanism has remained elusive. Recent studies have revealed the presence of a Rad52-type recombination system of bacteriophage origin in mitochondria, which operates by a single-strand annealing mechanism independent of the canonical RecA/Rad51-type recombinases. Increasing evidence supports the notion that, like in bacteriophages, mtDNA inheritance is a coordinated interplay between recombination, repair, and replication. These findings could have profound implications for understanding the mechanism of mtDNA inheritance and the generation of mtDNA deletions in aging cells. PMID:24006472

  18. Evolution of the paralogous hap and iga genes in Haemophilus influenzae: evidence for a conserved hap pseudogene associated with microcolony formation in the recently diverged Haemophilus aegyptius and H. influenzae biogroup aegyptius

    DEFF Research Database (Denmark)

    Kilian, Mogens; Poulsen, Knud; Lomholt, Hans Bredsted

    2002-01-01

    genetic polymorphism and pronounced mosaic-like patterns in both genes, but no evidence of intrastrain recombination between the two genes. A conserved hap pseudogene was present in all strains of H. aegyptius and H. influenzae biogroup aegyptius, each of which constituted distinct subpopulations...... on conjunctival cells, previously termed microcolony formation. The fact that individual hap pseudogenes differed from the ancestral sequence by zero to two positions within a 1.5 kb stretch suggests that the silencing event happened approximately 2000-11,000 years ago. Divergence of H. aegyptius and H...

  19. Live recombinant BHV/BRSV vaccine

    NARCIS (Netherlands)

    Keil, G.M.; Rijsewijk, F.A.M.

    1998-01-01

    The present invention refers to synthetic Bovine Respiratory Syncytium virus genes. Also the invention relates to live attenuated Bovine Herpesvirus recombinants carrying such synthetic genes. Furthermore, the invention relates to vaccines based on these live attenuated recombinants, for the

  20. Hadron production at RHIC: recombination of quarks

    Energy Technology Data Exchange (ETDEWEB)

    Fries, Rainer J [School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455 (United States)

    2005-01-01

    We discuss quark recombination applied to the hadronization of a quark gluon plasma. It has been shown that the quark recombination model can explain essential features of hadron production measured in high energy heavy ion collisions.

  1. Affinity purification of recombinant human plasminogen activator ...

    African Journals Online (AJOL)

    Affinity purification of recombinant human plasminogen activator from ... Screening antibody was performed using rhPA milk in an ELISA-elution assay. ... useful for purifying other tPA mutants or other novel recombinant milkderived proteins.

  2. Graded Recombination Layers for Multijunction Photovoltaics

    KAUST Repository

    Koleilat, Ghada I.; Wang, Xihua; Sargent, Edward H.

    2012-01-01

    it to achieve multicolor and spectrally tunable behavior. In series-connected current-matched multijunction devices, the recombination layers must allow the hole current from one cell to recombine, with high efficiency and low voltage loss, with the electron

  3. Recombinant innovation and endogenous technological transitions

    NARCIS (Netherlands)

    Frenken, K.; Izquierdo, L.R.; Zeppini, P.

    2012-01-01

    We propose a model of technological transitions based on two different types of innovations. Branching innovations refer to technological improvements along a particular path, while recombinant innovations represent fusions of multiple paths. Recombinant innovations create "short-cuts" which reduce

  4. Genetics of Genome-Wide Recombination Rate Evolution in Mice from an Isolated Island.

    Science.gov (United States)

    Wang, Richard J; Payseur, Bret A

    2017-08-01

    Recombination rate is a heritable quantitative trait that evolves despite the fundamentally conserved role that recombination plays in meiosis. Differences in recombination rate can alter the landscape of the genome and the genetic diversity of populations. Yet our understanding of the genetic basis of recombination rate evolution in nature remains limited. We used wild house mice ( Mus musculus domesticus ) from Gough Island (GI), which diverged recently from their mainland counterparts, to characterize the genetics of recombination rate evolution. We quantified genome-wide autosomal recombination rates by immunofluorescence cytology in spermatocytes from 240 F 2 males generated from intercrosses between GI-derived mice and the wild-derived inbred strain WSB/EiJ. We identified four quantitative trait loci (QTL) responsible for inter-F 2 variation in this trait, the strongest of which had effects that opposed the direction of the parental trait differences. Candidate genes and mutations for these QTL were identified by overlapping the detected intervals with whole-genome sequencing data and publicly available transcriptomic profiles from spermatocytes. Combined with existing studies, our findings suggest that genome-wide recombination rate divergence is not directional and its evolution within and between subspecies proceeds from distinct genetic loci. Copyright © 2017 by the Genetics Society of America.

  5. Enrichment of intersubtype HIV-1 recombinants in a dual infection system using HIV-1 strain-specific siRNAs

    Science.gov (United States)

    2011-01-01

    Background Intersubtype HIV-1 recombinants in the form of unique or stable circulating recombinants forms (CRFs) are responsible for over 20% of infections in the worldwide epidemic. Mechanisms controlling the generation, selection, and transmission of these intersubtype HIV-1 recombinants still require further investigation. All intersubtype HIV-1 recombinants are generated and evolve from initial dual infections, but are difficult to identify in the human population. In vitro studies provide the most practical system to study mechanisms, but the recombination rates are usually very low in dual infections with primary HIV-1 isolates. This study describes the use of HIV-1 isolate-specific siRNAs to enrich intersubtype HIV-1 recombinants and inhibit the parental HIV-1 isolates from a dual infection. Results Following a dual infection with subtype A and D primary HIV-1 isolates and two rounds of siRNA treatment, nearly 100% of replicative virus was resistant to a siRNA specific for an upstream target sequence in the subtype A envelope (env) gene as well as a siRNA specific for a downstream target sequence in the subtype D env gene. Only 20% (10/50) of the replicating virus had nucleotide substitutions in the siRNA-target sequence whereas the remaining 78% (39/50) harbored a recombination breakpoint that removed both siRNA target sequences, and rendered the intersubtype D/A recombinant virus resistant to the dual siRNA treatment. Since siRNAs target the newly transcribed HIV-1 mRNA, the siRNAs only enrich intersubtype env recombinants and do not influence the recombination process during reverse transcription. Using this system, a strong bias is selected for recombination breakpoints in the C2 region, whereas other HIV-1 env regions, most notably the hypervariable regions, were nearly devoid of intersubtype recombination breakpoints. Sequence conservation plays an important role in selecting for recombination breakpoints, but the lack of breakpoints in many conserved

  6. Population inversion in recombining hydrogen plasma

    International Nuclear Information System (INIS)

    Furukane, Utaro; Yokota, Toshiaki; Oda, Toshiatsu.

    1978-11-01

    The collisional-radiative model is applied to a recombining hydrogen plasma in order to investigate the plasma condition in which the population inversion between the energy levels of hydrogen can be generated. The population inversion is expected in a plasma where the three body recombination has a large contribution to the recombining processes and the effective recombination rate is beyond a certain value for a given electron density and temperature. Calculated results are presented in figures and tables. (author)

  7. Regulation of homologous recombination in eukaryotes

    OpenAIRE

    Heyer, Wolf-Dietrich; Ehmsen, Kirk T.; Liu, Jie

    2010-01-01

    Homologous recombination is required for accurate chromosome segregation during the first meiotic division and constitutes a key repair and tolerance pathway for complex DNA damage including DNA double-stranded breaks, interstrand crosslinks, and DNA gaps. In addition, recombination and replication are inextricably linked, as recombination recovers stalled and broken replication forks enabling the evolution of larger genomes/replicons. Defects in recombination lead to genomic instability and ...

  8. The effect of a single recombination event

    DEFF Research Database (Denmark)

    Schierup, Mikkel Heide; Jensen, Thomas Mailund; Wiuf, Carsten

    We investigate the variance in how visible a single recombination event is in a SNP data set as a function of the type of recombination event and its age. Data is simulated under the coalescent with recombination and inference is by the popular composite likelihood methods. The major determinant...

  9. Regulatory Control of the Resolution of DNA Recombination Intermediates during Meiosis and Mitosis

    OpenAIRE

    Matos, Joao; Blanco, Miguel G.; Maslen, Sarah; Skehel, J. Mark; West, Stephen C.

    2011-01-01

    The efficient and timely resolution of DNA recombination intermediates is essential for bipolar chromosome segregation. Here, we show that the specialized chromosome segregation patterns of meiosis and mitosis, which require the coordination of recombination with cell-cycle progression, are achieved by regulating the timing of activation of two crossover-promoting endonucleases. In yeast meiosis, Mus81-Mms4 and Yen1 are controlled by phosphorylation events that lead to their sequential activa...

  10. Vegetation patterns and environmental gradients in Benin

    NARCIS (Netherlands)

    Adomou, A.

    2005-01-01

    Key words: West Africa, Benin, vegetation patterns, floristic areas, phytogeography, chorology, floristic gradients, climatic factors, water availability, Dahomey Gap, threatened plants, biodiversity, conservation.Understanding plant species distribution patterns and the underlying factors is a

  11. Cocirculation of Two env Molecular Variants, of Possible Recombinant Origin, in Gorilla and Chimpanzee Simian Foamy Virus Strains from Central Africa.

    Science.gov (United States)

    Richard, Léa; Rua, Réjane; Betsem, Edouard; Mouinga-Ondémé, Augustin; Kazanji, Mirdad; Leroy, Eric; Njouom, Richard; Buseyne, Florence; Afonso, Philippe V; Gessain, Antoine

    2015-12-01

    Simian foamy virus (SFV) is a ubiquitous retrovirus in nonhuman primates (NHPs) that can be transmitted to humans, mostly through severe bites. In the past few years, our laboratory has identified more than 50 hunters from central Africa infected with zoonotic SFVs. Analysis of the complete sequences of five SFVs obtained from these individuals revealed that env was the most variable gene. Furthermore, recombinant SFV strains, some of which involve sequences in the env gene, were recently identified. Here, we investigated the variability of the env genes of zoonotic SFV strains and searched for possible recombinants. We sequenced the complete env gene or its surface glycoprotein region (SU) from DNA amplified from the blood of (i) a series of 40 individuals from Cameroon or Gabon infected with a gorilla or chimpanzee foamy virus (FV) strain and (ii) 1 gorilla and 3 infected chimpanzees living in the same areas as these hunters. Phylogenetic analyses revealed the existence of two env variants among both the gorilla and chimpanzee FV strains that were present in zoonotic and NHP strains. These variants differ greatly (>30% variability) in a 753-bp-long region located in the receptor-binding domain of SU, whereas the rest of the gene is very conserved. Although the organizations of the Env protein sequences are similar, the potential glycosylation patterns differ between variants. Analysis of recombination suggests that the variants emerged through recombination between different strains, although all parental strains could not be identified. SFV infection in humans is a great example of a zoonotic retroviral infection that has not spread among human populations, in contrast to human immunodeficiency viruses (HIVs) and human T-lymphotropic viruses (HTLVs). Recombination was a major mechanism leading to the emergence of HIV. Here, we show that two SFV molecular envelope gene variants circulate among ape populations in Central Africa and that both can be transmitted to

  12. Conservation: Toward firmer ground

    Science.gov (United States)

    1975-01-01

    The following aspects of energy conservation were reviewed in order to place the problems in proper perspective: history and goals, conservation accounting-criteria, and a method to overcome obstacles. The effect of changing prices and available supplies of energy sources and their causes on consumption levels during the last few decades were described. Some examples of attainable conservation goals were listed and justified. A number of specific criteria applicable to conservation accounting were given. Finally, a discussion was presented to relate together the following aspects of energy conservation: widespread impact, involvement of government, industry, politics, moral and ethical aspects, urgency and time element.

  13. Recombination Catalysts for Hypersonic Fuels

    Science.gov (United States)

    Chinitz, W.

    1998-01-01

    The goal of commercially-viable access to space will require technologies that reduce propulsion system weight and complexity, while extracting maximum energy from the products of combustion. This work is directed toward developing effective nozzle recombination catalysts for the supersonic and hypersonic aeropropulsion engines used to provide such access to space. Effective nozzle recombination will significantly reduce rk=le length (hence, propulsion system weight) and reduce fuel requirements, further decreasing the vehicle's gross lift-off weight. Two such catalysts have been identified in this work, barium and antimony compounds, by developing chemical kinetic reaction mechanisms for these materials and determining the engine performance enhancement for a typical flight trajectory. Significant performance improvements are indicated, using only 2% (mole or mass) of these compounds in the combustor product gas.

  14. Mechanisms of sister chromatid recombination

    International Nuclear Information System (INIS)

    Nakai, Sayaka; Machida, Isamu; Tsuji, Satsuki

    1985-01-01

    Studies using T948 as a model system have been carried out aimed at elucidating the mechanism of sister chromatid recombination (SCR). Characterization of U.V. light- and x-ray-induced SCR, the relationiship between SCR induction and DNA repair using rad mutations, and the relationship between SCR induction and the time of cell division using cdc mutations are presented. It has been supposed that SCR is induced at the phase of S-G 2 following DNA replication, that postreplication break of DNA strands is strongly involved in the induction of SCR, and that induction type of SCR, i.e., conversion type or recombination type, is dependent upon the type of molecular damage of DNA. (Namekawa, K.)

  15. Variation in human recombination rates and its genetic determinants.

    Directory of Open Access Journals (Sweden)

    Adi Fledel-Alon

    Full Text Available Despite the fundamental role of crossing-over in the pairing and segregation of chromosomes during human meiosis, the rates and placements of events vary markedly among individuals. Characterizing this variation and identifying its determinants are essential steps in our understanding of the human recombination process and its evolution.Using three large sets of European-American pedigrees, we examined variation in five recombination phenotypes that capture distinct aspects of crossing-over patterns. We found that the mean recombination rate in males and females and the historical hotspot usage are significantly heritable and are uncorrelated with one another. We then conducted a genome-wide association study in order to identify loci that influence them. We replicated associations of RNF212 with the mean rate in males and in females as well as the association of Inversion 17q21.31 with the female mean rate. We also replicated the association of PRDM9 with historical hotspot usage, finding that it explains most of the genetic variance in this phenotype. In addition, we identified a set of new candidate regions for further validation.These findings suggest that variation at broad and fine scales is largely separable and that, beyond three known loci, there is no evidence for common variation with large effects on recombination phenotypes.

  16. Recombination difference between sexes: a role for haploid selection.

    Directory of Open Access Journals (Sweden)

    Thomas Lenormand

    2005-03-01

    Full Text Available Why the autosomal recombination rate differs between female and male meiosis in most species has been a genetic enigma since the early study of meiosis. Some hypotheses have been put forward to explain this widespread phenomenon and, up to now, only one fact has emerged clearly: In species in which meiosis is achiasmate in one sex, it is the heterogametic one. This pattern, known as the Haldane-Huxley rule, is thought to be a side effect, on autosomes, of the suppression of recombination between the sex chromosomes. However, this rule does not hold for heterochiasmate species (i.e., species in which recombination is present in both sexes but varies quantitatively between sexes and does not apply to species lacking sex chromosomes, such as hermaphroditic plants. In this paper, we show that in plants, heterochiasmy is due to a male-female difference in gametic selection and is not influenced by the presence of heteromorphic sex chromosomes. This finding provides strong empirical support in favour of a population genetic explanation for the evolution of heterochiasmy and, more broadly, for the evolution of sex and recombination.

  17. Recombination Proteins Mediate Meiotic Spatial Chromosome Organization and Pairing

    Science.gov (United States)

    Storlazzi, Aurora; Gargano, Silvana; Ruprich-Robert, Gwenael; Falque, Matthieu; David, Michelle; Kleckner, Nancy; Zickler, Denise

    2010-01-01

    SUMMARY Meiotic chromosome pairing involves not only recognition of homology but also juxtaposition of entire chromosomes in a topologically regular way. Analysis of filamentous fungus Sordaria macrospora reveals that recombination proteins Mer3, Msh4 and Mlh1 play direct roles in all of these aspects, in advance of their known roles in recombination. Absence of Mer3 helicase results in interwoven chromosomes, thereby revealing the existence of features that specifically ensure “entanglement avoidance”. Entanglements that remain at zygotene, i.e. “interlockings”, require Mlh1 for resolution, likely to eliminate constraining recombinational connections. Patterns of Mer3 and Msh4 foci along aligned chromosomes show that the double-strand breaks mediating homologous alignment have spatially separated ends, one localized to each partner axis, and that pairing involves interference among developing interhomolog interactions. We propose that Mer3, Msh4 and Mlh1 execute all of these roles during pairing by modulating the state of nascent double-strand break/partner DNA contacts within axis-associated recombination complexes. PMID:20371348

  18. Interface recombination influence on carrier transport

    International Nuclear Information System (INIS)

    Konin, A

    2013-01-01

    A theory of interface recombination in the semiconductor–semiconductor junction is developed. The interface recombination rate dependence on the nonequilibrium carrier densities is derived on the basis of a model in which the interface recombination occurs through the mechanism of trapping. The general relation between the interface recombination parameters at small carrier density deviation from the equilibrium ones is obtained. The validity of this relation is proved considering the generation of the Hall electric field in the extrinsic semiconductor sample. The anomalous Hall electromotive force in a weak magnetic field was investigated and interpreted by means of a new interface recombination model. The experimental data corroborate the developed theory. (paper)

  19. Recombinant Cyclophilins Lack Nuclease Activity

    OpenAIRE

    Manteca, Angel; Sanchez, Jesus

    2004-01-01

    Several single-domain prokaryotic and eukaryotic cyclophilins have been identified as also being unspecific nucleases with a role in DNA degradation during the lytic processes that accompany bacterial cell death and eukaryotic apoptosis. Evidence is provided here that the supposed nuclease activity of human and bacterial recombinant cyclophilins is due to contamination of the proteins by the host Escherichia coli endonuclease and is not an intrinsic property of these proteins.

  20. Workshop on Radio Recombination Lines

    CERN Document Server

    1980-01-01

    Since their first detection 15 years ago, radio recombination lines from several elements have been observed in a wide variety of objects including HII regions, planetary nebulae, molecular clouds, the diffuse interstellar medium, and recently, other galaxies. The observations span almost the entire range from 0.1 to 100 GHz, and employ both single­ djsh and aperture synthesis techniques. The theory of radio recombination lines has also advanced strongly, to the point where it is perhaps one of the best-understood in astro­ physics. In a parallel development, it has become possible over the last decade to study these same highly-excited atoms in the laboratory; this work provides further confirmation of the theoretical framework. However there has been continuing controversy over the astrophysical interpre­ tation of radio recombination line observations, especially regarding the role of stimulated emission. A workshop was held in Ottawa on 24-25 August, 1979, bringing together many of the active scientist...

  1. Consequences of recombination on traditional phylogenetic analysis

    DEFF Research Database (Denmark)

    Schierup, M H; Hein, J

    2000-01-01

    We investigate the shape of a phylogenetic tree reconstructed from sequences evolving under the coalescent with recombination. The motivation is that evolutionary inferences are often made from phylogenetic trees reconstructed from population data even though recombination may well occur (mt......DNA or viral sequences) or does occur (nuclear sequences). We investigate the size and direction of biases when a single tree is reconstructed ignoring recombination. Standard software (PHYLIP) was used to construct the best phylogenetic tree from sequences simulated under the coalescent with recombination....... With recombination present, the length of terminal branches and the total branch length are larger, and the time to the most recent common ancestor smaller, than for a tree reconstructed from sequences evolving with no recombination. The effects are pronounced even for small levels of recombination that may...

  2. Genetic recombination is associated with intrinsic disorder in plant proteomes.

    Science.gov (United States)

    Yruela, Inmaculada; Contreras-Moreira, Bruno

    2013-11-09

    Intrinsically disordered proteins, found in all living organisms, are essential for basic cellular functions and complement the function of ordered proteins. It has been shown that protein disorder is linked to the G + C content of the genome. Furthermore, recent investigations have suggested that the evolutionary dynamics of the plant nucleus adds disordered segments to open reading frames alike, and these segments are not necessarily conserved among orthologous genes. In the present work the distribution of intrinsically disordered proteins along the chromosomes of several representative plants was analyzed. The reported results support a non-random distribution of disordered proteins along the chromosomes of Arabidopsis thaliana and Oryza sativa, two model eudicot and monocot plant species, respectively. In fact, for most chromosomes positive correlations between the frequency of disordered segments of 30+ amino acids and both recombination rates and G + C content were observed. These analyses demonstrate that the presence of disordered segments among plant proteins is associated with the rates of genetic recombination of their encoding genes. Altogether, these findings suggest that high recombination rates, as well as chromosomal rearrangements, could induce disordered segments in proteins during evolution.

  3. B chromosomes are associated with redistribution of genetic recombination towards lower recombination chromosomal regions in perennial ryegrass.

    Science.gov (United States)

    Harper, John; Phillips, Dylan; Thomas, Ann; Gasior, Dagmara; Evans, Caron; Powell, Wayne; King, Julie; King, Ian; Jenkins, Glyn; Armstead, Ian

    2018-04-09

    Supernumerary 'B' chromosomes are non-essential components of the genome present in a range of plant and animal species-including many grasses. Within diploid and polyploid ryegrass and fescue species, including the forage grass perennial ryegrass (Lolium perenne L.), the presence of B chromosomes has been reported as influencing both chromosome pairing and chiasma frequencies. In this study, the effects of the presence/absence of B chromosomes on genetic recombination has been investigated through generating DArT (Diversity Arrays Technology) marker genetic maps for six perennial ryegrass diploid populations, the pollen parents of which contained either two B or zero B chromosomes. Through genetic and cytological analyses of these progeny and their parents, we have identified that, while overall cytological estimates of chiasma frequencies were significantly lower in pollen mother cells with two B chromosomes as compared with zero B chromosomes, the recombination frequencies within some marker intervals were actually increased, particularly for marker intervals in lower recombination regions of chromosomes, namely pericentromeric regions. Thus, in perennial ryegrass, the presence of two B chromosomes redistributed patterns of meiotic recombination in pollen mother cells in ways which could increase the range of allelic variation available to plant breeders.

  4. Googling trends in conservation biology.

    Science.gov (United States)

    Proulx, Raphaël; Massicotte, Philippe; Pépino, Marc

    2014-02-01

    Web-crawling approaches, that is, automated programs data mining the internet to obtain information about a particular process, have recently been proposed for monitoring early signs of ecosystem degradation or for establishing crop calendars. However, lack of a clear conceptual and methodological framework has prevented the development of such approaches within the field of conservation biology. Our objective was to illustrate how Google Trends, a freely accessible web-crawling engine, can be used to track changes in timing of biological processes, spatial distribution of invasive species, and level of public awareness about key conservation issues. Google Trends returns the number of internet searches that were made for a keyword in a given region of the world over a defined period. Using data retrieved online for 13 countries, we exemplify how Google Trends can be used to study the timing of biological processes, such as the seasonal recurrence of pollen release or mosquito outbreaks across a latitudinal gradient. We mapped the spatial extent of results from Google Trends for 5 invasive species in the United States and found geographic patterns in invasions that are consistent with their coarse-grained distribution at state levels. From 2004 through 2012, Google Trends showed that the level of public interest and awareness about conservation issues related to ecosystem services, biodiversity, and climate change increased, decreased, and followed both trends, respectively. Finally, to further the development of research approaches at the interface of conservation biology, collective knowledge, and environmental management, we developed an algorithm that allows the rapid retrieval of Google Trends data. © 2013 Society for Conservation Biology.

  5. Ethics of conservation triage

    Directory of Open Access Journals (Sweden)

    Kerrie A Wilson

    2016-09-01

    Full Text Available Conservation triage seems to be at a stalemate between those who accept triage based on utilitarian rationalization, and those that reject it based on a number of ethical principles. We argue that without considered attention to the ethics of conservation triage we risk further polarization in the field of conservation. We draw lessons from the medical sector, where triage is more intuitive and acceptable, and also from disaster planning, to help navigate the challenges that triage entails for conservation science, practice, and policy. We clarify the consequentialist, deontological, and virtue ethical stances that influence the level of acceptance of triage. We emphasize the ethical dimensions of conservation triage in principle and in practice, particularly in the context of stakeholder diversity, a wide range of possible objectives and actions, broader institutions, and significant uncertainties. A focus on a more diverse set of ethics, more considered choice of triage as a conservation tool, open communication of triage objectives and protocols, greater consideration of risk preferences, and regular review and adaptation of triage protocols is required for conservation triage to become more acceptable among diverse conservation practitioners, institutions, and the general public. Accepting conservation triage as fundamentally an ethical problem would foster more open dialogue and constructive debate about the role of conservation triage in a wider system of care.

  6. Integrated conservation planning for coral reefs: Designing conservation zones for multiple conservation objectives in spatial prioritisation

    Directory of Open Access Journals (Sweden)

    Rafael A. Magris

    2017-07-01

    Full Text Available Decision-makers focus on representing biodiversity pattern, maintaining connectivity, and strengthening resilience to global warming when designing marine protected area (MPA systems, especially in coral reef ecosystems. The achievement of these broad conservation objectives will likely require large areas, and stretch limited funds for MPA implementation. We undertook a spatial prioritisation of Brazilian coral reefs that considered two types of conservation zones (i.e. no-take and multiple use areas and integrated multiple conservation objectives into MPA planning, while assessing the potential impact of different sets of objectives on implementation costs. We devised objectives for biodiversity, connectivity, and resilience to global warming, determined the extent to which existing MPAs achieved them, and designed complementary zoning to achieve all objectives combined in expanded MPA systems. In doing so, we explored interactions between different sets of objectives, determined whether refinements to the existing spatial arrangement of MPAs were necessary, and tested the utility of existing MPAs by comparing their cost effectiveness with an MPA system designed from scratch. We found that MPAs in Brazil protect some aspects of coral reef biodiversity pattern (e.g. threatened fauna and ecosystem types more effectively than connectivity or resilience to global warming. Expanding the existing MPA system was as cost-effective as designing one from scratch only when multiple objectives were considered and management costs were accounted for. Our approach provides a comprehensive assessment of the benefits of integrating multiple objectives in the initial stages of conservation planning, and yields insights for planners of MPAs tackling multiple objectives in other regions.

  7. A functional analysis of the spacer of V(DJ recombination signal sequences.

    Directory of Open Access Journals (Sweden)

    Alfred Ian Lee

    2003-10-01

    Full Text Available During lymphocyte development, V(DJ recombination assembles antigen receptor genes from component V, D, and J gene segments. These gene segments are flanked by a recombination signal sequence (RSS, which serves as the binding site for the recombination machinery. The murine Jbeta2.6 gene segment is a recombinationally inactive pseudogene, but examination of its RSS reveals no obvious reason for its failure to recombine. Mutagenesis of the Jbeta2.6 RSS demonstrates that the sequences of the heptamer, nonamer, and spacer are all important. Strikingly, changes solely in the spacer sequence can result in dramatic differences in the level of recombination. The subsequent analysis of a library of more than 4,000 spacer variants revealed that spacer residues of particular functional importance are correlated with their degree of conservation. Biochemical assays indicate distinct cooperation between the spacer and heptamer/nonamer along each step of the reaction pathway. The results suggest that the spacer serves not only to ensure the appropriate distance between the heptamer and nonamer but also regulates RSS activity by providing additional RAG:RSS interaction surfaces. We conclude that while RSSs are defined by a "digital" requirement for absolutely conserved nucleotides, the quality of RSS function is determined in an "analog" manner by numerous complex interactions between the RAG proteins and the less-well conserved nucleotides in the heptamer, the nonamer, and, importantly, the spacer. Those modulatory effects are accurately predicted by a new computational algorithm for "RSS information content." The interplay between such binary and multiplicative modes of interactions provides a general model for analyzing protein-DNA interactions in various biological systems.

