WorldWideScience

Sample records for evolutionary conserved regions

  1. ECRbase: Database of Evolutionary Conserved Regions, Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Loots, G; Ovcharenko, I

    2006-08-08

    Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. We have created a database of evolutionary conserved regions (ECRs) in vertebrate genomes entitled ECRbase that is constructed from a collection of pairwise vertebrate genome alignments produced by the ECR Browser database. ECRbase features a database of syntenic blocks that recapitulate the evolution of rearrangements in vertebrates and a collection of promoters in all vertebrate genomes presented in the database. The database also contains a collection of annotated transcription factor binding sites (TFBS) in all ECRs and promoter elements. ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish, and two pufferfish genomes. It is freely accessible at http://ECRbase.dcode.org.

  2. An evolutionary model for protein-coding regions with conserved RNA structure

    DEFF Research Database (Denmark)

    Pedersen, Jakob Skou; Forsberg, Roald; Meyer, Irmtraud Margret

    2004-01-01

    components of traditional phylogenetic models. We applied this to a data set of full-genome sequences from the hepatitis C virus where five RNA structures are mapped within the coding region. This allowed us to partition the effects of selection on different structural elements and to test various hypotheses...... concerning the relation of these effects. Of particular interest, we found evidence of a functional role of loop and bulge regions, as these were shown to evolve according to a different and more constrained selective regime than the nonpairing regions outside the RNA structures. Other potential applications......Here we present a model of nucleotide substitution in protein-coding regions that also encode the formation of conserved RNA structures. In such regions, apparent evolutionary context dependencies exist, both between nucleotides occupying the same codon and between nucleotides forming a base pair...

  3. Proteome-Wide Discovery of Evolutionary Conserved Sequences in Disordered Regions

    Science.gov (United States)

    Nguyen Ba, Alex N.; Yeh, Brian J.; van Dyk, Dewald; Davidson, Alan R.; Andrews, Brenda J.; Weiss, Eric L.; Moses, Alan M.

    2016-01-01

    At least 30% of human proteins are thought to contain intrinsically disordered regions, which lack stable structural conformation. Despite lacking enzymatic functions and having few protein domains, disordered regions are functionally important for protein regulation and contain short linear motifs (short peptide sequences involved in protein-protein interactions), but in most disordered regions, the functional amino acid residues remain unknown. We searched for evolutionarily conserved sequences within disordered regions according to the hypothesis that conservation would indicate functional residues. Using a phylogenetic hidden Markov model (phylo-HMM), we made accurate, specific predictions of functional elements in disordered regions even when these elements are only two or three amino acids long. Among the conserved sequences that we identified were previously known and newly identified short linear motifs, and we experimentally verified key examples, including a motif that may mediate interaction between protein kinase Cbk1 and its substrates. We also observed that hub proteins, which interact with many partners in a protein interaction network, are highly enriched in these conserved sequences. Our analysis enabled the systematic identification of the functional residues in disordered regions and suggested that at least 5% of amino acids in disordered regions are important for function. PMID:22416277

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

    Directory of Open Access Journals (Sweden)

    Haddley Kate

    2011-05-01

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

  5. cDNA sequence, genomic organization, and evolutionary conservation of a novel gene from the WAGR region

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    Schwartz, F.; Eisenman, R.; Knoll, J.; Bruns, G. [Children`s Hospital and Department of Pediatrics, Boston, MA (United States)

    1995-09-20

    A new gene (239FB) with predominant and differential expression in fetal brain has recently been isolated from a chromosome 11p13-p14 boundary area near FSHB. The corresponding mRNA has an open reading frame of 294 amino acids, a 3` untranslated region of 1247 nucleotides, and a highly GC-rich 5` untranslated region. The coding and 3` UT sequence is specified by 6 exons within nearly 87 kb of isolated genomic locus. The 5` end region of the transcript maps adjacent to the only genomically defined CpG island in a chromosomal subregion that may be associated with part of the mental retardation of some WAGR (Wilms tumor, aniridia, genitourinary anomalies, and mental retardation) syndrome patients. In addition to nucleotide and amino acid similarity to an EST from a normalized infant brain cDNA library, the predicted protein has extensive similarity to Caenorhbditis elegans polypeptides of, as yet, unknown function. The 239FB locus is, therefore, likely part of a family of genes with two members expressed in human brain. The extensive conservation of the predicted protein suggests a fundamental function of the gene product and will enable evaluation of the role of the 239FB gene in neurogenesis in model organisms. 48 refs., 4 figs., 1 tab.

  6. Global distribution and conservation of evolutionary distinctness in birds.

    Science.gov (United States)

    Jetz, Walter; Thomas, Gavin H; Joy, Jeffrey B; Redding, David W; Hartmann, Klaas; Mooers, Arne O

    2014-05-05

    Integrated, efficient, and global prioritization approaches are necessary to manage the ongoing loss of species and their associated function. "Evolutionary distinctness" measures a species' contribution to the total evolutionary history of its clade and is expected to capture uniquely divergent genomes and functions. Here we demonstrate how such a metric identifies species and regions of particular value for safeguarding evolutionary diversity. Among the world's 9,993 recognized bird species, evolutionary distinctness is very heterogeneously distributed on the phylogenetic tree and varies little with range size or threat level. Species representing the most evolutionary history over the smallest area (those with greatest "evolutionary distinctness rarity") as well as some of the most imperiled distinct species are often concentrated outside the species-rich regions and countries, suggesting they may not be well captured by current conservation planning. We perform global cross-species and spatial analyses and generate minimum conservation sets to assess the benefits of the presented species-level metrics. We find that prioritizing imperiled species by their evolutionary distinctness and geographic rarity is a surprisingly effective and spatially economical way to maintain the total evolutionary information encompassing the world's birds. We identify potential conservation gaps in relation to the existing reserve network that in particular highlight islands as effective priority areas. The presented distinctness metrics are effective yet easily communicable and versatile tools to assist objective global conservation decision making. Given that most species will remain ecologically understudied, combining growing phylogenetic and spatial data may be an efficient way to retain vital aspects of biodiversity. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  7. Evolutionary conservation of protein vibrational dynamics.

    Science.gov (United States)

    Maguid, Sandra; Fernandez-Alberti, Sebastian; Echave, Julian

    2008-10-01

    The aim of the present work is to study the evolutionary divergence of vibrational protein dynamics. To this end, we used the Gaussian Network Model to perform a systematic analysis of normal mode conservation on a large dataset of proteins classified into homologous sets of family pairs and superfamily pairs. We found that the lowest most collective normal modes are the most conserved ones. More precisely, there is, on average, a linear correlation between normal mode conservation and mode collectivity. These results imply that the previously observed conservation of backbone flexibility (B-factor) profiles is due to the conservation of the most collective modes, which contribute the most to such profiles. We discuss the possible roles of normal mode robustness and natural selection in the determination of the observed behavior. Finally, we draw some practical implications for dynamics-based protein alignment and classification and discuss possible caveats of the present approach.

  8. Evolutionary conservation of protein backbone flexibility.

    Science.gov (United States)

    Maguid, Sandra; Fernández-Alberti, Sebastián; Parisi, Gustavo; Echave, Julián

    2006-10-01

    Internal protein dynamics is essential for biological function. During evolution, protein divergence is functionally constrained: properties more relevant for function vary more slowly than less important properties. Thus, if protein dynamics is relevant for function, it should be evolutionary conserved. In contrast with the well-studied evolution of protein structure, the evolutionary divergence of protein dynamics has not been addressed systematically before, apart from a few case studies. X-Ray diffraction analysis gives information not only on protein structure but also on B-factors, which characterize the flexibility that results from protein dynamics. Here we study the evolutionary divergence of protein backbone dynamics by comparing the C(alpha) flexibility (B-factor) profiles for a large dataset of homologous proteins classified into families and superfamilies. We show that C(alpha) flexibility profiles diverge slowly, so that they are conserved at family and superfamily levels, even for pairs of proteins with nonsignificant sequence similarity. We also analyze and discuss the correlations among the divergences of flexibility, sequence, and structure.

  9. Special Issue: Evolutionary perspectives on salmonid conservation and management

    OpenAIRE

    Waples, Robin S; Hendry, Andrew P

    2008-01-01

    This special issue of Evolutionary Applications comprises 15 papers that illustrate how evolutionary principles can inform the conservation and management of salmonid fishes. Several papers address the past evolutionary history of salmonids to gain insights into their likely plastic and genetic responses to future environmental change. The remaining papers consider potential evolutionary responses to climate warming, biological invasions, artificial propagation, habitat alteration, and harves...

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

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

    2003-12-31

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

  11. Late replication domains are evolutionary conserved in the Drosophila genome.

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    Natalya G Andreyenkova

    Full Text Available Drosophila chromosomes are organized into distinct domains differing in their predominant chromatin composition, replication timing and evolutionary conservation. We show on a genome-wide level that genes whose order has remained unaltered across 9 Drosophila species display late replication timing and frequently map to the regions of repressive chromatin. This observation is consistent with the existence of extensive domains of repressive chromatin that replicate extremely late and have conserved gene order in the Drosophila genome. We suggest that such repressive chromatin domains correspond to a handful of regions that complete replication at the very end of S phase. We further demonstrate that the order of genes in these regions is rarely altered in evolution. Substantial proportion of such regions significantly coincide with large synteny blocks. This indicates that there are evolutionary mechanisms maintaining the integrity of these late-replicating chromatin domains. The synteny blocks corresponding to the extremely late-replicating regions in the D. melanogaster genome consistently display two-fold lower gene density across different Drosophila species.

  12. Evolutionary discrimination of mammalian conserved non-genic sequences (CNGs)

    NARCIS (Netherlands)

    Dermitzakis, ET; Reymond, A; Scamuffa, N; Ucla, C; Kirkness, E; Rossier, C; Antonarakis, SE

    2003-01-01

    Analysis of the human and mouse genomes identified an abundance of conserved non-genic sequences (CNGs). The significance and evolutionary depth of their conservation remain unanswered. We have quantified levels and patterns of conservation of 191 CNGs of human chromosome 21 in 14 mammalian species.

  13. The importance of an evolutionary perspective in conservation policy planning.

    Science.gov (United States)

    Moritz, Craig C; Potter, Sally

    2013-12-01

    Prioritization of taxa for conservation must rest on a foundation of correctly identified species boundaries, enhanced by an understanding of evolutionary history and phylogenetic relationships. Therefore, we can incorporate both evolutionary and ecological processes into efforts to sustain biodiversity. In this issue of Molecular Ecology, Malaney & Cook (2013) highlight the critical value of an evolutionary biogeographical approach, combining multilocus phylogeography with climatic niche modelling to infer phylogenetically weighted conservation priorities for evolutionary lineages of jumping mice across North America. Remarkably, they find that the Preble's meadow jumping mouse (Zapus hudsonius preblei), long debated as a threatened taxon, in fact represents the southern terminus of a relatively uniform lineage that expanded well into Alaska during the Holocene. By contrast, some other relictual and phylogenetically divergent taxa of jumping mice likely warrant greater conservation priority. This study highlights the value of integrative approaches that place current taxonomy in a broader evolutionary context to identify taxa for conservation assessment, but also highlights the challenges in maintaining potential for adaptive responses to environmental change. © 2013 John Wiley & Sons Ltd.

  14. Strategies for measuring evolutionary conservation of RNA secondary structures

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    Hofacker Ivo L

    2008-02-01

    Full Text Available Abstract Background Evolutionary conservation of RNA secondary structure is a typical feature of many functional non-coding RNAs. Since almost all of the available methods used for prediction and annotation of non-coding RNA genes rely on this evolutionary signature, accurate measures for structural conservation are essential. Results We systematically assessed the ability of various measures to detect conserved RNA structures in multiple sequence alignments. We tested three existing and eight novel strategies that are based on metrics of folding energies, metrics of single optimal structure predictions, and metrics of structure ensembles. We find that the folding energy based SCI score used in the RNAz program and a simple base-pair distance metric are by far the most accurate. The use of more complex metrics like for example tree editing does not improve performance. A variant of the SCI performed particularly well on highly conserved alignments and is thus a viable alternative when only little evolutionary information is available. Surprisingly, ensemble based methods that, in principle, could benefit from the additional information contained in sub-optimal structures, perform particularly poorly. As a general trend, we observed that methods that include a consensus structure prediction outperformed equivalent methods that only consider pairwise comparisons. Conclusion Structural conservation can be measured accurately with relatively simple and intuitive metrics. They have the potential to form the basis of future RNA gene finders, that face new challenges like finding lineage specific structures or detecting mis-aligned sequences.

  15. How conservative are evolutionary anthropologists?: a survey of political attitudes.

    Science.gov (United States)

    Lyle, Henry F; Smith, Eric A

    2012-09-01

    The application of evolutionary theory to human behavior has elicited a variety of critiques, some of which charge that this approach expresses or encourages conservative or reactionary political agendas. In a survey of graduate students in psychology, Tybur, Miller, and Gangestad (Human Nature, 18, 313-328, 2007) found that the political attitudes of those who use an evolutionary approach did not differ from those of other psychology grad students. Here, we present results from a directed online survey of a broad sample of graduate students in anthropology that assays political views. We found that evolutionary anthropology graduate students were very liberal in their political beliefs, overwhelmingly voted for a liberal U.S. presidential candidate in the 2008 election, and identified with liberal political parties; in this, they were almost indistinguishable from non-evolutionary anthropology students. Our results contradict the view that evolutionary anthropologists hold conservative or reactionary political views. We discuss some possible reasons for the persistence of this view in terms of the sociology of science.

  16. Comparative Analysis of the Mitochondrial Genomes of Callitettixini Spittlebugs (Hemiptera: Cercopidae) Confirms the Overall High Evolutionary Speed of the AT-Rich Region but Reveals the Presence of Short Conservative Elements at the Tribal Level

    Science.gov (United States)

    Liu, Jie; Bu, Cuiping; Wipfler, Benjamin; Liang, Aiping

    2014-01-01

    The present study compares the mitochondrial genomes of five species of the spittlebug tribe Callitettixini (Hemiptera: Cercopoidea: Cercopidae) from eastern Asia. All genomes of the five species sequenced are circular double-stranded DNA molecules and range from 15,222 to 15,637 bp in length. They contain 22 tRNA genes, 13 protein coding genes (PCGs) and 2 rRNA genes and share the putative ancestral gene arrangement of insects. The PCGs show an extreme bias of nucleotide and amino acid composition. Significant differences of the substitution rates among the different genes as well as the different codon position of each PCG are revealed by the comparative evolutionary analyses. The substitution speeds of the first and second codon position of different PCGs are negatively correlated with their GC content. Among the five species, the AT-rich region features great differences in length and pattern and generally shows a 2–5 times higher substitution rate than the fastest PCG in the mitochondrial genome, atp8. Despite the significant variability in length, short conservative segments were identified in the AT-rich region within Callitettixini, although absent from the other groups of the spittlebug superfamily Cercopoidea. PMID:25285442

  17. Does the evolutionary conservation of microsatellite loci imply function?

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    Shriver, M.D.; Deka, R.; Ferrell, R.E. [Univ. of Pittsburgh, PA (United States)] [and others

    1994-09-01

    Microsatellites are highly polymorphic tandem arrays of short (1-6 bp) sequence motifs which have been found widely distributed in the genomes of all eukaryotes. We have analyzed allele frequency data on 16 microsatellite loci typed in the great apes (human, chimp, orangutan, and gorilla). The majority of these loci (13) were isolated from human genomic libraries; three were cloned from chimpanzee genomic DNA. Most of these loci are not only present in all apes species, but are polymorphic with comparable levels of heterozygosity and have alleles which overlap in size. The extent of divergence of allele frequencies among these four species were studies using the stepwise-weighted genetic distance (Dsw), which was previously shown to conform to linearity with evolutionary time since divergence for loci where mutations exist in a stepwise fashion. The phylogenetic tree of the great apes constructed from this distance matrix was consistent with the expected topology, with a high bootstrap confidence (82%) for the human/chimp clade. However, the allele frequency distributions of these species are 10 times more similar to each other than expected when they were calibrated with a conservative estimate of the time since separation of humans and the apes. These results are in agreement with sequence-based surveys of microsatellites which have demonstrated that they are highly (90%) conserved over short periods of evolutionary time (< 10 million years) and moderately (30%) conserved over long periods of evolutionary time (> 60-80 million years). This evolutionary conservation has prompted some authors to speculate that there are functional constraints on microsatellite loci. In contrast, the presence of directional bias of mutations with constraints and/or selection against aberrant sized alleles can explain these results.