  8. A functional analysis of the spacer of V(D)J recombination signal sequences.

    Science.gov (United States)

    Lee, Alfred Ian; Fugmann, Sebastian D; Cowell, Lindsay G; Ptaszek, Leon M; Kelsoe, Garnett; Schatz, David G

    2003-10-01

    During lymphocyte development, V(D)J recombination assembles antigen receptor genes from component V, D, and J gene segments. These gene segments are flanked by a recombination signal sequence (RSS), which serves as the binding site for the recombination machinery. The murine Jbeta2.6 gene segment is a recombinationally inactive pseudogene, but examination of its RSS reveals no obvious reason for its failure to recombine. Mutagenesis of the Jbeta2.6 RSS demonstrates that the sequences of the heptamer, nonamer, and spacer are all important. Strikingly, changes solely in the spacer sequence can result in dramatic differences in the level of recombination. The subsequent analysis of a library of more than 4,000 spacer variants revealed that spacer residues of particular functional importance are correlated with their degree of conservation. Biochemical assays indicate distinct cooperation between the spacer and heptamer/nonamer along each step of the reaction pathway. The results suggest that the spacer serves not only to ensure the appropriate distance between the heptamer and nonamer but also regulates RSS activity by providing additional RAG:RSS interaction surfaces. We conclude that while RSSs are defined by a "digital" requirement for absolutely conserved nucleotides, the quality of RSS function is determined in an "analog" manner by numerous complex interactions between the RAG proteins and the less-well conserved nucleotides in the heptamer, the nonamer, and, importantly, the spacer. Those modulatory effects are accurately predicted by a new computational algorithm for "RSS information content." The interplay between such binary and multiplicative modes of interactions provides a general model for analyzing protein-DNA interactions in various biological systems.

  9. 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'.

  10. Towards a more conservative energy policy

    International Nuclear Information System (INIS)

    Forman, N.

    1977-01-01

    The subject is treated under the following headings: the meaning of energy policy; previous attempts to formulate United Kingdom energy policy; patterns of energy supply and demand (in the UK) (current and future); towards a more conservative energy policy (the use of energy in the various sectors, the conversion and distribution of energy (coal, nuclear power, electricity, oil and gas, renewable sources)); energy policy in broader perspective (international context, cost benefit assessments, contrasting patterns of energy use, ethical issues). (U.K.)

  11. Polarized recombination of acoustically transported carriers in GaAs nanowires

    Science.gov (United States)

    Möller, Michael; Hernández-Mínguez, Alberto; Breuer, Steffen; Pfüller, Carsten; Brandt, Oliver; de Lima, Mauricio M.; Cantarero, Andrés; Geelhaar, Lutz; Riechert, Henning; Santos, Paulo V.

    2012-05-01

    The oscillating piezoelectric field of a surface acoustic wave (SAW) is employed to transport photoexcited electrons and holes in GaAs nanowires deposited on a SAW delay line on a LiNbO3 crystal. The carriers generated in the nanowire by a focused light spot are acoustically transferred to a second location where they recombine. We show that the recombination of the transported carriers occurs in a zinc blende section on top of the predominant wurtzite nanowire. This allows contactless control of the linear polarized emission by SAWs which is governed by the crystal structure. Additional polarization-resolved photoluminescence measurements were performed to investigate spin conservation during transport.

  12. Ultrafast and band-selective Auger recombination in InGaN quantum wells

    International Nuclear Information System (INIS)

    Williams, Kristopher W.; Monahan, Nicholas R.; Zhu, X.-Y.; Koleske, Daniel D.; Crawford, Mary H.

    2016-01-01

    In InGaN quantum well based light-emitting diodes, Auger recombination is believed to limit the quantum efficiency at high injection currents. Here, we report the direct observation of carrier loss from Auger recombination on a sub-picosecond timescale in a single InGaN quantum well using time-resolved photoemission. Selective excitations of different valence sub-bands reveal that the Auger rate constant decreases by two orders of magnitude as the effective hole mass decreases, confirming the critical role of momentum conservation.

  13. Conservation: Toward firmer ground

    Science.gov (United States)

    1975-01-01

    The following aspects of energy conservation were discussed: conservation history and goals, conservation modes, conservation accounting-criteria, and a method to overcome obstacles. The conservation modes tested fall into one of the following categories: reduced energy consumption, increased efficiency of energy utilization, or substitution of one or more forms of energy for another which is in shorter supply or in some sense thought to be of more value. The conservation accounting criteria include net energy reduction, economic, and technical criteria. A method to overcome obstacles includes (approaches such as: direct personal impact (life style, income, security, aspiration), an element of crisis, large scale involvement of environmental, safety, and health issues, connections to big government, big business, big politics, involvement of known and speculative science and technology, appeal to moral and ethical standards, the transient nature of opportunities to correct the system.

  14. Econometric modelling of conservation

    International Nuclear Information System (INIS)

    Parker, J.C.; Seal, D.J.

    1990-01-01

    The issue of energy conservation in general, and conservation in the natural gas markets in particular, has recently had a much lower profile than in the past, when energy prices were significantly higher and energy costs composed a much larger proportion of industrial operating costs than today. The recent downward trend in energy prices has diverted attention away from this issue. In the face of expected significant real price increases, increasing pressure from environmental groups, and directives on the part of regulator authorities, conservation is once again becoming a topic of consideration in the energy industry. From the point of view of gas demand forecasting, conservation has received too little attention. The intentions of this paper are to establish the need for forecasting conservation in the natural gas utility sector, and to construct a model of industrial demand which incorporates conservation and is appropriate for use as a forecasting tool

  15. Handbook on energy conservation

    International Nuclear Information System (INIS)

    1989-12-01

    This book shows energy situation in recent years, which includes reserves of energy resource in the world, crude oil production records in OPEC and non OPEC, supply and demand of energy in important developed countries, prospect of supply and demand of energy and current situation of energy conservation in developed countries. It also deals with energy situation in Korea reporting natural resources status, energy conservation policy, measurement for alternative energy, energy management of Korea, investment in equipment and public education for energy conservation.

  16. Immunological and biological properties of recombinant Lol p 1.

    Science.gov (United States)

    Boutin, Y; Lamontagne, P; Boulanger, J; Brunet, C; Hébert, J

    1997-03-01

    Current forms of allergy diagnosis and therapies are based on the use of natural allergenic extracts. Despite strong evidence that higher therapeutic efficacy may be achieved with purified allergens, the purification of multiple allergic components from extracts is a fastidious and sometimes an impossible task. However, the use of recombinant allergens may be an alternative to overcome this problem. In this study, we compared the immunological properties of recombinant (r) Lol p 1 with those of the natural protein. We cloned directly the gene encoding Lol p 1 from genomic DNA of ryegrass pollen. This gene was subcloned into the expression vector pMAL-c and expressed as fusion protein. Subsequently, rLol p 1 was cleaved from maltose-binding protein using factor Xa. Using binding inhibition and proliferative assays, we assessed the immunological properties of the recombinant allergens. The capacity of rLol p 1 to trigger basophil histamine release and to elicit a skin reaction was also assessed and compared to those of its natural counterpart. We found that the Lol p 1 gene has no introns since we amplified this gene directly from genomic DNA. We demonstrated that the binding sites of anti-Lol p 1 monoclonal antibody, specific human IgG and IgE antibody are well conserved on rLol p 1 as no difference in the binding inhibition profile was observed when using either natural or recombinant protein. At the T-cell level, rLol p 1 elicited a T-cell response in mice comparable to that observed with the natural protein. In addition, we demonstrated that the biological characteristics of rLol p 1 were comparable to those of the natural counterpart, in that rLol p 1 elicited a skin wheal reaction and induced basophil histamine release in grass-allergic patients only. The data indicate that natural Lol p 1 and rLol p 1 shared identical immunological and biological properties.

  17. PRDM9 and Its Role in Genetic Recombination.

    Science.gov (United States)

    Paigen, Kenneth; Petkov, Petko M

    2018-04-01

    PRDM9 is a zinc finger protein that binds DNA at specific locations in the genome where it trimethylates histone H3 at lysines 4 and 36 at surrounding nucleosomes. During meiosis in many species, including humans and mice where PRDM9 has been most intensely studied, these actions determine the location of recombination hotspots, where genetic recombination occurs. In addition, PRDM9 facilitates the association of hotspots with the chromosome axis, the site of the programmed DNA double-strand breaks (DSBs) that give rise to genetic exchange between chromosomes. In the absence of PRDM9 DSBs are not properly repaired. Collectively, these actions determine patterns of genetic linkage and the possibilities for chromosome reorganization over successive generations. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Posttranslational modifications in human plasma MBL and human recombinant MBL

    DEFF Research Database (Denmark)

    Jensen, Pia Hønnerup; Laursen, Inga; Matthiesen, Finn

    2007-01-01

    the intact protein in its active conformation. For the first time, positions and occupation frequency of partial hydroxylations and partial glycosylations are reported in MBL. Hydroxylation and glycosylation patterns of both recombinant and plasma derived MBL were determined, using a combination of mass......Mannan-binding lectin (MBL) is a complex serum protein that plays an important role in innate immunity. In addition to assuming several different oligomeric forms, the polypeptide itself is highly heterogeneous. This heterogeneity is due to post-translational modifications, which help to stabilize......(202)) was modified in trace amounts to dehydroalanine, as detected by a 34 Da mass loss. This impairs the formation of a disulphide bond in the carbohydrate recognition domain. The dehydroalanine was identified in similar small amounts in both recombinant and plasma-derived MBL....

  19. The rise and fall of a human recombination hot spot.

    Science.gov (United States)

    Jeffreys, Alec J; Neumann, Rita

    2009-05-01

    Human meiotic crossovers mainly cluster into narrow hot spots that profoundly influence patterns of haplotype diversity and that may also affect genome instability and sequence evolution. Hot spots also seem to be ephemeral, but processes of hot-spot activation and their subsequent evolutionary dynamics remain unknown. We now analyze the life cycle of a recombination hot spot. Sperm typing revealed a polymorphic hot spot that was activated in cis by a single base change, providing evidence for a primary sequence determinant necessary, though not sufficient, to activate recombination. This activating mutation occurred roughly 70,000 y ago and has persisted to the present, most likely fortuitously through genetic drift despite its systematic elimination by biased gene conversion. Nonetheless, this self-destructive conversion will eventually lead to hot-spot extinction. These findings define a subclass of highly transient hot spots and highlight the importance of understanding hot-spot turnover and how it influences haplotype diversity.

  20. Effects of nuclear mutations for recombination and repair functions and of caffeine on mitochondrial recombination

    International Nuclear Information System (INIS)

    Fraenkel, A.H.M.

    1974-01-01

    Studies of both prokaryotic and eukaryotic organisms indicate that pathways governing repair of damage to nuclear DNA caused by x-ray or ultraviolet irradiation overlap with those controlling recombination. Fourteen nuclear mutants of Saccharomyces cerevisiae were tested in order to determine whether these mutant genes affected mitochondrial recombination. None of the mutations studied significantly affected mitochondrial recombination. The nuclear recombination and repair pathways studied do not overlap with the nuclear pathway which controls recombination of mitochondrial DNA. A second set of experiments was designed to test the effect of caffeine on both nuclear and mitochondrial recombination in Saccharomyces cerevisiae. (U.S.)

  1. Vaccine platform recombinant measles virus.

    Science.gov (United States)

    Mühlebach, Michael D

    2017-10-01

    The classic development of vaccines is lengthy, tedious, and may not necessarily be successful as demonstrated by the case of HIV. This is especially a problem for emerging pathogens that are newly introduced into the human population and carry the inherent risk of pandemic spread in a naïve population. For such situations, a considerable number of different platform technologies are under development. These are also under development for pathogens, where directly derived vaccines are regarded as too complicated or even dangerous due to the induction of inefficient or unwanted immune responses causing considerable side-effects as for dengue virus. Among platform technologies are plasmid-based DNA vaccines, RNA replicons, single-round infectious vector particles, or replicating vaccine-based vectors encoding (a) critical antigen(s) of the target pathogens. Among the latter, recombinant measles viruses derived from vaccine strains have been tested. Measles vaccines are among the most effective and safest life-attenuated vaccines known. Therefore, the development of Schwarz-, Moraten-, or AIK-C-strain derived recombinant vaccines against a wide range of mostly viral, but also bacterial pathogens was quite straightforward. These vaccines generally induce powerful humoral and cellular immune responses in appropriate animal models, i.e., transgenic mice or non-human primates. Also in the recent first clinical phase I trial, the results have been quite encouraging. The trial indicated the expected safety and efficacy also in human patients, interestingly independent from the level of prevalent anti-measles immunity before the trial. Thereby, recombinant measles vaccines expressing additional antigens are a promising platform for future vaccines.

  2. CRMAGE: CRISPR Optimized MAGE Recombineering

    DEFF Research Database (Denmark)

    Ronda, Carlotta; Pedersen, Lasse Ebdrup; Sommer, Morten Otto Alexander

    2016-01-01

    A bottleneck in metabolic engineering and systems biology approaches is the lack of efficient genome engineering technologies. Here, we combine CRISPR/Cas9 and λ Red recombineering based MAGE technology (CRMAGE) to create a highly efficient and fast method for genome engineering of Escherichia coli...... that are assembled by a USER-cloning approach enabling quick and cost efficient gRNA replacement. CRMAGE furthermore utilizes CRISPR/Cas9 for efficient plasmid curing, thereby enabling multiple engineering rounds per day. To facilitate the design process, a web-based tool was developed to predict both the λ Red...

  3. Structural Variation Shapes the Landscape of Recombination in Mouse.

    Science.gov (United States)

    Morgan, Andrew P; Gatti, Daniel M; Najarian, Maya L; Keane, Thomas M; Galante, Raymond J; Pack, Allan I; Mott, Richard; Churchill, Gary A; de Villena, Fernando Pardo-Manuel

    2017-06-01

    Meiotic recombination is an essential feature of sexual reproduction that ensures faithful segregation of chromosomes and redistributes genetic variants in populations. Multiparent populations such as the Diversity Outbred (DO) mouse stock accumulate large numbers of crossover (CO) events between founder haplotypes, and thus present a unique opportunity to study the role of genetic variation in shaping the recombination landscape. We obtained high-density genotype data from [Formula: see text] DO mice, and localized 2.2 million CO events to intervals with a median size of 28 kb. The resulting sex-averaged genetic map of the DO population is highly concordant with large-scale (order 10 Mb) features of previously reported genetic maps for mouse. To examine fine-scale (order 10 kb) patterns of recombination in the DO, we overlaid putative recombination hotspots onto our CO intervals. We found that CO intervals are enriched in hotspots compared to the genomic background. However, as many as [Formula: see text] of CO intervals do not overlap any putative hotspots, suggesting that our understanding of hotspots is incomplete. We also identified coldspots encompassing 329 Mb, or [Formula: see text] of observable genome, in which there is little or no recombination. In contrast to hotspots, which are a few kilobases in size, and widely scattered throughout the genome, coldspots have a median size of 2.1 Mb and are spatially clustered. Coldspots are strongly associated with copy-number variant (CNV) regions, especially multi-allelic clusters, identified from whole-genome sequencing of 228 DO mice. Genes in these regions have reduced expression, and epigenetic features of closed chromatin in male germ cells, which suggests that CNVs may repress recombination by altering chromatin structure in meiosis. Our findings demonstrate how multiparent populations, by bridging the gap between large-scale and fine-scale genetic mapping, can reveal new features of the recombination

  4. Development and characterization of recombinant ovine coagulation factor VIII.

    Directory of Open Access Journals (Sweden)

    Philip M Zakas

    Full Text Available Animal models of the bleeding disorder, hemophilia A, have been an integral component of the biopharmaceutical development process and have facilitated the development of recombinant coagulation factor VIII (fVIII products capable of restoring median survival of persons with hemophilia A to that of the general population. However, there remain several limitations to recombinant fVIII as a biotherapeutic, including invasiveness of intravenous infusion, short half-life, immunogenicity, and lack of availability to the majority of the world's population. The recently described ovine model of hemophilia A is the largest and most accurate phenocopy. Affected sheep die prematurely due to bleeding-related pathogenesis and display robust adaptive humoral immunity to non-ovine fVIII. Herein, we describe the development and characterization of recombinant ovine fVIII (ofVIII to support further the utility of the ovine hemophilia A model. Full-length and B-domain deleted (BDD ofVIII cDNAs were generated and demonstrated to facilitate greater biosynthetic rates than their human fVIII counterparts while both BDD constructs showed greater expression rates than the same-species full-length versions. A top recombinant BDD ofVIII producing baby hamster kidney clone was identified and used to biosynthesize raw material for purification and biochemical characterization. Highly purified recombinant BDD ofVIII preparations possess a specific activity nearly 2-fold higher than recombinant BDD human fVIII and display a differential glycosylation pattern. However, binding to the carrier protein, von Willebrand factor, which is critical for stability of fVIII in circulation, is indistinguishable. Decay of thrombin-activated ofVIIIa is 2-fold slower than human fVIII indicating greater intrinsic stability. Furthermore, intravenous administration of ofVIII effectively reverses the bleeding phenotype in the murine model of hemophilia A. Recombinant ofVIII should facilitate

  5. Integrating technologies for scalable ecology and conservation

    NARCIS (Netherlands)

    Marvin, D.C.; Koh, L.P.; Lynam, A.J.; Wich, S.; Davies, A.B.; Krishnamurthy, R.; Stokes, E.; Starkey, R.; Asner, G.P.

    Integration of multiple technologies greatly increases the spatial and temporal scales over which ecological patterns and processes can be studied, and threats to protected ecosystems can be identified and mitigated. A range of technology options relevant to ecologists and conservation practitioners

  6. Divergence, recombination and retention of functionality during protein evolution

    Directory of Open Access Journals (Sweden)

    Xu Yanlong O

    2005-09-01

    Full Text Available Abstract We have only a vague idea of precisely how protein sequences evolve in the context of protein structure and function. This is primarily because structural and functional contexts are not easily predictable from the primary sequence, and evaluating patterns of evolution at individual residue positions is also difficult. As a result of increasing biodiversity in genomics studies, progress is being made in detecting context-dependent variation in substitution processes, but it remains unclear exactly what context-dependent patterns we should be looking for. To address this, we have been simulating protein evolution in the context of structure and function using lattice models of proteins and ligands (or substrates. These simulations include thermodynamic features of protein stability and population dynamics. We refer to this approach as 'ab initio evolution' to emphasise the fact that the equilibrium details of fitness distributions arise from the physical principles of the system and not from any preconceived notions or arbitrary mathematical distributions. Here, we present results on the retention of functionality in homologous recombinants following population divergence. A central result is that protein structure characteristics can strongly influence recombinant functionality. Exceptional structures with many sequence options evolve quickly and tend to retain functionality -- even in highly diverged recombinants. By contrast, the more common structures with fewer sequence options evolve more slowly, but the fitness of recombinants drops off rapidly as homologous proteins diverge. These results have implications for understanding viral evolution, speciation and directed evolutionary experiments. Our analysis of the divergence process can also guide improved methods for accurately approximating folding probabilities in more complex but realistic systems.

  7. Atomic excitation and recombination in external fields

    International Nuclear Information System (INIS)

    Nayfeh, M.H.; Clark, C.W.

    1985-01-01

    This volume offers a timely look at Rydberg states of atoms in external fields and dielectronic recombination. Each topic provides authoritative coverage, presents a fresh account of a flourishing field of current atomic physics and introduces new opportunities for discovery and development. Topics considered include electron-atom scattering in external fields; observations of regular and irregular motion as exemplified by the quadratic zeeman effect and other systems; Rydberg atoms in external fields and the Coulomb geometry; crossed-field effects in the absorption spectrum of lithium in a magnetic field; precise studies of static electric field ionization; widths and shapes of stark resonances in sodium above the saddle point; studies of electric field effects and barium autoionizing resonances; autoionization and dielectronic recombination in plasma electric microfields; dielectronic recombination measurements on multicharged ions; merged beam studies of dielectronic recombination; Rydberg atoms and dielectronic recombination in astrophysics; and observations on dielectronic recombination

  8. Biodiversity Conservation and Conservation Biotechnology Tools

    Science.gov (United States)

    This special issue is dedicated to the in vitro tools and methods used to conserve the genetic diversity of rare and threatened species from around the world. Species that are on the brink of extinction, due to the rapid loss of genetic diversity and habitat, come mainly from resource poor areas the...

  9. No Evidence that Infection Alters Global Recombination Rate in House Mice.

    Directory of Open Access Journals (Sweden)

    Beth L Dumont

    Full Text Available Recombination rate is a complex trait, with genetic and environmental factors shaping observed patterns of variation. Although recent studies have begun to unravel the genetic basis of recombination rate differences between organisms, less attention has focused on the environmental determinants of crossover rates. Here, we test the effect of one ubiquitous environmental pressure-bacterial infection-on global recombination frequency in mammals. We applied MLH1 mapping to assay global crossover rates in male mice infected with the pathogenic bacterium Borrelia burgdorferi, the causative agent of Lyme Disease, and uninfected control animals. Despite ample statistical power to identify biologically relevant differences between infected and uninfected animals, we find no evidence for a global recombination rate response to bacterial infection. Moreover, broad-scale patterns of crossover distribution, including the number of achiasmate bivalents, are not affected by infection status. Although pathogen exposure can plastically increase recombination in some species, our findings suggest that recombination rates in house mice may be resilient to at least some forms of infection stress. This negative result motivates future experiments with alternative house mouse pathogens to evaluate the generality of this conclusion.

  10. Paradigms for parasite conservation.

    Science.gov (United States)

    Dougherty, Eric R; Carlson, Colin J; Bueno, Veronica M; Burgio, Kevin R; Cizauskas, Carrie A; Clements, Christopher F; Seidel, Dana P; Harris, Nyeema C

    2016-08-01

    Parasitic species, which depend directly on host species for their survival, represent a major regulatory force in ecosystems and a significant component of Earth's biodiversity. Yet the negative impacts of parasites observed at the host level have motivated a conservation paradigm of eradication, moving us farther from attainment of taxonomically unbiased conservation goals. Despite a growing body of literature highlighting the importance of parasite-inclusive conservation, most parasite species remain understudied, underfunded, and underappreciated. We argue the protection of parasitic biodiversity requires a paradigm shift in the perception and valuation of their role as consumer species, similar to that of apex predators in the mid-20th century. Beyond recognizing parasites as vital trophic regulators, existing tools available to conservation practitioners should explicitly account for the unique threats facing dependent species. We built upon concepts from epidemiology and economics (e.g., host-density threshold and cost-benefit analysis) to devise novel metrics of margin of error and minimum investment for parasite conservation. We define margin of error as the risk of accidental host extinction from misestimating equilibrium population sizes and predicted oscillations, while minimum investment represents the cost associated with conserving the additional hosts required to maintain viable parasite populations. This framework will aid in the identification of readily conserved parasites that present minimal health risks. To establish parasite conservation, we propose an extension of population viability analysis for host-parasite assemblages to assess extinction risk. In the direst cases, ex situ breeding programs for parasites should be evaluated to maximize success without undermining host protection. Though parasitic species pose a considerable conservation challenge, adaptations to conservation tools will help protect parasite biodiversity in the face of

  11. Density dependence of dielectronic recombination in selenium

    International Nuclear Information System (INIS)

    Hagelstein, P.L.; Rosen, M.D.; Jacobs, V.L.

    1986-01-01

    Dielectronic recombination has been found to be the dominant recombination process in the determination of the ionization balance of selenium near the Ne-like sequence under conditions relevant to the exploding-foil EUV laser plasmas. The dielectronic recombination process tends to populate excited levels, and these levels in turn are more susceptible to subsequent excitation and ionization than are the ground-state ions. If one defines an effective recombination rate which includes, in addition to the primary recombination, the subsequent excitation and ionization of the additional excited-state population due to the primary recombination, then this effective recombination rate can be density-sensitive at relatively low electron density. We present results for this effective dielectronic recombination rate at an electron density of 3 x 10/sup 20/ electrons/cm 3 for recombination from Ne-like to Na-like selenium and from F-like to Ne-like selenium. In the former case, the effective recombination rate coefficient is found to be 1.8 x 10/sup -11/ cm 3 /sec at 1.0 keV, which is to be compared with the zero-density value of 2.8 x 10/sup -11/ cm 3 /sec. In the latter case (F-like to Ne-like), the effective recombination rate coefficient is found to be 1.3 x 10/sup -11/ cm 3 /sec, which is substantially reduced from the zero-density result of 3.3 x 10/sup -11/ cm 3 /sec. We have examined the effects of dielectronic recombination on the laser gain of the dominant Ne-like 3p-3s transitions and have compared our results with those presented by Whitten et al. [Phys. Rev. A 33, 2171 (1986)

  12. Recent and historical recombination in the admixed Norwegian Red cattle breed

    Directory of Open Access Journals (Sweden)

    Grove Harald

    2011-01-01

    Full Text Available Abstract Background Comparison of recent patterns of recombination derived from linkage maps to historical patterns of recombination from linkage disequilibrium (LD could help identify genomic regions affected by strong artificial selection, appearing as reduced recent recombination. Norwegian Red cattle (NRF make an interesting case study for investigating these patterns as it is an admixed breed with an extensively recorded pedigree. NRF have been under strong artificial selection for traits such as milk and meat production, fertility and health. While measures of LD is also crucial for determining the number of markers required for association mapping studies, estimates of recombination rate can be used to assess quality of genomic assemblies. Results A dataset containing more than 17,000 genome-wide distributed SNPs and 2600 animals was used to assess recombination rates and LD in NRF. Although low LD measured by r2 was observed in NRF relative to some of the breeds from which this breed originates, reports from breeds other than those assessed in this study have described more rapid decline in r2 at short distances than what was found in NRF. Rate of decline in r2 for NRF suggested that to obtain an expected r2 between markers and a causal polymorphism of at least 0.5 for genome-wide association studies, approximately one SNP every 15 kb or a total of 200,000 SNPs would be required. For well known quantitative trait loci (QTLs for milk production traits on Bos Taurus chromosomes 1, 6 and 20, map length based on historic recombination was greater than map length based on recent recombination in NRF. Further, positions for 130 previously unpositioned contigs from assembly of the bovine genome sequence (Btau_4.0 found using comparative sequence analysis were validated by linkage analysis, and 28% of these positions corresponded to extreme values of population recombination rate. Conclusion While LD is reduced in NRF compared to some of the

  13. Rapid purification of recombinant histones.

    Science.gov (United States)

    Klinker, Henrike; Haas, Caroline; Harrer, Nadine; Becker, Peter B; Mueller-Planitz, Felix

    2014-01-01

    The development of methods to assemble nucleosomes from recombinant histones decades ago has transformed chromatin research. Nevertheless, nucleosome reconstitution remains time consuming to this day, not least because the four individual histones must be purified first. Here, we present a streamlined purification protocol of recombinant histones from bacteria. We termed this method "rapid histone purification" (RHP) as it circumvents isolation of inclusion bodies and thereby cuts out the most time-consuming step of traditional purification protocols. Instead of inclusion body isolation, whole cell extracts are prepared under strongly denaturing conditions that directly solubilize inclusion bodies. By ion exchange chromatography, the histones are purified from the extracts. The protocol has been successfully applied to all four canonical Drosophila and human histones. RHP histones and histones that were purified from isolated inclusion bodies had similar purities. The different purification strategies also did not impact the quality of octamers reconstituted from these histones. We expect that the RHP protocol can be readily applied to the purification of canonical histones from other species as well as the numerous histone variants.

  14. High-level secretion of native recombinant human calreticulin in yeast

    DEFF Research Database (Denmark)

    Čiplys, Evaldas; Žitkus, Eimantas; Gold, Leslie I.

    2015-01-01

    , Saccharomyces cerevisiae and Pichia pastoris. RESULTS: Expression of a full-length human CRT precursor including its native signal sequence resulted in high-level secretion of mature recombinant protein into the culture medium by both S. cerevisiae and P. pastoris. To ensure the structural and functional...... by non-denaturing PAGE. Moreover, limited trypsin digestion yielded identical fragment patterns of calcium-binding recombinant and native CRT suggesting that the yeast-derived CRT was correctly folded. Furthermore, both native and recombinant CRT induced cellular proliferation (MTS assay) and migration...... recombinant CRT protein with yields reaching 75 % of total secreted protein and with production levels of 60 and 200 mg/l from S. cerevisiae and P. pastoris, respectively. Finally, cultivation of P. pastoris in a bioreactor yielded CRT secretion titer to exceed 1.5 g/l of culture medium. CONCLUSIONS: Yeasts...

  15. Introducing Conservation of Momentum

    Science.gov (United States)

    Brunt, Marjorie; Brunt, Geoff

    2013-01-01

    The teaching of the principle of conservation of linear momentum is considered (ages 15 + ). From the principle, the momenta of two masses in an isolated system are considered. Sketch graphs of the momenta make Newton's laws appear obvious. Examples using different collision conditions are considered. Conservation of momentum is considered…

  16. Water Conservation Resource List.

    Science.gov (United States)

    NJEA Review, 1981

    1981-01-01

    Alarmed by the growing water shortage, the New Jersey State Office of Dissemination has prepared this annotated list of free or inexpensive instructional materials for teaching about water conservation, K-l2. A tipsheet for home water conservation is appended. (Editor/SJL)

  17. Controllability of conservative behaviours

    NARCIS (Netherlands)

    Rao, Shodhan

    2012-01-01

    In this article, we first define the class of J-conservative behaviours with observable storage functions, where J is a symmetric two-variable polynomial matrix. We then provide two main results. The first result states that if J(-xi,xi) is nonsingular, the input cardinality of a J-conservative

  18. Conservation Science Fair Projects.

    Science.gov (United States)

    Soil Conservation Society of America, Ankeny, IA.

    Included are ideas, suggestions, and examples for selecting and designing conservation science projects. Over 70 possible conservation subject areas are presented with suggested projects. References are cited with each of these subject areas, and a separate list of annotated references is included. The references pertain to general subject…

  19. Fixism and conservation science.

    Science.gov (United States)

    Robert, Alexandre; Fontaine, Colin; Veron, Simon; Monnet, Anne-Christine; Legrand, Marine; Clavel, Joanne; Chantepie, Stéphane; Couvet, Denis; Ducarme, Frédéric; Fontaine, Benoît; Jiguet, Frédéric; le Viol, Isabelle; Rolland, Jonathan; Sarrazin, François; Teplitsky, Céline; Mouchet, Maud

    2017-08-01

    The field of biodiversity conservation has recently been criticized as relying on a fixist view of the living world in which existing species constitute at the same time targets of conservation efforts and static states of reference, which is in apparent disagreement with evolutionary dynamics. We reviewed the prominent role of species as conservation units and the common benchmark approach to conservation that aims to use past biodiversity as a reference to conserve current biodiversity. We found that the species approach is justified by the discrepancy between the time scales of macroevolution and human influence and that biodiversity benchmarks are based on reference processes rather than fixed reference states. Overall, we argue that the ethical and theoretical frameworks underlying conservation research are based on macroevolutionary processes, such as extinction dynamics. Current species, phylogenetic, community, and functional conservation approaches constitute short-term responses to short-term human effects on these reference processes, and these approaches are consistent with evolutionary principles. © 2016 Society for Conservation Biology.

  20. Setting conservation priorities.

    Science.gov (United States)

    Wilson, Kerrie A; Carwardine, Josie; Possingham, Hugh P

    2009-04-01

    A generic framework for setting conservation priorities based on the principles of classic decision theory is provided. This framework encapsulates the key elements of any problem, including the objective, the constraints, and knowledge of the system. Within the context of this framework the broad array of approaches for setting conservation priorities are reviewed. While some approaches prioritize assets or locations for conservation investment, it is concluded here that prioritization is incomplete without consideration of the conservation actions required to conserve the assets at particular locations. The challenges associated with prioritizing investments through time in the face of threats (and also spatially and temporally heterogeneous costs) can be aided by proper problem definition. Using the authors' general framework for setting conservation priorities, multiple criteria can be rationally integrated and where, how, and when to invest conservation resources can be scheduled. Trade-offs are unavoidable in priority setting when there are multiple considerations, and budgets are almost always finite. The authors discuss how trade-offs, risks, uncertainty, feedbacks, and learning can be explicitly evaluated within their generic framework for setting conservation priorities. Finally, they suggest ways that current priority-setting approaches may be improved.

  1. Madagascar Conservation & Development

    African Journals Online (AJOL)

    Madagascar Conservation & Development welcomes the results of original research, field surveys, advances in field and laboratory techniques, book reviews, and informal status reports from research, conservation, development and management programs and in-field projects in Madagascar. In addition, notes on changes ...

  2. Resource Conservation Glossary.

    Science.gov (United States)

    Soil Conservation Society of America, Ankeny, IA.

    This glossary is a composite of terms selected from 13 technologies, and is the expanded revision of the original 1952 edition of "The Soil and Water Conservation Glossary." The terms were selected from these areas: agronomy, biology, conservation, ecology, economics, engineering, forestry, geology, hydrology, range, recreation, soils, and…

  3. Creative Soil Conservation

    Science.gov (United States)

    Smith, Martha

    2010-01-01

    Take plant lessons outdoors with this engaging and inquiry-based activity in which third-grade students learn how to apply soil conservation methods to growing plants. They also collect data and draw conclusions about the effectiveness of their method of soil conservation. An added benefit to this activity is that the third-grade students played…

  4. The extent and importance of intragenic recombination

    Directory of Open Access Journals (Sweden)

    de Silva Eric

    2004-11-01

    Full Text Available Abstract We have studied the recombination rate behaviour of a set of 140 genes which were investigated for their potential importance in inflammatory disease. Each gene was extensively sequenced in 24 individuals of African descent and 23 individuals of European descent, and the recombination process was studied separately in the two population samples. The results obtained from the two populations were highly correlated, suggesting that demographic bias does not affect our population genetic estimation procedure. We found evidence that levels of recombination correlate with levels of nucleotide diversity. High marker density allowed us to study recombination rate variation on a very fine spatial scale. We found that about 40 per cent of genes showed evidence of uniform recombination, while approximately 12 per cent of genes carried distinct signatures of recombination hotspots. On studying the locations of these hotspots, we found that they are not always confined to introns but can also stretch across exons. An investigation of the protein products of these genes suggested that recombination hotspots can sometimes separate exons belonging to different protein domains; however, this occurs much less frequently than might be expected based on evolutionary studies into the origins of recombination. This suggests that evolutionary analysis of the recombination process is greatly aided by considering nucleotide sequences and protein products jointly.

  5. Japan's energy conservation policy

    International Nuclear Information System (INIS)

    Yoda, Kenichi

    1990-01-01

    This article reviews developments in Japanese energy conservation since the 1970s. The industrial sector has achieved the greatest success, due to industrial restructuring as well as improvements in energy efficiency. In the residential/commercial sector, the efficiency of appliances has been much improved. Although improvements have been made in the fuel efficiency of passenger cars, energy consumption in the transportation sector has risen slightly owing to increased transport of passengers and freight. The overall responsibility for energy conservation policy rests with the Ministry of International Trade and Industry. MITI is also responsible for implementing specific conservation policies in regard to the industrial and commercial sectors. In the residential sector, MITI works with the Ministry of Construction and in the transportation sector with the Ministry of Transport. To realize the goals of energy conservation policy through general research, dissemination of public information and other activities, MITI works with the Energy Conservation Center (ECC). (author). 2 figs, 3 tabs

  6. Tests of conservation laws

    International Nuclear Information System (INIS)

    Goldhaber, M.

    1988-01-01

    For quite a while it has been realized that some discrete quantum numbers are conserved in some interactions but not in others. The most conspicuous cases are parity P, charge conjugation C, and the product CP which are conserved in strong and electromagnetic interactions but not in weak interactions. The question arises whether for some of the other conserved quantities, which are conserved in strong, electromagnetic and weak interactions, there is an interaction intermediate in strength between weak and gravitational which violates these quantum numbers, e.g., baryon number B and lepton number L. The possibility exists that these conservation laws, if they are broken at all, are only broken by the gravitational force which would make the mass of an intermediate boson which induces the break-down equal to the Planck mass. (orig.)

  7. Applications of recombinant antibodies in plant pathology.

    Science.gov (United States)

    Ziegler, Angelika; Torrance, Lesley

    2002-09-01

    Summary Advances in molecular biology have made it possible to produce antibody fragments comprising the binding domains of antibody molecules in diverse heterologous systems, such as Escherichia coli, insect cells, or plants. Antibody fragments specific for a wide range of antigens, including plant pathogens, have been obtained by cloning V-genes from lymphoid tissue, or by selection from large naive phage display libraries, thus avoiding the need for immunization. The antibody fragments have been expressed as fusion proteins to create different functional molecules, and fully recombinant assays have been devised to detect plant viruses. The defined binding properties and unlimited cheap supply of antibody fusion proteins make them useful components of standardized immunoassays. The expression of antibody fragments in plants was shown to confer resistance to several plant pathogens. However, the antibodies usually only slowed the progress of infection and durable 'plantibody' resistance has yet to be demonstrated. In future, it is anticipated that antibody fragments from large libraries will be essential tools in high-throughput approaches to post-genomics research, such as the assignment of gene function, characterization of spatio-temporal patterns of protein expression, and elucidation of protein-protein interactions.

  8. SPECIES DISTRIBUTIONS, SURROGACY, AND IMPORTANT CONSERVATION REGIONS IN CANADA

    Science.gov (United States)

    Conservation actions could be more efficient if there is congruence among taxa in the distribution of species. Patterns in the geographic distribution of species of six taxa were used to identify nationally important sites for conservation in Canada. Species richness and a meas...

  9. Auger recombination in Dirac materials: A tangle of many-body effects

    Science.gov (United States)

    Alymov, Georgy; Vyurkov, Vladimir; Ryzhii, Victor; Satou, Akira; Svintsov, Dmitry

    2018-05-01

    The peculiar electron dispersion in Dirac materials makes lowest-order Auger processes prohibited or marginally prohibited by energy and momentum conservation laws. Thus, Auger recombination (AR) in these materials is very sensitive to many-body effects. We incorporate them at the level of the G W approximation into the nonequilibrium Green's functions approach to AR and study the role of dynamic screening, spectrum broadening, and renormalization in the case of weakly pumped undoped graphene. We find that incorrect treatment of many-body effects can lead to an order-of-magnitude error in the recombination rate. We show that the AR time depends weakly (sublinearly) on the background dielectric constant, which limits the possibility to control recombination by the choice of substrate. However, the AR time can be considerably prolonged by placing graphene under a metal gate or by introducing a band gap. With carrier cooling taken into account, our results comply with experiments on photoexcited graphene.

  10. The sensitivity of $R_{pA}$ to colour recombination effects

    CERN Document Server

    Zapp, Korinna Christina; Wiedemann, Urs Achim

    2016-01-01

    In hadronization models with color recombination, partons are allowed to regroup into color singlet structures that are different from those determined by the perturbative parton shower. This aims at modeling the possibility that soft interactions of partons with the underlying event can change color connections. If such an effect is at play in proton-proton collisions, it may be expected to be enhanced in proton-nucleus collisions due to the higher color charge density in the underlying event. Here, we provide a qualitative argument that color recombination effects could lead to a multiplicity dependent hardening of single inclusive hadron spectra that dies out very weakly with increasing transverse momentum. We present results of a (conservative) model implementation in the cluster hadronization model of the SHERPA event generator. In this model, we find that color recombination effects harden indeed the single inclusive hadron spectra without affecting the jet spectra, but that this effect does not depend ...

  11. Global conservation priorities for marine turtles.

    Directory of Open Access Journals (Sweden)

    Bryan P Wallace

    Full Text Available Where conservation resources are limited and conservation targets are diverse, robust yet flexible priority-setting frameworks are vital. Priority-setting is especially important for geographically widespread species with distinct populations subject to multiple threats that operate on different spatial and temporal scales. Marine turtles are widely distributed and exhibit intra-specific variations in population sizes and trends, as well as reproduction and morphology. However, current global extinction risk assessment frameworks do not assess conservation status of spatially and biologically distinct marine turtle Regional Management Units (RMUs, and thus do not capture variations in population trends, impacts of threats, or necessary conservation actions across individual populations. To address this issue, we developed a new assessment framework that allowed us to evaluate, compare and organize marine turtle RMUs according to status and threats criteria. Because conservation priorities can vary widely (i.e. from avoiding imminent extinction to maintaining long-term monitoring efforts we developed a "conservation priorities portfolio" system using categories of paired risk and threats scores for all RMUs (n = 58. We performed these assessments and rankings globally, by species, by ocean basin, and by recognized geopolitical bodies to identify patterns in risk, threats, and data gaps at different scales. This process resulted in characterization of risk and threats to all marine turtle RMUs, including identification of the world's 11 most endangered marine turtle RMUs based on highest risk and threats scores. This system also highlighted important gaps in available information that is crucial for accurate conservation assessments. Overall, this priority-setting framework can provide guidance for research and conservation priorities at multiple relevant scales, and should serve as a model for conservation status assessments and priority

  12. Conservation value of clustered housing developments.

    Science.gov (United States)

    Lenth, Buffy A; Knight, Richard L; Gilgert, Wendell C

    2006-10-01

    Traditionally, exurban lands in Colorado have been subdivided into a grid of parcels ranging from 2 to 16 ha. From an ecological perspective, this dispersed pattern of development effectively maximizes the individual influence of each home on the land. Clustered housing developments, designed to maximize open space, are assumed to benefit plant and wildlife communities of conservation interest. They have become a popular alternative for rural development despite the lack of empirical evidence demonstrating their conservation benefits. To better inform rural land-use planning, we evaluated clustered housing developments by comparing their spatial pattern with that of dispersed housing developments and by comparing their conservation value with that of both dispersed housing developments and undeveloped areas in Boulder County, Colorado. We used four indicators to assess conservation value: (1) densities of songbirds, (2) nest density and survival of ground-nesting birds, (3) presence of mammals, and (4) percent cover and proportion of native and non-native plant species. Clustered and dispersed housing developments did not differ on the majority of variables we examined. Both types of housing development had significantly higher densities of non-native and human-commensal species and significantly lower densities of native and human-sensitive species than undeveloped areas. More rigorous ecological guidelines and planning on a regional scale may help create clustered developments with higher conservation value.

  13. Optimized spatial priorities for biodiversity conservation in China: a systematic conservation planning perspective.

    Science.gov (United States)

    Wu, Ruidong; Long, Yongcheng; Malanson, George P; Garber, Paul A; Zhang, Shuang; Li, Diqiang; Zhao, Peng; Wang, Longzhu; Duo, Hairui

    2014-01-01

    By addressing several key features overlooked in previous studies, i.e. human disturbance, integration of ecosystem- and species-level conservation features, and principles of complementarity and representativeness, we present the first national-scale systematic conservation planning for China to determine the optimized spatial priorities for biodiversity conservation. We compiled a spatial database on the distributions of ecosystem- and species-level conservation features, and modeled a human disturbance index (HDI) by aggregating information using several socioeconomic proxies. We ran Marxan with two scenarios (HDI-ignored and HDI-considered) to investigate the effects of human disturbance, and explored the geographic patterns of the optimized spatial conservation priorities. Compared to when HDI was ignored, the HDI-considered scenario resulted in (1) a marked reduction (∼9%) in the total HDI score and a slight increase (∼7%) in the total area of the portfolio of priority units, (2) a significant increase (∼43%) in the total irreplaceable area and (3) more irreplaceable units being identified in almost all environmental zones and highly-disturbed provinces. Thus the inclusion of human disturbance is essential for cost-effective priority-setting. Attention should be targeted to the areas that are characterized as moderately-disturbed, conservation. We delineated 23 primary large-scale priority areas that are significant for conserving China's biodiversity, but those isolated priority units in disturbed regions are in more urgent need of conservation actions so as to prevent immediate and severe biodiversity loss. This study presents a spatially optimized national-scale portfolio of conservation priorities--effectively representing the overall biodiversity of China while minimizing conflicts with economic development. Our results offer critical insights for current conservation and strategic land-use planning in China. The approach is transferable and easy

  14. Cloning of human and mouse genes homologous to RAD52, a yeast gene involved in DNA repair and recombination.

    NARCIS (Netherlands)

    D.F.R. Muris; O.Y. Bezzubova (Olga); J-M. Buerstedde; K. Vreeken; A.S. Balajee; C.J. Osgood; C. Troelstra (Christine); J.H.J. Hoeijmakers (Jan); K. Ostermann; H. Schmidt (Henning); A.T. Natarajan; J.C.J. Eeken; P.H.M. Lohmann (Paul); A. Pastink (Albert)

    1994-01-01

    textabstractThe RAD52 gene of Saccharomyces cerevisiae is required for recombinational repair of double-strand breaks. Using degenerate oligonucleotides based on conserved amino acid sequences of RAD52 and rad22, its counterpart from Schizosaccharomyces pombe, RAD52 homologs from man and mouse were

  15. Electron-ion recombination at low energy

    International Nuclear Information System (INIS)

    Andersen, L.H.

    1993-01-01

    The work is based on results obtained with a merged-beams experiment. A beam of electronics with a well characterized density and energy distribution was merged with a fast, monoenergetic ion beam. Results have been obtained for radiative recombination and dielectronic recombination at low relative energies (0 to ∼70eV). The obtained energy resolution was improved by about a factor of 30. High vacuum technology was used to suppress interactions with electrons from the environments. The velocity distribution of the electron beam was determined. State-selective dielectronic-recombination measurements were performable. Recombination processes were studied. The theoretical background for radiative recombination and Kramers' theory are reviewed. The quantum mechanical result and its relation to the semiclassical theory is discussed. Radiative recombination was also measured with several different non-bare ions, and the applicability of the semiclassical theory to non-bare ions was investigated. The use of an effective charge is discussed. For dielectronic recombination, the standard theoretical approach in the isolated resonance and independent-processes approximation is debated. The applicability of this method was tested. The theory was able to reproduce most of the experimental data except when the recombination process was sensitive to couplings between different electronic configurations. The influence of external perturbing electrostatic fields is discussed. (AB) (31 refs.)

  16. Recombination rate plasticity: revealing mechanisms by design

    Science.gov (United States)

    Sefick, Stephen; Rushton, Chase

    2017-01-01

    For over a century, scientists have known that meiotic recombination rates can vary considerably among individuals, and that environmental conditions can modify recombination rates relative to the background. A variety of external and intrinsic factors such as temperature, age, sex and starvation can elicit ‘plastic’ responses in recombination rate. The influence of recombination rate plasticity on genetic diversity of the next generation has interesting and important implications for how populations evolve. Further, many questions remain regarding the mechanisms and molecular processes that contribute to recombination rate plasticity. Here, we review 100 years of experimental work on recombination rate plasticity conducted in Drosophila melanogaster. We categorize this work into four major classes of experimental designs, which we describe via classic studies in D. melanogaster. Based on these studies, we highlight molecular mechanisms that are supported by experimental results and relate these findings to studies in other systems. We synthesize lessons learned from this model system into experimental guidelines for using recent advances in genotyping technologies, to study recombination rate plasticity in non-model organisms. Specifically, we recommend (1) using fine-scale genome-wide markers, (2) collecting time-course data, (3) including crossover distribution measurements, and (4) using mixed effects models to analyse results. To illustrate this approach, we present an application adhering to these guidelines from empirical work we conducted in Drosophila pseudoobscura. This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’. PMID:29109222

  17. Electron-ion recombination in merged beams

    International Nuclear Information System (INIS)

    Wolf, A.; Habs, D.; Lampert, A.; Neumann, R.; Schramm, U.; Schuessler, T.; Schwalm, D.

    1993-01-01

    Detailed studies of recombination processes between electrons and highly charged ions have become possible by recent improvements of merged-beams experiments. We discuss in particular measurements with stored cooled ion beams at the Test Storage Ring (TSR) in Heidelberg. The cross section of dielectronic recombination was measured with high energy resolution for few-electron systems up to the nuclear charge of Cu at a relative energy up to 2.6 keV. At low energy (∼0.1 eV) total recombination rates of several ions were measured and compared with calculated radiative recombination rates. Laser-stimulated recombination of protons and of C 6+ ions was investigated as a function of the photon energy using visible radiation. Both the total recombination rates and the stimulated recombination spectra indicate that in spite of the short interaction time in merged beams, also collisional capture of electrons into weakly bound levels (related to three-body recombination) could be important

  18. Electronic recombination in some physics problems

    International Nuclear Information System (INIS)

    Guzman, O.

    1988-01-01

    This work is related to calculations of electronic recombination rates, as a function of electronic density, electronic temperature, and ion nuclear charge. Recombination times can be calculated and compared to cooling time, in cooling processes of ion beans by electrons from storage rings. (A.C.A.S.) [pt

  19. Generation of Modified Pestiviruses by Targeted Recombination

    DEFF Research Database (Denmark)

    Rasmussen, Thomas Bruun; Friis, Martin Barfred; Risager, Peter Christian

    involves targeted modification of viral cDNA genomes, cloned within BACs, by Red/ET recombination-mediated mutagenesis in E.coli DH10B cells. Using recombination-mediated mutagenesis for the targeted design, the work can be expedited and focused in principal on any sequence within the viral genome...

  20. Cell biology of homologous recombination in yeast

    DEFF Research Database (Denmark)

    Eckert-Boulet, Nadine Valerie; Rothstein, Rodney; Lisby, Michael

    2011-01-01

    Homologous recombination is an important pathway for error-free repair of DNA lesions, such as single- and double-strand breaks, and for rescue of collapsed replication forks. Here, we describe protocols for live cell imaging of single-lesion recombination events in the yeast Saccharomyces...

  1. Recombinant Vaccinia Virus: Immunization against Multiple Pathogens

    Science.gov (United States)

    Perkus, Marion E.; Piccini, Antonia; Lipinskas, Bernard R.; Paoletti, Enzo

    1985-09-01

    The coding sequences for the hepatitis B virus surface antigen, the herpes simplex virus glycoprotein D, and the influenza virus hemagglutinin were inserted into a single vaccinia virus genome. Rabbits inoculated intravenously or intradermally with this polyvalent vaccinia virus recombinant produced antibodies reactive to all three authentic foreign antigens. In addition, the feasibility of multiple rounds of vaccination with recombinant vaccinia virus was demonstrated.

  2. Recombinant organisms for production of industrial products

    OpenAIRE

    Adrio, Jose-Luis; Demain, Arnold L

    2009-01-01

    A revolution in industrial microbiology was sparked by the discoveries of ther double-stranded structure of DNA and the development of recombinant DNA technology. Traditional industrial microbiology was merged with molecular biology to yield improved recombinant processes for the industrial production of primary and secondary metabolites, protein biopharmaceuticals and industrial enzymes. Novel genetic techniques such as metabolic engineering, combinatorial biosynthesis and molecular breeding...

  3. Molecular requirements for radiation-activated recombination

    International Nuclear Information System (INIS)

    Stevens, Craig W.; Zeng Ming; Stamato, Thomas; Cerniglia, George

    1997-01-01

    Purpose/Objective: The major stumbling block to successful gene therapy today is poor gene transfer. We hypothesized that ionizing radiation might activate cellular recombination, and so improve stable gene transfer. We further hypothesized that known DNA-damage-repair proteins might also be important in radiation-activated recombination. Materials and Methods: The effect of irradiation on stable gene transfer efficiency was determined in human (A549 and 39F) and rodent (NIH/3T3) cell lines. Continuous low dose rate and multiple radiation fractions were also tested. Nuclear extracts were made and the effect of irradiation on inter-plasmid recombination/ligation determined. Multiple DNA damage-repair deficient cell lines were tested for radiation-activated recombination. Results: A significant radiation dose-dependent improvement in stable plasmid transfection (by as much as 1300 fold) is demonstrated in neoplastic and primary cells. An improvement in transient plasmid transfection is also seen, with as much as 85% of cells transiently expressing b-galactosidase (20-50 fold improvement). Stable transfection is only improved for linearized or nicked plasmids. Cells have improved gene transfer for at least 96 hours after irradiation. Both fractionated and continuous low dose rate irradiation are effective at improving stable gene transfer in mammalian cells, thus making relatively high radiation dose delivery clinically feasible. Inter-plasmid recombination is radiation dose dependent in nuclear extract assays, and the type of overhang (3', 5' or blunt end) significantly affects recombination efficiency and the type of product. The most common end-joining activity involves filling-in of the overhang followed by blunt end ligation. Adenovirus is a linear, double stranded DNA virus. We demonstrate that adenoviral infection efficiency is increased by irradiation. The duration of transgene expression is lengthened because the virus integrates with high efficiency (∼10

  4. Recombination gives a new insight in the effective population size and the history of the old world human populations.

    Science.gov (United States)

    Melé, Marta; Javed, Asif; Pybus, Marc; Zalloua, Pierre; Haber, Marc; Comas, David; Netea, Mihai G; Balanovsky, Oleg; Balanovska, Elena; Jin, Li; Yang, Yajun; Pitchappan, R M; Arunkumar, G; Parida, Laxmi; Calafell, Francesc; Bertranpetit, Jaume

    2012-01-01

    The information left by recombination in our genomes can be used to make inferences on our recent evolutionary history. Specifically, the number of past recombination events in a population sample is a function of its effective population size (Ne). We have applied a method, Identifying Recombination in Sequences (IRiS), to detect specific past recombination events in 30 Old World populations to infer their Ne. We have found that sub-Saharan African populations have an Ne that is approximately four times greater than those of non-African populations and that outside of Africa, South Asian populations had the largest Ne. We also observe that the patterns of recombinational diversity of these populations correlate with distance out of Africa if that distance is measured along a path crossing South Arabia. No such correlation is found through a Sinai route, suggesting that anatomically modern humans first left Africa through the Bab-el-Mandeb strait rather than through present Egypt.

  5. RNAi and heterochromatin repress centromeric meiotic recombination

    DEFF Research Database (Denmark)

    Ellermeier, Chad; Higuchi, Emily C; Phadnis, Naina

    2010-01-01

    During meiosis, the formation of viable haploid gametes from diploid precursors requires that each homologous chromosome pair be properly segregated to produce an exact haploid set of chromosomes. Genetic recombination, which provides a physical connection between homologous chromosomes, is essen......During meiosis, the formation of viable haploid gametes from diploid precursors requires that each homologous chromosome pair be properly segregated to produce an exact haploid set of chromosomes. Genetic recombination, which provides a physical connection between homologous chromosomes....... Surprisingly, one mutant derepressed for recombination in the heterochromatic mating-type region during meiosis and several mutants derepressed for centromeric gene expression during mitotic growth are not derepressed for centromeric recombination during meiosis. These results reveal a complex relation between...... types of repression by heterochromatin. Our results also reveal a previously undemonstrated role for RNAi and heterochromatin in the repression of meiotic centromeric recombination and, potentially, in the prevention of birth defects by maintenance of proper chromosome segregation during meiosis....

  6. BIOTECHNOLOGY OF RECOMBINANT HORMONES IN DOPING

    Directory of Open Access Journals (Sweden)

    Biljana Vitošević

    2011-09-01

    Full Text Available Recombinant DNA technology has allowed rapid progress in creating biosynthetic gene products for the treatment of many diseases. In this way it can produce large amounts of hormone, which is intended for the treatment of many pathological conditions. Recombinant hormones that are commonly used are insulin, growth hormone and erythropoietin. Precisely because of the availability of these recombinant hormones, it started their abuse by athletes. Experiments in animal models confirmed the potential effects of some of these hormones in increasing physical abilities, which attracted the attention of athletes who push the limits of their competitive capability by such manipulation. The risks of the use of recombinant hormones in doping include serious consequences for the health of athletes. Methods of detection of endogenous hormones from recombined based on the use of a monoclonal antibodies, capillary zone electrophoresis and protein biomarkers

  7. Effects of UV radiation on genetic recombination

    International Nuclear Information System (INIS)

    Vlahovic, K.; Zahradka, D.; Petranovic, M.; Petranovic, D.

    1996-01-01

    We have used the model consisting of Escherichia coli cells and l phage to study the effects of UV radiation on genetic recombination. We found two radiation induced processes that reduce or inhibit genetic recombination. One such process leads to the inability of prophage to excise itself from the irradiated bacterial chromosome by the site-specific recombination. The other process was shown to inhibit a type of general recombination by which the prophage transfers one of its genetic markers to the infecting homologous phage. Loss of the prophage ability to take part in both site-specific and general recombination was shown to develop in recB + but not in recB cells. From this we infer that the loss of prophage recombinogenicity in irradiated cells is a consequence of one process in which RecBCD enzyme (the product of recB, recC and recD genes) plays an essential role. (author)

  8. Water conservation in semiarid dryland agriculture

    International Nuclear Information System (INIS)

    Willis, W.O.

    1980-01-01

    Factors affecting water conservation in semiarid dryland regions are discussed. Because precipitation is the only source of water for plant growth in most semiarid regions, a good understanding of precipitation patterns (quantity, distribution, and their probable frequency) is needed for each dryland area. The various dryland practices, e.g. tillage, cultivars, residue management, fertility, erosion control, and grazing, must be considered as integral parts of an entire system to develop best management practices and to gain most efficient water conservation for food and fiber production. (author)

  9. A Resource Conservation Unit.

    Science.gov (United States)

    Porter, Philip D.

    1979-01-01

    Describes a variety of learning activities for teaching elementary and junior high students about air, water, and energy conservation techniques. Suggests community resources, social studies objectives, language skills, and 20 activities. (CK)

  10. Hearing Conservation Team

    Data.gov (United States)

    Federal Laboratory Consortium — The Hearing Conservation Team focuses on ways to identify the early stages of noise-induced damage to the human ear.Our current research involves the evaluation of...