  18. Making evolutionary history count: biodiversity planning for coral reef fishes and the conservation of evolutionary processes

    Science.gov (United States)

    von der Heyden, Sophie

    2017-03-01

    Anthropogenic activities are having devastating impacts on marine systems with numerous knock-on effects on trophic functioning, species interactions and an accelerated loss of biodiversity. Establishing conservation areas can not only protect biodiversity, but also confer resilience against changes to coral reefs and their inhabitants. Planning for protection and conservation in marine systems is complex, but usually focuses on maintaining levels of biodiversity and protecting special and unique landscape features while avoiding negative impacts to socio-economic benefits. Conversely, the integration of evolutionary processes that have shaped extant species assemblages is rarely taken into account. However, it is as important to protect processes as it is to protect patterns for maintaining the evolutionary trajectories of populations and species. This review focuses on different approaches for integrating genetic analyses, such as phylogenetic diversity, phylogeography and the delineation of management units, temporal and spatial monitoring of genetic diversity and quantification of adaptive variation for protecting evolutionary resilience, into marine spatial planning, specifically for coral reef fishes. Many of these concepts are not yet readily applied to coral reef fish studies, but this synthesis highlights their potential and the importance of including historical processes into systematic biodiversity planning for conserving not only extant, but also future, biodiversity and its evolutionary potential.

  19. Linkage disequilibrium of evolutionarily conserved regions in the human genome

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    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.

  20. Evolutionary rescue: linking theory for conservation and medicine.

    Science.gov (United States)

    Alexander, Helen K; Martin, Guillaume; Martin, Oliver Y; Bonhoeffer, Sebastian

    2014-12-01

    Evolutionary responses that rescue populations from extinction when drastic environmental changes occur can be friend or foe. The field of conservation biology is concerned with the survival of species in deteriorating global habitats. In medicine, in contrast, infected patients are treated with chemotherapeutic interventions, but drug resistance can compromise eradication of pathogens. These contrasting biological systems and goals have created two quite separate research communities, despite addressing the same central question of whether populations will decline to extinction or be rescued through evolution. We argue that closer integration of the two fields, especially of theoretical understanding, would yield new insights and accelerate progress on these applied problems. Here, we overview and link mathematical modelling approaches in these fields, suggest specific areas with potential for fruitful exchange, and discuss common ideas and issues for empirical testing and prediction.

  1. Evolutionary conservation and changes in insect TRP channels

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    Tominaga Makoto

    2009-09-01

    Full Text Available Abstract Background TRP (Transient Receptor Potential channels respond to diverse stimuli and thus function as the primary integrators of varied sensory information. They are also activated by various compounds and secondary messengers to mediate cell-cell interactions as well as to detect changes in the local environment. Their physiological roles have been primarily characterized only in mice and fruit flies, and evolutionary studies are limited. To understand the evolution of insect TRP channels and the mechanisms of integrating sensory inputs in insects, we have identified and compared TRP channel genes in Drosophila melanogaster, Bombyx mori, Tribolium castaneum, Apis mellifera, Nasonia vitripennis, and Pediculus humanus genomes as part of genome sequencing efforts. Results All the insects examined have 2 TRPV, 1 TRPN, 1 TRPM, 3 TRPC, and 1 TRPML subfamily members, demonstrating that these channels have the ancient origins in insects. The common pattern also suggests that the mechanisms for detecting mechanical and visual stimuli and maintaining lysosomal functions may be evolutionarily well conserved in insects. However, a TRPP channel, the most ancient TRP channel, is missing in B. mori, A. mellifera, and N. vitripennis. Although P. humanus and D. melanogaster contain 4 TRPA subfamily members, the other insects have 5 TRPA subfamily members. T. castaneum, A. mellifera, and N. vitripennis contain TRPA5 channels, which have been specifically retained or gained in Coleoptera and Hymenoptera. Furthermore, TRPA1, which functions for thermotaxis in Drosophila, is missing in A. mellifera and N. vitripennis; however, they have other Hymenoptera-specific TRPA channels (AmHsTRPA and NvHsTRPA. NvHsTRPA expressed in HEK293 cells is activated by temperature increase, demonstrating that HsTRPAs function as novel thermal sensors in Hymenoptera. Conclusion The total number of insect TRP family members is 13-14, approximately half that of mammalian TRP

  2. Evolutionary placement of Xanthomonadales based on conserved protein signature sequences.

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    Cutiño-Jiménez, Ania M; Martins-Pinheiro, Marinalva; Lima, Wanessa C; Martín-Tornet, Alexander; Morales, Osleidys G; Menck, Carlos F M

    2010-02-01

    Xanthomonadales comprises one of the largest phytopathogenic bacterial groups, and is currently classified within the gamma-proteobacteria. However, the phylogenetic placement of this group is not clearly resolved, and the results of different studies contradict one another. In this work, the evolutionary position of Xanthomonadales was determined by analyzing the presence of shared insertions and deletions (INDELs) in highly conserved proteins. Several distinctive insertions found in most of the members of the gamma-proteobacteria are absent in Xanthomonadales and groups such as Legionelalles, Chromatiales, Methylococcales, Thiotrichales and Cardiobacteriales. These INDELs were most likely introduced after the branching of Xanthomonadales from most of the gamma-proteobacteria and provide evidence for the phylogenetic placement of the early gamma-proteobacteria. Moreover, other proteins contain insertions exclusive to the Xanthomonadales order, confirming that this is a monophyletic group and provide important specific genetic markers. Thus, the data presented clearly support the Xanthomonadales group as an independent subdivision, and constitute one of the deepest branching lineage within the gamma-proteobacteria clade. Copyright (c) 2009 Elsevier Inc. All rights reserved.

  3. Evolutionary Conservation of ABA Signaling for Stomatal Closure1[OPEN

    Science.gov (United States)

    Huang, Yuqing; Dai, Fei; Franks, Peter J.; Nevo, Eviatar; Soltis, Douglas E.; Soltis, Pamela S.; Xue, Dawei; Zhang, Guoping; Pogson, Barry J.

    2017-01-01

    Abscisic acid (ABA)-driven stomatal regulation reportedly evolved after the divergence of ferns, during the early evolution of seed plants approximately 360 million years ago. This hypothesis is based on the observation that the stomata of certain fern species are unresponsive to ABA, but exhibit passive hydraulic control. However, ABA-induced stomatal closure was detected in some mosses and lycophytes. Here, we observed that a number of ABA signaling and membrane transporter protein families diversified over the evolutionary history of land plants. The aquatic ferns Azolla filiculoides and Salvinia cucullata have representatives of 23 families of proteins orthologous to those of Arabidopsis (Arabidopsis thaliana) and all other land plant species studied. Phylogenetic analysis of the key ABA signaling proteins indicates an evolutionarily conserved stomatal response to ABA. Moreover, comparative transcriptomic analysis has identified a suite of ABA-responsive genes that differentially expressed in a terrestrial fern species, Polystichum proliferum. These genes encode proteins associated with ABA biosynthesis, transport, reception, transcription, signaling, and ion and sugar transport, which fit the general ABA signaling pathway constructed from Arabidopsis and Hordeum vulgare. The retention of these key ABA-responsive genes could have had a profound effect on the adaptation of ferns to dry conditions. Furthermore, stomatal assays have shown the primary evidence for ABA-induced closure of stomata in two terrestrial fern species P. proliferum and Nephrolepis exaltata. In summary, we report, to our knowledge, new molecular and physiological evidence for the presence of active stomatal control in ferns. PMID:28232585

  4. Investigating evolutionary conservation of dendritic cell subset identity and functions

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    Thien-Phong eVu Manh

    2015-06-01

    Full Text Available Dendritic cells (DC were initially defined as mononuclear phagocytes with a dendritic morphology and an exquisite efficiency for naïve T cell activation. DC encompass several subsets initially identified by their expression of specific cell surface molecules and later shown to excel in distinct functions and to develop under the instruction of different transcription factors or cytokines. Very few cell surface molecules are expressed in a specific manner on any immune cell type. Hence, to identify cell types, the sole use of a small number of cell surface markers in classical flow cytometry can be deceiving. Moreover, the markers currently used to define mononuclear phagocyte subsets vary depending on the tissue and animal species studied and even between laboratories. This has led to confusion in the definition of DC subset identity and in their attribution of specific functions. There is a strong need to identify a rigorous and consensus way to define mononuclear phagocyte subsets, with precise guidelines potentially applicable throughout tissues and species. We will discuss the advantages, drawbacks and complementarities of different methodologies: cell surface phenotyping, ontogeny, functional characterization and molecular profiling. We will advocate that gene expression profiling is a very rigorous, largely unbiased and accessible method to define the identity of mononuclear phagocyte subsets, which strengthens and refines surface phenotyping. It is uniquely powerful to yield new, experimentally testable, hypotheses on the ontogeny or functions of mononuclear phagocyte subsets, their molecular regulation and their evolutionary conservation. We propose defining cell populations based on a combination of cell surface phenotyping, expression analysis of hallmark genes and robust functional assays, in order to reach a consensus and integrate faster the huge but scattered knowledge accumulated by different laboratories on different cell types

  5. Evolutionary Conservation of ABA Signaling for Stomatal Closure.

    Science.gov (United States)

    Cai, Shengguan; Chen, Guang; Wang, Yuanyuan; Huang, Yuqing; Marchant, D Blaine; Wang, Yizhou; Yang, Qian; Dai, Fei; Hills, Adrian; Franks, Peter J; Nevo, Eviatar; Soltis, Douglas E; Soltis, Pamela S; Sessa, Emily; Wolf, Paul G; Xue, Dawei; Zhang, Guoping; Pogson, Barry J; Blatt, Michael R; Chen, Zhong-Hua

    2017-06-01

    Abscisic acid (ABA)-driven stomatal regulation reportedly evolved after the divergence of ferns, during the early evolution of seed plants approximately 360 million years ago. This hypothesis is based on the observation that the stomata of certain fern species are unresponsive to ABA, but exhibit passive hydraulic control. However, ABA-induced stomatal closure was detected in some mosses and lycophytes. Here, we observed that a number of ABA signaling and membrane transporter protein families diversified over the evolutionary history of land plants. The aquatic ferns Azolla filiculoides and Salvinia cucullata have representatives of 23 families of proteins orthologous to those of Arabidopsis (Arabidopsis thaliana) and all other land plant species studied. Phylogenetic analysis of the key ABA signaling proteins indicates an evolutionarily conserved stomatal response to ABA. Moreover, comparative transcriptomic analysis has identified a suite of ABA-responsive genes that differentially expressed in a terrestrial fern species, Polystichum proliferum These genes encode proteins associated with ABA biosynthesis, transport, reception, transcription, signaling, and ion and sugar transport, which fit the general ABA signaling pathway constructed from Arabidopsis and Hordeum vulgare The retention of these key ABA-responsive genes could have had a profound effect on the adaptation of ferns to dry conditions. Furthermore, stomatal assays have shown the primary evidence for ABA-induced closure of stomata in two terrestrial fern species Pproliferum and Nephrolepis exaltata In summary, we report, to our knowledge, new molecular and physiological evidence for the presence of active stomatal control in ferns. © 2017 American Society of Plant Biologists. All Rights Reserved.

  6. Evolutionary conservation of P-selectin glycoprotein ligand-1 primary structure and function

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    Schapira Marc

    2007-09-01

    Full Text Available Abstract Background P-selectin glycoprotein ligand-1 (PSGL-1 plays a critical role in recruiting leukocytes in inflammatory lesions by mediating leukocyte rolling on selectins. Core-2 O-glycosylation of a N-terminal threonine and sulfation of at least one tyrosine residue of PSGL-1 are required for L- and P-selectin binding. Little information is available on the intra- and inter-species evolution of PSGL-1 primary structure. In addition, the evolutionary conservation of selectin binding site on PSGL-1 has not been previously examined in detail. Therefore, we performed multiple sequence alignment of PSGL-1 amino acid sequences of 14 mammals (human, chimpanzee, rhesus monkey, bovine, pig, rat, tree-shrew, bushbaby, mouse, bat, horse, cat, sheep and dog and examined mammalian PSGL-1 interactions with human selectins. Results A signal peptide was predicted in each sequence and a propeptide cleavage site was found in 9/14 species. PSGL-1 N-terminus is poorly conserved. However, each species exhibits at least one tyrosine sulfation site and, except in horse and dog, a T [D/E]PP [D/E] motif associated to the core-2 O-glycosylation of a N-terminal threonine. A mucin-like domain of 250–280 amino acids long was disclosed in all studied species. It lies between the conserved N-terminal O-glycosylated threonine (Thr-57 in human and the transmembrane domain, and contains a central region exhibiting a variable number of decameric repeats (DR. Interspecies and intraspecies polymorphisms were observed. Transmembrane and cytoplasmic domain sequences are well conserved. The moesin binding residues that serve as adaptor between PSGL-1 and Syk, and are involved in regulating PSGL-1-dependent rolling on P-selectin are perfectly conserved in all analyzed mammalian sequences. Despite a poor conservation of PSGL-1 N-terminal sequence, CHO cells co-expressing human glycosyltransferases and human, bovine, pig or rat PSGL-1 efficiently rolled on human L- or P

  7. Characterization of five evolutionary conserved regions of the human tyrosine hydroxylase (TH) promoter: implications for the engineering of a human TH minimal promoter assembled in a self-inactivating lentiviral vector system.

    Science.gov (United States)

    Romano, Gaetano; Suon, Sokreine; Jin, Hao; Donaldson, Angela E; Iacovitti, Lorraine

    2005-08-01

    A DNA fragment of about 13 kb containing the human tyrosine hydroxylase (TH) promoter was previously isolated from a genomic DNA library and sequenced. The 11 kb from the transcription start of the human TH promoter was successively joined to the green fluorescent protein (GFP) to generate a transgenic mouse model. High levels of GFP expression could be observed in TH-positive cells of the Substantia nigra of embryonic and adult mice. Intriguingly, the sequence of the human TH promoter showed a low degree of homology with the mouse and rat TH promoters. In fact, comparative analysis of the sequences of human, rat, and mouse TH promoters revealed only five small regions of high homology. These five evolutionarily conserved regions were numbered in numeric progression from the 5' end of human TH promoter. In the present study, a panel of minimal human TH promoters was generated to analyze the transcriptional activity and specificity of gene expression conferred by the five conserved regions (CRs). The series of constructs was termed 250 bp and contained the first -194 bp of the human TH promoter immediately upstream of the transcription start, the first 35 bp the human TH messenger RNA leader, plus one or more of the five CRs. All the constructs were assembled in a self-inactivating form of the latest series of lentiviral vector system based on the human immunodeficiency virus type 1 (HIV-1). Lentiviral-mediated gene transfer was highly efficient for the in vitro transduction of human neuronal progenitor cells (hNPCs). Since a subset of hNPCs express TH following in vitro treatment with a mixture of differentiating agents, it was possible to assess specificity of expression for all the minimal human TH promoters. Overall, the successive addition of the five conserved regions produced a greater degree of specificity in induced TH-positive hNPCs, in particular after the addition of CRI (-8,917, -8,876). However, the human TH minimal promoters did not show any

  8. Plant conservation priorities of Xinjiang region, China

    Science.gov (United States)

    Li, L. P.; Cui, W. H.; Wang, T.; Tian, S.; Xing, W. J.; Yin, L. K.; Abdusalih, N.; Jiang, Y. M.

    2017-02-01

    As an important region in the Silk Road, Xinjiang is getting a good chance of developing economy. However at the same time, its natural environment is facing a big challenge. To better protect the plant diversity, it is urgent to make a thorough conservation plan. With a full database of vascular and medicinal plant distributions and nature reserve plant lists and boundaries in Xinjiang of China, we analysed the plant diversity hotspots, protection gaps and proposed the plant conservation priorities of this region. Differed from the widely accepted viewpoints that lots of plants were not included in nature reserves, we found that most of the plants ( > 90%) were actually included in the current nature reserves. We believe that compared with establishing more nature reserves, improving the management of the existing ones is also important. Furthermore, the very few unprotected plants ( < 10%) were distributed mostly in the regions of Aletai, Tacheng, Zhaosu, Manasi, Qitai and Hetian which could be the future conservation priorities.

  9. Evolutionary biology in biodiversity science, conservation, and policy: a call to action.

    Science.gov (United States)

    Hendry, Andrew P; Lohmann, Lúcia G; Conti, Elena; Cracraft, Joel; Crandall, Keith A; Faith, Daniel P; Häuser, Christoph; Joly, Carlos A; Kogure, Kazuhiro; Larigauderie, Anne; Magallón, Susana; Moritz, Craig; Tillier, Simon; Zardoya, Rafael; Prieur-Richard, Anne-Hélène; Walther, Bruno A; Yahara, Tetsukazu; Donoghue, Michael J

    2010-05-01

    Evolutionary biologists have long endeavored to document how many species exist on Earth, to understand the processes by which biodiversity waxes and wanes, to document and interpret spatial patterns of biodiversity, and to infer evolutionary relationships. Despite the great potential of this knowledge to improve biodiversity science, conservation, and policy, evolutionary biologists have generally devoted limited attention to these broader implications. Likewise, many workers in biodiversity science have underappreciated the fundamental relevance of evolutionary biology. The aim of this article is to summarize and illustrate some ways in which evolutionary biology is directly relevant. We do so in the context of four broad areas: (1) discovering and documenting biodiversity, (2) understanding the causes of diversification, (3) evaluating evolutionary responses to human disturbances, and (4) implications for ecological communities, ecosystems, and humans. We also introduce bioGENESIS, a new project within DIVERSITAS launched to explore the potential practical contributions of evolutionary biology. In addition to fostering the integration of evolutionary thinking into biodiversity science, bioGENESIS provides practical recommendations to policy makers for incorporating evolutionary perspectives into biodiversity agendas and conservation. We solicit your involvement in developing innovative ways of using evolutionary biology to better comprehend and stem the loss of biodiversity.

  10. Periostin shows increased evolutionary plasticity in its alternatively spliced region

    Directory of Open Access Journals (Sweden)

    Hoersch Sebastian

    2010-01-01

    Full Text Available Abstract Background Periostin (POSTN is a secreted extracellular matrix protein of poorly defined function that has been related to bone and heart development as well as to cancer. In human and mouse, it is known to undergo alternative splicing in its C-terminal region, which is devoid of known protein domains. Differential expression of periostin, sometimes of specific splicing isoforms, is observed in a broad range of human cancers, including breast, pancreatic, and colon cancer. Here, we combine genomic and transcriptomic sequence data from vertebrate organisms to study the evolution of periostin and particularly of its C-terminal region. Results We found that the C-terminal part of periostin is markedly more variable among vertebrates than the rest of periostin in terms of exon count, length, and splicing pattern, which we interpret as a consequence of neofunctionalization after the split between periostin and its paralog transforming growth factor, beta-induced (TGFBI. We also defined periostin's sequential 13-amino acid repeat units - well conserved in teleost fish, but more obscure in higher vertebrates - whose secondary structure is predicted to be consecutive beta strands. We suggest that these beta strands may mediate binding interactions with other proteins through an extended beta-zipper in a manner similar to the way repeat units in bacterial cell wall proteins have been reported to bind human fibronectin. Conclusions Our results, obtained with the help of the increasingly large collection of complete vertebrate genomes, document the evolutionary plasticity of periostin's C-terminal region, and for the first time suggest a basis for its functional role.

  11. Effectiveness of conservation easements in agricultural regions.

    Science.gov (United States)

    Braza, Mark

    2017-08-01

    Conservation easements are a standard technique for preventing habitat loss, particularly in agricultural regions with extensive cropland cultivation, yet little is known about their effectiveness. I developed a spatial econometric approach to propensity-score matching and used the approach to estimate the amount of habitat loss prevented by a grassland conservation easement program of the U.S. federal government. I used a spatial autoregressive probit model to predict tract enrollment in the easement program as of 2001 based on tract agricultural suitability, habitat quality, and spatial interactions among neighboring tracts. Using the predicted values from the model, I matched enrolled tracts with similar unenrolled tracts to form a treatment group and a control group. To measure the program's impact on subsequent grassland loss, I estimated cropland cultivation rates for both groups in 2014 with a second spatial probit model. Between 2001 and 2014, approximately 14.9% of control tracts were cultivated and 0.3% of treated tracts were cultivated. Therefore, approximately 14.6% of the protected land would have been cultivated in the absence of the program. My results demonstrate that conservation easements can significantly reduce habitat loss in agricultural regions; however, the enrollment of tracts with low cropland suitability may constrain the amount of habitat loss they prevent. My results also show that spatial econometric models can improve the validity of control groups and thereby strengthen causal inferences about program effectiveness in situations when spatial interactions influence conservation decisions. © 2017 Society for Conservation Biology.

  12. 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...

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

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    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

  14. An Evolutionary Approach to Regional Systems of Innovation

    DEFF Research Database (Denmark)

    Gunnarsson, Jan Sture Gunnar; Wallin, Torsten

    This article examines how the birth and the development of regional systems of innovation are connected with economic selection and points to implications for regional-level policies. The research questions are explored using an evolutionary model, which emphasises geographical spaces...... using computer simulations. The primary findings are, firstly, that the model generates predictions suited for empirical research on how economic selection influences cooperative behaviour of innovative factors. Secondly, we demonstrate how a region's entrepreneurial activity and growth can...... be controlled in a decentralised way by regions....

  15. Evolutionary refugia and ecological refuges: key concepts for conserving Australian arid zone freshwater biodiversity under climate change.

    Science.gov (United States)

    Davis, Jenny; Pavlova, Alexandra; Thompson, Ross; Sunnucks, Paul

    2013-07-01

    Refugia have been suggested as priority sites for conservation under climate change because of their ability to facilitate survival of biota under adverse conditions. Here, we review the likely role of refugial habitats in conserving freshwater biota in arid Australian aquatic systems where the major long-term climatic influence has been aridification. We introduce a conceptual model that characterizes evolutionary refugia and ecological refugees based on our review of the attributes of aquatic habitats and freshwater taxa (fishes and aquatic invertebrates) in arid Australia. We also identify methods of recognizing likely future refugia and approaches to assessing the vulnerability of arid-adapted freshwater biota to a warming and drying climate. Evolutionary refugia in arid areas are characterized as permanent, groundwater-dependent habitats (subterranean aquifers and springs) supporting vicariant relicts and short-range endemics. Ecological refugees can vary across space and time, depending on the dispersal abilities of aquatic taxa and the geographical proximity and hydrological connectivity of aquatic habitats. The most important are the perennial waterbodies (both groundwater and surface water fed) that support obligate aquatic organisms. These species will persist where suitable habitats are available and dispersal pathways are maintained. For very mobile species (invertebrates with an aerial dispersal phase) evolutionary refugia may also act as ecological refugees. Evolutionary refugia are likely future refugia because their water source (groundwater) is decoupled from local precipitation. However, their biota is extremely vulnerable to changes in local conditions because population extinction risks cannot be abated by the dispersal of individuals from other sites. Conservation planning must incorporate a high level of protection for aquifers that support refugial sites. Ecological refuges are vulnerable to changes in regional climate because they have

  16. Teaching the Toolkit: A Laboratory Series to Demonstrate the Evolutionary Conservation of Metazoan Cell Signaling Pathways

    Science.gov (United States)

    LeClair, Elizabeth E.

    2008-01-01

    A major finding of comparative genomics and developmental genetics is that metazoans share certain conserved, embryonically deployed signaling pathways that instruct cells as to their ultimate fate. Because the DNA encoding these pathways predates the evolutionary split of most animal groups, it should in principle be possible to clone…

  17. Integrating Traditional and Evolutionary Knowledge in Biodiversity Conservation: a Population Level Case Study

    Directory of Open Access Journals (Sweden)

    Dylan J. Fraser

    2006-12-01

    Full Text Available Despite their dual importance in the assessment of endangered/threatened species, there have been few attempts to integrate traditional ecological knowledge (TEK and evolutionary biology knowledge (EBK at the population level. We contrasted long-term aboriginal TEK with previously obtained EBK in the context of seasonal migratory habits and population biology of a salmonid fish, brook charr, (Salvelinus fontinalis inhabiting a large, remote postglacial lake. Compilation of TEK spanning four decades involved analytical workshops, semidirective interviews, and collaborative fieldwork with local aboriginal informants and fishing guides. We found that TEK complemented EBK of brook charr by providing concordant and additional information about (1 population viability; (2 breeding areas and migration patterns of divergent populations; and (3 the behavioral ecology of populations within feeding areas; all of which may ultimately affect the maintenance of population diversity. Aboriginal concerns related to human pressures on this species, not revealed by EBK, also help to focus future conservation initiatives for divergent populations and to encourage restoration of traditional fishing practices. However, relative to EBK, the relevance of TEK to salmonid biodiversity conservation was evident mainly at a smaller spatial scale, for example, that of individual rivers occupied by populations or certain lake sectors. Nevertheless, EBK was only collected over a 4-yr period, so TEK provided an essential long-term temporal window to evaluate population differences and persistence. We concluded that, despite different conceptual underpinnings, spatially and temporally varying TEK and EBK both contribute to the knowledge base required to achieve sustainability and effective biodiversity conservation planning for a given species. Such integration may be particularly relevant in many isolated regions, where intraspecific diversity can go unrecognized due to sparse

  18. Evolutionary Conservation in Genes Underlying Human Psychiatric Disorders

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    Lisa Michelle Ogawa

    2014-05-01

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

  19. Evolutionary Conserved Protein Features From Analysis of Virus Shapes

    CERN Document Server

    Bozic, Anze Losdorfer; Podgornik, Rudolf

    2013-01-01

    From the shape and size analysis of approximately 130 small icosahedral viruses we conclude that there is a typical structural capsid protein, having a mean diameter of 5 nm and a mean thickness of 3 nm, with more than two thirds of the analyzed capsid proteins having thicknesses between 2 nm and 4 nm. To investigate whether, in addition to the conserved geometry, capsid proteins show similarities in the way they interact with one another, we examined the shapes of the capsids in detail. We classified them numerically according to their similarity to sphere and icosahedron and a set of shapes in between, all obtained from the theory of elasticity of shells. In order to make a unique and straightforward connection between an idealized, numerically calculated shape of an elastic shell and a capsid, we devised a special shape fitting procedure, the outcome of which is the idealized elastic shape fitting the capsid best. Using such a procedure we performed statistical analysis of a series of virus shapes and we f...

  20. Evolutionary Relationships and Taxa-Specific Conserved Signature Indels Among Cellulases of Archaea, Bacteria, and Eukarya.

    Science.gov (United States)

    Thomas, Lebin; Ram, Hari; Singh, Ved Pal

    2017-10-01

    The cellulases from different cellulolytic organisms have evolutionary relationships, which range from single-celled prokaryotes to the complex eukaryotes of the living world. This in silico analysis revealed the presence of a conserved cellulase domain along with evolutionary relationships among cellulases from several species of Archaea, Bacteria, and Eukarya. The amino acid sequences of cellulases from Archaea and Bacteria showed closer identity with their domain or phylum members that provided insights into convergent and divergent evolution of cellulases from other enzymes with different substrate specificities. Evolutionary relatedness was also observed in phylogenetic trees among a number of cellulase sequences of diverse taxa. In cellulases, propensity for alanine, glycine, leucine, serine, and threonine was high, but low for cysteine, histidine, and methionine. Catalytic aspartic acid had a higher propensity than glutamic acid, and both were involved in regular expression patterns. Characteristic group and multigroup-specific conserved signature indels located in the catalytic domains of cellulases were observed that further clarified evolutionary relationships. These indels can be distinctive molecular tools for understanding phylogeny and identification of unknown cellulolytic species of common evolutionary descent in different environments.

  1. Evolutionary conservation of sequence and secondary structures inCRISPR repeats

    Energy Technology Data Exchange (ETDEWEB)

    Kunin, Victor; Sorek, Rotem; Hugenholtz, Philip

    2006-09-01

    Clustered Regularly Interspaced Palindromic Repeats (CRISPRs) are a novel class of direct repeats, separated by unique spacer sequences of similar length, that are present in {approx}40% of bacterial and all archaeal genomes analyzed to date. More than 40 gene families, called CRISPR-associated sequences (CAS), appear in conjunction with these repeats and are thought to be involved in the propagation and functioning of CRISPRs. It has been proposed that the CRISPR/CAS system samples, maintains a record of, and inactivates invasive DNA that the cell has encountered, and therefore constitutes a prokaryotic analog of an immune system. Here we analyze CRISPR repeats identified in 195 microbial genomes and show that they can be organized into multiple clusters based on sequence similarity. All individual repeats in any given cluster were inferred to form characteristic RNA secondary structure, ranging from non-existent to pronounced. Stable secondary structures included G:U base pairs and exhibited multiple compensatory base changes in the stem region, indicating evolutionary conservation and functional importance. We also show that the repeat-based classification corresponds to, and expands upon, a previously reported CAS gene-based classification including specific relationships between CRISPR and CAS subtypes.

  2. An evolutionary approach to regional systems of innovation

    DEFF Research Database (Denmark)

    Gunnarsson, Jan Sture Gunnar; Wallin, Torsten

    2011-01-01

    and production of intermediate goods. In particular we are concerned with how cooperative behaviour of technology producers is affected by the need to protect technological secrecies and of being financially constrained by firms demanding innovative input. Based on the theoretical model, we provide an analysis...... using computer simulations. The primary findings are, firstly, that the model generates predictions suited for empirical research on how economic selection influences cooperative behaviour of innovative actors. Secondly, we demonstrate how a region's entrepreneurial activity and growth can be controlled......This article examines how the birth and the development of regional systems of innovation are connected with economic selection and points to implications for regional-level policies. The research questions are explored using an evolutionary model, which emphasises geographical spaces...

  3. A Syntenic Region Conserved from Fish to Mammalian X Chromosome

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    Guijun Guan

    2014-01-01

    Full Text Available Sex chromosomes bearing the sex-determining gene initiate development along the male or female pathway, no matter which sex is determined by XY male or ZW female heterogamety. Sex chromosomes originate from ancient autosomes but evolved rapidly after the acquisition of sex-determining factors which are highly divergent between species. In the heterogametic male system (XY system, the X chromosome is relatively evolutionary silent and maintains most of its ancestral genes, in contrast to its Y counterpart that has evolved rapidly and degenerated. Sex in a teleost fish, the Nile tilapia (Oreochromis niloticus, is determined genetically via an XY system, in which an unpaired region is present in the largest chromosome pair. We defined the differences in DNA contents present in this chromosome with a two-color comparative genomic hybridization (CGH and the random amplified polymorphic DNA (RAPD approach in XY males. We further identified a syntenic segment within this region that is well conserved in several teleosts. Through comparative genome analysis, this syntenic segment was also shown to be present in mammalian X chromosomes, suggesting a common ancestral origin of vertebrate sex chromosomes.

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

    Science.gov (United States)

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

    2011-02-01

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

  5. Spatial multiobjective optimization of agricultural conservation practices using a SWAT model and an evolutionary algorithm.

    Science.gov (United States)

    Rabotyagov, Sergey; Campbell, Todd; Valcu, Adriana; Gassman, Philip; Jha, Manoj; Schilling, Keith; Wolter, Calvin; Kling, Catherine

    2012-12-09

    Finding the cost-efficient (i.e., lowest-cost) ways of targeting conservation practice investments for the achievement of specific water quality goals across the landscape is of primary importance in watershed management. Traditional economics methods of finding the lowest-cost solution in the watershed context (e.g.,(5,12,20)) assume that off-site impacts can be accurately described as a proportion of on-site pollution generated. Such approaches are unlikely to be representative of the actual pollution process in a watershed, where the impacts of polluting sources are often determined by complex biophysical processes. The use of modern physically-based, spatially distributed hydrologic simulation models allows for a greater degree of realism in terms of process representation but requires a development of a simulation-optimization framework where the model becomes an integral part of optimization. Evolutionary algorithms appear to be a particularly useful optimization tool, able to deal with the combinatorial nature of a watershed simulation-optimization problem and allowing the use of the full water quality model. Evolutionary algorithms treat a particular spatial allocation of conservation practices in a watershed as a candidate solution and utilize sets (populations) of candidate solutions iteratively applying stochastic operators of selection, recombination, and mutation to find improvements with respect to the optimization objectives. The optimization objectives in this case are to minimize nonpoint-source pollution in the watershed, simultaneously minimizing the cost of conservation practices. A recent and expanding set of research is attempting to use similar methods and integrates water quality models with broadly defined evolutionary optimization methods(3,4,9,10,13-15,17-19,22,23,25). In this application, we demonstrate a program which follows Rabotyagov et al.'s approach and integrates a modern and commonly used SWAT water quality model(7) with a

  6. Identification of putative regulatory upstream ORFs in the yeast genome using heuristics and evolutionary conservation

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    Bilsland Elizabeth

    2007-08-01

    Full Text Available Abstract Background The translational efficiency of an mRNA can be modulated by upstream open reading frames (uORFs present in certain genes. A uORF can attenuate translation of the main ORF by interfering with translational reinitiation at the main start codon. uORFs also occur by chance in the genome, in which case they do not have a regulatory role. Since the sequence determinants for functional uORFs are not understood, it is difficult to discriminate functional from spurious uORFs by sequence analysis. Results We have used comparative genomics to identify novel uORFs in yeast with a high likelihood of having a translational regulatory role. We examined uORFs, previously shown to play a role in regulation of translation in Saccharomyces cerevisiae, for evolutionary conservation within seven Saccharomyces species. Inspection of the set of conserved uORFs yielded the following three characteristics useful for discrimination of functional from spurious uORFs: a length between 4 and 6 codons, a distance from the start of the main ORF between 50 and 150 nucleotides, and finally a lack of overlap with, and clear separation from, neighbouring uORFs. These derived rules are inherently associated with uORFs with properties similar to the GCN4 locus, and may not detect most uORFs of other types. uORFs with high scores based on these rules showed a much higher evolutionary conservation than randomly selected uORFs. In a genome-wide scan in S. cerevisiae, we found 34 conserved uORFs from 32 genes that we predict to be functional; subsequent analysis showed the majority of these to be located within transcripts. A total of 252 genes were found containing conserved uORFs with properties indicative of a functional role; all but 7 are novel. Functional content analysis of this set identified an overrepresentation of genes involved in transcriptional control and development. Conclusion Evolutionary conservation of uORFs in yeasts can be traced up to 100

  7. Wildlife conservation and animal temperament: causes and consequences of evolutionary change for captive, reintroduced, and wild populations

    NARCIS (Netherlands)

    McDougall, P.T.; Réale, D.; Sol, D.; Reader, S.M.