  11. Madagascar Conservation & Development

    African Journals Online (AJOL)

    Madagascar Conservation & Development. Journal Home · ABOUT THIS JOURNAL · Advanced Search · Current Issue · Archives · Journal Home > Vol 9, No 1 (2014) >. Log in or Register to get access to full text downloads.

  12. Metro Conservation Corridors

    Data.gov (United States)

    Minnesota Department of Natural Resources — The Metro Conservation Corridors (MeCC) grow out of the natural resource analysis work done by the DNR in the late '90's, documented in the Metro Greenprint...

  13. Madagascar Conservation & Development

    African Journals Online (AJOL)

    www.journalmcd.com

    2012-02-19

    Feb 19, 2012 ... MADAGASCAR CONSERVATION & DEVELOPMENT. VOLUME 7 ... die within a short period of time (e.g., infanticide) (Erhart and. Overdorff 1998 .... been as deep or may have healed by the time of examination. Falls during ...

  14. Birds of Conservation Concern

    Data.gov (United States)

    Department of the Interior — The 1988 amendment to the Fish and Wildlife Conservation Act mandates the U.S. Fish and Wildlife Service (USFWS) to “identify species, subspecies, and populations of...

  15. Containment air circulation for optimal hydrogen recombination

    International Nuclear Information System (INIS)

    Spinks, N.; Krause, M.

    1997-01-01

    An accepted first-line defense for hydrogen mitigation is to design for the hydrogen to be rapidly mixed with the containment atmosphere and diluted to below flammability concentrations. Then, as hydrogen continues to be produced in the longer term, recombiners can be used to remove hydrogen: recombiners can be located in forced-air ducts or passive recombiners can be distributed within containment and the heat of recombination used to promote local air circulation. However, this principle does not eliminate the possibility of high hydrogen concentrations at locations removed from the recombiners. An improvement on this strategy is to arrange for a specific, buoyancy-driven, overall circulation of the containment atmosphere such that the recombiners can be located within the recirculation flow, immediately downstream of the hydrogen source. This would make the mixing process more predictable and solve the mass-transfer problem associated with distributed recombiners. Ideally, the recombiners would be located just above the hydrogen source so that the heat of recombination would assist the overall circulation. In this way, the hydrogen would be removed as close as possible to the source, thereby minimizing the amount of hydrogen immediately downstream of the source and reducing the hydrogen concentration to acceptable levels at other locations. Such a strategy requires the containment volume to be divided into an upflow path, past the hydrogen source and the recombiner, and a downflow path to complete the circuit. The flow could be generated actively using fans or passively using buoyancy forces arising from the difference in density of gases in the upfiow and downflow paths; the gases in the downflow path being cooled at an elevated heat sink. (author)

  16. Mesocycles in conserving plastics

    DEFF Research Database (Denmark)

    Shashoua, Yvonne

    2016-01-01

    driven by the need to balance the requirements for reversibility in conservation practices with the artist’s intent and significance. Developments within each of the three mesocycles from the 1990s to date are discussed in this article. Environmental science and toxicology of waste plastics offer a novel...... source of information about real time degradation in terrestrial and marine microenvironments that seems likely to contribute to the conservation of similar materials in contemporary artworks....

  17. Soil conservation measures: exercises

    OpenAIRE

    Figueiredo, Tomás de; Fonseca, Felícia

    2009-01-01

    Exercises proposed under the topic of Soil Conservation Measures addresses to the design of structural measure, namely waterways in the context of a soil conservation plan. However, to get a better insight on the actual meaning of soil loss as a resource loss, a prior exercise is proposed to students. It concerns calculations of soil loss due to sheet (interrill) erosion and to gully erosion, and allows the perception through realistic number of the impact of these mechanism...

  18. The unconventional xer recombination machinery of Streptococci/Lactococci

    NARCIS (Netherlands)

    Le Bourgeois, Pascal; Bugarel, Marie; Campo, Nathalie; Daveran-Mingot, Marie-Line; Labonte, Jessica; Lanfranchi, Daniel; Lautier, Thomas; Pages, Carine; Ritzenthaler, Paul

    Homologous recombination between circular sister chromosomes during DNA replication in bacteria can generate chromosome dimers that must be resolved into monomers prior to cell division. In Escherichia coli, dimer resolution is achieved by site-specific recombination, Xer recombination, involving

  19. A novel computational method identifies intra- and inter-species recombination events in Staphylococcus aureus and Streptococcus pneumoniae.

    Directory of Open Access Journals (Sweden)

    Lisa Sanguinetti

    Full Text Available Advances in high-throughput DNA sequencing technologies have determined an explosion in the number of sequenced bacterial genomes. Comparative sequence analysis frequently reveals evidences of homologous recombination occurring with different mechanisms and rates in different species, but the large-scale use of computational methods to identify recombination events is hampered by their high computational costs. Here, we propose a new method to identify recombination events in large datasets of whole genome sequences. Using a filtering procedure of the gene conservation profiles of a test genome against a panel of strains, this algorithm identifies sets of contiguous genes acquired by homologous recombination. The locations of the recombination breakpoints are determined using a statistical test that is able to account for the differences in the natural rate of evolution between different genes. The algorithm was tested on a dataset of 75 genomes of Staphylococcus aureus and 50 genomes comprising different streptococcal species, and was able to detect intra-species recombination events in S. aureus and in Streptococcus pneumoniae. Furthermore, we found evidences of an inter-species exchange of genetic material between S. pneumoniae and Streptococcus mitis, a closely related commensal species that colonizes the same ecological niche. The method has been implemented in an R package, Reco, which is freely available from supplementary material, and provides a rapid screening tool to investigate recombination on a genome-wide scale from sequence data.

  20. RecO protein initiates DNA recombination and strand annealing through two alternative DNA binding mechanisms.

    Science.gov (United States)

    Ryzhikov, Mikhail; Gupta, Richa; Glickman, Michael; Korolev, Sergey

    2014-10-17

    Recombination mediator proteins (RMPs) are important for genome stability in all organisms. Several RMPs support two alternative reactions: initiation of homologous recombination and DNA annealing. We examined mechanisms of RMPs in both reactions with Mycobacterium smegmatis RecO (MsRecO) and demonstrated that MsRecO interacts with ssDNA by two distinct mechanisms. Zinc stimulates MsRecO binding to ssDNA during annealing, whereas the recombination function is zinc-independent and is regulated by interaction with MsRecR. Thus, different structural motifs or conformations of MsRecO are responsible for interaction with ssDNA during annealing and recombination. Neither annealing nor recombinase loading depends on MsRecO interaction with the conserved C-terminal tail of single-stranded (ss) DNA-binding protein (SSB), which is known to bind Escherichia coli RecO. However, similarly to E. coli proteins, MsRecO and MsRecOR do not dismiss SSB from ssDNA, suggesting that RMPs form a complex with SSB-ssDNA even in the absence of binding to the major protein interaction motif. We propose that alternative conformations of such complexes define the mechanism by which RMPs initiate the repair of stalled replication and support two different functions during recombinational repair of DNA breaks. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  1. Recombination kinetics of photogenerated electrons in InGaAs/InP quantum wells

    Science.gov (United States)

    Tito, M. A.; Pusep, Yu. A.; Gold, A.; Teodoro, M. D.; Marques, G. E.; LaPierre, R. R.

    2016-03-01

    The electron transport and recombination processes of photoexcited electron-hole pairs were studied in InGaAs/InP single quantum wells. Comprehensive transport data analysis reveals a asymmetric shape of the quantum well potential where the electron mobility was found to be dominated by interface-roughness scattering. The low-temperature time-resolved photoluminescence was employed to investigate recombination kinetics of photogenerated electrons. Remarkable modification of Auger recombination was observed with variation of the electron mobility. In high mobility quantum wells, the increasing pump power resulted in a new and unexpected phenomenon: a considerably enhanced Auger non-radiative recombination time. We propose that the distribution of the photoexcited electrons over different conduction band valleys might account for this effect. In low mobility quantum wells, disorder-induced relaxation of the momentum conservation rule causes inter-valley transitions to be insignificant; as a consequence, the non-radiative recombination time is reduced with the increase in pump power. Thus, interface-roughness scattering was found responsible for both transport properties and dynamic optical response in InGaAs/InP quantum wells.

  2. The typical RB76 recombination breakpoint of the invasive recombinant tomato yellow leaf curl virus of Morocco can be generated experimentally but is not positively selected in tomato.

    Science.gov (United States)

    Belabess, Z; Urbino, C; Granier, M; Tahiri, A; Blenzar, A; Peterschmitt, M

    2018-01-02

    TYLCV-IS76 is an unusual recombinant between the highly recombinogenic tomato yellow leaf curl virus (TYLCV) and tomato yellow leaf curl Sardinia virus (TYLCSV), two Mediterranean begomoviruses (Geminiviridae). In contrast with the previously reported TYLCV/TYLCSV recombinants, it has a TYLCSV derived fragment of only 76 nucleotides, and has replaced its parental viruses in natural conditions (Morocco, Souss region). The viral population shift coincided with the deployment of the popular Ty-1 resistant tomato cultivars, and according to experimental studies, has been driven by a strong positive selection in such resistant plants. However, although Ty-1 cultivars were extensively used in Mediterranean countries, TYLCV-IS76 was not reported outside Morocco. This, in combination with its unusual recombination pattern suggests that it was generated through a rare and possibly multistep process. The potential generation of a recombination breakpoint (RB) at locus 76 (RB76) was investigated over time in 10 Ty-1 resistant and 10 nearly isogenic susceptible tomato plants co-inoculated with TYLCV and TYLCSV clones. RB76 could not be detected in the recombinant progeny using the standard PCR/sequencing approach that was previously designed to monitor the emergence of TYLCV-IS76 in Morocco. Using a more sensitive PCR test, RB76 was detected in one resistant and five susceptible plants. The results are consistent with a very low intra-plant frequency of RB76 bearing recombinants throughout the test and support the hypothesis of a rare emergence of TYLCV-IS76. More generally, RBs were more scattered in resistant than in susceptible plants and an unusual RB at position 141 (RB141) was positively selected in the resistant cultivar; interestingly, RB141 bearing recombinants were detected in resistant tomato plants from the field. Scenarios of TYLCV-IS76 pre-emergence are proposed. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Electron-ion recombination rates for merged-beams experiments

    International Nuclear Information System (INIS)

    Pajek, M.

    1994-01-01

    Energy dependence of the electron-ion recombination rates are studied for different recombination processes (radiative recombination, three-body recombination, dissociative recombination) for Maxwellian relative velocity distribution of arbitrary asymmetry. The results are discussed in context of the electron-ion merged beams experiments in cooling ion storage rings. The question of indication of a possible contribution of the three-body recombination to the measured recombination rates versus relative energy is particularly addressed. Its influence on the electron beam temperature derived from the energy dependence of recombination rate is discussed

  4. First-principles study of Frenkel pair recombination in tungsten

    International Nuclear Information System (INIS)

    Qin, Shi-Yao; Jin, Shuo; Li, Yu-Hao; Zhou, Hong-Bo; Zhang, Ying; Lu, Guang-Hong

    2017-01-01

    The recombination of one Frenkel pair in tungsten has been investigated through first-principles simulation. Two different recombination types have been identified: instantaneous and thermally activated. The small recombination barriers for thermally activated recombination cases indicate that recombination can occur easily with a slightly increased temperature. For both of the two recombination types, recombination occurs through the self-interstitial atom moving towards the vacancy. The recombination process can be direct or through replacement sequences, depending on the vertical distance between the vacancy and the 〈1 1 1〉 line of self-interstitial atom pair.

  5. Induction of homologous recombination in Saccharomyces cerevisiae.

    Science.gov (United States)

    Simon, J R; Moore, P D

    1988-09-01

    We have investigated the effects of UV irradiation of Saccharomyces cerevisiae in order to distinguish whether UV-induced recombination results from the induction of enzymes required for homologous recombination, or the production of substrate sites for recombination containing regions of DNA damage. We utilized split-dose experiments to investigate the induction of proteins required for survival, gene conversion, and mutation in a diploid strain of S. cerevisiae. We demonstrate that inducing doses of UV irradiation followed by a 6 h period of incubation render the cells resistant to challenge doses of UV irradiation. The effects of inducing and challenge doses of UV irradiation upon interchromosomal gene conversion and mutation are strictly additive. Using the yeast URA3 gene cloned in non-replicating single- and double-stranded plasmid vectors that integrate into chromosomal genes upon transformation, we show that UV irradiation of haploid yeast cells and homologous plasmid DNA sequences each stimulate homologous recombination approximately two-fold, and that these effects are additive. Non-specific DNA damage has little effect on the stimulation of homologous recombination, as shown by studies in which UV-irradiated heterologous DNA was included in transformation/recombination experiments. We further demonstrate that the effect of competing single- and double-stranded heterologous DNA sequences differs in UV-irradiated and unirradiated cells, suggesting an induction of recombinational machinery in UV-irradiated S. cerevisiae cells.

  6. Homologous Recombination in Protozoan Parasites and Recombinase Inhibitors

    Directory of Open Access Journals (Sweden)

    Andrew A. Kelso

    2017-09-01

    Full Text Available Homologous recombination (HR is a DNA double-strand break (DSB repair pathway that utilizes a homologous template to fully repair the damaged DNA. HR is critical to maintain genome stability and to ensure genetic diversity during meiosis. A specialized class of enzymes known as recombinases facilitate the exchange of genetic information between sister chromatids or homologous chromosomes with the help of numerous protein accessory factors. The majority of the HR machinery is highly conserved among eukaryotes. In many protozoan parasites, HR is an essential DSB repair pathway that allows these organisms to adapt to environmental conditions and evade host immune systems through genetic recombination. Therefore, small molecule inhibitors, capable of disrupting HR in protozoan parasites, represent potential therapeutic options. A number of small molecule inhibitors were identified that disrupt the activities of the human recombinase RAD51. Recent studies have examined the effect of two of these molecules on the Entamoeba recombinases. Here, we discuss the current understandings of HR in the protozoan parasites Trypanosoma, Leishmania, Plasmodium, and Entamoeba, and we review the small molecule inhibitors known to disrupt human RAD51 activity.

  7. Differences in mutagenic and recombinational DNA repair in enterobacteria

    International Nuclear Information System (INIS)

    Sedgwick, S.G.; Goodwin, P.A.

    1985-01-01

    The incidence of recombinational DNA repair and inducible mutagenic DNA repair has been examined in Escherichia coli and 11 related species of enterobacteria. Recombinational repair was found to be a common feature of the DNA repair repertoire of at least 6 genera of enterobacteria. This conclusion is based on observations of (i) damage-induced synthesis of RecA-like proteins, (ii) nucleotide hybridization between E. coli recA sequences and some chromosomal DNAs, and (iii) recA-negative complementation by plasmids showing SOS-inducible expression of truncated E. coli recA genes. The mechanism of DNA damage-induced gene expression is therefore sufficiently conserved to allow non-E. coli regulatory elements to govern expression of these cloned truncated E. coli recA genes. In contrast, the process of mutagenic repair, which uses umuC+ umuD+ gene products in E. coli, appeared less widespread. Little ultraviolet light-induced mutagenesis to rifampicin resistance was detected outside the genus Escherichia, and even within the genus induced mutagenesis was detected in only 3 out of 6 species. Nucleotide hybridization showed that sequences like the E. coli umuCD+ gene are not found in these poorly mutable organisms. Evolutionary questions raised by the sporadic incidence of inducible mutagenic repair are discussed

  8. Hydrogen Recombination Rates of Plate-type Passive Auto-catalytic Recombiner

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jongtae; Hong, Seong-Wan [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of); Kim, Gun Hong [Kyungwon E-C Co., Seongnam (Korea, Republic of)

    2014-10-15

    The hydrogen mitigation system may include igniters, passive autocatalytic recombiner (PAR), and venting or dilution system. Recently PAR is commonly used as a main component of HMS in a NPP containment because of its passive nature. PARs are categorized by the shape and material of catalytic surface. Catalytic surface coated by platinum is mostly used for the hydrogen recombiners. The shapes of the catalytic surface can be grouped into plate type, honeycomb type and porous media type. Among them, the plate-type PAR is well tested by many experiments. PAR performance analysis can be approached by a multi-scale method which is composed of micro, meso and macro scales. The criterion of the scaling is the ratio of thickness of boundary layer developed on a catalytic surface to representative length of a computational domain. Mass diffusion in the boundary layer must be resolved in the micro scale analysis. In a lumped parameter (LP) analysis using a system code such as MAAP or MELCOR, the chamber of the PAR is much smaller than a computational node. The hydrogen depletion by a PAR is modeled as a source of mass and energy conservation equations. Te catalytic surface reaction of hydrogen must be modeled by a volume-averaged correlation. In this study, a micro scale analysis method is developed using libraries in OpenFOAM to evaluate a hydrogen depletion rate depending on parameters such as size and number of plates and plate arrangement. The analysis code is validated by simulating REKO-3 experiment. And hydrogen depletion analysis is conducted by changing the plate arrangement as a trial of the performance enhancement of a PAR. In this study, a numerical code for an analysis of a PAR performance in a micro scale has been developed by using OpenFOAM libraries. The physical and numerical models were validated by simulating the REKO-3 experiment. As a try to enhance the performance of the plate-type PAR, it was proposed to apply a staggered two-layer arrangement of the

  9. Hydrogen Recombination Rates of Plate-type Passive Auto-catalytic Recombiner

    International Nuclear Information System (INIS)

    Kim, Jongtae; Hong, Seong-Wan; Kim, Gun Hong

    2014-01-01

    The hydrogen mitigation system may include igniters, passive autocatalytic recombiner (PAR), and venting or dilution system. Recently PAR is commonly used as a main component of HMS in a NPP containment because of its passive nature. PARs are categorized by the shape and material of catalytic surface. Catalytic surface coated by platinum is mostly used for the hydrogen recombiners. The shapes of the catalytic surface can be grouped into plate type, honeycomb type and porous media type. Among them, the plate-type PAR is well tested by many experiments. PAR performance analysis can be approached by a multi-scale method which is composed of micro, meso and macro scales. The criterion of the scaling is the ratio of thickness of boundary layer developed on a catalytic surface to representative length of a computational domain. Mass diffusion in the boundary layer must be resolved in the micro scale analysis. In a lumped parameter (LP) analysis using a system code such as MAAP or MELCOR, the chamber of the PAR is much smaller than a computational node. The hydrogen depletion by a PAR is modeled as a source of mass and energy conservation equations. Te catalytic surface reaction of hydrogen must be modeled by a volume-averaged correlation. In this study, a micro scale analysis method is developed using libraries in OpenFOAM to evaluate a hydrogen depletion rate depending on parameters such as size and number of plates and plate arrangement. The analysis code is validated by simulating REKO-3 experiment. And hydrogen depletion analysis is conducted by changing the plate arrangement as a trial of the performance enhancement of a PAR. In this study, a numerical code for an analysis of a PAR performance in a micro scale has been developed by using OpenFOAM libraries. The physical and numerical models were validated by simulating the REKO-3 experiment. As a try to enhance the performance of the plate-type PAR, it was proposed to apply a staggered two-layer arrangement of the

  10. Polyhedral patterns

    KAUST Repository

    Jiang, Caigui; Tang, Chengcheng; Vaxman, Amir; Wonka, Peter; Pottmann, Helmut

    2015-01-01

    We study the design and optimization of polyhedral patterns, which are patterns of planar polygonal faces on freeform surfaces. Working with polyhedral patterns is desirable in architectural geometry and industrial design. However, the classical

  11. Extreme Recombination Frequencies Shape Genome Variation and Evolution in the Honeybee, Apis mellifera

    Science.gov (United States)

    Wallberg, Andreas; Glémin, Sylvain; Webster, Matthew T.

    2015-01-01

    Meiotic recombination is a fundamental cellular process, with important consequences for evolution and genome integrity. However, we know little about how recombination rates vary across the genomes of most species and the molecular and evolutionary determinants of this variation. The honeybee, Apis mellifera, has extremely high rates of meiotic recombination, although the evolutionary causes and consequences of this are unclear. Here we use patterns of linkage disequilibrium in whole genome resequencing data from 30 diploid honeybees to construct a fine-scale map of rates of crossing over in the genome. We find that, in contrast to vertebrate genomes, the recombination landscape is not strongly punctate. Crossover rates strongly correlate with levels of genetic variation, but not divergence, which indicates a pervasive impact of selection on the genome. Germ-line methylated genes have reduced crossover rate, which could indicate a role of methylation in suppressing recombination. Controlling for the effects of methylation, we do not infer a strong association between gene expression patterns and recombination. The site frequency spectrum is strongly skewed from neutral expectations in honeybees: rare variants are dominated by AT-biased mutations, whereas GC-biased mutations are found at higher frequencies, indicative of a major influence of GC-biased gene conversion (gBGC), which we infer to generate an allele fixation bias 5 – 50 times the genomic average estimated in humans. We uncover further evidence that this repair bias specifically affects transitions and favours fixation of CpG sites. Recombination, via gBGC, therefore appears to have profound consequences on genome evolution in honeybees and interferes with the process of natural selection. These findings have important implications for our understanding of the forces driving molecular evolution. PMID:25902173

  12. Recombination every day: abundant recombination in a virus during a single multi-cellular host infection.

    Directory of Open Access Journals (Sweden)

    Remy Froissart

    2005-03-01

    Full Text Available Viral recombination can dramatically impact evolution and epidemiology. In viruses, the recombination rate depends on the frequency of genetic exchange between different viral genomes within an infected host cell and on the frequency at which such co-infections occur. While the recombination rate has been recently evaluated in experimentally co-infected cell cultures for several viruses, direct quantification at the most biologically significant level, that of a host infection, is still lacking. This study fills this gap using the cauliflower mosaic virus as a model. We distributed four neutral markers along the viral genome, and co-inoculated host plants with marker-containing and wild-type viruses. The frequency of recombinant genomes was evaluated 21 d post-inoculation. On average, over 50% of viral genomes recovered after a single host infection were recombinants, clearly indicating that recombination is very frequent in this virus. Estimates of the recombination rate show that all regions of the genome are equally affected by this process. Assuming that ten viral replication cycles occurred during our experiment-based on data on the timing of coat protein detection-the per base and replication cycle recombination rate was on the order of 2 x 10(-5 to 4 x 10(-5. This first determination of a virus recombination rate during a single multi-cellular host infection indicates that recombination is very frequent in the everyday life of this virus.

  13. Recombinant DNA production of spider silk proteins.

    Science.gov (United States)

    Tokareva, Olena; Michalczechen-Lacerda, Valquíria A; Rech, Elíbio L; Kaplan, David L

    2013-11-01

    Spider dragline silk is considered to be the toughest biopolymer on Earth due to an extraordinary combination of strength and elasticity. Moreover, silks are biocompatible and biodegradable protein-based materials. Recent advances in genetic engineering make it possible to produce recombinant silks in heterologous hosts, opening up opportunities for large-scale production of recombinant silks for various biomedical and material science applications. We review the current strategies to produce recombinant spider silks. © 2013 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  14. Hydrology and Conservation Ecology

    Science.gov (United States)

    Narayanan, M.

    2006-12-01

    Responses to change in the behavior of ecological systems are largely governed by interactions at different levels. Research is essential and is to be necessarily designed to gain insights into various interactions at the community level. Sustainable resource management is only possible if conservation of biodiversity can be accomplished by properly using the knowledge discovered. It is well known that the United States Department of Agriculture provides technical information, resources, and data necessary to assist the researchers in addressing their conservation needs. Conservation aims to protect, preserve and conserve the earth's natural resources. These include, but not limited to the conservation of soil, water, minerals, air, plants and all living beings. The United States Department of Agriculture also encourages farmers and ranchers to voluntarily address threats to soil and water. Protection of wetlands and wildlife habitat has been on the radar screen of conservation experts for a very long time. The main objective has always been to help farmers and landowners conform and comply with federal and state environmental laws. During the implementation phase, farmers should be encouraged to make beneficial, cost-effective changes to methods of irrigation systems. In some cases, the hydrologic regime of the project area can be thought of as principally an issue of river flow regimes for floodplain forests. In this presentation, the author tries to focus on the impact of hydrology and conservation ecology on global warming. He also discusses the impact of hydrology and conservation ecology global air concerns such as greenhouse gas concentrations in the atmosphere. References: Chow, V. T, D. R. Maidment, and L. W. Mays. 1988. Applied Hydrology. McGraw-Hill, Inc. U.S. Soil Conservation Service. Technical Release 55: Urban Hydrology for Small Watersheds. USDA (U.S. Department of Agriculture). June 1986. Lehner, B. and P. Döll (2004). Development and validation

  15. Advances in recombinant antibody manufacturing.

    Science.gov (United States)

    Kunert, Renate; Reinhart, David

    2016-04-01

    Since the first use of Chinese hamster ovary (CHO) cells for recombinant protein expression, production processes have steadily improved through numerous advances. In this review, we have highlighted several key milestones that have contributed to the success of CHO cells from the beginning of their use for monoclonal antibody (mAb) expression until today. The main factors influencing the yield of a production process are the time to accumulate a desired amount of biomass, the process duration, and the specific productivity. By comparing maximum cell densities and specific growth rates of various expression systems, we have emphasized the limiting parameters of different cellular systems and comprehensively described scientific approaches and techniques to improve host cell lines. Besides the quantitative evaluation of current systems, the quality-determining properties of a host cell line, namely post-translational modifications, were analyzed and compared to naturally occurring polyclonal immunoglobulin fractions from human plasma. In summary, numerous different expression systems for mAbs are available and also under scientific investigation. However, CHO cells are the most frequently investigated cell lines and remain the workhorse for mAb production until today.

  16. U-Pb, Nd isotope and REE geochemistry in eclogites from the Cabo Ortegal Complex, Galicia, Spain: an example of REE immobility conserving MORB-like patterns during high-grade metamorphism

    International Nuclear Information System (INIS)

    Bernard-Griffiths, J.; Peucat, J.-J.; Cornichet, J.; Iglesias Ponce de Leon, M.; Gil Ibarguchi, J.I.

    1985-01-01

    REE abundances and Nd isotopic compositions were determined on representative samples of eclogite from the Cabo Ortegal Complex of northern Spain. Zircons were also separated from a whole-rock eclogite and analysed by the U-Pb radiometric method. Results indicate that eclogite facies metamorphism occurred between 480 and 420 Ma ago, but no precise constraint can be placed on the protolith age. The REE patterns observed suggest that there has been no significant alteration of the protolith whole-rock systems and that high-grade metamorphism has had little effect on the more mobile LREE. The eclogite protoliths were probably derived from ancient mantle sources with geochemical characteristics very similar to present-day MORB sources. This implies that LREE-depleted (N-type) tholeiites have been erupted at constructive plate margins since at least the early Palaeozoic and possibly long before. The Cabo Ortegal eclogites are allochthonous. They have been thrust up on to the continent and thus they can be compared to other eclogites which also show MORB-like characteristics (e.g., 90% of the eclogites of Vendee area of western France). (orig.)

  17. Direct bacterial killing in vitro by recombinant Nod2 is compromised by Crohn's disease-associated mutations.

    Directory of Open Access Journals (Sweden)

    Laurent-Herve Perez

    2010-06-01

    Full Text Available A homeostatic relationship with the intestinal microflora is increasingly appreciated as essential for human health and wellbeing. Mutations in the leucine-rich repeat (LRR domain of Nod2, a bacterial recognition protein, are associated with development of the inflammatory bowel disorder, Crohn's disease. We investigated the molecular mechanisms underlying disruption of intestinal symbiosis in patients carrying Nod2 mutations.In this study, using purified recombinant LRR domains, we demonstrate that Nod2 is a direct antimicrobial agent and this activity is generally deficient in proteins carrying Crohn's-associated mutations. Wild-type, but not Crohn's-associated, Nod2 LRR domains directly interacted with bacteria in vitro, altered their metabolism and disrupted the integrity of the plasma membrane. Antibiotic activity was also expressed by the LRR domains of Nod1 and other pattern recognition receptors suggesting that the LRR domain is a conserved anti-microbial motif supporting innate cellular immunity.The lack of anti-bacterial activity demonstrated with Crohn's-associated Nod2 mutations in vitro, supports the hypothesis that a deficiency in direct bacterial killing contributes to the association of Nod2 polymorphisms with the disease.