    2006-01-01

    We argue that animal temperament is an important concept for wildlife conservation science and review causes and consequences of evolutionary changes in temperament traits that may occur in captive-breeding programmes. An evolutionary perspective is valid because temperament traits are heritable,

  8. Evolutionary mirages: selection on binding site composition creates the illusion of conserved grammars in Drosophila enhancers.

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    Richard W Lusk

    2010-01-01

    Full Text Available The clustering of transcription factor binding sites in developmental enhancers and the apparent preferential conservation of clustered sites have been widely interpreted as proof that spatially constrained physical interactions between transcription factors are required for regulatory function. However, we show here that selection on the composition of enhancers alone, and not their internal structure, leads to the accumulation of clustered sites with evolutionary dynamics that suggest they are preferentially conserved. We simulated the evolution of idealized enhancers from Drosophila melanogaster constrained to contain only a minimum number of binding sites for one or more factors. Under this constraint, mutations that destroy an existing binding site are tolerated only if a compensating site has emerged elsewhere in the enhancer. Overlapping sites, such as those frequently observed for the activator Bicoid and repressor Krüppel, had significantly longer evolutionary half-lives than isolated sites for the same factors. This leads to a substantially higher density of overlapping sites than expected by chance and the appearance that such sites are preferentially conserved. Because D. melanogaster (like many other species has a bias for deletions over insertions, sites tended to become closer together over time, leading to an overall clustering of sites in the absence of any selection for clustered sites. Since this effect is strongest for the oldest sites, clustered sites also incorrectly appear to be preferentially conserved. Following speciation, sites tend to be closer together in all descendent species than in their common ancestors, violating the common assumption that shared features of species' genomes reflect their ancestral state. Finally, we show that selection on binding site composition alone recapitulates the observed number of overlapping and closely neighboring sites in real D. melanogaster enhancers. Thus, this study calls into

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

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    Martin Poot

    2011-05-01

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

  10. How conserved are the conserved 16S-rRNA regions?

    Directory of Open Access Journals (Sweden)

    Marcel Martinez-Porchas

    2017-02-01

    Full Text Available The 16S rRNA gene has been used as master key for studying prokaryotic diversity in almost every environment. Despite the claim of several researchers to have the best universal primers, the reality is that no primer has been demonstrated to be truly universal. This suggests that conserved regions of the gene may not be as conserved as expected. The aim of this study was to evaluate the conservation degree of the so-called conserved regions flanking the hypervariable regions of the 16S rRNA gene. Data contained in SILVA database (release 123 were used for the study. Primers reported as matches of each conserved region were assembled to form contigs; sequences sizing 12 nucleotides (12-mers were extracted from these contigs and searched into the entire set of SILVA sequences. Frequency analysis shown that extreme regions, 1 and 10, registered the lowest frequencies. 12-mer frequencies revealed segments of contigs that were not as conserved as expected (≤90%. Fragments corresponding to the primer contigs 3, 4, 5b and 6a were recovered from all sequences in SILVA database. Nucleotide frequency analysis in each consensus demonstrated that only a small fraction of these so-called conserved regions is truly conserved in non-redundant sequences. It could be concluded that conserved regions of the 16S rRNA gene exhibit considerable variation that has to be considered when using this gene as biomarker.

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

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    Marek Ostaszewski

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

  12. Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery.

    Science.gov (United States)

    Davey, Norman E; Shields, Denis C; Edwards, Richard J

    2009-02-15

    Short linear motifs (SLiMs) are important mediators of protein-protein interactions. Their short and degenerate nature presents a challenge for computational discovery. We sought to improve SLiM discovery by incorporating evolutionary information, since SLiMs are more conserved than surrounding residues. We have developed a new method that assesses the evolutionary signal of a residue in its sequence and structural context. Under-conserved residues are masked out prior to SLiM discovery, allowing incorporation into the existing statistical model employed by SLiMFinder. The method shows considerable robustness in terms of both the conservation score used for individual residues and the size of the sequence neighbourhood. Optimal parameters significantly improve return of known functional motifs from benchmarking data, raising the return of significant validated SLiMs from typical human interaction datasets from 20% to 60%, while retaining the high level of stringency needed for application to real biological data. The success of this regime indicates that it could be of general benefit to computational annotation and prediction of protein function at the sequence level. All data and tools in this article are available at http://bioware.ucd.ie/~slimdisc/slimfinder/conmasking/.

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

    Directory of Open Access Journals (Sweden)

    Shirai Leila T

    2012-02-01

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

  14. Identification of the novel evolutionary conserved obstructor multigene family in invertebrates.

    Science.gov (United States)

    Behr, Matthias; Hoch, Michael

    2005-12-19

    Insects have evolved chitin-containing structures such as the cuticle or peritrophic membranes that serve to protect their bodies against the hostile environment. The specific mechanisms by which these structures are produced, are mostly unknown. We have identified a novel multigene family, the obstructor family, which encodes ten putatively secreted chitin-binding proteins that are characterized by a stereotype arrangement of a N-terminal signaling peptide and 3 chitin-binding-domains. Gene expression studies in Drosophila melanogaster embryos demonstrate that obstructor family members are expressed in cuticle forming tissues. Using computational and phylogenetic analysis, we show that obstructor genes represent an evolutionary conserved multigene family in invertebrates.

  15. Cross-species genome-wide identification of evolutionary conserved microproteins

    DEFF Research Database (Denmark)

    Straub, Daniel; Wenkel, Stephan

    2017-01-01

    Protein concept beyond transcription factors to other protein families. Here, we reveal potential microProtein candidates in several plant and animal reference genomes. A large number of these microProteins are species-specific while others evolved early and are evolutionary highly conserved. Most known micro......MicroProteins are small single-domain proteins that act by engaging their targets into different, sometimes nonproductive protein complexes. In order to identify novel microProteins in any sequenced genome of interest, we have developed miPFinder, a program that identifies and classifies potential...

  16. Maximizing species conservation in continental Ecuador: a case of systematic conservation planning for biodiverse regions

    Science.gov (United States)

    Lessmann, Janeth; Muñoz, Jesús; Bonaccorso, Elisa

    2014-01-01

    Ecuador has the largest number of species by area worldwide, but also a low representation of species within its protected areas. Here, we applied systematic conservation planning to identify potential areas for conservation in continental Ecuador, with the aim of increasing the representation of terrestrial species diversity in the protected area network. We selected 809 terrestrial species (amphibians, birds, mammals, and plants), for which distributions were estimated via species distribution models (SDMs), using Maxent. For each species we established conservation goals based on conservation priorities, and estimated new potential protected areas using Marxan conservation planning software. For each selected area, we determined their conservation priority and feasibility of establishment, two important aspects in the decision-making processes. We found that according to our conservation goals, the current protected area network contains large conservation gaps. Potential areas for conservation almost double the surface area of currently protected areas. Most of the newly proposed areas are located in the Coast, a region with large conservation gaps and irreversible changes in land use. The most feasible areas for conservation were found in the Amazon and Andes regions, which encompass more undisturbed habitats, and already harbor most of the current reserves. Our study allows defining a viable strategy for preserving Ecuador's biodiversity, by combining SDMs, GIS-based decision-support software, and priority and feasibility assessments of the selected areas. This approach is useful for complementing protected area networks in countries with great biodiversity, insufficient biological information, and limited resources for conservation. PMID:25360277

  17. Evolutionary conserved regulation of HIF-1β by NF-κB.

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    Patrick van Uden

    2011-01-01

    Full Text Available Hypoxia Inducible Factor-1 (HIF-1 is essential for mammalian development and is the principal transcription factor activated by low oxygen tensions. HIF-α subunit quantities and their associated activity are regulated in a post-translational manner, through the concerted action of a class of enzymes called Prolyl Hydroxylases (PHDs and Factor Inhibiting HIF (FIH respectively. However, alternative modes of HIF-α regulation such as translation or transcription are under-investigated, and their importance has not been firmly established. Here, we demonstrate that NF-κB regulates the HIF pathway in a significant and evolutionary conserved manner. We demonstrate that NF-κB directly regulates HIF-1β mRNA and protein. In addition, we found that NF-κB-mediated changes in HIF-1β result in modulation of HIF-2α protein. HIF-1β overexpression can rescue HIF-2α protein levels following NF-κB depletion. Significantly, NF-κB regulates HIF-1β (tango and HIF-α (sima levels and activity (Hph/fatiga, ImpL3/ldha in Drosophila, both in normoxia and hypoxia, indicating an evolutionary conserved mode of regulation. These results reveal a novel mechanism of HIF regulation, with impact in the development of novel therapeutic strategies for HIF-related pathologies including ageing, ischemia, and cancer.

  18. Evolutionary conserved regulation of HIF-1β by NF-κB.

    Science.gov (United States)

    van Uden, Patrick; Kenneth, Niall S; Webster, Ryan; Müller, H Arno; Mudie, Sharon; Rocha, Sonia

    2011-01-27

    Hypoxia Inducible Factor-1 (HIF-1) is essential for mammalian development and is the principal transcription factor activated by low oxygen tensions. HIF-α subunit quantities and their associated activity are regulated in a post-translational manner, through the concerted action of a class of enzymes called Prolyl Hydroxylases (PHDs) and Factor Inhibiting HIF (FIH) respectively. However, alternative modes of HIF-α regulation such as translation or transcription are under-investigated, and their importance has not been firmly established. Here, we demonstrate that NF-κB regulates the HIF pathway in a significant and evolutionary conserved manner. We demonstrate that NF-κB directly regulates HIF-1β mRNA and protein. In addition, we found that NF-κB-mediated changes in HIF-1β result in modulation of HIF-2α protein. HIF-1β overexpression can rescue HIF-2α protein levels following NF-κB depletion. Significantly, NF-κB regulates HIF-1β (tango) and HIF-α (sima) levels and activity (Hph/fatiga, ImpL3/ldha) in Drosophila, both in normoxia and hypoxia, indicating an evolutionary conserved mode of regulation. These results reveal a novel mechanism of HIF regulation, with impact in the development of novel therapeutic strategies for HIF-related pathologies including ageing, ischemia, and cancer.

  19. Setting priorities for regional conservation planning in the Mediterranean Sea.

    Science.gov (United States)

    Micheli, Fiorenza; Levin, Noam; Giakoumi, Sylvaine; Katsanevakis, Stelios; Abdulla, Ameer; Coll, Marta; Fraschetti, Simonetta; Kark, Salit; Koutsoubas, Drosos; Mackelworth, Peter; Maiorano, Luigi; Possingham, Hugh P

    2013-01-01

    Spatial prioritization in conservation is required to direct limited resources to where actions are most urgently needed and most likely to produce effective conservation outcomes. In an effort to advance the protection of a highly threatened hotspot of marine biodiversity, the Mediterranean Sea, multiple spatial conservation plans have been developed in recent years. Here, we review and integrate these different plans with the goal of identifying priority conservation areas that represent the current consensus among the different initiatives. A review of six existing and twelve proposed conservation initiatives highlights gaps in conservation and management planning, particularly within the southern and eastern regions of the Mediterranean and for offshore and deep sea habitats. The eighteen initiatives vary substantially in their extent (covering 0.1-58.5% of the Mediterranean Sea) and in the location of additional proposed conservation and management areas. Differences in the criteria, approaches and data used explain such variation. Despite the diversity among proposals, our analyses identified ten areas, encompassing 10% of the Mediterranean Sea, that are consistently identified among the existing proposals, with an additional 10% selected by at least five proposals. These areas represent top priorities for immediate conservation action. Despite the plethora of initiatives, major challenges face Mediterranean biodiversity and conservation. These include the need for spatial prioritization within a comprehensive framework for regional conservation planning, the acquisition of additional information from data-poor areas, species or habitats, and addressing the challenges of establishing transboundary governance and collaboration in socially, culturally and politically complex conditions. Collective prioritised action, not new conservation plans, is needed for the north, western, and high seas of the Mediterranean, while developing initial information-based plans

  20. Setting Priorities for Regional Conservation Planning in the Mediterranean Sea

    Science.gov (United States)

    Micheli, Fiorenza; Levin, Noam; Giakoumi, Sylvaine; Katsanevakis, Stelios; Abdulla, Ameer; Coll, Marta; Fraschetti, Simonetta; Kark, Salit; Koutsoubas, Drosos; Mackelworth, Peter; Maiorano, Luigi; Possingham, Hugh P.

    2013-01-01

    Spatial prioritization in conservation is required to direct limited resources to where actions are most urgently needed and most likely to produce effective conservation outcomes. In an effort to advance the protection of a highly threatened hotspot of marine biodiversity, the Mediterranean Sea, multiple spatial conservation plans have been developed in recent years. Here, we review and integrate these different plans with the goal of identifying priority conservation areas that represent the current consensus among the different initiatives. A review of six existing and twelve proposed conservation initiatives highlights gaps in conservation and management planning, particularly within the southern and eastern regions of the Mediterranean and for offshore and deep sea habitats. The eighteen initiatives vary substantially in their extent (covering 0.1–58.5% of the Mediterranean Sea) and in the location of additional proposed conservation and management areas. Differences in the criteria, approaches and data used explain such variation. Despite the diversity among proposals, our analyses identified ten areas, encompassing 10% of the Mediterranean Sea, that are consistently identified among the existing proposals, with an additional 10% selected by at least five proposals. These areas represent top priorities for immediate conservation action. Despite the plethora of initiatives, major challenges face Mediterranean biodiversity and conservation. These include the need for spatial prioritization within a comprehensive framework for regional conservation planning, the acquisition of additional information from data-poor areas, species or habitats, and addressing the challenges of establishing transboundary governance and collaboration in socially, culturally and politically complex conditions. Collective prioritised action, not new conservation plans, is needed for the north, western, and high seas of the Mediterranean, while developing initial information

  1. SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions.

    Science.gov (United States)

    Davey, Norman E; Cowan, Joanne L; Shields, Denis C; Gibson, Toby J; Coldwell, Mark J; Edwards, Richard J

    2012-11-01

    Large portions of higher eukaryotic proteomes are intrinsically disordered, and abundant evidence suggests that these unstructured regions of proteins are rich in regulatory interaction interfaces. A major class of disordered interaction interfaces are the compact and degenerate modules known as short linear motifs (SLiMs). As a result of the difficulties associated with the experimental identification and validation of SLiMs, our understanding of these modules is limited, advocating the use of computational methods to focus experimental discovery. This article evaluates the use of evolutionary conservation as a discriminatory technique for motif discovery. A statistical framework is introduced to assess the significance of relatively conserved residues, quantifying the likelihood a residue will have a particular level of conservation given the conservation of the surrounding residues. The framework is expanded to assess the significance of groupings of conserved residues, a metric that forms the basis of SLiMPrints (short linear motif fingerprints), a de novo motif discovery tool. SLiMPrints identifies relatively overconstrained proximal groupings of residues within intrinsically disordered regions, indicative of putatively functional motifs. Finally, the human proteome is analysed to create a set of highly conserved putative motif instances, including a novel site on translation initiation factor eIF2A that may regulate translation through binding of eIF4E.

  2. Comparative phylogeography reveals deep lineages and regional evolutionary hotspots in the Mojave and Sonoran Deserts

    Science.gov (United States)

    Wood, Dustin A.; Vandergast, Amy G.; Barr, Kelly R.; Inman, Richard D.; Esque, Todd C.; Nussear, Kenneth E.; Fisher, Robert N.

    2013-01-01

    Aim: We explored lineage diversification within desert-dwelling fauna. Our goals were (1) to determine whether phylogenetic lineages and population expansions were consistent with younger Pleistocene climate fluctuation hypotheses or much older events predicted by pre-Pleistocene vicariance hypotheses, (2) to assess concordance in spatial patterns of genetic divergence and diversity among species and (3) to identify regional evolutionary hotspots of divergence and diversity and assess their conservation status. Location: Mojave, Colorado, and Sonoran Deserts, USA. Methods: We analysed previously published gene sequence data for twelve species. We used Bayesian gene tree methods to estimate lineages and divergence times. Within each lineage, we tested for population expansion and age of expansion using coalescent approaches. We mapped interpopulation genetic divergence and intra-population genetic diversity in a GIS to identify hotspots of highest genetic divergence and diversity and to assess whether protected lands overlapped with evolutionary hotspots. Results: In seven of the 12 species, lineage divergence substantially predated the Pleistocene. Historical population expansion was found in eight species, but expansion events postdated the Last Glacial Maximum (LGM) in only four. For all species assessed, six hotspots of high genetic divergence and diversity were concentrated in the Colorado Desert, along the Colorado River and in the Mojave/Sonoran ecotone. At least some proportion of the land within each recovered hotspot was categorized as protected, yet four of the six also overlapped with major areas of human development. Main conclusions: Most of the species studied here diversified into distinct Mojave and Sonoran lineages prior to the LGM – supporting older diversification hypotheses. Several evolutionary hotspots were recovered but are not strategically paired with areas of protected land. Long-term preservation of species-level biodiversity would

  3. Developmental evolutionary biology of the vertebrate ear: conserving mechanoelectric transduction and developmental pathways in diverging morphologies

    Science.gov (United States)

    Fritzsch, B.; Beisel, K. W.; Bermingham, N. A.

    2000-01-01

    This brief overview shows that a start has been made to molecularly dissect vertebrate ear development and its evolutionary conservation to the development of the insect hearing organ. However, neither the patterning process of the ear nor the patterning process of insect sensory organs is sufficiently known at the moment to provide more than a first glimpse. Moreover, hardly anything is known about otocyst development of the cephalopod molluscs, another triploblast lineage that evolved complex 'ears'. We hope that the apparent conserved functional and cellular components present in the ciliated sensory neurons/hair cells will also be found in the genes required for vertebrate ear and insect sensory organ morphogenesis (Fig. 3). Likewise, we expect that homologous pre-patterning genes will soon be identified for the non-sensory cell development, which is more than a blocking of neuronal development through the Delta/Notch signaling system. Generation of the apparently unique ear could thus represent a multiplication of non-sensory cells by asymmetric and symmetric divisions as well as modification of existing patterning process by implementing novel developmental modules. In the final analysis, the vertebrate ear may come about by increasing the level of gene interactions in an already existing and highly conserved interactive cascade of bHLH genes. Since this was apparently achieved in all three lineages of triploblasts independently (Fig. 3), we now need to understand how much of the morphogenetic cascades are equally conserved across phyla to generate complex ears. The existing mutations in humans and mice may be able to point the direction of future research to understand the development of specific cell types and morphologies in the formation of complex arthropod, cephalopod, and vertebrate 'ears'.

  4. Evolutionary conserved mechanisms pervade structure and transcriptional modulation of allograft inflammatory factor-1 from sea anemone Anemonia viridis.

    Science.gov (United States)

    Cuttitta, Angela; Ragusa, Maria Antonietta; Costa, Salvatore; Bennici, Carmelo; Colombo, Paolo; Mazzola, Salvatore; Gianguzza, Fabrizio; Nicosia, Aldo

    2017-08-01

    Gene family encoding allograft inflammatory factor-1 (AIF-1) is well conserved among organisms; however, there is limited knowledge in lower organisms. In this study, the first AIF-1 homologue from cnidarians was identified and characterised in the sea anemone Anemonia viridis. The full-length cDNA of AvAIF-1 was of 913 bp with a 5' -untranslated region (UTR) of 148 bp, a 3'-UTR of 315 and an open reading frame (ORF) of 450 bp encoding a polypeptide with149 amino acid residues and predicted molecular weight of about 17 kDa. The predicted protein possesses evolutionary conserved EF hand Ca2+ binding motifs, post-transcriptional modification sites and a 3D structure which can be superimposed with human members of AIF-1 family. The AvAIF-1 transcript was constitutively expressed in all tested tissues of unchallenged sea anemone, suggesting that AvAIF-1 could serve as a general protective factor under normal physiological conditions. Moreover, we profiled the transcriptional activation of AvAIF-1 after challenges with different abiotic/biotic stresses showing induction by warming conditions, heavy metals exposure and immune stimulation. Thus, mechanisms associated to inflammation and immune challenges up-regulated AvAIF-1 mRNA levels. Our results suggest its involvement in the inflammatory processes and immune response of A. viridis. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Developments in conservation tillage in rainfed regions of North China

    NARCIS (Netherlands)

    Wang, X.B.; Cai, D.X.; Hoogmoed, W.B.; Oenema, O.; Perdok, U.D.

    2007-01-01

    Dryland regions in northern China account for over 50% of the nation's total area, where farming development is constrained by adverse weather, topography and water resource conditions, low fertility soils, and poor soil management. Conservation tillage research and application in dryland regions of

  6. Integration of Regional Mitigation Assessment and Conservation Planning

    Directory of Open Access Journals (Sweden)

    James H. Thorne

    2009-06-01

    Full Text Available Government agencies that develop infrastructure such as roads, waterworks, and energy delivery often impact natural ecosystems, but they also have unique opportunities to contribute to the conservation of regional natural resources through compensatory mitigation. Infrastructure development requires a planning, funding, and implementation cycle that can frequently take a decade or longer, but biological mitigation is often planned and implemented late in this process, in a project-by-project piecemeal manner. By adopting early regional mitigation needs assessment and planning for habitat-level impacts from multiple infrastructure projects, agencies could secure time needed to proactively integrate these obligations into regional conservation objectives. Such practice can be financially and ecologically beneficial due to economies of scale, and because earlier mitigation implementation means potentially developable critical parcels may still be available for conservation. Here, we compare the integration of regional conservation designs, termed greenprints, with early multi-project mitigation assessment for two areas in California, USA. The expected spatial extent of habitat impacts and associated mitigation requirements from multiple projects were identified for each area. We used the reserve-selection algorithm MARXAN to identify a regional greenprint for each site and to seek mitigation solutions through parcel acquisition that would contribute to the greenprint, as well as meet agency obligations. The two areas differed in the amount of input data available, the types of conservation objectives identified, and local land-management capacity. They are representative of the range of conditions that conservation practitioners may encounter, so contrasting the two illustrates how regional advanced mitigation can be generalized for use in a wide variety of settings. Environmental organizations can benefit from this approach because it provides a

  7. Conservation of the Keap1-Nrf2 System: An Evolutionary Journey through Stressful Space and Time

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    Yuji Fuse

    2017-03-01

    Full Text Available The Keap1-Nrf2 system is an evolutionarily conserved defense mechanism against oxidative and xenobiotic stress. Its regulatory mechanisms, e.g., stress-sensing mechanism, proteasome-based regulation of Nrf2 activity and selection of target genes, have been elucidated mainly in mammals. In addition, emerging model animals, such as zebrafish, fruit fly and Caenorhabditis elegans, have been shown to have similar anti-stress systems to mammals, suggesting that analogous defense systems are widely conserved throughout the animal kingdom. Experimental evidence in lower animals provides important information beyond mere laboratory-confined utility, such as regarding how these systems transformed during evolution, which may help characterize the mammalian system in greater detail. Recent advances in genome projects of both model and non-model animals have provided a great deal of useful information toward this end. We herein review the research on Keap1-Nrf2 and its analogous systems in both mammals and lower model animals. In addition, by comparing the amino acid sequences of Nrf2 and Keap1 proteins from various species, we can deduce the evolutionary history of the anti-stress system. This combinatorial approach using both experimental and genetic data will suggest perspectives of approach for researchers studying the stress response.

  8. Conservation of the Keap1-Nrf2 System: An Evolutionary Journey through Stressful Space and Time.

    Science.gov (United States)

    Fuse, Yuji; Kobayashi, Makoto

    2017-03-09

    The Keap1-Nrf2 system is an evolutionarily conserved defense mechanism against oxidative and xenobiotic stress. Its regulatory mechanisms, e.g., stress-sensing mechanism, proteasome-based regulation of Nrf2 activity and selection of target genes, have been elucidated mainly in mammals. In addition, emerging model animals, such as zebrafish, fruit fly and Caenorhabditis elegans , have been shown to have similar anti-stress systems to mammals, suggesting that analogous defense systems are widely conserved throughout the animal kingdom. Experimental evidence in lower animals provides important information beyond mere laboratory-confined utility, such as regarding how these systems transformed during evolution, which may help characterize the mammalian system in greater detail. Recent advances in genome projects of both model and non-model animals have provided a great deal of useful information toward this end. We herein review the research on Keap1-Nrf2 and its analogous systems in both mammals and lower model animals. In addition, by comparing the amino acid sequences of Nrf2 and Keap1 proteins from various species, we can deduce the evolutionary history of the anti-stress system. This combinatorial approach using both experimental and genetic data will suggest perspectives of approach for researchers studying the stress response.

  9. Evolutionary conservation of mammalian sperm proteins associates with overall, not tyrosine, phosphorylation in human spermatozoa.

    Science.gov (United States)

    Schumacher, Julia; Ramljak, Sanja; Asif, Abdul R; Schaffrath, Michael; Zischler, Hans; Herlyn, Holger

    2013-12-06

    We investigated possible associations between sequence evolution of mammalian sperm proteins and their phosphorylation status in humans. As a reference, spermatozoa from three normozoospermic men were analyzed combining two-dimensional gel electrophoresis, immunoblotting, and mass spectrometry. We identified 99 sperm proteins (thereof 42 newly described) and determined the phosphorylation status for most of them. Sequence evolution was studied across six mammalian species using nonsynonymous/synonymous rate ratios (dN/dS) and amino acid distances. Site-specific purifying selection was assessed employing average ratios of evolutionary rates at phosphorylated versus nonphosphorylated amino acids (α). According to our data, mammalian sperm proteins do not show statistically significant sequence conservation difference, no matter if the human ortholog is a phosphoprotein with or without tyrosine (Y) phosphorylation. In contrast, overall phosphorylation of human sperm proteins, i.e., phosphorylation at serine (S), threonine (T), and/or Y residues, associates with above-average conservation of sequences. Complementary investigations suggest that numerous protein-protein interactants constrain sequence evolution of sperm phosphoproteins. Although our findings reject a special relevance of Y phosphorylation for sperm functioning, they still indicate that overall phosphorylation substantially contributes to proper functioning of sperm proteins. Hence, phosphorylated sperm proteins might be considered as prime candidates for diagnosis and treatment of reduced male fertility.

  10. 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.

  11. Evolutionary Diversifaction of Aminopeptidase N in Lepidoptera by Conserved Clade-specific Amino Acid Residues

    Science.gov (United States)

    Hughes, Austin L.

    2015-01-01

    Members of the aminopepidase N (APN) gene family of the insect order Lepidoptera (moths and butterflies) bind the naturally insecticidal Cry toxins produced by the bacterium Bacillus thuringiensis. Phylogenetic analysis of amino acid sequences of seven lepidopteran APN classes provided strong support for the hypothesis that lepidopteran APN2 class arose by gene duplication prior to the most recent common ancestor of Lepidoptera and Diptera. The Cry toxin-binding region (BR) of lepidopteran and dipteran APNs was subject to stronger purifying selection within APN classes than was the remainder of the molecule, reflecting conservation of catalytic site and adjoining residues within the BR. Of lepidopteran APN classes, APN2, APN6, and APN8 showed the strongest evidence of functional specialization, both in expression patterns and in the occurrence of conserved derived amino acid residues. The latter three APN classes also shared a convergently evolved conserved residue close to the catalytic site. APN8 showed a particularly strong tendency towards class-specific conserved residues, including one of the catalytic site residues in the BR and ten others in close vicinity to the catalytic site residues. The occurrence of class-specific sequences along with the conservation of enzymatic function is consistent with the hypothesis that the presence of Cry toxins in the environment has been a factor shaping the evolution of this multi-gene family. PMID:24675701

  12. Evolutionary diversification of aminopeptidase N in Lepidoptera by conserved clade-specific amino acid residues.

    Science.gov (United States)

    Hughes, Austin L

    2014-07-01

    Members of the aminopepidase N (APN) gene family of the insect order Lepidoptera (moths and butterflies) bind the naturally insecticidal Cry toxins produced by the bacterium Bacillus thuringiensis. Phylogenetic analysis of amino acid sequences of seven lepidopteran APN classes provided strong support for the hypothesis that lepidopteran APN2 class arose by gene duplication prior to the most recent common ancestor of Lepidoptera and Diptera. The Cry toxin-binding region (BR) of lepidopteran and dipteran APNs was subject to stronger purifying selection within APN classes than was the remainder of the molecule, reflecting conservation of catalytic site and adjoining residues within the BR. Of lepidopteran APN classes, APN2, APN6, and APN8 showed the strongest evidence of functional specialization, both in expression patterns and in the occurrence of conserved derived amino acid residues. The latter three APN classes also shared a convergently evolved conserved residue close to the catalytic site. APN8 showed a particularly strong tendency towards class-specific conserved residues, including one of the catalytic site residues in the BR and ten others in close vicinity to the catalytic site residues. The occurrence of class-specific sequences along with the conservation of enzymatic function is consistent with the hypothesis that the presence of Cry toxins in the environment has been a factor shaping the evolution of this multi-gene family. Copyright © 2014 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

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

    2015-11-24

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

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

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    Scharfe Maren

    2010-04-01

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

  15. Systematic analysis of head-to-head gene organization: evolutionary conservation and potential biological relevance.

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    Yuan-Yuan Li

    2006-07-01

    Full Text Available Several "head-to-head" (or "bidirectional" gene pairs have been studied in individual experiments, but genome-wide analysis of this gene organization, especially in terms of transcriptional correlation and functional association, is still insufficient. We conducted a systematic investigation of head-to-head gene organization focusing on structural features, evolutionary conservation, expression correlation and functional association. Of the present 1,262, 1,071, and 491 head-to-head pairs identified in human, mouse, and rat genomes, respectively, pairs with 1- to 400-base pair distance between transcription start sites form the majority (62.36%, 64.15%, and 55.19% for human, mouse, and rat,respectively of each dataset, and the largest group is always the one with a transcription start site distance of 101 to 200 base pairs. The phylogenetic analysis among Fugu, chicken, and human indicates a negative selection on the separation of head-to-head genes across vertebrate evolution, and thus the ancestral existence of this gene organization. The expression analysis shows that most of the human head-to-head genes are significantly correlated,and the correlation could be positive, negative, or alternative depending on the experimental conditions. Finally, head to-head genes statistically tend to perform similar functions, and gene pairs associated with the significant cofunctions seem to have stronger expression correlations. The findings indicate that the head-to-head gene organization is ancient and conserved, which subjects functionally related genes to correlated transcriptional regulation and thus provides an exquisite mechanism of transcriptional regulation based on gene organization. These results have significantly expanded the knowledge about head-to-head gene organization. Supplementary materials for this study are available at http://www.scbit.org/h2h.

  16. Evolutionary conservation of Kv3.1 in the barn owl Tyto alba.

    Science.gov (United States)

    Kullmann, Lars; Schlüter, Tina; Wagner, Hermann; Nothwang, Hans Gerd

    2013-01-01

    For prey capture in the dark, the barn owl Tyto alba has evolved into an auditory specialist with an exquisite capability of sound localization. Adaptations include asymmetrical ears, enlarged auditory processing centers, the utilization of minute interaural time differences, and phase locking along the entire hearing range up to 10 kHz. Adaptations on the molecular level have not yet been investigated. Here, we tested the hypothesis that divergence in the amino acid sequence of the voltage-gated K(+) channel Kv3.1 contributes to the accuracy and high firing rates of auditory neurons in the barn owl. We therefore cloned both splice variants of Kcnc1, the gene encoding Kv3.1. Both splice variants, Kcnc1a and Kcnc1b, encode amino acids identical to those of the chicken, an auditory generalist. Expression analyses confirmed neural-restricted expression of the channel. In summary, our data reveal strong evolutionary conservation of Kcnc1 in the barn owl and point to other genes involved in auditory specializations of this animal. The data also demonstrate the feasibility to address neuroethological questions in organisms with no reference genome by molecular approaches. This will open new avenues for neuroethologists working in these organisms. Copyright © 2013 S. Karger AG, Basel.