  18. Applying the dark diversity concept to nature conservation

    DEFF Research Database (Denmark)

    Lewis, Rob; de Bello, Francesco; A Bennett, Jonathan

    2017-01-01

    is currently an underappreciated source of information that is valuable for conservation applications ranging from macroscale conservation prioritization to more locally scaled restoration ecology and the management of invasive species. Introduction Conservation biology has strong scientific underpinnings (e...... to improve understanding of how biological diversity is governed and maintained. We illustrate our viewpoint by clarifying how measuring, monitoring, and understanding dark diversity can prove beneficial in the context of 3 facets of conservation biology: biodiversity conservation, habitat restoration......Linking diversity to biological processes is central for developing informed and effective conservation decisions. Unfortunately, observable patterns provide only a proportion of the information necessary for fully understanding the mechanisms and processes acting on a particular population...

  19. Tourism and Conservation

    DEFF Research Database (Denmark)

    Budeanu, Adriana

    2017-01-01

    Tourism is promoted by policy makers and international organizations as a tool for advancing conservation agendas, while contributing to poverty alleviation and human development, under the banner of ecotourism or sustainable tourism. However, the indiscriminating use of complex and ambiguous...... concepts such as “poverty” and “sustainability” hide important nuances with regards to the variety of processes and subsequent effects that are triggered when tourism and conservation are being adjoined. Experiences with tourism developments show that destinations that are weak economically find it harder...... to draw benefits from tourism developments or to decline participation in tourism with only little or no losses of sources of income and wealth. If tourism should fulfil sustainability goals related to conservation, poverty, and human development, it needs consistent governmental intervention...

  20. Conservation of Mangifera sylvatica

    DEFF Research Database (Denmark)

    Akhter, Sayma

    and conservation of these valuable species. The present study considers an underutilised and threatened species of Bangladesh, namely wild mango (Mangifera sylvatica Roxb.). Although this wild mango is one of the genetically closest species to the common mango (Mangifera indica L.) research is very limited...... and mostly focused on wood quality and phylogenetic relationships. Therefore, this study investigated the conservation potential of wild mango considering its contribution for food, nutrition and livelihoods. To do so, an assessment was made of the current and future distribution of the species, which...... explored. The study conveyed five key messages: 1. Wild mango may become extinct under future climate change scenarios so it is high time to start thinking about conservation initiatives. 2. Wild mango is a small sized mango with a large kernel in relation to other Mangifera species which provides...

  1. Resource conservation management

    International Nuclear Information System (INIS)

    Miller, W.

    1999-01-01

    Resource conservation management is a management program similar to financial management in that its success requires commitment by all levels of the organization to the process as well as an accounting procedure and auditing of critical components. Resource conservation management provides a framework for all elements of efficient building operations and maintenance. The savings connected with the program are principally connected with changes in the way buildings are operated and maintained. Given the reduction in rebates for the installation of energy-efficient equipment, this approach has considerable promise. This paper discusses the evolution of the resource conservation management service and the savings associated with a two-year pilot effort with seven school districts, as well as the critical components of a successful program

  2. Conservation reaches new heights.

    Science.gov (United States)

    Pepall, J; Khanal, P

    1992-10-01

    The conservation program with the management assistance of the Woodlands Mountain Institute in 2 contiguous parks, the Mount Everest National Park in Nepal and the Qomolangma Nature Reserve in China, in 2 countries is described. The focus is on conservation of the complex ecosystem with sustainable development by showing local people how to benefit from the park without environmental damage. Cultural diversity is as important as biological diversity. The area has been designated by UNESCO as a World Heritage Site with the "last pure ecological seed" of the Himalayas. The regional geography and culture are presented. Population growth has impacted natural resources through overgrazing, cultivation of marginal land, and deforestation; future plans to build a dam and road bordering the nature reserve pose other threats. Proposed management plans for the Makalu-Barun Nature Park (established in November 1991) and Conservation Area include a division of the park into nature reserve areas free of human activity, protected areas which permit traditional land use, and special sites and trail for tourists and religious pilgrims. The conservation area will act as a buffer for the park and provide economic opportunities; further subdivisions include land use for biodiversity protection, community forest and pasture, agroforestry, and agriculture and settlement. Efforts will be made to increase the welfare of women and local people; proposed projects include the introduction of higher milk-producing animals for stall feeding. Also proposed is a cultural and natural history museum. 70% of the project's resources will be directed to local community participation in consultation and park maintenance. The project is a model of how conservation and protection of natural resources can coexist with local economic development and participation; an integration of preservation of biological diversity, mountain wisdom, and the value of local people as resources for conservation.

  3. Laser-induced electron--ion recombination used to study enhanced spontaneous recombination during electron cooling

    International Nuclear Information System (INIS)

    Schramm, U.; Wolf, A.; Schuess ler, T.; Habs, D.; Schwalm, D.; Uwira, O.; Linkemann, J.; Mueller, A.

    1997-01-01

    Spontaneous recombination of highly charged ions with free electrons in merged velocity matched electron and ion beams has been observed in earlier experiments to occur at rates significantly higher than predicted by theoretical estimates. To study this enhanced spontaneous recombination, laser induced recombination spectra were measured both in velocity matched beams and in beams with well defined relative velocities, corresponding to relative electron-ion detuning energies ranging from 1 meV up to 6.5 meV where the spontaneous recombination enhancement was found to be strongly reduced. Based on a comparison with simplified calculations, the development of the recombination spectra for decreasing detuning energies indicates additional contributions at matched velocities which could be related to the energy distribution of electrons causing the spontaneous recombination rate enhancement

  4. Energy conservation in industry

    International Nuclear Information System (INIS)

    Pembleton, P.

    1992-01-01

    Energy Conservation in Industry is the first number in the Energy and Environmental Series of the Industrial and Technological Information Bank (INTIB). The Series supersedes the INECA Journal and reflects the broader information programme undertaken by INTIB. The present number of the Series contains contributions from three major international databases and five topic-specific sources, including three United Nations Organizations. The present publication consists of a recent technical report on a current topic: reducing energy loss in four industrial sectors and improving energy conservation through waste-heat recovery, followed by two sections containing abstracts of technical materials

  5. Local instant conservation equations

    International Nuclear Information System (INIS)

    Delaje, Dzh.

    1984-01-01

    Local instant conservation equations for two-phase flow are derived. Derivation of the equation starts from the recording of integral laws of conservation for a fixed reference volume, containing both phases. Transformation of the laws, using the Leibniz rule and Gauss theory permits to obtain the sum of two integrals as to the volume and integral as to the surface. Integrals as to the volume result in local instant differential equations, in particular derivatives for each phase, and integrals as to the surface reflect local instant conditions of a jump on interface surface

  6. Diesel conservation: GSRTC'S experience

    Energy Technology Data Exchange (ETDEWEB)

    Ramesh Kumar, I V

    1980-01-01

    The Gujarat State Road Transport Corporation (GSRTC) in India has a fleet of about 6000 buses. The increasing cost of fuel and lubricants added to uncertainty in supplies, has necessitated the need for conserving High Speed Diesel Oil (HSD). GSRTC had achieved an overall average Kilometre Per Litre (kmpl) of 4.44 in the year 1976-1977 due to a variety of measures. In the year 1978-1979 the average kmpl was 4.52 and it is expected to be 4.60 for 1979-1980. The case study outlined describes the measures taken by GSRTC in conserving high speed diesel oil by various methods.

  7. Information, conservation and retrieval

    Energy Technology Data Exchange (ETDEWEB)

    Eng, T [Swedish Nuclear Fuel and Waste Management Co., Stockholm (Sweden); Norberg, E [National Swedish Archives, Stockholm (Sweden); Torbacke, J [Stockholm Univ. (Sweden). Dept. of History; Jensen, M [Swedish Radiation Protection Inst., Stockholm (Sweden)

    1996-12-01

    The seminar took place on the Swedish ship for transportation of radioactive wastes, M/S Sigyn, which at summer time is used for exhibitions. The seminar treated items related to general information needs in society and questions related to radioactive waste, i.e. how knowledge about a waste repository should be passed on to future generations. Three contributions are contained in the report from the seminar and are indexed separately: `Active preservation - otherwise no achieves`; `The conservation and dissemination of information - A democratic issue`; and, `Conservation and retrieval of information - Elements of a strategy to inform future societies about nuclear waste repositories`.

  8. Information, conservation and retrieval

    International Nuclear Information System (INIS)

    Eng, T.; Norberg, E.; Torbacke, J.

    1996-12-01

    The seminar took place on the Swedish ship for transportation of radioactive wastes, M/S Sigyn, which at summer time is used for exhibitions. The seminar treated items related to general information needs in society and questions related to radioactive waste, i.e. how knowledge about a waste repository should be passed on to future generations. Three contributions are contained in the report from the seminar and are indexed separately: 'Active preservation - otherwise no achieves'; 'The conservation and dissemination of information - A democratic issue'; and, 'Conservation and retrieval of information - Elements of a strategy to inform future societies about nuclear waste repositories'

  9. Recombinant Human Papillomavirus (HPV) Bivalent Vaccine

    Science.gov (United States)

    This page contains brief information about recombinant human papillomavirus (HPV) bivalent vaccine and a collection of links to more information about the use of this vaccine, research results, and ongoing clinical trials.

  10. Recombinant Human Papillomavirus (HPV) Nonavalent Vaccine

    Science.gov (United States)

    This page contains brief information about recombinant human papillomavirus (HPV) nonavalent vaccine and a collection of links to more information about the use of this vaccine, research results, and ongoing clinical trials.

  11. Recombinant Human Papillomavirus (HPV) Quadrivalent Vaccine

    Science.gov (United States)

    This page contains brief information about recombinant human papillomavirus (HPV) quadrivalent vaccine and a collection of links to more information about the use of this vaccine, research results, and ongoing clinical trials.

  12. Ultramicroscopic observation of recombinant adenoassociated virus ...

    African Journals Online (AJOL)

    Ultramicroscopic observation of recombinant adenoassociated virus type 2 on the surface of formvarcarbon coated copper grids under different relative humidity and incubation time using negative stain transmission electron microscopy.

  13. Recombinant vaccines: experimental and applied aspects

    DEFF Research Database (Denmark)

    Lorenzen, Niels

    1999-01-01

    Development of vaccines for aquaculture fish represent an important applied functional aspect of fish immunology research. Particularly in the case of recombinant vaccines, where a single antigen is usually expected to induce immunity to a specific pathogen, knowledge of mechanisms involved...... in induction of a protective immune response may become vital. The few recombinant vaccines licensd so far, despite much research during the last decade, illustrate that this is not a straightforward matter. However, as vaccine technology as well as our knowledge of the fish immune system is steadily improved......, these fields will open up a number of interesting research objectives of mutual benefit. Recent aspects of recombinant protein vaccines, live recombinant vaccines and DNA vaccines are discussed....

  14. New perspectives on recombinant human antibodies

    NARCIS (Netherlands)

    J. de Kruif (John); A.-R. van der Vuurst de Vries (Anne); L. Cilenti (L.); E. Boel (E.); W. van Ewijk (Willem); T. Logtenberg (Ton)

    1996-01-01

    textabstractThe limited potential of murine monoclonal antibodies for human immunotherapy has driven recent progress in recombinant antibody technology. Here, de Kruif and colleagues report on advances in the development and use of phage-antibody-display libraries.

  15. Construction of retroviral recombinant containing human tissue ...

    African Journals Online (AJOL)

    USER

    2010-03-29

    Mar 29, 2010 ... Recombinant retroviral vector containing human tissue inhibitor of matrix metalloproteinase-2 (TIMP-2) gene was ..... heavy metal ions, the protein could be express in an .... involves adhesion, degradation and movement. To.

  16. French industry and the energy conservation challenge

    Energy Technology Data Exchange (ETDEWEB)

    Serpette, M.

    1979-07-01

    The general position of France and its energy conservation objectives; the action taken by the government to stimulate this policy; and government cooperation with industrial circles and the action of industry itself are discussed. It is observed that the potential for future energy savings are smaller in France than in other countries because consumptions are already down to minimal levels. Consumption patterns in France are illustrated. (MCW)

  17. Integrating technologies for scalable ecology and conservation

    OpenAIRE

    David C. Marvin; Lian Pin Koh; Antony J. Lynam; Serge Wich; Andrew B. Davies; Ramesh Krishnamurthy; Emma Stokes; Ruth Starkey; Gregory P. Asner

    2016-01-01

    Integration of multiple technologies greatly increases the spatial and temporal scales over which ecological patterns and processes can be studied, and threats to protected ecosystems can be identified and mitigated. A range of technology options relevant to ecologists and conservation practitioners are described, including ways they can be linked to increase the dimensionality of data collection efforts. Remote sensing, ground-based, and data fusion technologies are broadly discussed in the ...

  18. Of mice and men: divergence of gene expression patterns in kidney.

    Directory of Open Access Journals (Sweden)

    Lydie Cheval

    Full Text Available Since the development of methods for homologous gene recombination, mouse models have played a central role in research in renal pathophysiology. However, many published and unpublished results show that mice with genetic changes mimicking human pathogenic mutations do not display the human phenotype. These functional differences may stem from differences in gene expression between mouse and human kidneys. However, large scale comparison of gene expression networks revealed conservation of gene expression among a large panel of human and mouse tissues including kidneys. Because renal functions result from the spatial integration of elementary processes originating in the glomerulus and the successive segments constituting the nephron, we hypothesized that differences in gene expression profiles along the human and mouse nephron might account for different behaviors. Analysis of SAGE libraries generated from the glomerulus and seven anatomically defined nephron segments from human and mouse kidneys allowed us to identify 4644 pairs of gene orthologs expressed in either one or both species. Quantitative analysis shows that many transcripts are present at different levels in the two species. It also shows poor conservation of gene expression profiles, with less than 10% of the 4644 gene orthologs displaying a higher conservation of expression profiles than the neutral expectation (p<0.05. Accordingly, hierarchical clustering reveals a higher degree of conservation of gene expression patterns between functionally unrelated kidney structures within a given species than between cognate structures from the two species. Similar findings were obtained for sub-groups of genes with either kidney-specific or housekeeping functions. Conservation of gene expression at the scale of the whole organ and divergence at the level of its constituting sub-structures likely account for the fact that although kidneys assume the same global function in the two species

  19. Live recombinant BHV/BRSV vaccine

    OpenAIRE

    Keil, G.M.; Rijsewijk, F.A.M.

    1998-01-01

    The present invention refers to synthetic Bovine Respiratory Syncytium virus genes. Also the invention relates to live attenuated Bovine Herpesvirus recombinants carrying such synthetic genes. Furthermore, the invention relates to vaccines based on these live attenuated recombinants, for the protection of cattle against both Bovine herpesvirus infection and against Bovine Respiratory Syncytium virus infection. Also the invention relates to methods for the preparation of such live attenuated r...

  20. Co-factor activated recombinant adenovirus proteinases

    Science.gov (United States)

    Anderson, Carl W.; Mangel, Walter F.

    1996-08-06

    This application describes methods and expression constructs for producing activatable recombinant adenovirus proteinases. Purified activatable recombinant adenovirus proteinases and methods of purification are described. Activated adenovirus proteinases and methods for obtaining activated adenovirus proteinases are further included. Isolated peptide cofactors of adenovirus proteinase activity, methods of purifying and identifying said peptide cofactors are also described. Antibodies immunoreactive with adenovirus proteinases, immunospecific antibodies, and methods for preparing them are also described. Other related methods and materials are also described.

  1. Hadron correlations from recombination and fragmentation

    Energy Technology Data Exchange (ETDEWEB)

    Fries, Rainer J [School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455 (United States)

    2005-04-01

    We review the formalism of quark recombination applied to the hadronization of a quark-gluon plasma. Evidence in favour of the quark recombination model is outlined. Recent work on parton correlations, leading to detectable correlations between hadrons, is discussed. Hot spots from completely quenched jets are a likely source of such correlations which appear to be jet like. It will be discussed how such a picture compares with measurement of associated hadron yields at RHIC.

  2. Recombination of a fast expanding plasma

    International Nuclear Information System (INIS)

    Salvat, M.

    1979-05-01

    The goal of the following calculations is to determine numerically the recombination of dense plasmas (for instance of laser-produced plasmas). The recombination is computed for plasmas with initial densities of 10 24 27 [m -3 ] and with initial temperatures >= 50 eV. The ionization of the plasma remains essentially constant during the early phase of expansion. The time for which the ionization is 'frozen-in' grows with decreasing initial density and with increasing initial temperature. (orig.) [de

  3. A multispecies framework for landscape conservation planning.

    Science.gov (United States)

    Schwenk, W Scott; Donovan, Therese M

    2011-10-01

    Rapidly changing landscapes have spurred the need for quantitative methods for conservation assessment and planning that encompass large spatial extents. We devised and tested a multispecies framework for conservation planning to complement single-species assessments and ecosystem-level approaches. Our framework consisted of 4 elements: sampling to effectively estimate population parameters, measuring how human activity affects landscapes at multiple scales, analyzing the relation between landscape characteristics and individual species occurrences, and evaluating and comparing the responses of multiple species to landscape modification. We applied the approach to a community of terrestrial birds across 25,000 km(2) with a range of intensities of human development. Human modification of land cover, road density, and other elements of the landscape, measured at multiple spatial extents, had large effects on occupancy of the 67 species studied. Forest composition within 1 km of points had a strong effect on occupancy of many species and a range of negative, intermediate, and positive associations. Road density within 1 km of points, percent evergreen forest within 300 m, and distance from patch edge were also strongly associated with occupancy for many species. We used the occupancy results to group species into 11 guilds that shared patterns of association with landscape characteristics. Our multispecies approach to conservation planning allowed us to quantify the trade-offs of different scenarios of land-cover change in terms of species occupancy. Conservation Biology © 2011 Society for Conservation Biology. No claim to original US government works.

  4. Dissociation of recombinant prion autocatalysis from infectivity.

    Science.gov (United States)

    Noble, Geoffrey P; Supattapone, Surachai

    2015-01-01

    Within the mammalian prion field, the existence of recombinant prion protein (PrP) conformers with self-replicating (ie. autocatalytic) activity in vitro but little to no infectious activity in vivo challenges a key prediction of the protein-only hypothesis of prion replication--that autocatalytic PrP conformers should be infectious. To understand this dissociation of autocatalysis from infectivity, we recently performed a structural and functional comparison between a highly infectious and non-infectious pair of autocatalytic recombinant PrP conformers derived from the same initial prion strain. (1) We identified restricted, C-terminal structural differences between these 2 conformers and provided evidence that these relatively subtle differences prevent the non-infectious conformer from templating the conversion of native PrP(C) substrates containing a glycosylphosphatidylinositol (GPI) anchor. (1) In this article we discuss a model, consistent with these findings, in which recombinant PrP, lacking post-translational modifications and associated folding constraints, is capable of adopting a wide variety of autocatalytic conformations. Only a subset of these recombinant conformers can be adopted by post-translationally modified native PrP(C), and this subset represents the recombinant conformers with high specific infectivity. We examine this model's implications for the generation of highly infectious recombinant prions and the protein-only hypothesis of prion replication.

  5. Mitigating Mitochondrial Genome Erosion Without Recombination.

    Science.gov (United States)

    Radzvilavicius, Arunas L; Kokko, Hanna; Christie, Joshua R

    2017-11-01

    Mitochondria are ATP-producing organelles of bacterial ancestry that played a key role in the origin and early evolution of complex eukaryotic cells. Most modern eukaryotes transmit mitochondrial genes uniparentally, often without recombination among genetically divergent organelles. While this asymmetric inheritance maintains the efficacy of purifying selection at the level of the cell, the absence of recombination could also make the genome susceptible to Muller's ratchet. How mitochondria escape this irreversible defect accumulation is a fundamental unsolved question. Occasional paternal leakage could in principle promote recombination, but it would also compromise the purifying selection benefits of uniparental inheritance. We assess this tradeoff using a stochastic population-genetic model. In the absence of recombination, uniparental inheritance of freely-segregating genomes mitigates mutational erosion, while paternal leakage exacerbates the ratchet effect. Mitochondrial fusion-fission cycles ensure independent genome segregation, improving purifying selection. Paternal leakage provides opportunity for recombination to slow down the mutation accumulation, but always at a cost of increased steady-state mutation load. Our findings indicate that random segregation of mitochondrial genomes under uniparental inheritance can effectively combat the mutational meltdown, and that homologous recombination under paternal leakage might not be needed. Copyright © 2017 by the Genetics Society of America.

  6. The kissing-loop motif is a preferred site of 5' leader recombination during replication of SL3-3 murine leukemia viruses in mice

    DEFF Research Database (Denmark)

    Lund, Anders Henrik; Mikkelsen, J G; Schmidt, J

    1999-01-01

    , and the upstream part of the 5' untranslated region, enabled us to map recombination sites, guided by distinct scattered nucleotide differences. In 30 of 44 analyzed sequences, recombination was mapped to a 33-nucleotide similarity window coinciding with the kissing-loop stem-loop motif implicated in dimerization...... of the diploid genome. Interestingly, the recombination pattern preference found in replication-competent viruses from T-cell tumors is very similar to the pattern previously reported for retroviral vectors in cell culture experiments. The data therefore sustain the hypothesis that the kissing loop, presumably...

  7. Electron - ion recombination processes - an overview

    International Nuclear Information System (INIS)

    Hahn, Yukap

    1997-01-01

    Extensive theoretical and experimental studies have been carried out for the past 20 years on electron - ion recombination processes, as they are applied to the analysis of astrophysical and laboratory plasmas. We review the basic understanding gained through these efforts, with emphasis on some of the more recent progress made in recombination theory as the recombining system is affected by time-dependent electric fields and plasma particles at low temperature. Together with collisional ionization and excitation processes, recombination is important in determining ionization balance and excited-state population in non-equilibrium plasmas. The radiation emitted by plasmas is usually the principal medium with which to study the plasma condition, as it is produced mainly during the recombination and decay of excited states of ions inside the plasma. This is especially true when the plasma under study is not readily accessible by direct probes, as in astrophysical plasmas. Moreover, external probes may sometimes cause undesirable disturbances of the plasma. Electron-ion recombination proceeds in several different modes. The direct modes include three-body recombination (TBR) and one-step radiative recombination (RR), all to the ground- and singly-excited states of the target ions. By contrast, the indirect resonant mode is a two-step dielectronic recombination (DR), which proceeds first with the formation of doubly-excited states by radiationless excitation/capture. The resonant states thus formed may relax by autoionization and/or radiative cascades. For more exotic modes of recombination, we consider off-shell dielectronic recombination (radiative DR = RDR), in which an electron capture is accompanied by simultaneous radiative emission and excitation of the target ion. Some discussion on attachment of electrons to neutral atoms, resulting in the formation of negative ions, is also given. When resonance states involve one or more electrons in high Rydberg states

  8. Science Experience Unit: Conservation.

    Science.gov (United States)

    Ferguson-Florissant School District, Ferguson, MO.

    GRADES OR AGES: Intermediate grades. SUBJECT MATTER: Conservation. ORGANIZATION AND PHYSICAL APPEARANCE: The guide is divided into 24 experiments. It is mimeographed and staple-bound with a paper cover. OBJECTIVES AND ACTIVITIES: A specific skill or knowledge objective is stated at the beginning of each experiment. Detailed procedures are listed…

  9. (ICTs) And Environmental Conservation

    African Journals Online (AJOL)

    ICTs have a potential for improving the accessibility of environmental information, and if appropriately applied, they can empower local people to make informed decisions regarding environmental issues, thus enhancing environmental conservation. However, the challenge is on how to define particular roles that ...

  10. Conservative Delta Hedging

    Science.gov (United States)

    1997-09-01

    an exact method for converting such intervals into arbitrage based prices of financial derivatives or industrial or contractual options. We call this...procedure conservative delta hedging . As existing procedures are of an ad hoc nature, the proposed approach will permit an institution’s man agement a greater oversight of its exposure to risk.

  11. [Lateral epicondylitis: conservative - operative].

    Science.gov (United States)

    Altintas, Burak; Greiner, Stefan

    2016-10-01

    Lateral epicondylitis is a common disease of the common extensor origin at the lateral humerus. Despite its common self-limitation it can lead to chronic therapy-resistant pain with remarkable functional disability of the affected arm. Different conservative and operative treatment options of lateral epicondylitis are described and compared regarding benefits and risks. Additionally, recent surgical techniques and their complications are mentioned. Based on the current literature, it is shown which treatment option can be recommended. This review was based on the literature analysis in PubMed regarding "conservative and operative therapy of lateral epicondylitis" as well as the clinical experience of the authors. Conservative treatment is the primary choice for the treatment of lateral epicondylitis if concomitant pathologies such as instability among others can be excluded. It should include strengthening against resistance with eccentric stretching of the extensor group. In persistent cases, operative treatment is warranted. Resection of the pathologic tissue at the extensor origin with debridement and refixation of the healthy tendinous tissue yields good results. Most patients with lateral epicondylitis can be treated conservatively with success. Radiological evaluation should be performed in therapy-resistant cases. In the case of partial or complete rupture of the extensor origin, operative therapy is indicated.

  12. Biological science in conservation

    Science.gov (United States)

    David M. Johns

    2000-01-01

    Large-scale wildlands reserve systems offer one of the best hopes for slowing, if not reversing, the loss of biodiversity and wilderness. Establishing such reserves requires both sound biology and effective advocacy. Attempts by The Wildlands Project and its cooperators to meld science and advocacy in the service of conservation is working, but is not without some...

  13. Speyeria (Lepidoptera: Nymphalidae Conservation

    Directory of Open Access Journals (Sweden)

    Steven R. Sims

    2017-04-01

    Full Text Available Speyeria (Nymphalidae are a conspicuous component of the North American butterfly fauna. There are approximately 16 species and >100 associated subspecies (or geographical variants. Speyeria are univoltine, occupy a wide range of habitats, overwinter as first instar larvae, and feed only on native violets. Speyeria species have become a model group for studies of evolution, speciation, and conservation. Several species and subspecies are threatened or endangered. The reasons for this vary with the taxa involved, but always involve the degradation or loss of quality habitat for larvae and adults. The impacts of climate change must be considered among the causes for habitat degradation and in the establishment of conservation measures. In addition to increasing the available habitat, conservation efforts should consider maintaining habitat in a seral “disturbed” successional stage that selectively favors the growth of violets and preferred adult nectar sources. A major future challenge will be determining the most effective allocation of conservation resources to those species and subspecies that have the greatest potential to respond favorably to these efforts.

  14. 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 ...

  15. Human developmental enhancers conserved between deuterostomes and protostomes.

    Directory of Open Access Journals (Sweden)

    Shoa L Clarke

    Full Text Available The identification of homologies, whether morphological, molecular, or genetic, is fundamental to our understanding of common biological principles. Homologies bridging the great divide between deuterostomes and protostomes have served as the basis for current models of animal evolution and development. It is now appreciated that these two clades share a common developmental toolkit consisting of conserved transcription factors and signaling pathways. These patterning genes sometimes show common expression patterns and genetic interactions, suggesting the existence of similar or even conserved regulatory apparatus. However, previous studies have found no regulatory sequence conserved between deuterostomes and protostomes. Here we describe the first such enhancers, which we call bilaterian conserved regulatory elements (Bicores. Bicores show conservation of sequence and gene synteny. Sequence conservation of Bicores reflects conserved patterns of transcription factor binding sites. We predict that Bicores act as response elements to signaling pathways, and we show that Bicores are developmental enhancers that drive expression of transcriptional repressors in the vertebrate central nervous system. Although the small number of identified Bicores suggests extensive rewiring of cis-regulation between the protostome and deuterostome clades, additional Bicores may be revealed as our understanding of cis-regulatory logic and sample of bilaterian genomes continue to grow.

  16. Crowdfunding biodiversity conservation.

    Science.gov (United States)

    Gallo-Cajiao, E; Archibald, C; Friedman, R; Steven, R; Fuller, R A; Game, E T; Morrison, T H; Ritchie, E G

    2018-05-26

    Raising funds is critical for conserving biodiversity and hence so too is scrutinizing emerging financial mechanisms that might help achieve this goal. In this context, anecdotal evidence indicates crowdfunding is being used to support a variety of activities needed for biodiversity conservation, yet its magnitude and allocation remain largely unknown. We conducted a global analysis to help address this knowledge gap, based on empirical data from conservation-focused projects extracted from crowdfunding platforms. For each project, we determined the funds raised, date, country of implementation, proponent characteristics, activity type, biodiversity realm, and target taxa. We identified 72 relevant platforms and 577 conservation-focused projects that have raised US$4 790 634 since 2009. Whilst proponents were based in 38 countries, projects were delivered across 80 countries, indicating a potential mechanism of resource mobilization. Proponents were from non-governmental organizations (35%), universities (30%), or were freelancers (26%). Most projects were for research (40%), persuasion (31%), and on-ground actions (21%). Projects have focused primarily on species (57.7%) and terrestrial ecosystems (20.3%), and less on marine (8.8%) and freshwater ecosystems (3.6%). Projects have focused on 208 species, including a disproportionate number of threatened bird and mammal species. Crowdfunding for biodiversity conservation has now become a global phenomenon and presents signals for potential expansion, despite possible pitfalls. Opportunities arise from its spatial amplifying effect, steady increase over time, inclusion of Cinderella species, adoption by multiple actors, and funding of a range of activities beyond research. Our study paves the way for further research on key questions, such as campaign success rates, effectiveness, and drivers of adoption. Even though the capital input of crowdfunding so far has been modest compared to other conservation finance

  17. Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies.

    Directory of Open Access Journals (Sweden)

    Ranyee A Chiang

    2008-08-01

    Full Text Available The evolution of enzymes affects how well a species can adapt to new environmental conditions. During enzyme evolution, certain aspects of molecular function are conserved while other aspects can vary. Aspects of function that are more difficult to change or that need to be reused in multiple contexts are often conserved, while those that vary may indicate functions that are more easily changed or that are no longer required. In analogy to the study of conservation patterns in enzyme sequences and structures, we have examined the patterns of conservation and variation in enzyme function by analyzing graph isomorphisms among enzyme substrates of a large number of enzyme superfamilies. This systematic analysis of substrate substructures establishes the conservation patterns that typify individual superfamilies. Specifically, we determined the chemical substructures that are conserved among all known substrates of a superfamily and the substructures that are reacting in these substrates and then examined the relationship between the two. Across the 42 superfamilies that were analyzed, substantial variation was found in how much of the conserved substructure is reacting, suggesting that superfamilies may not be easily grouped into discrete and separable categories. Instead, our results suggest that many superfamilies may need to be treated individually for analyses of evolution, function prediction, and guiding enzyme engineering strategies. Annotating superfamilies with these conserved and reacting substructure patterns provides information that is orthogonal to information provided by studies of conservation in superfamily sequences and structures, thereby improving the precision with which we can predict the functions of enzymes of unknown function and direct studies in enzyme engineering. Because the method is automated, it is suitable for large-scale characterization and comparison of fundamental functional capabilities of both characterized

  18. Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies.

    Science.gov (United States)

    Chiang, Ranyee A; Sali, Andrej; Babbitt, Patricia C

    2008-08-01

    The evolution of enzymes affects how well a species can adapt to new environmental conditions. During enzyme evolution, certain aspects of molecular function are conserved while other aspects can vary. Aspects of function that are more difficult to change or that need to be reused in multiple contexts are often conserved, while those that vary may indicate functions that are more easily changed or that are no longer required. In analogy to the study of conservation patterns in enzyme sequences and structures, we have examined the patterns of conservation and variation in enzyme function by analyzing graph isomorphisms among enzyme substrates of a large number of enzyme superfamilies. This systematic analysis of substrate substructures establishes the conservation patterns that typify individual superfamilies. Specifically, we determined the chemical substructures that are conserved among all known substrates of a superfamily and the substructures that are reacting in these substrates and then examined the relationship between the two. Across the 42 superfamilies that were analyzed, substantial variation was found in how much of the conserved substructure is reacting, suggesting that superfamilies may not be easily grouped into discrete and separable categories. Instead, our results suggest that many superfamilies may need to be treated individually for analyses of evolution, function prediction, and guiding enzyme engineering strategies. Annotating superfamilies with these conserved and reacting substructure patterns provides information that is orthogonal to information provided by studies of conservation in superfamily sequences and structures, thereby improving the precision with which we can predict the functions of enzymes of unknown function and direct studies in enzyme engineering. Because the method is automated, it is suitable for large-scale characterization and comparison of fundamental functional capabilities of both characterized and uncharacterized

  19. Oligonucleotide recombination enabled site-specific mutagenesis in bacteria

    Science.gov (United States)

    Recombineering refers to a strategy for engineering DNA sequences using a specialized mode of homologous recombination. This technology can be used for rapidly constructing precise changes in bacterial genome sequences in vivo. Oligo recombination is one type of recombineering that uses ssDNA olig...

  20. Recombination analysis based on the complete genome of bocavirus

    Directory of Open Access Journals (Sweden)

    Chen Shengxia

    2011-04-01

    Full Text Available Abstract Bocavirus include bovine parvovirus, minute virus of canine, porcine bocavirus, gorilla bocavirus, and Human bocaviruses 1-4 (HBoVs. Although recent reports showed that recombination happened in bocavirus, no systematical study investigated the recombination of bocavirus. The present study performed the phylogenetic and recombination analysis of bocavirus over the complete genomes available in GenBank. Results confirmed that recombination existed among bocavirus, including the likely inter-genotype recombination between HBoV1 and HBoV4, and intra-genotype recombination among HBoV2 variants. Moreover, it is the first report revealing the recombination that occurred between minute viruses of canine.

  1. Expression variation in connected recombinant populations of Arabidopsis thaliana highlights distinct transcriptome architectures

    Directory of Open Access Journals (Sweden)

    Cubillos Francisco A

    2012-03-01

    Full Text Available Abstract Background Expression traits can vary quantitatively between individuals and have a complex inheritance. Identification of the genetics underlying transcript variation can help in the understanding of phenotypic variation due to genetic factors regulating transcript abundance and shed light into divergence patterns. So far, only a limited number of studies have addressed this subject in Arabidopsis, with contrasting results due to dissimilar statistical power. Here, we present the transcriptome architecture in leaf tissue of two RIL sets obtained from a connected-cross design involving 3 commonly used accessions. We also present the transcriptome architecture observed in developing seeds of a third independent cross. Results The utilisation of the novel R/eqtl package (which goal is to automatize and extend functions from the R/qtl package allowed us to map 4,290 and 6,534 eQTLs in the Cvi-0 × Col-0 and Bur-0 × Col-0 recombinant populations respectively. In agreement with previous studies, we observed a larger phenotypic variance explained by eQTLs in linkage with the controlled gene (potentially cis-acting, compared to distant loci (acting necessarily indirectly or in trans. Distant eQTLs hotspots were essentially not conserved between crosses, but instead, cross-specific. Accounting for confounding factors using a probabilistic approach (VBQTL increased the mapping resolution and the number of significant associations. Moreover, using local eQTLs obtained from this approach, we detected evidence for a directional allelic effect in genes with related function, where significantly more eQTLs than expected by chance were up-regulated from one of the accessions. Primary experimental data, analysis parameters, eQTL results and visualisation of LOD score curves presented here are stored and accessible through the QTLstore service database http://qtlstore.versailles.inra.fr/. Conclusions Our results demonstrate the extensive diversity and

  2. Genetic recombination of the hepatitis C virus: clinical implications.

    Science.gov (United States)

    Morel, V; Fournier, C; François, C; Brochot, E; Helle, F; Duverlie, G; Castelain, S

    2011-02-01

    Genetic recombination is a well-known feature of RNA viruses that plays a significant role in their evolution. Although recombination is well documented for Flaviviridae family viruses, the first natural recombinant strain of hepatitis C virus (HCV) was identified as recently as 2002. Since then, a few other natural inter-genotypic, intra-genotypic and intra-subtype recombinant HCV strains have been described. However, the frequency of recombination may have been underestimated because not all known HCV recombinants are screened for in routine practice. Furthermore, the choice of treatment regimen and its predictive outcome remain problematic as the therapeutic strategy for HCV infection is genotype dependent. HCV recombination also raises many questions concerning its mechanisms and effects on the epidemiological and physiopathological features of the virus. This review provides an update on recombinant HCV strains, the process that gives rise to recombinants and clinical implications of recombination. © 2010 Blackwell Publishing Ltd.

  3. A role for recombination junctions in the segregation of mitochondrial DNA in yeast.

    Science.gov (United States)

    Lockshon, D; Zweifel, S G; Freeman-Cook, L L; Lorimer, H E; Brewer, B J; Fangman, W L

    1995-06-16

    In S. cerevisiae, mitochondrial DNA (mtDNA) molecules, in spite of their high copy number, segregate as if there were a small number of heritable units. The rapid segregation of mitochondrial genomes can be analyzed using mtDNA deletion variants. These small, amplified genomes segregate preferentially from mixed zygotes relative to wild-type mtDNA. This segregation advantage is abolished by mutations in a gene, MGT1, that encodes a recombination junction-resolving enzyme. We show here that resolvase deficiency causes a larger proportion of molecules to be linked together by recombination junctions, resulting in the aggregation of mtDNA into a small number of cytological structures. This change in mtDNA structure can account for the increased mitotic loss of mtDNA and the altered pattern of mtDNA segregation from zygotes. We propose that the level of unresolved recombination junctions influences the number of heritable units of mtDNA.

  4. Investigations for the implementation of catalytic recombiners in large dry containments in Germany

    International Nuclear Information System (INIS)

    Rohde, J.; Tiltmann, M.; Froehmel, T.

    1997-01-01

    During the past few years, several concepts of mitigation have been developed and tested to limit the hydrogen concentrations in the containment atmosphere during the course of a severe accident. Extensive efforts have been given, especially in Germany and Canada, to investigate the use of catalytic recombiners. Based on the outcome of these research efforts in Germany it was recommended by the Reactor Safety Commission (RSK) in June 1994 to implement a hydrogen mitigation system, based on catalytic recombiners in large dry containments of PWR plants. Investigations are carried out at GRS, sponsored by the German Ministry of Environment, Nature Conservation and Nuclear Safety (BMU), to develop basic requirements for the implementation of a catalytic recombiner system in large dry containments. Severe accidents scenarios were calculated with the system code MELCOR to determine the mass- and energy release rates from the primary system into the containment, necessary to prepare the input data for the containment code calculations. A detailed nodalisation of the containment system of a German PWR plant (Konvoi-type) was developed for the code RA-LOC MOD4 to investigate the effectiveness of a catalytic recombiner system which consists of 53 of such devices, being distributed in the complex room arrangement. The effectiveness of such a system is demonstrated by comparing a representative severe accident sequence without and with the catalytic recombination of hydrogen. The results showed, that only in some limited areas in the containment combustible gas mixtures were formed for a limited time span and that at the end of the first day after the onset of the accident the catalytic reaction is limited due to oxygen depletion. The work is still in progress while additional severe accident sequences have to be analyzed to develop some generic guidelines for the implementation of a catalytic recombiner system in large dry containments. (author)

  5. Homologous recombination in mammalian cells: effect of p53 and Bcl-2 proteins, replication inhibition and ionizing radiations

    International Nuclear Information System (INIS)

    Saintigny, Yannick

    1999-01-01

    The control of cell cycle, associated with the mechanisms of replication, DNA repair/recombination allows the cells to maintain their genetic integrity. The p53 protein ensures the control of G1/S transition. Its inactivation would allow to initial replication on damaged matrix and lead to the block of replication forks followed by DNA strand breaks, good substrates for recombination. This work shows that the expression of mutant p53 protein stimulates both spontaneous and radio-induced homologous recombination, independently of the control of cell cycle. Moreover, the use of a set of replication inhibitors show that inhibition of the replication elongation stimulates recombination more strongly than the initiation inhibition. Replication arrest by these inhibitors also significantly increases the number of DNA strand breaks. These results highlighted a point of action of p53 protein on the ultimate stages of the homologous recombination mechanism. Lastly, the expression of Bcl-2 protein inhibits apoptosis and increases survival, but specifically inhibits conservative recombination, after radiation as well as in absence of apoptotic stress. The extinction of this mechanism of DNA repair is associated with an increase of mutagenesis. Taken together, these results allow ta consider the maintenance of the genetic stability as a cellular network involving different pathways. A multiple stages model for tumoral progression can be deduced. (author) [fr

  6. Conservation businesses and conservation planning in a biological diversity hotspot.

    Science.gov (United States)

    Di Minin, Enrico; Macmillan, Douglas Craig; Goodman, Peter Styan; Escott, Boyd; Slotow, Rob; Moilanen, Atte

    2013-08-01

    The allocation of land to biological diversity conservation competes with other land uses and the needs of society for development, food, and extraction of natural resources. Trade-offs between biological diversity conservation and alternative land uses are unavoidable, given the realities of limited conservation resources and the competing demands of society. We developed a conservation-planning assessment for the South African province of KwaZulu-Natal, which forms the central component of the Maputaland-Pondoland-Albany biological diversity hotspot. Our objective was to enhance biological diversity protection while promoting sustainable development and providing spatial guidance in the resolution of potential policy conflicts over priority areas for conservation at risk of transformation. The conservation-planning assessment combined spatial-distribution models for 646 conservation features, spatial economic-return models for 28 alternative land uses, and spatial maps for 4 threats. Nature-based tourism businesses were competitive with other land uses and could provide revenues of >US$60 million/year to local stakeholders and simultaneously help meeting conservation goals for almost half the conservation features in the planning region. Accounting for opportunity costs substantially decreased conflicts between biological diversity, agricultural use, commercial forestry, and mining. Accounting for economic benefits arising from conservation and reducing potential policy conflicts with alternative plans for development can provide opportunities for successful strategies that combine conservation and sustainable development and facilitate conservation action. © 2013 Society for Conservation Biology.

  7. Heterogeneous recombination among Hepatitis B virus genotypes.

    Science.gov (United States)

    Castelhano, Nadine; Araujo, Natalia M; Arenas, Miguel

    2017-10-01

    The rapid evolution of Hepatitis B virus (HBV) through both evolutionary forces, mutation and recombination, allows this virus to generate a large variety of adapted variants at both intra and inter-host levels. It can, for instance, generate drug resistance or the diverse viral genotypes that currently exist in the HBV epidemics. Concerning the latter, it is known that recombination played a major role in the emergence and genetic diversification of novel genotypes. In this regard, the quantification of viral recombination in each genotype can provide relevant information to devise expectations about the evolutionary trends of the epidemic. Here we measured the amount of this evolutionary force by estimating global and local recombination rates in >4700 HBV complete genome sequences corresponding to nine (A to I) HBV genotypes. Counterintuitively, we found that genotype E presents extremely high levels of recombination, followed by genotypes B and C. On the other hand, genotype G presents the lowest level, where recombination is almost negligible. We discuss these findings in the light of known characteristics of these genotypes. Additionally, we present a phylogenetic network to depict the evolutionary history of the studied HBV genotypes. This network clearly classified all genotypes into specific groups and indicated that diverse pairs of genotypes are derived from a common ancestor (i.e., C-I, D-E and, F-H) although still the origin of this virus presented large uncertainty. Altogether we conclude that the amount of observed recombination is heterogeneous among HBV genotypes and that this heterogeneity can influence on the future expansion of the epidemic. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Linkage disequilibrium of evolutionarily conserved regions in the human genome

    Directory of Open Access Journals (Sweden)

    Johnson Todd A

    2006-12-01

    Full Text Available Abstract Background The strong linkage disequilibrium (LD recently found in genic or exonic regions of the human genome demonstrated that LD can be increased by evolutionary mechanisms that select for functionally important loci. This suggests that LD might be stronger in regions conserved among species than in non-conserved regions, since regions exposed to natural selection tend to be conserved. To assess this hypothesis, we used genome-wide polymorphism data from the HapMap project and investigated LD within DNA sequences conserved between the human and mouse genomes. Results Unexpectedly, we observed that LD was significantly weaker in conserved regions than in non-conserved regions. To investigate why, we examined sequence features that may distort the relationship between LD and conserved regions. We found that interspersed repeats, and not other sequence features, were associated with the weak LD tendency in conserved regions. To appropriately understand the relationship between LD and conserved regions, we removed the effect of repetitive elements and found that the high degree of sequence conservation was strongly associated with strong LD in coding regions but not with that in non-coding regions. Conclusion Our work demonstrates that the degree of sequence conservation does not simply increase LD as predicted by the hypothesis. Rather, it implies that purifying selection changes the polymorphic patterns of coding sequences but has little influence on the patterns of functional units such as regulatory elements present in non-coding regions, since the former are generally restricted by the constraint of maintaining a functional protein product across multiple exons while the latter may exist more as individually isolated units.

  9. Polyhedral patterns

    KAUST Repository

    Jiang, Caigui

    2015-10-27

    We study the design and optimization of polyhedral patterns, which are patterns of planar polygonal faces on freeform surfaces. Working with polyhedral patterns is desirable in architectural geometry and industrial design. However, the classical tiling patterns on the plane must take on various shapes in order to faithfully and feasibly approximate curved surfaces. We define and analyze the deformations these tiles must undertake to account for curvature, and discover the symmetries that remain invariant under such deformations. We propose a novel method to regularize polyhedral patterns while maintaining these symmetries into a plethora of aesthetic and feasible patterns.

  10. Methods of equipment conservation of a carboelectric

    International Nuclear Information System (INIS)

    Hurtado Higuera, Julio Cesar

    2001-01-01

    Several conservation methods are mentioned like they are those of conservation in dry, in humid, conservation of bombs of water conservation, of turbines, of generators, of transformers, of electric motors and conservation of coal piles

  11. On momentum conservation

    International Nuclear Information System (INIS)

    Karastoyanov, A.

    1990-01-01

    The relativistic law of momentum transformation shows that the sum of momenta of even isolated particles is not invariable in all inertial reference systems. This is connected with the relativistic change of kinetic energy and mass of a system of particles in result of internal interactions. The paper proposes a short and simple proof on the necessity of potential momentum. The momentum conservation law (for all interactions in the Minkowski world) is expressed in a generalized form. The constancy of the sum of kinetic and potential momentum of closed system of particles is shown. The energy conservation is a necessary condition. The potential momentum is defined as usual (e.g. as in the Berkeley Physics Course). (author). 13 refs

  12. Conservation laws shape dissipation

    Science.gov (United States)

    Rao, Riccardo; Esposito, Massimiliano

    2018-02-01

    Starting from the most general formulation of stochastic thermodynamics—i.e. a thermodynamically consistent nonautonomous stochastic dynamics describing systems in contact with several reservoirs—we define a procedure to identify the conservative and the minimal set of nonconservative contributions in the entropy production. The former is expressed as the difference between changes caused by time-dependent drivings and a generalized potential difference. The latter is a sum over the minimal set of flux-force contributions controlling the dissipative flows across the system. When the system is initially prepared at equilibrium (e.g. by turning off drivings and forces), a finite-time detailed fluctuation theorem holds for the different contributions. Our approach relies on identifying the complete set of conserved quantities and can be viewed as the extension of the theory of generalized Gibbs ensembles to nonequilibrium situations.

  13. Promoting household energy conservation

    International Nuclear Information System (INIS)

    Steg, Linda

    2008-01-01

    It is commonly assumed that households must change their behaviour to reduce the problems caused by increasing levels of fossil energy use. Strategies for behaviour change will be more effective if they target the most important causes of the behaviour in question. Therefore, this paper first discusses the factors influencing household energy use. Three barriers to fossil fuel energy conservation are discussed: insufficient knowledge of effective ways to reduce household energy use, the low priority and high costs of energy savings, and the lack of feasible alternatives. Next, the paper elaborates on the effectiveness and acceptability of strategies aimed to promote household energy savings. Informational strategies aimed at changing individuals' knowledge, perceptions, cognitions, motivations and norms, as well as structural strategies aimed at changing the context in which decisions are made, are discussed. This paper focuses on the psychological literature on household energy conservation, which mostly examined the effects of informational strategies. Finally, this paper lists important topics for future research

  14. Widespread evolutionary conservation of alternatively spliced exons in caenorhabditis

    DEFF Research Database (Denmark)

    Irimia, Manuel; Rukov, Jakob L; Penny, David

    2007-01-01

    Alternative splicing (AS) contributes to increased transcriptome and proteome diversity in various eukaryotic lineages. Previous studies showed low levels of conservation of alternatively spliced (cassette) exons within mammals and within dipterans. We report a strikingly different pattern...... in Caenorhabditis nematodes-more than 92% of cassette exons from Caenorhabditis elegans are conserved in Caenorhabditis briggsae and/or Caenorhabditis remanei. High levels of conservation extend to minor-form exons (present in a minority of transcripts) and are particularly pronounced for exons showing complex...... patterns of splicing. The functionality of the vast majority of cassette exons is underscored by various other features. We suggest that differences in conservation between lineages reflect differences in levels of functionality and further suggest that these differences are due to differences in intron...

  15. Specialization Patterns

    DEFF Research Database (Denmark)

    Schultz, Ulrik Pagh; Lawall, Julia Laetitia; Consel, Charles

    2000-01-01

    Design patterns offer many advantages for software development, but can introduce inefficiency into the final program. Program specialization can eliminate such overheads, but is most effective when targeted by the user to specific bottlenecks. Consequently, we propose that these concepts...... are complementary. Program specialization can optimize programs written using design patterns, and design patterns provide information about the program structure that can guide specialization. Concretely, we propose specialization patterns, which describe how to apply program specialization to optimize uses...... of design patterns. In this paper, we analyze the specialization opportunities provided by specific uses of design patterns. Based on the analysis of each design pattern, we define the associated specialization pattern. These specialization opportunities can be declared using the specialization classes...

  16. Anti-angiogenesis and anti-tumor activity of recombinant anginex

    International Nuclear Information System (INIS)

    Brandwijk, Ricardo J.M.G.E.; Dings, Ruud P.M.; Linden, Edith van der; Mayo, Kevin H.; Thijssen, Victor L.J.L.; Griffioen, Arjan W.

    2006-01-01

    Anginex, a synthetic 33-mer angiostatic peptide, specifically inhibits vascular endothelial cell proliferation and migration along with induction of apoptosis in endothelial cells. Here we report on the in vivo characterization of recombinant anginex and use of the artificial anginex gene for gene therapy approaches. Tumor growth of human MA148 ovarian carcinoma in athymic mice was inhibited by 80% when treated with recombinant anginex. Histological analysis of the tumors showed an approximate 2.5-fold reduction of microvessel density, suggesting that angiogenesis inhibition is the cause of the anti-tumor effect. Furthermore, there was a significant correlation between the gene expression patterns of 16 angiogenesis-related factors after treatment with both recombinant and synthetic anginex. To validate the applicability of the anginex gene for gene therapy, stable transfectants of murine B16F10 melanoma cells expressing recombinant anginex were made. Supernatants of these cells inhibited endothelial cell proliferation in vitro. Furthermore, after subcutaneous injection of these cells in C57BL/6 mice, an extensive delay in tumor growth was observed. These data show that the artificial anginex gene can be used to produce a recombinant protein with similar activity as its synthetic counterpart and that the gene can be applied in gene therapy approaches for cancer treatment

  17. Mini review: Recombinant production of tailored bio-pharmaceuticals in different Bacillus strains and future perspectives.

    Science.gov (United States)

    Lakowitz, Antonia; Godard, Thibault; Biedendieck, Rebekka; Krull, Rainer

    2018-05-01

    Bio-pharmaceuticals like antibodies, hormones and growth factors represent about one-fifth of commercial pharmaceuticals. Host candidates of growing interest for recombinant production of these proteins are strains of the genus Bacillus, long being established for biotechnological production of homologous and heterologous proteins. Bacillus strains benefit from development of efficient expression systems in the last decades and emerge as major industrial workhorses for recombinant proteins due to easy cultivation, non-pathogenicity and their ability to secrete recombinant proteins directly into extracellular medium allowing cost-effective downstream processing. Their broad product portfolio of pharmaceutically relevant recombinant proteins described in research include antibody fragments, growth factors, interferons and interleukins, insulin, penicillin G acylase, streptavidin and different kinases produced in various cultivation systems like microtiter plates, shake flasks and bioreactor systems in batch, fed-batch and continuous mode. To further improve production and secretion performance of Bacillus, bottlenecks and limiting factors concerning proteases, chaperones, secretion machinery or feedback mechanisms can be identified on different cell levels from genomics and transcriptomics via proteomics to metabolomics and fluxomics. For systematical identification of recurring patterns characteristic of given regulatory systems and key genetic targets, systems biology and omics-technology provide suitable and promising approaches, pushing Bacillus further towards industrial application for recombinant pharmaceutical protein production. Copyright © 2017. Published by Elsevier B.V.

  18. Graded Recombination Layers for Multijunction Photovoltaics

    KAUST Repository

    Koleilat, Ghada I.

    2012-06-13

    Multijunction devices consist of a stack of semiconductor junctions having bandgaps tuned across a broad spectrum. In solar cells this concept is used to increase the efficiency of photovoltaic harvesting, while light emitters and detectors use it to achieve multicolor and spectrally tunable behavior. In series-connected current-matched multijunction devices, the recombination layers must allow the hole current from one cell to recombine, with high efficiency and low voltage loss, with the electron current from the next cell. We recently reported a tandem solar cell in which the recombination layer was implemented using a progression of n-type oxides whose doping densities and work functions serve to connect, with negligible resistive loss at solar current densities, the constituent cells. Here we present the generalized conditions for design of efficient graded recombination layer solar devices. We report the number of interlayers and the requirements on work function and doping of each interlayer, to bridge an work function difference as high as 1.6 eV. We also find solutions that minimize the doping required of the interlayers in order to minimize optical absorption due to free carriers in the graded recombination layer (GRL). We demonstrate a family of new GRL designs experimentally and highlight the benefits of the progression of dopings and work functions in the interlayers. © 2012 American Chemical Society.

  19. Polyploidization increases meiotic recombination frequency in Arabidopsis

    Directory of Open Access Journals (Sweden)

    Rehmsmeier Marc

    2011-04-01

    Full Text Available Abstract Background Polyploidization is the multiplication of the whole chromosome complement and has occurred frequently in vascular plants. Maintenance of stable polyploid state over generations requires special mechanisms to control pairing and distribution of more than two homologous chromosomes during meiosis. Since a minimal number of crossover events is essential for correct chromosome segregation, we investigated whether polyploidy has an influence on the frequency of meiotic recombination. Results Using two genetically linked transgenes providing seed-specific fluorescence, we compared a high number of progeny from diploid and tetraploid Arabidopsis plants. We show that rates of meiotic recombination in reciprocal crosses of genetically identical diploid and autotetraploid Arabidopsis plants were significantly higher in tetraploids compared to diploids. Although male and female gametogenesis differ substantially in meiotic recombination frequency, both rates were equally increased in tetraploids. To investigate whether multivalent formation in autotetraploids was responsible for the increased recombination rates, we also performed corresponding experiments with allotetraploid plants showing strict bivalent pairing. We found similarly increased rates in auto- and allotetraploids, suggesting that the ploidy effect is independent of chromosome pairing configurations. Conclusions The evolutionary success of polyploid plants in nature and under domestication has been attributed to buffering of mutations and sub- and neo-functionalization of duplicated genes. Should the data described here be representative for polyploid plants, enhanced meiotic recombination, and the resulting rapid creation of genetic diversity, could have also contributed to their prevalence.

  20. SequenceLDhot: detecting recombination hotspots.

    Science.gov (United States)

    Fearnhead, Paul

    2006-12-15

    There is much local variation in recombination rates across the human genome--with the majority of recombination occurring in recombination hotspots--short regions of around approximately 2 kb in length that have much higher recombination rates than neighbouring regions. Knowledge of this local variation is important, e.g. in the design and analysis of association studies for disease genes. Population genetic data, such as that generated by the HapMap project, can be used to infer the location of these hotspots. We present a new, efficient and powerful method for detecting recombination hotspots from population data. We compare our method with four current methods for detecting hotspots. It is orders of magnitude quicker, and has greater power, than two related approaches. It appears to be more powerful than HotspotFisher, though less accurate at inferring the precise positions of the hotspot. It was also more powerful than LDhot in some situations: particularly for weaker hotspots (10-40 times the background rate) when SNP density is lower (maths.lancs.ac.uk/~fearnhea/Hotspot.