  17. An evolutionary conserved role for anaplastic lymphoma kinase in behavioral responses to ethanol.

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    Amy W Lasek

    Full Text Available Anaplastic lymphoma kinase (Alk is a gene expressed in the nervous system that encodes a receptor tyrosine kinase commonly known for its oncogenic function in various human cancers. We have determined that Alk is associated with altered behavioral responses to ethanol in the fruit fly Drosophila melanogaster, in mice, and in humans. Mutant flies containing transposon insertions in dAlk demonstrate increased resistance to the sedating effect of ethanol. Database analyses revealed that Alk expression levels in the brains of recombinant inbred mice are negatively correlated with ethanol-induced ataxia and ethanol consumption. We therefore tested Alk gene knockout mice and found that they sedate longer in response to high doses of ethanol and consume more ethanol than wild-type mice. Finally, sequencing of human ALK led to the discovery of four polymorphisms associated with a low level of response to ethanol, an intermediate phenotype that is predictive of future alcohol use disorders (AUDs. These results suggest that Alk plays an evolutionary conserved role in ethanol-related behaviors. Moreover, ALK may be a novel candidate gene conferring risk for AUDs as well as a potential target for pharmacological intervention.

  18. Evolutionary conserved role of c-Jun-N-terminal kinase in CO2-induced epithelial dysfunction.

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    István Vadász

    Full Text Available Elevated CO(2 levels (hypercapnia occur in patients with respiratory diseases and impair alveolar epithelial integrity, in part, by inhibiting Na,K-ATPase function. Here, we examined the role of c-Jun N-terminal kinase (JNK in CO(2 signaling in mammalian alveolar epithelial cells as well as in diptera, nematodes and rodent lungs. In alveolar epithelial cells, elevated CO(2 levels rapidly induced activation of JNK leading to downregulation of Na,K-ATPase and alveolar epithelial dysfunction. Hypercapnia-induced activation of JNK required AMP-activated protein kinase (AMPK and protein kinase C-ζ leading to subsequent phosphorylation of JNK at Ser-129. Importantly, elevated CO(2 levels also caused a rapid and prominent activation of JNK in Drosophila S2 cells and in C. elegans. Paralleling the results with mammalian epithelial cells, RNAi against Drosophila JNK fully prevented CO(2-induced downregulation of Na,K-ATPase in Drosophila S2 cells. The importance and specificity of JNK CO(2 signaling was additionally demonstrated by the ability of mutations in the C. elegans JNK homologs, jnk-1 and kgb-2 to partially rescue the hypercapnia-induced fertility defects but not the pharyngeal pumping defects. Together, these data provide evidence that deleterious effects of hypercapnia are mediated by JNK which plays an evolutionary conserved, specific role in CO(2 signaling in mammals, diptera and nematodes.

  19. Comprehensive characterization of evolutionary conserved breakpoints in four New World Monkey karyotypes compared to Chlorocebus aethiops and Homo sapiens.

    Science.gov (United States)

    Fan, Xiaobo; Supiwong, Weerayuth; Weise, Anja; Mrasek, Kristin; Kosyakova, Nadezda; Tanomtong, Alongkoad; Pinthong, Krit; Trifonov, Vladimir A; Cioffi, Marcelo de Bello; Grothmann, Pierre; Liehr, Thomas; Oliveira, Edivaldo H C de

    2015-11-01

    Comparative cytogenetic analysis in New World Monkeys (NWMs) using human multicolor banding (MCB) probe sets were not previously done. Here we report on an MCB based FISH-banding study complemented with selected locus-specific and heterochromatin specific probes in four NWMs and one Old World Monkey (OWM) species, i.e. in Alouatta caraya (ACA), Callithrix jacchus (CJA), Cebus apella (CAP), Saimiri sciureus (SSC), and Chlorocebus aethiops (CAE), respectively. 107 individual evolutionary conserved breakpoints (ECBs) among those species were identified and compared with those of other species in previous reports. Especially for chromosomal regions being syntenic to human chromosomes 6, 8, 9, 10, 11, 12 and 16 previously cryptic rearrangements could be observed. 50.4% (54/107) NWM-ECBs were colocalized with those of OWMs, 62.6% (62/99) NWM-ECBs were related with those of Hylobates lar (HLA) and 66.3% (71/107) NWM-ECBs corresponded with those known from other mammalians. Furthermore, human fragile sites were aligned with the ECBs found in the five studied species and interestingly 66.3% ECBs colocalized with those fragile sites (FS). Overall, this study presents detailed chromosomal maps of one OWM and four NWM species. This data will be helpful to further investigation on chromosome evolution in NWM and hominoids in general and is prerequisite for correct interpretation of future sequencing based genomic studies in those species.

  20. Comprehensive characterization of evolutionary conserved breakpoints in four New World Monkey karyotypes compared to Chlorocebus aethiops and Homo sapiens

    Directory of Open Access Journals (Sweden)

    Xiaobo Fan

    2015-11-01

    Full Text Available Comparative cytogenetic analysis in New World Monkeys (NWMs using human multicolor banding (MCB probe sets were not previously done. Here we report on an MCB based FISH-banding study complemented with selected locus-specific and heterochromatin specific probes in four NWMs and one Old World Monkey (OWM species, i.e. in Alouatta caraya (ACA, Callithrix jacchus (CJA, Cebus apella (CAP, Saimiri sciureus (SSC, and Chlorocebus aethiops (CAE, respectively. 107 individual evolutionary conserved breakpoints (ECBs among those species were identified and compared with those of other species in previous reports. Especially for chromosomal regions being syntenic to human chromosomes 6, 8, 9, 10, 11, 12 and 16 previously cryptic rearrangements could be observed. 50.4% (54/107 NWM-ECBs were colocalized with those of OWMs, 62.6% (62/99 NWM-ECBs were related with those of Hylobates lar (HLA and 66.3% (71/107 NWM-ECBs corresponded with those known from other mammalians. Furthermore, human fragile sites were aligned with the ECBs found in the five studied species and interestingly 66.3% ECBs colocalized with those fragile sites (FS. Overall, this study presents detailed chromosomal maps of one OWM and four NWM species. This data will be helpful to further investigation on chromosome evolution in NWM and hominoids in general and is prerequisite for correct interpretation of future sequencing based genomic studies in those species.

  1. Fungal conservation: Protected species of fungi in South Serbia region

    Directory of Open Access Journals (Sweden)

    Sadiković, D.

    2013-12-01

    Full Text Available Protection and conservation of fungi has only recently became an issue of concern. Main motives for increased attention are uncontrolled, mass collecting of edible wild mushrooms and environmental pollution which leads to the rapid decline of their natural habitats, some of which are rich with rare and endangered species. By Serbian Nature Conservation Law 2010. there are 38 strictly protected fungal species of which 17 species are recorded in this paper. 11 of those recorded species are on European and/or National Red List of endangered fungal species. All investigated territories were in South Serbia region. This study is a contribution to conservation of protected and threatened fungi and their respective habitats in Serbia.

  2. Predicting DNA-binding amino acid residues from electrostatic stabilization upon mutation to Asp/Glu and evolutionary conservation.

    Science.gov (United States)

    Chen, Yao Chi; Wu, Chih Yuan; Lim, Carmay

    2007-05-15

    Binding of polyanionic DNA depends on the cluster of electropositive atoms in the binding site of a DNA-binding protein. Such a cluster of electropositive protein atoms would be electrostatically unfavorable without stabilizing interactions from the respective electronegative DNA atoms and would likely be evolutionary conserved due to its critical biological role. Consequently, our strategy for predicting DNA-binding residues is based on detecting a cluster of evolutionary conserved surface residues that are electrostatically stabilized upon mutation to negatively charged Asp/Glu residues. The method requires as input the protein structure and sufficient sequence homologs to define each residue's relative conservation, and it yields as output experimentally testable residues that are predicted to bind DNA. By incorporating characteristic DNA-binding site features (i.e., electrostatic strain and amino acid conservation), the new method yields a prediction accuracy of 83%, which is much higher than methods based on only electrostatic strain (57%) or conservation alone (50%). It is also less sensitive to protein conformational changes upon DNA binding than methods that mainly depend on the 3D protein structure. 2007 Wiley-Liss, Inc.

  3. Lessons from Transportation Agency Participation In Regional Conservation Initiatives

    OpenAIRE

    Lederman, Jaimee

    2017-01-01

    Transportation agencies struggle to maximize the benefits of transportation infrastructure while minimizing environmental harm. This dissertation examines institutional collaborations that integrate capital investments (e.g. highway and rail projects) with regional Habitat Conservation Plans (RHCPs) under the Endangered Species Act (ESA). It addresses ways of maintaining these collaborations over time. The ESA requires that public and private project developers mitigate any harm to endangered...

  4. Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific Amino Acid Preferences throughout Evolutionary History

    Science.gov (United States)

    Risso, Valeria A.; Manssour-Triedo, Fadia; Delgado-Delgado, Asunción; Arco, Rocio; Barroso-delJesus, Alicia; Ingles-Prieto, Alvaro; Godoy-Ruiz, Raquel; Gavira, Jose A.; Gaucher, Eric A.; Ibarra-Molero, Beatriz; Sanchez-Ruiz, Jose M.

    2015-01-01

    Local protein interactions (“molecular context” effects) dictate amino acid replacements and can be described in terms of site-specific, energetic preferences for any different amino acid. It has been recently debated whether these preferences remain approximately constant during evolution or whether, due to coevolution of sites, they change strongly. Such research highlights an unresolved and fundamental issue with far-reaching implications for phylogenetic analysis and molecular evolution modeling. Here, we take advantage of the recent availability of phenotypically supported laboratory resurrections of Precambrian thioredoxins and β-lactamases to experimentally address the change of site-specific amino acid preferences over long geological timescales. Extensive mutational analyses support the notion that evolutionary adjustment to a new amino acid may occur, but to a large extent this is insufficient to erase the primitive preference for amino acid replacements. Generally, site-specific amino acid preferences appear to remain conserved throughout evolutionary history despite local sequence divergence. We show such preference conservation to be readily understandable in molecular terms and we provide crystallographic evidence for an intriguing structural-switch mechanism: Energetic preference for an ancestral amino acid in a modern protein can be linked to reorganization upon mutation to the ancestral local structure around the mutated site. Finally, we point out that site-specific preference conservation naturally leads to one plausible evolutionary explanation for the existence of intragenic global suppressor mutations. PMID:25392342

  5. The Drosophila surface glia transcriptome: evolutionary conserved blood-brain barrier processes.

    Directory of Open Access Journals (Sweden)

    Michael K DeSalvo

    2014-11-01

    Full Text Available AbstractCentral nervous system (CNS function is dependent on the stringent regulation of metabolites, drugs, cells, and pathogens exposed to the CNS space. Cellular blood-brain barrier (BBB structures are highly specific checkpoints governing entry and exit of all small molecules to and from the brain interstitial space, but the precise mechanisms that regulate the BBB are not well understood. In addition, the BBB has long been a challenging obstacle to the pharmacologic treatment of CNS diseases; thus model systems that can parse the functions of the BBB are highly desirable. In this study, we sought to define the transcriptome of the adult Drosophila melanogaster BBB by isolating the BBB surface glia with FACS and profiling their gene expression with microarrays. By comparing the transcriptome of these surface glia to that of all brain glia, brain neurons, and whole brains, we present a catalog of transcripts that are selectively enriched at the Drosophila BBB. We found that the fly surface glia show high expression of many ABC and SLC transporters, cell adhesion molecules, metabolic enzymes, signaling molecules, and components of xenobiotic metabolism pathways. Using gene sequence-based alignments, we compare the Drosophila and Murine BBB transcriptomes and discover many shared chemoprotective and small molecule control pathways, thus affirming the relevance of invertebrate models for studying evolutionary conserved BBB properties. The Drosophila BBB transcriptome is valuable to vertebrate and insect biologists alike as a resource for studying proteins underlying diffusion barrier development and maintenance, glial biology, and regulation of drug transport at tissue barriers.

  6. The Drosophila surface glia transcriptome: evolutionary conserved blood-brain barrier processes.

    Science.gov (United States)

    DeSalvo, Michael K; Hindle, Samantha J; Rusan, Zeid M; Orng, Souvinh; Eddison, Mark; Halliwill, Kyle; Bainton, Roland J

    2014-01-01

    Central nervous system (CNS) function is dependent on the stringent regulation of metabolites, drugs, cells, and pathogens exposed to the CNS space. Cellular blood-brain barrier (BBB) structures are highly specific checkpoints governing entry and exit of all small molecules to and from the brain interstitial space, but the precise mechanisms that regulate the BBB are not well understood. In addition, the BBB has long been a challenging obstacle to the pharmacologic treatment of CNS diseases; thus model systems that can parse the functions of the BBB are highly desirable. In this study, we sought to define the transcriptome of the adult Drosophila melanogaster BBB by isolating the BBB surface glia with fluorescence activated cell sorting (FACS) and profiling their gene expression with microarrays. By comparing the transcriptome of these surface glia to that of all brain glia, brain neurons, and whole brains, we present a catalog of transcripts that are selectively enriched at the Drosophila BBB. We found that the fly surface glia show high expression of many ATP-binding cassette (ABC) and solute carrier (SLC) transporters, cell adhesion molecules, metabolic enzymes, signaling molecules, and components of xenobiotic metabolism pathways. Using gene sequence-based alignments, we compare the Drosophila and Murine BBB transcriptomes and discover many shared chemoprotective and small molecule control pathways, thus affirming the relevance of invertebrate models for studying evolutionary conserved BBB properties. The Drosophila BBB transcriptome is valuable to vertebrate and insect biologists alike as a resource for studying proteins underlying diffusion barrier development and maintenance, glial biology, and regulation of drug transport at tissue barriers.

  7. Polycomb repressive complex's evolutionary conserved function: the role of EZH2 status and cellular background.

    Science.gov (United States)

    Gall Trošelj, Koraljka; Novak Kujundzic, Renata; Ugarkovic, Djurdjica

    2016-01-01

    When assembled in multiprotein polycomb repressive complexes (PRCs), highly evolutionary conserved polycomb group (PcG) proteins epigenetically control gene activity. Although the composition of PRCs may vary considerably, it is well established that the embryonic ectoderm development (EED) 1, suppressor of zeste (SUZ) 12, and methyltransferase enhancer of zeste (EZH2)-containing complex, PRC2, which is abundant in highly proliferative cells (including cancer cells), establishes a repressive methylation mark on histone 3 (H3K27me3). From the perspective of molecular cancer pathogenesis, this effect, when directed towards a promoter of tumor suppressor genes, represents pro-tumorigenic effect. This mode of action was shown in several cancer models. However, EZH2 function extends beyond this scenario. The highly specific cellular background, related to the origin of cell and numerous external stimuli during a given time-window, may be the trigger for EZH2 interaction with other proteins, not necessarily histones. This is particularly relevant for cancer. This review provides a critical overview of the evolutional importance of PRC and discusses several important aspects of EZH2 functioning within PRC. The review also deals with mutational studies on EZH2. Due to the existence of several protein (and messenger RNA (mRNA)) isoforms, these mutations were stratified, using the protein sequence which is considered canonical. This approach showed that there is an urgent need for the uniformed positioning of currently known EZH2 mutations (somatic-in tumors, as well as germline mutations in the Weaver's syndrome). Finally, we discuss EZH2 function with respect to amount of trimethylated H3K27, in a specific cellular milieu, through presenting the most recent data related to EZH2-H3K27m3 relationship in cancer. All these points are significant in considering EZH2 as a therapeutic target.