  1. MEIOB targets single-strand DNA and is necessary for meiotic recombination.

    Directory of Open Access Journals (Sweden)

    Benoit Souquet

    Full Text Available Meiotic recombination is a mandatory process for sexual reproduction. We identified a protein specifically implicated in meiotic homologous recombination that we named: meiosis specific with OB domain (MEIOB. This protein is conserved among metazoan species and contains single-strand DNA binding sites similar to those of RPA1. Our studies in vitro revealed that both recombinant and endogenous MEIOB can be retained on single-strand DNA. Those in vivo demonstrated the specific expression of Meiob in early meiotic germ cells and the co-localization of MEIOB protein with RPA on chromosome axes. MEIOB localization in Dmc1 (-/- spermatocytes indicated that it accumulates on resected DNA. Homologous Meiob deletion in mice caused infertility in both sexes, due to a meiotic arrest at a zygotene/pachytene-like stage. DNA double strand break repair and homologous chromosome synapsis were impaired in Meiob (-/- meiocytes. Interestingly MEIOB appeared to be dispensable for the initial loading of recombinases but was required to maintain a proper number of RAD51 and DMC1 foci beyond the zygotene stage. In light of these findings, we propose that RPA and this new single-strand DNA binding protein MEIOB, are essential to ensure the proper stabilization of recombinases which is required for successful homology search and meiotic recombination.

  2. Characterization of canine herpesvirus glycoprotein C expressed by a recombinant baculovirus in insect cells.

    Science.gov (United States)

    Xuan, X; Maeda, K; Mikami, T; Otsuka, H

    1996-12-01

    The gene encoding the canine herpesvirus (CHV) glycoprotein C (gC) homologue has been identified by sequence homology analyses with other well studied herpesviruses. Previously, we have identified three CHV glycoproteins, gp145/112, gp80 and gp47 using a panel of monoclonal antibodies (MAbs). To determine which CHV glycoprotein corresponds to gC, a recombinant baculovirus which contains the putative CHV gC structural gene under the baculovirus polyhedrin promoter was constructed. The recombinant baculovirus expressed gC-related polypeptides (44-62 kDa), which reacted only with MAbs against CHV gp80, indicating that the previously identified CHV gp80 is the translation product of the gC gene. The baculovirus expressed gC was glycosylated and transported to the surface of infected cells. At least seven neutralizing epitopes were conserved on the gC produced in insect cells. It was found that the recombinant baculovirus infected cells adsorbed murine erythrocytes as is the case for CHV-infected cells. The hemadsorption activity was inhibited by heparin, indicating that the CHV gC binds to heparan sulfate on the surface of murine erythrocytes. Mice immunized with the recombinant gC produced strong neutralizing antibodies. Our results suggest that CHV gC produced in insect cells may be useful as a subunit vaccine to control CHV infections.

  3. Recombinant expression of a functional myo-inositol-1-phosphate synthase (MIPS) in Mycobacterium smegmatis.

    Science.gov (United States)

    Huang, Xinyi; Hernick, Marcy

    2015-10-01

    Myo-inositol-1-phosphate synthase (MIPS, E.C. 5.5.1.4) catalyzes the first step in inositol production-the conversion of glucose-6-phosphate (Glc-6P) to myo-inositol-1-phosphate. While the three dimensional structure of MIPS from Mycobacterium tuberculosis has been solved, biochemical studies examining the in vitro activity have not been reported to date. Herein we report the in vitro activity of mycobacterial MIPS expressed in E. coli and Mycobacterium smegmatis. Recombinant expression in E. coli yields a soluble protein capable of binding the NAD(+) cofactor; however, it has no significant activity with the Glc-6P substrate. In contrast, recombinant expression in M. smegmatis mc(2)4517 yields a functionally active protein. Examination of structural data suggests that MtMIPS expressed in E. coli adopts a fold that is missing a key helix containing two critical (conserved) Lys side chains, which likely explains the inability of the E. coli expressed protein to bind and turnover the Glc-6P substrate. Recombinant expression in M. smegmatis may yield a protein that adopts a fold in which this key helix is formed enabling proper positioning of important side chains, thereby allowing for Glc-6P substrate binding and turnover. Detailed mechanistic studies may be feasible following optimization of the recombinant MIPS expression protocol in M. smegmatis.

  4. Evidence for positive selection and recombination hotspots in Deformed wing virus (DWV).

    Science.gov (United States)

    Dalmon, A; Desbiez, C; Coulon, M; Thomasson, M; Le Conte, Y; Alaux, C; Vallon, J; Moury, B

    2017-01-25

    Deformed wing virus (DWV) is considered one of the most damaging pests in honey bees since the spread of its vector, Varroa destructor. In this study, we sequenced the whole genomes of two virus isolates and studied the evolutionary forces that act on DWV genomes. The isolate from a Varroa-tolerant bee colony was characterized by three recombination breakpoints between DWV and the closely related Varroa destructor virus-1 (VDV-1), whereas the variant from the colony using conventional Varroa management was similar to the originally described DWV. From the complete sequence dataset, nine independent DWV-VDV-1 recombination breakpoints were detected, and recombination hotspots were found in the 5' untranslated region (5' UTR) and the conserved region encoding the helicase. Partial sequencing of the 5' UTR and helicase-encoding region in 41 virus isolates suggested that most of the French isolates were recombinants. By applying different methods based on the ratio between non-synonymous (dN) and synonymous (dS) substitution rates, we identified four positions that showed evidence of positive selection. Three of these positions were in the putative leader protein (Lp), and one was in the polymerase. These findings raise the question of the putative role of the Lp in viral evolution.

  5. Genome-wide recombination rate variation in a recombination map of cotton.

    Science.gov (United States)

    Shen, Chao; Li, Ximei; Zhang, Ruiting; Lin, Zhongxu

    2017-01-01

    Recombination is crucial for genetic evolution, which not only provides new allele combinations but also influences the biological evolution and efficacy of natural selection. However, recombination variation is not well understood outside of the complex species' genomes, and it is particularly unclear in Gossypium. Cotton is the most important natural fibre crop and the second largest oil-seed crop. Here, we found that the genetic and physical maps distances did not have a simple linear relationship. Recombination rates were unevenly distributed throughout the cotton genome, which showed marked changes along the chromosome lengths and recombination was completely suppressed in the centromeric regions. Recombination rates significantly varied between A-subgenome (At) (range = 1.60 to 3.26 centimorgan/megabase [cM/Mb]) and D-subgenome (Dt) (range = 2.17 to 4.97 cM/Mb), which explained why the genetic maps of At and Dt are similar but the physical map of Dt is only half that of At. The translocation regions between A02 and A03 and between A04 and A05, and the inversion regions on A10, D10, A07 and D07 indicated relatively high recombination rates in the distal regions of the chromosomes. Recombination rates were positively correlated with the densities of genes, markers and the distance from the centromere, and negatively correlated with transposable elements (TEs). The gene ontology (GO) categories showed that genes in high recombination regions may tend to response to environmental stimuli, and genes in low recombination regions are related to mitosis and meiosis, which suggested that they may provide the primary driving force in adaptive evolution and assure the stability of basic cell cycle in a rapidly changing environment. Global knowledge of recombination rates will facilitate genetics and breeding in cotton.

  6. Live hot, die young: transmission distortion in recombination hotspots.

    Directory of Open Access Journals (Sweden)

    Graham Coop

    2007-03-01

    Full Text Available There is strong evidence that hotspots of meiotic recombination in humans are transient features of the genome. For example, hotspot locations are not shared between human and chimpanzee. Biased gene conversion in favor of alleles that locally disrupt hotspots is a possible explanation of the short lifespan of hotspots. We investigate the implications of such a bias on human hotspots and their evolution. Our results demonstrate that gene conversion bias is a sufficiently strong force to produce the observed lack of sharing of intense hotspots between species, although sharing may be much more common for weaker hotspots. We investigate models of how hotspots arise, and find that only models in which hotspot alleles do not initially experience drive are consistent with observations of rather hot hotspots in the human genome. Mutations acting against drive cannot successfully introduce such hotspots into the population, even if there is direct selection for higher recombination rates, such as to ensure correct segregation during meiosis. We explore the impact of hotspot alleles on patterns of haplotype variation, and show that such alleles mask their presence in population genetic data, making them difficult to detect.

  7. Water Well Locations - Conservation Wells

    Data.gov (United States)

    NSGIC Education | GIS Inventory — The conservation well layer identifies the permitted surface location of oil and gas conservation wells that have not been plugged. These include active, regulatory...

  8. How hot are drosophila hotspots? examining recombination rate variation and associations with nucleotide diversity, divergence, and maternal age in Drosophila pseudoobscura.

    Directory of Open Access Journals (Sweden)

    Brenda Manzano-Winkler

    Full Text Available Fine scale meiotic recombination maps have uncovered a large amount of variation in crossover rate across the genomes of many species, and such variation in mammalian and yeast genomes is concentrated to <5kb regions of highly elevated recombination rates (10-100x the background rate called "hotspots." Drosophila exhibit substantial recombination rate heterogeneity across their genome, but evidence for these highly-localized hotspots is lacking. We assayed recombination across a 40Kb region of Drosophila pseudoobscura chromosome 2, with one 20kb interval assayed every 5Kb and the adjacent 20kb interval bisected into 10kb pieces. We found that recombination events across the 40kb stretch were relatively evenly distributed across each of the 5kb and 10kb intervals, rather than concentrated in a single 5kb region. This, in combination with other recent work, indicates that the recombination landscape of Drosophila may differ from the punctate recombination pattern observed in many mammals and yeast. Additionally, we found no correlation of average pairwise nucleotide diversity and divergence with recombination rate across the 20kb intervals, nor any effect of maternal age in weeks on recombination rate in our sample.

  9. Recombinant human erythropoietin in sports: a review

    Directory of Open Access Journals (Sweden)

    Rafael Maia de Almeida Bento

    2003-06-01

    Full Text Available Erythropoietin is an endogenous hormone of glicoproteic nature secreted by the kidneys and is the main regulator of the erythropoiesis. An alteration in its production generates a disturbance in the plasmatic concentration giving rise to several types of pathologies related to the hematopoietic system. The recombinant forms of erythropoietin have indiscriminately been used by athletes, mainly in endurance sports, by increasing the erythrocytes concentration, generating a better delivery of oxygen to the muscle tissue. The administration of recombinant erythropoietin was prohibited by the International Olympic Committee and its use considered as doping. This review has the intention to describe the physical, biological and pharmacokinetic properties of the endogenous erythropoietin, as well as its recombinant form, describing also its use in sports and the process of searching methodologies for its detection in doping control.

  10. Regulation of Homologous Recombination by SUMOylation

    DEFF Research Database (Denmark)

    Pinela da Silva, Sonia Cristina

    factors such as the homologous recombination (HR) machinery. HR constitutes the main DSB repair pathway in Saccharomyces cerevisiae and despite being largely considered an error-free process and essential for genome stability, uncontrolled recombination can lead to loss of heterozygosity, translocations......, deletions, and genome rearrangements that can lead to cell death or cancer in humans. The post-translational modification by SUMO (small ubiquitinlike modifier) has proven to be an important regulator of HR and genome integrity, but the molecular mechanisms responsible for these roles are still unclear....... In this study I present new insights for the role of SUMOylation in regulating HR by dissecting the role of SUMO in the interaction between the central HR-mediator protein Rad52 and its paralogue Rad59 and the outcome of recombination. This data provides evidence for the importance of SUMO in promoting protein...

  11. Determination of recombination in Mycoplasma hominis

    DEFF Research Database (Denmark)

    Jacobsen, Iben Søgaard; Boesen, Thomas; Mygind, Tina

    2002-01-01

    disequilibrium and distance between the segregating sites, by the homoplasy ratio (H ratio), and by compatibility matrices. The gap gene showed well-supported evidence for high levels of recombination, whereas recombination was less frequent and not significant within the other genes. The analysis revealed......B-hitL, excinuclease ABC subunit A (uvrA) and glyceraldehyde-3-phosphate dehydrogenase (gap) genes. The level of variability of these M. hominis genes was low compared with the housekeeping genes from Helicobacter pylori and Neisseria meningitidis, but only few M. hominis isolates had identical sequences in all genes...... intergenic and intragenic recombination in M. hominis and this may explain the high intraspecies variability. The results obtained in the present study may be of importance for future population studies of Mycoplasma species....

  12. Constraints from jet calculus on quark recombination

    International Nuclear Information System (INIS)

    Jones, L.M.; Lassila, K.E.; Willen, D.

    1979-01-01

    Within the QCD jet calculus formalism, we deduce an equation describing recombination of quarks and antiquarks into mesons within a quark or gluon jet. This equation relates the recombination function R(x 1 ,x 2 ,x) used in current literature to the fragmentation function for producing that same meson out of the parton initiating the jet. We submit currently used recombination functions to our consistency test, taking as input mainly the u-quark fragmentation data into π + mesons, but also s-quark fragmentation into K - mesons. The constraint is well satisfied at large Q 2 for large moments. Our results depend on one parameter, Q 0 2 , the constraint equation being satisfied for small values of this parameter

  13. Recombination Processes and Nonlinear Markov Chains.

    Science.gov (United States)

    Pirogov, Sergey; Rybko, Alexander; Kalinina, Anastasia; Gelfand, Mikhail

    2016-09-01

    Bacteria are known to exchange genetic information by horizontal gene transfer. Since the frequency of homologous recombination depends on the similarity between the recombining segments, several studies examined whether this could lead to the emergence of subspecies. Most of them simulated fixed-size Wright-Fisher populations, in which the genetic drift should be taken into account. Here, we use nonlinear Markov processes to describe a bacterial population evolving under mutation and recombination. We consider a population structure as a probability measure on the space of genomes. This approach implies the infinite population size limit, and thus, the genetic drift is not assumed. We prove that under these conditions, the emergence of subspecies is impossible.

  14. Transcription and recombination: when RNA meets DNA.

    Science.gov (United States)

    Aguilera, Andrés; Gaillard, Hélène

    2014-08-01

    A particularly relevant phenomenon in cell physiology and proliferation is the fact that spontaneous mitotic recombination is strongly enhanced by transcription. The most accepted view is that transcription increases the occurrence of double-strand breaks and/or single-stranded DNA gaps that are repaired by recombination. Most breaks would arise as a consequence of the impact that transcription has on replication fork progression, provoking its stalling and/or breakage. Here, we discuss the mechanisms responsible for the cross talk between transcription and recombination, with emphasis on (1) the transcription-replication conflicts as the main source of recombinogenic DNA breaks, and (2) the formation of cotranscriptional R-loops as a major cause of such breaks. The new emerging questions and perspectives are discussed on the basis of the interference between transcription and replication, as well as the way RNA influences genome dynamics. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

  15. Exceptionally high levels of recombination across the honey bee genome.

    Science.gov (United States)

    Beye, Martin; Gattermeier, Irene; Hasselmann, Martin; Gempe, Tanja; Schioett, Morten; Baines, John F; Schlipalius, David; Mougel, Florence; Emore, Christine; Rueppell, Olav; Sirviö, Anu; Guzmán-Novoa, Ernesto; Hunt, Greg; Solignac, Michel; Page, Robert E

    2006-11-01

    The first draft of the honey bee genome sequence and improved genetic maps are utilized to analyze a genome displaying 10 times higher levels of recombination (19 cM/Mb) than previously analyzed genomes of higher eukaryotes. The exceptionally high recombination rate is distributed genome-wide, but varies by two orders of magnitude. Analysis of chromosome, sequence, and gene parameters with respect to recombination showed that local recombination rate is associated with distance to the telomere, GC content, and the number of simple repeats as described for low-recombining genomes. Recombination rate does not decrease with chromosome size. On average 5.7 recombination events per chromosome pair per meiosis are found in the honey bee genome. This contrasts with a wide range of taxa that have a uniform recombination frequency of about 1.6 per chromosome pair. The excess of recombination activity does not support a mechanistic role of recombination in stabilizing pairs of homologous chromosome during chromosome pairing. Recombination rate is associated with gene size, suggesting that introns are larger in regions of low recombination and may improve the efficacy of selection in these regions. Very few transposons and no retrotransposons are present in the high-recombining genome. We propose evolutionary explanations for the exceptionally high genome-wide recombination rate.

  16. Overview of energy demand and opportunities for conservation

    Energy Technology Data Exchange (ETDEWEB)

    Graham, P. J.

    1977-10-15

    The widespread practice of conservation could make a substantial reduction in the rate of growth of demand and hence in the rate at which resources need to be developed and consumed. An attempt is not made to show that conservation is an alternative to increasing energy supply. After reviewing the consumption of energy before the 1973 energy crisis, the main features of conservation which have brought it to the forefront of energy policy are examined. Some information on present consumption patterns in New Zealand is presented.

  17. Conservation of myeloid surface antigens on primate granulocytes.

    Science.gov (United States)

    Letvin, N L; Todd, R F; Palley, L S; Schlossman, S F; Griffin, J D

    1983-02-01

    Monoclonal antibodies reactive with myeloid cell surface antigens were used to study evolutionary changes in granulocyte surface antigens from primate species. Certain of these granulocyte membrane antigens are conserved in phylogenetically distant species, indicating the potential functional importance of these structures. The degree of conservation of these antigens reflects the phylogenetic relationship between primate species. Furthermore, species of the same genus show similar patterns of binding to this panel of anti-human myeloid antibodies. This finding of conserved granulocyte surface antigens suggests that non-human primates may provide a model system for exploring uses of monoclonal antibodies in the treatment of human myeloid disorders.

  18. Conservation Education: A Position Statement.

    Science.gov (United States)

    Soil Conservation Society of America, Ankeny, IA.

    The Soil Conservation Society of America's (SCSA) aim is to advance the science and art of good land and water use. Conservation education has a significant role in achieving the wise use of these resources. In this report, perspectives are offered on: (1) the requirements for effective conservation education programs; (2) rationale for…

  19. Madagascar Conservation & Development: Editorial Policies

    African Journals Online (AJOL)

    ... of the Madagascar Conservation & Development community. Finally, Madagascar Conservation & Development serves as a conduit for debate and discussion and welcomes contributions on any aspect of the legal or scientific status of any species living in Madagascar, or on conservation and development philosophy.

  20. Thermal recombination: Beyond the valence quark approximation

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, B. [Department of Physics, Duke University, Durham, NC 27708 (United States); Fries, R.J. [School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455 (United States)]. E-mail: fries@physics.umn.edu; Bass, S.A. [Department of Physics, Duke University, Durham, NC 27708 (United States); RIKEN BNL Research Center, Brookhaven National Laboratory, Upton, NY 11973 (United States)

    2005-07-07

    Quark counting rules derived from recombination models agree well with data on hadron production at intermediate transverse momenta in relativistic heavy-ion collisions. They convey a simple picture of hadrons consisting only of valence quarks. We discuss the inclusion of higher Fock states that add sea quarks and gluons to the hadron structure. We show that, when recombination occurs from a thermal medium, hadron spectra remain unaffected by the inclusion of higher Fock states. However, the quark number scaling for elliptic flow is somewhat affected. We discuss the implications for our understanding of data from the Relativistic Heavy Ion Collider.

  1. The recombination of a helium plasma

    International Nuclear Information System (INIS)

    Hollenstein, C.; Sayasov, Y.; Schneider, H.

    1975-01-01

    A helium plasma (Tsub(e) 15 cm -3 ) in the afterglow without magnetic field was investigated. The measurements of the electron density and temperature are presented. Laser interferometry and radiowave diagnostics were used. The measured exponential decay of the electron density and temperature was explained with the collisional-radiative recombination and the thermal conduction of the electrons towards the wall of the discharge vessel. The measured recombination coefficients were compared with measurements and calculations of other authors. The best agreement was found with the calculations by Drawin. (Auth.)

  2. Theoretical models for recombination in expanding gas

    International Nuclear Information System (INIS)

    Avron, Y.; Kahane, S.

    1978-09-01

    In laser isotope separation of atomic uranium, one is confronted with the theoretical problem of estimating the concentration of thermally ionized uranium atoms. To investigate this problem theoretical models for recombination in an expanding gas and in the absence of local thermal equilibrium have been constructed. The expansion of the gas is described by soluble models of the hydrodynamic equation, and the recombination by rate equations. General results for the freezing effect for the suitable ranges of the gas parameters are obtained. The impossibility of thermal equilibrium in expanding two-component systems is proven

  3. Integrating conservation costs into sea level rise adaptive conservation prioritization

    Directory of Open Access Journals (Sweden)

    Mingjian Zhu

    2015-07-01

    Full Text Available Biodiversity conservation requires strategic investment as resources for conservation are often limited. As sea level rises, it is important and necessary to consider both sea level rise and costs in conservation decision making. In this study, we consider costs of conservation in an integrated modeling process that incorporates a geomorphological model (SLAMM, species habitat models, and conservation prioritization (Zonation to identify conservation priorities in the face of landscape dynamics due to sea level rise in the Matanzas River basin of northeast Florida. Compared to conservation priorities that do not consider land costs in the analysis process, conservation priorities that consider costs in the planning process change significantly. The comparison demonstrates that some areas with high conservation values might be identified as lower priorities when integrating economic costs in the planning process and some areas with low conservation values might be identified as high priorities when considering costs in the planning process. This research could help coastal resources managers make informed decisions about where and how to allocate conservation resources more wisely to facilitate biodiversity adaptation to sea level rise.

  4. Inactivated Recombinant Rabies Viruses Displaying Canine Distemper Virus Glycoproteins Induce Protective Immunity against Both Pathogens.

    Science.gov (United States)

    da Fontoura Budaszewski, Renata; Hudacek, Andrew; Sawatsky, Bevan; Krämer, Beate; Yin, Xiangping; Schnell, Matthias J; von Messling, Veronika

    2017-04-15

    The development of multivalent vaccines is an attractive methodology for the simultaneous prevention of several infectious diseases in vulnerable populations. Both canine distemper virus (CDV) and rabies virus (RABV) cause lethal disease in wild and domestic carnivores. While RABV vaccines are inactivated, the live-attenuated CDV vaccines retain residual virulence for highly susceptible wildlife species. In this study, we developed recombinant bivalent vaccine candidates based on recombinant vaccine strain rabies virus particles, which concurrently display the protective CDV and RABV glycoprotein antigens. The recombinant viruses replicated to near-wild-type titers, and the heterologous glycoproteins were efficiently expressed and incorporated in the viral particles. Immunization of ferrets with beta-propiolactone-inactivated recombinant virus particles elicited protective RABV antibody titers, and animals immunized with a combination of CDV attachment protein- and fusion protein-expressing recombinant viruses were protected from lethal CDV challenge. However, animals that were immunized with only a RABV expressing the attachment protein of CDV vaccine strain Onderstepoort succumbed to infection with a more recent wild-type strain, indicating that immune responses to the more conserved fusion protein contribute to protection against heterologous CDV strains. IMPORTANCE Rabies virus and canine distemper virus (CDV) cause high mortality rates and death in many carnivores. While rabies vaccines are inactivated and thus have an excellent safety profile and high stability, live-attenuated CDV vaccines can retain residual virulence in highly susceptible species. Here we generated recombinant inactivated rabies viruses that carry one of the CDV glycoproteins on their surface. Ferrets immunized twice with a mix of recombinant rabies viruses carrying the CDV fusion and attachment glycoproteins were protected from lethal CDV challenge, whereas all animals that received

  5. Patterns of distribution and conservation status of freshwater fishes ...

    African Journals Online (AJOL)

    1995-02-15

    Feb 15, 1995 ... Treur River barb Barhus treurensis in the Blyde River; orange-fringed largemouth Chetia brevis in the Komati-. Incomati and Incomati suckermouth ChiJogJanis blfurcus in the Crocodile-Incomati River) (Table I). In addition to the endemic species there are 15 or 16 species like the lungfish. Protopterus ...

  6. Spatial patterns and biodiversity conservation of snakes from Cerrado biome

    OpenAIRE

    Couto, Larice de Fátima; UCG; Terribile, Levi Carina; UNB; Diniz Filho, José Alexandre Felizola; UFG

    2007-01-01

    Em geral, as tentativas para estabelecer áreas prioritárias para conservação no Cerrado têm sido baseadas em critérios subjetivos. No presente trabalho, foram utilizados dados macroecológicos de distribuição de 129 espécies de serpentes distribuídas em 181 células com 1o de latitude/longitude do Cerrado para analisar padrões espaciais na riqueza e propor uma estratégia de conservação para essas espécies. Verificou-se que as cinco variáveis ambientais analisadas explicaram apenas 34,65% da var...

  7. Functional mitochondrial ATP synthase proteolipid gene produced by recombination of parental genes in a petunia somatic hybrid

    International Nuclear Information System (INIS)

    Rothenberg, M.; Hanson, M.R.

    1988-01-01

    A novel ATP synthase subunit 9 gene (atp9) was identified in the mitochondrial genome of a Petunia somatic hybrid line (13-133) which was produced from a fusion between Petunia lines 3688 and 3704. The novel gene was generated by intergenomic recombination between atp9 genes from the two parental plant lines. The entire atp9 coding region is represented on the recombinant gene. Comparison of gene sequences using electrophoresis and autoradiography, indicate that the 5' transcribed region is contributed by an atp9 gene from 3704 and the 3' transcribed region is contributed by an atp9 gene from 3688. The recombinant atp9 gene is transcriptionally active. The location of the 5' and 3' transcript termini are conserved with respect to the parental genes, resulting in the production of hybrid transcripts

  8. Recombination coefficients in extrinsic n-InSb

    International Nuclear Information System (INIS)

    Schneider, W.; Groh, H.; Huebner, K.

    1976-01-01

    The bulk recombination coefficients for linear recombination via recombination centers as well as for direct recombination have been determined measuring the conductivity decay after two-photon absorption with a CO 2 laser. The Suhl effect was applied to measure the surface recombination velocity. The corresponding literature is discussed and compared with our results. We conclude that two different kinds of recombination centers are possible in n-InSb, with energy levels (0.1-0.12)eV above the valence band, or (0.14-0.2)eV respectively. (orig.) [de

  9. Hearing Conservation Live #2430

    Energy Technology Data Exchange (ETDEWEB)

    Chochoms, Michael [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-08-09

    Occupational hearing loss is one of the most common work-related illnesses in the United States (US). From 22 to 30 million US workers are exposed to hazardous noise levels at work, and 25% of these workers will develop permanent hearing loss. Hearing loss from noise is slow and painless, and you can have a disability before you notice it. This course presents the hazards associated with workplace noise, the purpose and elements of the Los Alamos National Laboratory (LANL) Hearing Conservation Program (HCP), and controls that are available to reduce your exposure to hazardous levels of noise.

  10. Energy conservation technologies

    Energy Technology Data Exchange (ETDEWEB)

    Courtright, H.A. [Electric Power Research Inst., Palo Alto, CA (United States)

    1993-12-31

    The conservation of energy through the efficiency improvement of existing end-uses and the development of new technologies to replace less efficient systems is an important component of the overall effort to reduce greenhouse gases which may contribute to global climate change. Even though uncertainties exist on the degree and causes of global warming, efficiency improvements in end-use applications remain in the best interest of utilities, their customers and society because efficiency improvements not only reduce environmental exposures but also contribute to industrial productivity, business cost reductions and consumer savings in energy costs.

  11. Integrating Agriculture and Conservation

    Science.gov (United States)

    Vandever, Mark W.

    2010-01-01

    The USGS produces the needed science-based information to guide management actions and policy decisions that support wildlife habitat and other environmental services compatible with USDA conservation goals and farm operations. The Policy Analysis and Science Assistance Branch of the Fort Collins Science Center (FORT) has conducted research involving a national landowner survey and numerous short- and long-term evaluations regarding vegetation responses to land management practices. This research helps land and resource managers to make informed decisions and resolve resource management conflicts.

  12. Analysis of sectoral energy conservation in Malaysia

    Energy Technology Data Exchange (ETDEWEB)

    Al-Mofleh, Anwar; Taib, Soib; Salah, Wael [School of Electrical and Electronics Engineering, Universiti Sains Malaysia, 14300 Nibong Tebal, Penang (Malaysia); Mujeebu, M. Abdul [School of Mechanical Engineering, Universiti Sains Malaysia, 14300 Nibong Tebal, Penang (Malaysia)

    2009-06-15

    The electrical energy consumption in Malaysia has increased sharply in the past few years, and modern energy efficient technologies are desperately needed for the national energy policy. This article presents a comprehensive picture of the current status of energy consumption and various energy conservation options viable for Malaysian environment. A detailed survey is made to assess the consumption pattern and the existing techniques for energy efficiency. Based on the survey, the feasibility of improving the available systems and adopting new programs in different sectors is investigated. The study reveals the fact that the energy conservation policy of the country has been fairly improved in the last ten years. However the country has to pay more attention to this area and make urgent measures to adopt more energy efficient technologies in various sectors. (author)

  13. Analysis of sectoral energy conservation in Malaysia

    International Nuclear Information System (INIS)

    Al-Mofleh, Anwar; Taib, Soib; Mujeebu, M. Abdul; Salah, Wael

    2009-01-01

    The electrical energy consumption in Malaysia has increased sharply in the past few years, and modern energy efficient technologies are desperately needed for the national energy policy. This article presents a comprehensive picture of the current status of energy consumption and various energy conservation options viable for Malaysian environment. A detailed survey is made to assess the consumption pattern and the existing techniques for energy efficiency. Based on the survey, the feasibility of improving the available systems and adopting new programs in different sectors is investigated. The study reveals the fact that the energy conservation policy of the country has been fairly improved in the last ten years. However the country has to pay more attention to this area and make urgent measures to adopt more energy efficient technologies in various sectors.