  8. Dynamic routing problems with fruitful regions: models and evolutionary computation

    NARCIS (Netherlands)

    J.I. van Hemert; J.A. La Poutré (Han)

    2004-01-01

    textabstractWe introduce the concept of fruitful regions in a dynamic routing context: regions that have a high potential of generating loads to be transported. The objective is to maximise the number of loads transported, while keeping to capacity and time constraints. Loads arrive while the

  9. Phylogeography of Camellia taliensis (Theaceae) inferred from chloroplast and nuclear DNA: insights into evolutionary history and conservation

    Science.gov (United States)

    2012-01-01

    Background As one of the most important but seriously endangered wild relatives of the cultivated tea, Camellia taliensis harbors valuable gene resources for tea tree improvement in the future. The knowledge of genetic variation and population structure may provide insights into evolutionary history and germplasm conservation of the species. Results Here, we sampled 21 natural populations from the species' range in China and performed the phylogeography of C. taliensis by using the nuclear PAL gene fragment and chloroplast rpl32-trnL intergenic spacer. Levels of haplotype diversity and nucleotide diversity detected at rpl32-trnL (h = 0.841; π = 0.00314) were almost as high as at PAL (h = 0.836; π = 0.00417). Significant chloroplast DNA population subdivision was detected (GST = 0.988; NST = 0.989), suggesting fairly high genetic differentiation and low levels of recurrent gene flow through seeds among populations. Nested clade phylogeographic analysis of chlorotypes suggests that population genetic structure in C. taliensis has been affected by habitat fragmentation in the past. However, the detection of a moderate nrDNA population subdivision (GST = 0.222; NST = 0.301) provided the evidence of efficient pollen-mediated gene flow among populations and significant phylogeographical structure (NST > GST; P < 0.01). The analysis of PAL haplotypes indicates that phylogeographical pattern of nrDNA haplotypes might be caused by restricted gene flow with isolation by distance, which was also supported by Mantel’s test of nrDNA haplotypes (r = 0.234, P < 0.001). We found that chlorotype C1 was fixed in seven populations of Lancang River Region, implying that the Lancang River might have provided a corridor for the long-distance dispersal of the species. Conclusions We found that C. taliensis showed fairly high genetic differentiation resulting from restricted gene flow and habitat fragmentation. This phylogeographical

  10. Conservation of regional gene expression in mouse and human brain.

    Directory of Open Access Journals (Sweden)

    Andrew D Strand

    2007-04-01

    Full Text Available Many neurodegenerative diseases have a hallmark regional and cellular pathology. Gene expression analysis of healthy tissues may provide clues to the differences that distinguish resistant and sensitive tissues and cell types. Comparative analysis of gene expression in healthy mouse and human brain provides a framework to explore the ability of mice to model diseases of the human brain. It may also aid in understanding brain evolution and the basis for higher order cognitive abilities. Here we compare gene expression profiles of human motor cortex, caudate nucleus, and cerebellum to one another and identify genes that are more highly expressed in one region relative to another. We separately perform identical analysis on corresponding brain regions from mice. Within each species, we find that the different brain regions have distinctly different expression profiles. Contrasting between the two species shows that regionally enriched genes in one species are generally regionally enriched genes in the other species. Thus, even when considering thousands of genes, the expression ratios in two regions from one species are significantly correlated with expression ratios in the other species. Finally, genes whose expression is higher in one area of the brain relative to the other areas, in other words genes with patterned expression, tend to have greater conservation of nucleotide sequence than more widely expressed genes. Together these observations suggest that region-specific genes have been conserved in the mammalian brain at both the sequence and gene expression levels. Given the general similarity between patterns of gene expression in healthy human and mouse brains, we believe it is reasonable to expect a high degree of concordance between microarray phenotypes of human neurodegenerative diseases and their mouse models. Finally, these data on very divergent species provide context for studies in more closely related species that address

  11. The 3D organization of chromatin explains evolutionary fragile genomic regions.

    Science.gov (United States)

    Berthelot, Camille; Muffato, Matthieu; Abecassis, Judith; Roest Crollius, Hugues

    2015-03-24

    Genomic rearrangements are a major source of evolutionary divergence in eukaryotic genomes, a cause of genetic diseases and a hallmark of tumor cell progression, yet the mechanisms underlying their occurrence and evolutionary fixation are poorly understood. Statistical associations between breakpoints and specific genomic features suggest that genomes may contain elusive “fragile regions” with a higher propensity for breakage. Here, we use ancestral genome reconstructions to demonstrate a near-perfect correlation between gene density and evolutionary rearrangement breakpoints. Simulations based on functional features in the human genome show that this pattern is best explained as the outcome of DNA breaks that occur in open chromatin regions coming into 3D contact in the nucleus. Our model explains how rearrangements reorganize the order of genes in an evolutionary neutral fashion and provides a basis for understanding the susceptibility of “fragile regions” to breakage.

  12. The 3D Organization of Chromatin Explains Evolutionary Fragile Genomic Regions

    Directory of Open Access Journals (Sweden)

    Camille Berthelot

    2015-03-01

    Full Text Available Genomic rearrangements are a major source of evolutionary divergence in eukaryotic genomes, a cause of genetic diseases and a hallmark of tumor cell progression, yet the mechanisms underlying their occurrence and evolutionary fixation are poorly understood. Statistical associations between breakpoints and specific genomic features suggest that genomes may contain elusive “fragile regions” with a higher propensity for breakage. Here, we use ancestral genome reconstructions to demonstrate a near-perfect correlation between gene density and evolutionary rearrangement breakpoints. Simulations based on functional features in the human genome show that this pattern is best explained as the outcome of DNA breaks that occur in open chromatin regions coming into 3D contact in the nucleus. Our model explains how rearrangements reorganize the order of genes in an evolutionary neutral fashion and provides a basis for understanding the susceptibility of “fragile regions” to breakage.

  13. The relevance of the Mediterranean Region to colonial waterbird conservation

    Science.gov (United States)

    Erwin, R.M.; Crivelli, Alain J.; Hafner, Heinz; Fasola, Mauro; Erwin, R. Michael; McCrimmon, Donald A.=

    1996-01-01

    The Mediterranean Sea is the largest partially enclosed sea in the world and provides habitat to more than 100 species of waterbirds from the Palearctic-North African-Middle Eastern regions. Even though the Mediterranean suffers from pollution, has little tidal influence, and is oligotrophic, more than half of the western Palearctic populations of numerous waterfowl species winter in the region. Thirty-three species of colonial waterbirds breed along the 46,000 km Mediterranean coastline with nine species considered threatened or endangered, mostly because of wetland loss and degradation. The long history of human activity and scientific investigations in the region has taught some valuable lessons. In the area of colonial waterbird biology and conservation, we have learned important lessons about the value of long-term monitoring and research on selected populations. From marking studies of Greater Flamingos (Phoenicopterus ruber roseus) and Little Egrets (Egretta garzetta) results have been used to derive useful information about metapopulation dynamics. Involvement of both African and European biologists allowed year-round Studies of these species that yielded valuable spin-offs for training in avian and wetland conservation. We have also learned the value of man-made wetlands as feeding and nesting sites for some colonial waterbirds. Careful evaluations of the habitat quality of different types of wetlands are required, as in contaminant levels such as lead shot and pesticides. Wetland conservationists have also learned from some instructive mistakes. Dam construction and agricultural incentive programs sponsored by the European Community, the World Bank, and others from the past have largely ignored impacts on wetlands and wildlife. In some areas, economic ventures such as aquaculture operations and salt mining have not involved waterbird habitat needs in their planning. Research and conservation needs include: (1) establishing regional monitoring programs and

  14. A new region of conservation is defined between human and mouse X chromosomes

    Energy Technology Data Exchange (ETDEWEB)

    Dinulos, M.B.; Disteche, C.M. [Univ. of Washington, Seattle, WA (United States); Bassi, M.T. [Univ. of Siena (Italy)] [and others

    1996-07-01

    Comparative mapping of the X chromosome in eutherian mammals have revealed distinct regions of conservation as well as evolutionary rearrangements between human and mouse. Recently, we and others mapped the murine homologue of CLCN4 (Chloride channel 4) to band F4 of the X chromosome in Mus spretus but to chromosome 7 in laboratory strains. We now report the mapping of the murine homologues of APXL (Apical protein Xenopus laevis-like) and OA1 (Ocular albinism type I), two genes that are located on the human X chromosome at band p22.3 and in close proximity to CLCN4. Interestingly, Oa1 and Apxl map to bands F2-F3 in both M. spretus and the laboratory strain C57BL/6J, defining a new rearrangement between human and mouse X chromosomes. 17 refs., 2 figs., 1 tab.

  15. [Morphologic variation of the parthenogenetic lizard Aspidoscelis rodecki (Squamata: Teiidae): evolutionary and conservation implications].

    Science.gov (United States)

    Elizalde-Rocha, Sandra P; Méndez-de la Cruz, Fausto R; Méndez-Sánchez, J Fernando; Granados-González, Gisela; Hernândez-Gallegos, Oswaldo

    2008-12-01

    Post-formational divergence has been used for the recognition of new parthenogenetic species. Currently, the parthenogenetic lizard Aspidoscelis rodecki McCoy and Maslin 1962 is recognized as a single taxon that was derived from a single, parthenogenetically capable, hybrid. This lizard had been derived via hybridization between individuals of two gonochoristic species, Aspidoscelis ungusticeps Cope 1878 and Aspidoscelis deppii Wiegmann 1834. The distribution of A. rodecki includes Isla Contoy and Isla Mujeres and the adjacent mainland of Quintana Roo, México. Previous studies have found post-formational divergence in genetic, chromatic and life-history characteristics among a continental population (Puerto Juárez) and an insular population (Isla Contoy). A meristic analysis was carried out to evaluate the morphological divergence among both populations of A. rodecki. We used 38 individuals from Puerto Juárez and 23 individuals from Isla Contoy. Nine meristic characters with discrimination value among species of the genus Aspidoscelis were used in both univariate (t-Student) and multivariate analyses (principal components and canonical variate analysis). According to both analyses, Puerto Juárez is meristically distinguishable from Isla Contoy. Both populations differ in five meristic characters and were a high correct classification in the canonical variate analysis: 97% of Puerto Juárez and 100% of Isla Contoy. A small sample from Isla Mujeres and a single specimen from Punta Sam (mainland) may represent different morphological groups. Due to the patterns of phenotypic variation, A. rodecki is considered as a single variable parthenogenetic species with high priority to conservation. The populations of A. rodecki have been extremely affected by the tourism developers. If the habitat of the parthenogenetic lizard (beach grasses) is allowed to stay, the expansion by the developers will not affect the survivorship of these populations. Nevertheless, the first

  16. Evolutionary Game Analysis of Co-opetition Relationship between Regional Logistics Nodes

    Directory of Open Access Journals (Sweden)

    D.Z. Wang

    2014-04-01

    Full Text Available The evolutionary game of co-opetition relationship between regional logistics nodes is studied in this paper. A replicator dynamic model is built to obtain the Evolutionary Stable Strategy (ESS of the game. Then, according to the status and level of logistics nodes, the symmetric and asymmetric game models based on evolutionary game theory are proposed, respectively. The former is used to analyze the changing trends of co-opetition relationship between logistics nodes from a same layer of a logistics network. While the latter can be used to deal with the relationship forecasting problems between logistics nodes from different layers. The result of the case study reveals that the proposed models have good practicability and accuracy in dealing with the relationship forecasting problems within a regional logistics network.

  17. Evolutionary analysis of DNA-protein-coding regions based on a genetic code cube metric.

    Science.gov (United States)

    Sanchez, Robersy

    2014-01-01

    The right estimation of the evolutionary distance between DNA or protein sequences is the cornerstone of the current phylogenetic analysis based on distance methods. Herein, it is demonstrated that the Manhattan distance (dw), weighted by the evolutionary importance of the nucleotide bases in the codon, is a naturally derived metric in the standard genetic code cube inserted into the three-dimensional Euclidean space. Based on the application of distance dw, a novel evolutionary model is proposed. This model includes insertion/deletion mutations that are very important for cancer studies, but usually discarded in classical evolutionary models. In this study, the new evolutionary model was applied to the phylogenetic analysis of the DNA protein-coding regions of 13 mammal mitochondrial genomes and of four cancer genetic- susceptibility genes (ATM, BRCA1, BRCA2 and p53) from nine mammals. The opossum (a marsupial) was used as an out-group species for both sets of sequences. The new evolutionary model yielded the correct topology, while the current models failed to separate the evolutionarily distant species of mouse and opossum.

  18. Integrating regional conservation priorities for multiple objectives into national policy

    Science.gov (United States)

    Beger, Maria; McGowan, Jennifer; Treml, Eric A.; Green, Alison L.; White, Alan T.; Wolff, Nicholas H.; Klein, Carissa J.; Mumby, Peter J.; Possingham, Hugh P.

    2015-01-01

    Multinational conservation initiatives that prioritize investment across a region invariably navigate trade-offs among multiple objectives. It seems logical to focus where several objectives can be achieved efficiently, but such multi-objective hotspots may be ecologically inappropriate, or politically inequitable. Here we devise a framework to facilitate a regionally cohesive set of marine-protected areas driven by national preferences and supported by quantitative conservation prioritization analyses, and illustrate it using the Coral Triangle Initiative. We identify areas important for achieving six objectives to address ecosystem representation, threatened fauna, connectivity and climate change. We expose trade-offs between areas that contribute substantially to several objectives and those meeting one or two objectives extremely well. Hence there are two strategies to guide countries choosing to implement regional goals nationally: multi-objective hotspots and complementary sets of single-objective priorities. This novel framework is applicable to any multilateral or global initiative seeking to apply quantitative information in decision making. PMID:26364769

  19. Evolutionary conservation of an atypical glucocorticoid-responsive element in the human tyrosine hydroxylase gene.

    Science.gov (United States)

    Sheela Rani, C S; Soto-Pina, Alexandra; Iacovitti, Lorraine; Strong, Randy

    2013-07-01

    The human tyrosine hydroxylase (hTH) gene has a 42 bp evolutionarily conserved region designated (CR) II at -7.24 kb, which bears 93% homology to the region we earlier identified as containing the glucocorticoid response element, a 7 bp activator protein-1 (AP-1)-like motif in the rat TH gene. We cloned this hTH-CRII region upstream of minimal basal hTH promoter in luciferase (Luc) reporter vector, and tested glucocorticoid responsiveness in human cell lines. Dexamethasone (Dex) stimulated Luc activity of hTH-CRII in HeLa cells, while mifepristone, a glucocorticoid receptor (GR) antagonist, prevented Dex stimulation. Deletion of the 7 bp 5'-TGACTAA at -7243 bp completely abolished the Dex-stimulated Luc activity of hTH-CRII construct. The AP-1 agonist, tetradeconoyl-12,13-phorbol acetate (TPA), also stimulated hTH promoter activity, and Dex and TPA together further accentuated this response. Chromatin immunoprecipitation assays revealed the presence of both GR and AP-1 proteins, especially Jun family members, at this hTH promoter site. Dex did not stimulate hTH promoter activity in a catecholaminergic cell line, which had low endogenous GR levels, but did activate the response when GR was expressed exogenously. Thus, our studies have clearly identified a glucocorticoid-responsive element in a 7 bp AP-1-like motif in the promoter region at -7.24 kb of the human TH gene. © 2013 International Society for Neurochemistry.

  20. Conserved Units of Co-Expression in Bacterial Genomes: An Evolutionary Insight into Transcriptional Regulation

    Science.gov (United States)

    Junier, Ivan; Rivoire, Olivier

    2016-01-01

    Genome-wide measurements of transcriptional activity in bacteria indicate that the transcription of successive genes is strongly correlated beyond the scale of operons. Here, we analyze hundreds of bacterial genomes to identify supra-operonic segments of genes that are proximal in a large number of genomes. We show that these synteny segments correspond to genomic units of strong transcriptional co-expression. Structurally, the segments contain operons with specific relative orientations (co-directional or divergent) and nucleoid-associated proteins are found to bind at their boundaries. Functionally, operons inside a same segment are highly co-expressed even in the apparent absence of regulatory factors at their promoter regions. Remote operons along DNA can also be co-expressed if their corresponding segments share a transcriptional or sigma factor, without requiring these factors to bind directly to the promoters of the operons. As evidence that these results apply across the bacterial kingdom, we demonstrate them both in the Gram-negative bacterium Escherichia coli and in the Gram-positive bacterium Bacillus subtilis. The underlying process that we propose involves only RNA-polymerases and DNA: it implies that the transcription of an operon mechanically enhances the transcription of adjacent operons. In support of a primary role of this regulation by facilitated co-transcription, we show that the transcription en bloc of successive operons as a result of transcriptional read-through is strongly and specifically enhanced in synteny segments. Finally, our analysis indicates that facilitated co-transcription may be evolutionary primitive and may apply beyond bacteria. PMID:27195891

  1. Evidence of a Direct Evolutionary Selection for Strong Folding and Mutational Robustness Within HIV Coding Regions.

    Science.gov (United States)

    Goz, Eli; Tuller, Tamir

    2016-08-01

    A large number of studies demonstrated the importance of different HIV RNA structural elements at all stages of the viral life cycle. Nevertheless, the significance of many of these structures is unknown, and plausibly new regions containing RNA structure-mediated regulatory signals remain to be identified. An important characteristic of genomic regions carrying functionally significant secondary structures is their mutational robustness, that is, the extent to which a sequence remains constant in spite of despite mutations in terms of its underlying secondary structure. Structural robustness to mutations is expected to be important in the case of functional RNA structures in viruses with high mutation rate; it may prevent fitness loss due to disruption of possibly functional conformations, pointing to the specific significance of the corresponding genomic region. In the current work, we perform a genome-wide computational analysis to detect signals of a direct evolutionary selection for strong folding and RNA structure-based mutational robustness within HIV coding sequences. We provide evidence that specific regions of HIV structural genes undergo an evolutionary selection for strong folding; in addition, we demonstrate that HIV Rev responsive element seems to undergo a direct evolutionary selection for increased secondary structure robustness to point mutations. We believe that our analysis may enable a better understanding of viral evolutionary dynamics at the RNA structural level and may benefit to practical efforts of engineering antiviral vaccines and novel therapeutic approaches.