  14. Studies of the cytosolic thymidine kinase in human cells and comparison to the recombinantly expressed enzyme

    DEFF Research Database (Denmark)

    Kock Jensen, Helle

    by recombinant technics to examine the relation between the TKl gene and the TKl protein. In the second part of this investigation a direct expression system for human TKl in E.coli was developed to produce a source of high amounts of TKl, to be able to examine the structure of TKl. The resulting recombinant TKl...... cells and that this modification can not be performed in E.coli....... infections. In the first part of the present investigation a sensitive test for quantitating TKl mRNA (competitive PCR) is developed and the results show that PHA stimulated lymphocytes reveal the same pattern concerning expression of TKl mRNA and TKl enzyme activity as serum-stimulated cells. This pattern...

  15. Switch junction sequences in PMS2-deficient mice reveal a microhomology-mediated mechanism of Ig class switch recombination

    Science.gov (United States)

    Ehrenstein, Michael R.; Rada, Cristina; Jones, Anne-Marie; Milstein, César; Neuberger, Michael S.

    2001-01-01

    Isotype switching involves a region-specific, nonhomologous recombinational deletion that has been suggested to occur by nonhomologous joining of broken DNA ends. Here, we find increased donor/acceptor homology at switch junctions from PMS2-deficient mice and propose that class switching can occur by microhomology-mediated end-joining. Interestingly, although isotype switching and somatic hypermutation show many parallels, we confirm that PMS2 deficiency has no major effect on the pattern of nucleotide substitutions generated during somatic hypermutation. This finding is in contrast to MSH2 deficiency. With MSH2, the altered pattern of switch recombination and hypermutation suggests parallels in the mechanics of the two processes, whereas the fact that PMS2 deficiency affects only switch recombination may reflect differences in the pathways of break resolution. PMID:11717399

  16. What is a conservation actor?

    Directory of Open Access Journals (Sweden)

    Paul Jepson

    2011-01-01

    Full Text Available As a crisis-oriented discipline, conservation biology needs actions to understand the state of nature and thwart declines in biodiversity. Actors-traditionally individuals, institutions, and collectives-have been central to delivering such goals in practice. However, the definition of actors within the discipline has been narrow and their role in influencing conservation outcomes inadequately conceptualised. In this paper, we examine the question ′What is a conservation actor?′ Who or what creates the capacity to influence conservation values and actions? Drawing from theoretical developments in Actor-Network Theory and collective governance, we argue that the concept of an actor in conservation biology should be broadened to include non-humans, such as species and devices, because they have the agency and ability to influence project goals and outcomes. We illustrate this through four examples: the Asian elephant, International Union for Conservation of Nature red lists, the High Conservation Value approach, and an Integrated Conservation and Development Project. We argue that a broader conceptualisation of actors in conservation biology will produce new forms of understanding that could open up new areas of conservation research, enhance practice and draw attention to spheres of conservation activity that might require stronger oversight and governance.

  17. 18 CFR 701.5 - Organization pattern.

    Science.gov (United States)

    2010-04-01

    ... 18 Conservation of Power and Water Resources 2 2010-04-01 2010-04-01 false Organization pattern... ORGANIZATION Introduction § 701.5 Organization pattern. (a) The Office of the Water Resources Council is... Council Staff headed by a Director, and Field Organizations within its jurisdiction. (b) The Water...

  18. An outbreak of severe infections among Australian infants caused by a novel recombinant strain of human parechovirus type 3.

    Science.gov (United States)

    Nelson, Tiffanie M; Vuillermin, Peter; Hodge, Jason; Druce, Julian; Williams, David T; Jasrotia, Rekha; Alexandersen, Soren

    2017-03-14

    Human parechovirus types 1-16 (HPeV1-16) are positive strand RNA viruses in the family Picornaviridae. We investigated a 2015 outbreak of HPeV3 causing illness in infants in Victoria, Australia. Virus genome was extracted from clinical material and isolates and sequenced using a combination of next generation and Sanger sequencing. The HPeV3 outbreak genome was 98.7% similar to the HPeV3 Yamagata 2011 lineage for the region encoding the structural proteins up to nucleotide position 3115, but downstream of that the genome varied from known HPeV sequences with a similarity of 85% or less. Analysis indicated that recombination had occurred, may have involved multiple types of HPeV and that the recombination event/s occurred between March 2012 and November 2013. However the origin of the genome downstream of the recombination site is unknown. Overall, the capsid of this virus is highly conserved, but recombination provided a different non-structural protein coding region that may convey an evolutionary advantage. The indication that the capsid encoding region is highly conserved at the amino acid level may be helpful in directing energy towards the development of a preventive vaccine for expecting mothers or antibody treatment of young infants with severe disease.

  19. Beyond conservation agriculture.

    Science.gov (United States)

    Giller, Ken E; Andersson, Jens A; Corbeels, Marc; Kirkegaard, John; Mortensen, David; Erenstein, Olaf; Vanlauwe, Bernard

    2015-01-01

    Global support for Conservation Agriculture (CA) as a pathway to Sustainable Intensification is strong. CA revolves around three principles: no-till (or minimal soil disturbance), soil cover, and crop rotation. The benefits arising from the ease of crop management, energy/cost/time savings, and soil and water conservation led to widespread adoption of CA, particularly on large farms in the Americas and Australia, where farmers harness the tools of modern science: highly-sophisticated machines, potent agrochemicals, and biotechnology. Over the past 10 years CA has been promoted among smallholder farmers in the (sub-) tropics, often with disappointing results. Growing evidence challenges the claims that CA increases crop yields and builds-up soil carbon although increased stability of crop yields in dry climates is evident. Our analyses suggest pragmatic adoption on larger mechanized farms, and limited uptake of CA by smallholder farmers in developing countries. We propose a rigorous, context-sensitive approach based on Systems Agronomy to analyze and explore sustainable intensification options, including the potential of CA. There is an urgent need to move beyond dogma and prescriptive approaches to provide soil and crop management options for farmers to enable the Sustainable Intensification of agriculture.

  20. Beyond conservation agriculture

    Science.gov (United States)

    Giller, Ken E.; Andersson, Jens A.; Corbeels, Marc; Kirkegaard, John; Mortensen, David; Erenstein, Olaf; Vanlauwe, Bernard

    2015-01-01

    Global support for Conservation Agriculture (CA) as a pathway to Sustainable Intensification is strong. CA revolves around three principles: no-till (or minimal soil disturbance), soil cover, and crop rotation. The benefits arising from the ease of crop management, energy/cost/time savings, and soil and water conservation led to widespread adoption of CA, particularly on large farms in the Americas and Australia, where farmers harness the tools of modern science: highly-sophisticated machines, potent agrochemicals, and biotechnology. Over the past 10 years CA has been promoted among smallholder farmers in the (sub-) tropics, often with disappointing results. Growing evidence challenges the claims that CA increases crop yields and builds-up soil carbon although increased stability of crop yields in dry climates is evident. Our analyses suggest pragmatic adoption on larger mechanized farms, and limited uptake of CA by smallholder farmers in developing countries. We propose a rigorous, context-sensitive approach based on Systems Agronomy to analyze and explore sustainable intensification options, including the potential of CA. There is an urgent need to move beyond dogma and prescriptive approaches to provide soil and crop management options for farmers to enable the Sustainable Intensification of agriculture. PMID:26579139

  1. Beyond Conservation Agriculture

    Directory of Open Access Journals (Sweden)

    Ken E Giller

    2015-10-01

    Full Text Available Global support for Conservation Agriculture (CA as a pathway to Sustainable Intensification is strong. CA revolves around three principles: no-till (or minimal soil disturbance, soil cover, and crop rotation. The benefits arising from the ease of crop management, energy/cost/time savings and soil and water conservation led to widespread adoption of CA, particularly on large farms in the Americas and Australia, where farmers harness the tools of modern science: highly-sophisticated machines, potent agrochemicals and biotechnology. Over the past ten years CA has been promoted among smallholder farmers in the (sub- tropics, often with disappointing results. Growing evidence challenges the claims that CA increases crop yields and builds-up soil carbon although increased stability of crop yields in dry climates is evident. Our analyses suggest pragmatic adoption on larger mechanized farms, and limited uptake of CA by smallholder farmers in developing countries. We propose a rigorous, context-sensitive approach based on Systems Agronomy to analyze and explore sustainable intensification options, including the potential of CA. There is an urgent need to move beyond dogma and prescriptive approaches to provide soil and crop management options for farmers to enable the Sustainable Intensification of agriculture.

  2. Selling energy conservation.

    Science.gov (United States)

    Hinrichsen, D

    1995-01-01

    This article concerns the Organization of the Petroleum Exporting Countries (OPEC) crisis and its impact on energy efficiency measures in the US. In 1985, when the OPEC collapsed, the US government had avoided the need to construct 350 gigawatts of new electric capacity. The most successful efficiency improvements, especially in household appliances and equipment, lighting and tightened energy efficiency standards in new buildings, resulted from the OPEC event. The real innovation of that time was the change in profit rules for utilities. This revolution and the way some US utilities view energy have not caught on elsewhere. Despite the initiative toward improving energy efficiency in homes, offices and industries, the change has been slow. Partly to blame are the big development banks, which pointed out that short-term conservation and efficiency measures could save at least 15% of the total energy demand without the need for major investment. The benefits of energy conservation was shown during the oil shock when per capita energy consumption fell by 5% in the member states of the Organization of Economic Cooperation and Development, while the per capita gross domestic product grew by a third. There has been a decrease in energy expenditure worldwide, and the scope for further energy savings is enormous, but governments need to recognize and seize the opportunity.

  3. Lyme disease and conservation

    Science.gov (United States)

    Ginsberg, H.

    1994-01-01

    Lyme disease is a tick-borne illness that is wide-spread in North America, especially in the northeastern and northcentral United States. This disease could negatively influence efforts to conserve natural populations in two ways: (1) the disease could directly affect wild animal health; and (2) tick control efforts could adversely affect natural populations and communities. Lyme disease affects several domestic animals, but symptoms have been reported in only a few wild species. Direct effects of Lyme disease on wild animal populations have not been reported, but the disease should be considered as a possible cause in cases of unexplained population declines in endemic areas. Methods available to manage ticks and Lyme disease include human self-protection techniques, manipulation of habitats and hosts species populations, biological control, and pesticide applications. The diversity of available techniques allows selection of approaches to minimize environmental effects by (1) emphasizing personal protection techniques, (2) carefully targeting management efforts to maximize efficiency, and (3) integrating environmentally benign techniques to improve management while avoiding broad-scale environmentally destructive approaches. The environmental effects of Lyme disease depend, to a large extent, on the methods chosen to minimize human exposure to infected ticks. Conservation biologists can help design tick management programs that effectively lower the incidence of human Lyme disease while simultaneously minimizing negative effects on natural populations.

  4. Intensity Conserving Spectral Fitting

    Science.gov (United States)

    Klimchuk, J. A.; Patsourakos, S.; Tripathi, D.

    2015-01-01

    The detailed shapes of spectral line profiles provide valuable information about the emitting plasma, especially when the plasma contains an unresolved mixture of velocities, temperatures, and densities. As a result of finite spectral resolution, the intensity measured by a spectrometer is the average intensity across a wavelength bin of non-zero size. It is assigned to the wavelength position at the center of the bin. However, the actual intensity at that discrete position will be different if the profile is curved, as it invariably is. Standard fitting routines (spline, Gaussian, etc.) do not account for this difference, and this can result in significant errors when making sensitive measurements. Detection of asymmetries in solar coronal emission lines is one example. Removal of line blends is another. We have developed an iterative procedure that corrects for this effect. It can be used with any fitting function, but we employ a cubic spline in a new analysis routine called Intensity Conserving Spline Interpolation (ICSI). As the name implies, it conserves the observed intensity within each wavelength bin, which ordinary fits do not. Given the rapid convergence, speed of computation, and ease of use, we suggest that ICSI be made a standard component of the processing pipeline for spectroscopic data.

  5. Landscape Conservation Cooperatives: Creating a Collaborative Conservation Vision in the Face of Climate Change Uncertainty

    Science.gov (United States)

    Athearn, N.; Schlafmann, D.

    2015-12-01

    The 22 Landscape Conservation Cooperatives (LCCs) form a "network of networks," each defined by the characteristics of its ecoregion and its unique community of conservation managers, practitioners, and scientists. As self-directed partnerships, LCCs are strongly influenced not only by the landscape but by the evolving cultures and values that define the multi-faceted relationships between people and place. LCCs maintain an ecologically connected network across these diverse landscapes by transcending borders and leveraging resources. Natural resource managers are challenged to make decisions in the face of multiple uncertainties, and several partners across the network have recognized that climate change is one important uncertainty that spans boundaries - both across the conservation community and beyond. The impacts of climate change across the LCC Network are likely to be as diverse as the network itself - manifesting as, for example, sea level rise, ocean acidification, loss of sea ice, and shifts in climate patterns and timing - but synergies are being leveraged within and between LCCs and national climate-focused programs to systematically address the needs of the network to support a collaborative conservation vision that addresses multiple landscape-scale stressors in the face of climate uncertainties. This vision is being achieved by leveraging the convening power of the LCCs and collaborating with DOI Climate Science Centers and others. Selected case studies will demonstrate how the network finds strength in its differences, but also reveals powerful collaborative opportunities through integrated science, shared conservation strategies, and strategic approaches for translating targeted science to conservation action. These examples exemplify past successes as well as ongoing efforts as the network continues to bring about effective application of climate science to achieve conservation outcomes across the LCC Network in an uncertain future climate.

  6. Conserved Transcriptional Regulatory Programs Underlying Rice and Barley Germination

    Science.gov (United States)

    Lin, Li; Tian, Shulan; Kaeppler, Shawn; Liu, Zongrang; An, Yong-Qiang (Charles)

    2014-01-01

    Germination is a biological process important to plant development and agricultural production. Barley and rice diverged 50 million years ago, but share a similar germination process. To gain insight into the conservation of their underlying gene regulatory programs, we compared transcriptomes of barley and rice at start, middle and end points of germination, and revealed that germination regulated barley and rice genes (BRs) diverged significantly in expression patterns and/or protein sequences. However, BRs with higher protein sequence similarity tended to have more conserved expression patterns. We identified and characterized 316 sets of conserved barley and rice genes (cBRs) with high similarity in both protein sequences and expression patterns, and provided a comprehensive depiction of the transcriptional regulatory program conserved in barley and rice germination at gene, pathway and systems levels. The cBRs encoded proteins involved in a variety of biological pathways and had a wide range of expression patterns. The cBRs encoding key regulatory components in signaling pathways often had diverse expression patterns. Early germination up-regulation of cell wall metabolic pathway and peroxidases, and late germination up-regulation of chromatin structure and remodeling pathways were conserved in both barley and rice. Protein sequence and expression pattern of a gene change quickly if it is not subjected to a functional constraint. Preserving germination-regulated expression patterns and protein sequences of those cBRs for 50 million years strongly suggests that the cBRs are functionally significant and equivalent in germination, and contribute to the ancient characteristics of germination preserved in barley and rice. The functional significance and equivalence of the cBR genes predicted here can serve as a foundation to further characterize their biological functions and facilitate bridging rice and barley germination research with greater confidence. PMID

  7. Specialization Patterns

    OpenAIRE

    Schultz , Ulrik Pagh; Lawall , Julia ,; Consel , Charles

    1999-01-01

    Design patterns offer numerous advantages for software development, but can introduce inefficiency into the finished program. Program specialization can eliminate such overheads, but is most effective when targeted by the user to specific bottlenecks. Consequently, we propose to consider program specialization and design patterns as complementary concepts. On the one hand, program specialization can optimize object-oriented programs written using design patterns. On the other hand, design pat...

  8. Catalytic hydrogen recombination for nuclear containments

    International Nuclear Information System (INIS)

    Koroll, G.W.; Lau, D.W.P.; Dewit, W.A.; Graham, W.R.C.

    1994-01-01

    Catalytic recombiners appear to be a credible option for hydrogen mitigation in nuclear containments. The passive operation, versatility and ease of back fitting are appealing for existing stations and new designs. Recently, a generation of wet-proofed catalyst materials have been developed at AECL which are highly specific to H 2 -O 2 , are active at ambient temperatures and are being evaluated for containment applications. Two types of catalytic recombiners were evaluated for hydrogen removal in containments based on the AECL catalyst. The first is a catalytic combustor for application in existing air streams such as provided by fans or ventilation systems. The second is an autocatalytic recombiner which uses the enthalpy of reaction to produce natural convective flow over the catalyst elements. Intermediate-scale results obtained in 6 m 3 and 10 m 3 spherical and cylindrical vessels are given to demonstrate self-starting limits, operating limits, removal capacity, scaling parameters, flow resistance, mixing behaviour in the vicinity of an operating recombiner and sensitivity to poisoning, fouling and radiation. (author). 13 refs., 10 figs

  9. Recombinant protein blends: silk beyond natural design.

    Science.gov (United States)

    Dinjaski, Nina; Kaplan, David L

    2016-06-01

    Recombinant DNA technology and new material concepts are shaping future directions in biomaterial science for the design and production of the next-generation biomaterial platforms. Aside from conventionally used synthetic polymers, numerous natural biopolymers (e.g., silk, elastin, collagen, gelatin, alginate, cellulose, keratin, chitin, polyhydroxyalkanoates) have been investigated for properties and manipulation via bioengineering. Genetic engineering provides a path to increase structural and functional complexity of these biopolymers, and thereby expand the catalog of available biomaterials beyond that which exists in nature. In addition, the integration of experimental approaches with computational modeling to analyze sequence-structure-function relationships is starting to have an impact in the field by establishing predictive frameworks for determining material properties. Herein, we review advances in recombinant DNA-mediated protein production and functionalization approaches, with a focus on hybrids or combinations of proteins; recombinant protein blends or 'recombinamers'. We highlight the potential biomedical applications of fibrous protein recombinamers, such as Silk-Elastin Like Polypeptides (SELPs) and Silk-Bacterial Collagens (SBCs). We also discuss the possibility for the rationale design of fibrous proteins to build smart, stimuli-responsive biomaterials for diverse applications. We underline current limitations with production systems for these proteins and discuss the main trends in systems/synthetic biology that may improve recombinant fibrous protein design and production. Copyright © 2016. Published by Elsevier Ltd.

  10. Algae-based oral recombinant vaccines

    Science.gov (United States)

    Specht, Elizabeth A.; Mayfield, Stephen P.

    2014-01-01

    Recombinant subunit vaccines are some of the safest and most effective vaccines available, but their high cost and the requirement of advanced medical infrastructure for administration make them impractical for many developing world diseases. Plant-based vaccines have shifted that paradigm by paving the way for recombinant vaccine production at agricultural scale using an edible host. However, enthusiasm for “molecular pharming” in food crops has waned in the last decade due to difficulty in developing transgenic crop plants and concerns of contaminating the food supply. Microalgae could be poised to become the next candidate in recombinant subunit vaccine production, as they present several advantages over terrestrial crop plant-based platforms including scalable and contained growth, rapid transformation, easily obtained stable cell lines, and consistent transgene expression levels. Algae have been shown to accumulate and properly fold several vaccine antigens, and efforts are underway to create recombinant algal fusion proteins that can enhance antigenicity for effective orally delivered vaccines. These approaches have the potential to revolutionize the way subunit vaccines are made and delivered – from costly parenteral administration of purified protein, to an inexpensive oral algae tablet with effective mucosal and systemic immune reactivity. PMID:24596570

  11. Correlations in the Parton Recombination Model

    Energy Technology Data Exchange (ETDEWEB)

    Bass, S.A. [Department of Physics, Duke University, Durham, NC 27708-0305 (United States); RIKEN BNL Research Center, Brookhaven Nat. Lab., Upton, NY 11973 (United States); Fries, R.J. [School of Physics and Astronomy, Univ. of Minnesota, Minneapolis, MN 55455 (United States); Mueller, B. [Department of Physics, Duke University, Durham, NC 27708-0305 (United States)

    2006-08-07

    We describe how parton recombination can address the recent measurement of dynamical jet-like two particle correlations. In addition we discuss the possible effect realistic light-cone wave-functions including higher Fock-states may have on the well-known elliptic flow valence-quark number scaling law.

  12. Radiative recombination of excitons in amorphous semiconductors

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Jai [School of Engineering and Logistics, Faculty Technology, B-41, Charles Darwin University, Darwin, NT 0909 (Australia)]. E-mail: jai.singh@cdu.edu.au

    2005-04-15

    A theory for calculating the radiative lifetime of excitons in amorphous semiconductors is presented. Four possibilities of excitonic radiative recombination are considered and the corresponding rates are derived at thermal equilibrium. The radiative lifetime is calculated from the inverse of the maximum rate for all the four possibilities. Results agree very well with experiments.

  13. Precise genotyping and recombination detection of Enterovirus

    Science.gov (United States)

    2015-01-01

    Enteroviruses (EV) with different genotypes cause diverse infectious diseases in humans and mammals. A correct EV typing result is crucial for effective medical treatment and disease control; however, the emergence of novel viral strains has impaired the performance of available diagnostic tools. Here, we present a web-based tool, named EVIDENCE (EnteroVirus In DEep conception, http://symbiont.iis.sinica.edu.tw/evidence), for EV genotyping and recombination detection. We introduce the idea of using mixed-ranking scores to evaluate the fitness of prototypes based on relatedness and on the genome regions of interest. Using phylogenetic methods, the most possible genotype is determined based on the closest neighbor among the selected references. To detect possible recombination events, EVIDENCE calculates the sequence distance and phylogenetic relationship among sequences of all sliding windows scanning over the whole genome. Detected recombination events are plotted in an interactive figure for viewing of fine details. In addition, all EV sequences available in GenBank were collected and revised using the latest classification and nomenclature of EV in EVIDENCE. These sequences are built into the database and are retrieved in an indexed catalog, or can be searched for by keywords or by sequence similarity. EVIDENCE is the first web-based tool containing pipelines for genotyping and recombination detection, with updated, built-in, and complete reference sequences to improve sensitivity and specificity. The use of EVIDENCE can accelerate genotype identification, aiding clinical diagnosis and enhancing our understanding of EV evolution. PMID:26678286

  14. Theory of dielectronic recombination and plasma effects

    International Nuclear Information System (INIS)

    Yukap Hahn

    2000-01-01

    Current status of the various theoretical approaches to calculation of dielectronic recombination rates is summarized, with emphasis on the available data base and on the plasma effects of both the plasma ion (and external) fields and plasma electron collisional effects which seriously affect the rates and complicate compilation of data. (author)

  15. Optimization, purification and characterization of recombinant L ...

    African Journals Online (AJOL)

    We studied optimal L-asparaginase sequence from GenBank accession number X12746 encoding for Lasparaginase from Erwinia chrysanthemi NCPPB1125. The expression level of recombinant Lasparaginase was determined as 78% of the total proteins. The purified L-asparaginase had a molecular mass of 37 kDa with ...

  16. Asthma and Therapeutics: Recombinant Therapies in Asthma

    Directory of Open Access Journals (Sweden)

    Cockcroft Donald W

    2005-03-01

    Full Text Available Abstract Numerous recombinant therapies are being investigated for the treatment of asthma. This report reviews the current status of several of these novel agents. Anti-immunoglobulin (IgE (omalizumab, Xolair markedly inhibits all aspects of the allergen challenge in subjects who have reduction of free serum IgE to undetectable levels. Several clinical studies in atopic asthma have demonstrated benefit by improved symptoms and lung function and a reduction in corticosteroid requirements. Early use in atopic asthmatics may be even more effective. Several approaches target interleukin (IL-4. Soluble IL-4 receptor has been shown to effectively replace inhaled corticosteroid; further studies are under way. Recombinant anti-IL-5 and recombinant IL-12 inhibit blood and sputum eosinophils and allergen-induced eosinophilia without any effect on airway responsiveness, allergen-induced airway responses, or allergen-induced airway hyperresponsiveness. Efalizumab, a recombinant antibody that inhibits lymphocyte trafficking, is effective in psoriasis. A bronchoprovocation study showed a reduction in allergen-induced late asthmatic response and allergen-induced eosinophilia, which suggests that it should be effective in clinical asthma. These exciting novel therapies provide not only promise of new therapies for asthma but also valuable tools for investigation of asthma mechanisms.

  17. Recombination in disordered regions at semiconductors

    International Nuclear Information System (INIS)

    Artem'ev, V.A.; Mikhnovich, V.V.

    1987-01-01

    Theoretical estimates indicate the need to allow for the heating of carriers by the electrostatic field in disordered regions when studies are made of recombination properties. An analysis is made of the experiments in which the influence of heating on the properties of disordered regions may be manifested and experimentally verifiable effects of this influence are considered

  18. Dielectronic recombination of highly ionized iron

    International Nuclear Information System (INIS)

    Griffin, D.C.; Pindzola, M.S.

    1987-01-01

    Dielectronic recombination of the iron ions Fe/sup 15+/, Fe/sup 23+/, and Fe/sup 25+/ has been studied in the isolated-resonance, distorted-wave approximation. The cross-section calculations include the dielec- tronic transitions associated with the 3s→3l and 3s→4l excitations in Fe/sup 15+/, the 2s→2p and 2s→3l excitations in Fe/sup 23+/, and the 1s→2l excitations in Fe/sup 25+/. The effects of external electric fields have been included by employing intermediate-coupled, field-mixed eigenvectors for the doubly excited Rydberg states, determined by diagonalizing a Hamiltonian matrix which includes the internal electrostatic and spin-orbit terms, as well as the Stark matrix elements. The field effects are found to be quite large in Fe/sup 15+/, relatively small in Fe/sup 23+/, and negligible in Fe/sup 25+/. The calculations indicate that there are large resonances near threshold in Fe/sup 23+/ that are unaffected by external fields and may be measurable in new experiments currently being designed. In addition, the contributions of radiative recombination and the possible interference between radiative and dielectronic recombination in low-lying resonances are considered. Even though the radiative recombination cross sections may be appreciable near threshold in Fe/sup 15+/ and Fe/sup 23+/, the interference between these processes appears to be completely negligible

  19. Expression of recombinant Streptokinase from local Egyptian ...

    African Journals Online (AJOL)

    We reported for the first time the expression of a recombinant SK from a local Streptococcus strain. When produced on industrial scale this r-SK may substantially contribute to reducing the costs of thrombolytic therapy in developing countries. In this study, a highly purified r-SK from Streptococcus sp. isolated from Egyptian ...

  20. Algae-based oral recombinant vaccines

    Directory of Open Access Journals (Sweden)

    Elizabeth A Specht

    2014-02-01

    Full Text Available Recombinant subunit vaccines are some of the safest and most effective vaccines available, but their high cost and the requirement of advanced medical infrastructure for administration make them impractical for many developing world diseases. Plant-based vaccines have shifted that paradigm by paving the way for recombinant vaccine production at agricultural scale using an edible host. However, enthusiasm for molecular pharming in food crops has waned in the last decade due to difficulty in developing transgenic crop plants and concerns of contaminating the food supply. Microalgae are poised to become the next candidate in recombinant subunit vaccine production, and they present several advantages over terrestrial crop plant-based platforms including scalable and contained growth, rapid transformation, easily obtained stable cell lines, and consistent transgene expression levels. Algae have been shown to accumulate and properly fold several vaccine antigens, and efforts are underway to create recombinant algal fusion proteins that can enhance antigenicity for effective orally-delivered vaccines. These approaches have the potential to revolutionize the way subunit vaccines are made and delivered – from costly parenteral administration of purified protein, to an inexpensive oral algae tablet with effective mucosal and system immune reactivity.