  2. In situ conservation-harnessing natural and human-derived evolutionary forces to ensure future crop adaptation.

    Science.gov (United States)

    Bellon, Mauricio R; Dulloo, Ehsan; Sardos, Julie; Thormann, Imke; Burdon, Jeremy J

    2017-12-01

    Ensuring the availability of the broadest possible germplasm base for agriculture in the face of increasingly uncertain and variable patterns of biotic and abiotic change is fundamental for the world's future food supply. While ex situ conservation plays a major role in the conservation and availability of crop germplasm, it may be insufficient to ensure this. In situ conservation aims to maintain target species and the collective genotypes they represent under evolution. A major rationale for this view is based on the likelihood that continued exposure to changing selective forces will generate and favor new genetic variation and an increased likelihood that rare alleles that may be of value to future agriculture are maintained. However, the evidence that underpins this key rationale remains fragmented and has not been examined systematically, thereby decreasing the perceived value and support for in situ conservation for agriculture and food systems and limiting the conservation options available. This study reviews evidence regarding the likelihood and rate of evolutionary change in both biotic and abiotic traits for crops and their wild relatives, placing these processes in a realistic context in which smallholder farming operates and crop wild relatives continue to exist. It identifies areas of research that would contribute to a deeper understanding of these processes as the basis for making them more useful for future crop adaptation.

  3. Evolutionary analysis of two complement C4 genes: Ancient duplication and conservation during jawed vertebrate evolution.

    Science.gov (United States)

    Nonaka, Mayumi I; Terado, Tokio; Kimura, Hiroshi; Nonaka, Masaru

    2017-03-01

    The complement C4 is a thioester-containing protein, and a histidine (H) residue catalyzes the cleavage of the thioester to allow covalent binding to carbohydrates on target cells. Some mammalian and teleost species possess an additional isotype where the catalytic H is replaced by an aspartic acid (D), which binds preferentially to proteins. We found the two C4 isotypes in many other jawed vertebrates, including sharks and birds/reptiles. Phylogenetic analysis suggested that C4 gene duplication occurred in the early days of the jawed vertebrate evolution. The D-type C4 of bony fish except for mammals formed a cluster, termed D-lineage. The D-lineage genes were located in a syntenic region outside MHC, and evolved conservatively. Mammals lost the D-lineage before speciation, but D-type C4 was regenerated by recent gene duplication in some mammalian species or groups. Dual C4 molecules with different substrate specificities would have contributed to development of the antibody-dependent classical pathway. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Deciphering the cause of evolutionary variance within intrinsically disordered regions in human proteins.

    Science.gov (United States)

    Banerjee, Sanghita; Chakraborty, Sandip; De, Rajat K

    2017-02-01

    Why the intrinsically disordered regions evolve within human proteome has became an interesting question for a decade. Till date, it remains an unsolved yet an intriguing issue to investigate why some of the disordered regions evolve rapidly while the rest are highly conserved across mammalian species. Identifying the key biological factors, responsible for the variation in the conservation rate of different disordered regions within the human proteome, may revisit the above issue. We emphasized that among the other biological features (multifunctionality, gene essentiality, protein connectivity, number of unique domains, gene expression level and expression breadth) considered in our study, the number of unique protein domains acts as a strong determinant that negatively influences the conservation of disordered regions. In this context, we justified that proteins having a fewer types of domains preferably need to conserve their disordered regions to enhance their structural flexibility which in turn will facilitate their molecular interactions. In contrast, the selection pressure acting on the stretches of disordered regions is not so strong in the case of multi-domains proteins. Therefore, we reasoned that the presence of conserved disordered stretches may compensate the functions of multiple domains within a single domain protein. Interestingly, we noticed that the influence of the unique domain number and expression level acts differently on the evolution of disordered regions from that of well-structured ones.

  5. Disentangling evolutionary signals: conservation, specificity determining positions and coevolution. Implication for catalytic residue prediction

    DEFF Research Database (Denmark)

    Teppa, Elin; Wilkins, Angela D.; Nielsen, Morten

    2012-01-01

    predictive potential compared to others when it comes to, in particular, the identification of catalytic residues (CR) in proteins. Using a large set of enzymatic protein families and measures based on different evolutionary signals, we sought to break up the different components of the information content......Background: A large panel of methods exists that aim to identify residues with critical impact on protein function based on evolutionary signals, sequence and structure information. However, it is not clear to what extent these different methods overlap, and if any of the methods have higher...... within a multiple sequence alignment to investigate their predictive potential and degree of overlap. Results: Our results demonstrate that the different methods included in the benchmark in general can be divided into three groups with a limited mutual overlap. One group containing real...

  6. Using evolutionary conserved modules in gene networks as a strategy to leverage high throughput gene expression queries.

    Directory of Open Access Journals (Sweden)

    Jeanne M Serb

    Full Text Available BACKGROUND: Large-scale gene expression studies have not yielded the expected insight into genetic networks that control complex processes. These anticipated discoveries have been limited not by technology, but by a lack of effective strategies to investigate the data in a manageable and meaningful way. Previous work suggests that using a pre-determined seed-network of gene relationships to query large-scale expression datasets is an effective way to generate candidate genes for further study and network expansion or enrichment. Based on the evolutionary conservation of gene relationships, we test the hypothesis that a seed network derived from studies of retinal cell determination in the fly, Drosophila melanogaster, will be an effective way to identify novel candidate genes for their role in mouse retinal development. METHODOLOGY/PRINCIPAL FINDINGS: Our results demonstrate that a number of gene relationships regulating retinal cell differentiation in the fly are identifiable as pairwise correlations between genes from developing mouse retina. In addition, we demonstrate that our extracted seed-network of correlated mouse genes is an effective tool for querying datasets and provides a context to generate hypotheses. Our query identified 46 genes correlated with our extracted seed-network members. Approximately 54% of these candidates had been previously linked to the developing brain and 33% had been previously linked to the developing retina. Five of six candidate genes investigated further were validated by experiments examining spatial and temporal protein expression in the developing retina. CONCLUSIONS/SIGNIFICANCE: We present an effective strategy for pursuing a systems biology approach that utilizes an evolutionary comparative framework between two model organisms, fly and mouse. Future implementation of this strategy will be useful to determine the extent of network conservation, not just gene conservation, between species and will

  7. Phylogeography of Camellia taliensis (Theaceae) inferred from chloroplast and nuclear DNA: insights into evolutionary history and conservation.

    Science.gov (United States)

    Liu, Yang; Yang, Shi-xiong; Ji, Peng-zhang; Gao, Li-zhi

    2012-06-21

    As one of the most important but seriously endangered wild relatives of the cultivated tea, Camellia taliensis harbors valuable gene resources for tea tree improvement in the future. The knowledge of genetic variation and population structure may provide insights into evolutionary history and germplasm conservation of the species. Here, we sampled 21 natural populations from the species' range in China and performed the phylogeography of C. taliensis by using the nuclear PAL gene fragment and chloroplast rpl32-trnL intergenic spacer. Levels of haplotype diversity and nucleotide diversity detected at rpl32-trnL (h = 0.841; π = 0.00314) were almost as high as at PAL (h = 0.836; π = 0.00417). Significant chloroplast DNA population subdivision was detected (GST = 0.988; NST = 0.989), suggesting fairly high genetic differentiation and low levels of recurrent gene flow through seeds among populations. Nested clade phylogeographic analysis of chlorotypes suggests that population genetic structure in C. taliensis has been affected by habitat fragmentation in the past. However, the detection of a moderate nrDNA population subdivision (GST = 0.222; NST = 0.301) provided the evidence of efficient pollen-mediated gene flow among populations and significant phylogeographical structure (NST > GST; P conservation strategies for germplasm sampling and developing in situ conservation of natural populations.

  8. Conservation genomics reveals multiple evolutionary units within Bell’s Vireo (Vireo bellii).

    Science.gov (United States)

    Klicka, Luke B.; Kus, Barbara E.; Title, Pascal O.; Burns, Kevin J.

    2016-01-01

    The Bell’s Vireo (Vireo bellii) is a widespread North American species of bird that has declined since the mid-1960s primarily due to habitat modification. Throughout its range, Bell’s Vireo populations are regulated under varying degrees of protection; however, the species has never been characterized genetically. Therefore, the current taxonomy used to guide management decisions may misrepresent the true evolutionary history for the species. We sequenced 86 individuals for ND2 and genotyped 48 individuals for genome-wide SNPs to identify distinct lineages within Bell’s Vireo. Phylogenetic analyses uncovered two distinct clades that are separated in the arid southwestern United States, near the border of the Chihuahuan and Sonoran Deserts. These clades diverged from each other approximately 1.11–2.04 mya. The timing of diversification, geographic location, and niche modeling of the east/west divergence suggest vicariance as a mode of diversification for these two lineages. Analyses of the SNP dataset provided additional resolution and indicated the Least Bell’s Vireo populations are a distinct evolutionary lineage. Our genetic evidence, together with information from morphology and behavior, suggests that the Bell’s Vireo complex involves two species, each containing two separate subspecies. This new information has implications for the federal, state and other listing status of Bell’s Vireo throughout its range.

  9. Structural proteomics of minimal organisms: conservation ofprotein fold usage and evolutionary implications

    Energy Technology Data Exchange (ETDEWEB)

    Chandonia, John-Marc; Kim, Sung-Hou

    2006-03-15

    Background: Determining the complete repertoire of proteinstructures for all soluble, globular proteins in a single organism hasbeen one of the major goals of several structural genomics projects inrecent years. Results: We report that this goal has nearly been reachedfor several "minimal organisms"--parasites or symbionts with reducedgenomes--for which over 95 percent of the soluble, globular proteins maynow be assigned folds, overall 3-D backbone structures. We analyze thestructures of these proteins as they relate to cellular functions, andcompare conservation off old usage between functional categories. We alsocompare patterns in the conservation off olds among minimal organisms andthose observed between minimal organisms and other bacteria. Conclusion:We find that proteins performing essential cellular functions closelyrelated to transcription and translation exhibit a higher degree ofconservation in fold usage than proteins in other functional categories.Folds related to transcription and translation functional categories werealso over represented in minimal organisms compared to otherbacteria.

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

    Directory of Open Access Journals (Sweden)

    Igor R. Costa

    2014-12-01

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

  11. Integrated Migratory Bird Planning in the Lower Great Lakes/St. Lawrence Plain Bird Conservation Region

    Science.gov (United States)

    Chuck Hayes; Andrew Milliken; Randy Dettmers; Kevin Loftus; Brigitte Collins; Isabelle Ringuet

    2005-01-01

    The Atlantic Coast and Eastern Habitat Joint Ventures hosted two international planning workshops to begin the process of integrating bird conservation strategies under the North American Bird Conservation Initiative in the Lower Great Lakes/St. Lawrence Plain Bird Conservation Region. The workshops identified priority species and habitats, delineated focus areas,...

  12. 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.

  13. Antibodies directed against monomorphic and evolutionary conserved self epitopes may be generated in 'knock-out' mice. Development of monoclonal antibodies directed against monomorphic MHC class I determinants

    DEFF Research Database (Denmark)

    Claesson, M H; Endel, B; Ulrik, J

    1994-01-01

    of culture. It is concluded that MoAbs reacting with monomorphic self epitopes may be generated using animals deleted of the gene of interest. The implications may be far reaching since such MoAbs potentially identify evolutionary conserved and physiologically important epitopes....

  14. Evolutionary Conservation and Diversification of the Translation Initiation Apparatus in Trypanosomatids

    Directory of Open Access Journals (Sweden)

    Alexandra Zinoviev

    2012-01-01

    Full Text Available Trypanosomatids are ancient eukaryotic parasites that migrate between insect vectors and mammalian hosts, causing a range of diseases in humans and domestic animals. Trypanosomatids feature a multitude of unusual molecular features, including polycistronic transcription and subsequent processing by trans-splicing and polyadenylation. Regulation of protein coding genes is posttranscriptional and thus, translation regulation is fundamental for activating the developmental program of gene expression. The spliced-leader RNA is attached to all mRNAs. It contains an unusual hypermethylated cap-4 structure in its 5 end. The cap-binding complex, eIF4F, has gone through evolutionary changes in accordance with the requirement to bind cap-4. The eIF4F components in trypanosomatids are highly diverged from their orthologs in higher eukaryotes, and their potential functions are discussed. The cap-binding activity in all eukaryotes is a target for regulation and plays a similar role in trypanosomatids. Recent studies revealed a novel eIF4E-interacting protein, involved in directing stage-specific and stress-induced translation pathways. Translation regulation during stress also follows unusual regulatory cues, as the increased translation of Hsp83 following heat stress is driven by a defined element in the 3 UTR, unlike higher eukaryotes. Overall, the environmental switches experienced by trypanosomatids during their life cycle seem to affect their translational machinery in unique ways.

  15. New Insights on Coffea miRNAs: Features and Evolutionary Conservation.

    Science.gov (United States)

    Chaves, S S; Fernandes-Brum, C N; Silva, G F F; Ferrara-Barbosa, B C; Paiva, L V; Nogueira, F T S; Cardoso, T C S; Amaral, L R; de Souza Gomes, M; Chalfun-Junior, A

    2015-10-01

    Small RNAs influence the gene expression at the post-transcriptional level by guiding messenger RNA (mRNA) cleavage, translational repression, and chromatin modifications. In addition to model plants, the microRNAs (miRNAs) have been identified in different crop species. In this work, we developed a specific pipeline to search for coffee miRNA homologs on expressed sequence tags (ESTs) and genome survey sequences (GSS) databases. As a result, 36 microRNAs were identified and a total of 616 and 362 potential targets for Coffea arabica and Coffea canephora, respectively. The evolutionary analyses of these molecules were performed by comparing the primary and secondary structures of precursors and mature miRNAs with their orthologs. Moreover, using a stem-loop RT-PCR assay, we evaluated the accumulation of mature miRNAs in genomes with different ploidy levels, detecting an increase in the miRNAs accumulation according to the ploidy raising. Finally, a 5' RACE (Rapid Amplification of cDNA Ends) assay was performed to verify the regulation of auxin responsive factor 8 (ARF8) by MIR167 in coffee plants. The great variety of target genes indicates the functional plasticity of these molecules and reinforces the importance of understanding the RNAi-dependent regulatory mechanisms. Our results expand the study of miRNAs and their target genes in this crop, providing new challenges to understand the biology of these species.

  16. Phylogeography of Camellia taliensis (Theaceae inferred from chloroplast and nuclear DNA: insights into evolutionary history and conservation

    Directory of Open Access Journals (Sweden)

    Liu Yang

    2012-06-01

    Full Text Available Abstract Background As one of the most important but seriously endangered wild relatives of the cultivated tea, Camellia taliensis harbors valuable gene resources for tea tree improvement in the future. The knowledge of genetic variation and population structure may provide insights into evolutionary history and germplasm conservation of the species. Results Here, we sampled 21 natural populations from the species' range in China and performed the phylogeography of C. taliensis by using the nuclear PAL gene fragment and chloroplast rpl32-trnL intergenic spacer. Levels of haplotype diversity and nucleotide diversity detected at rpl32-trnL (h = 0.841; π = 0.00314 were almost as high as at PAL (h = 0.836; π = 0.00417. Significant chloroplast DNA population subdivision was detected (GST = 0.988; NST = 0.989, suggesting fairly high genetic differentiation and low levels of recurrent gene flow through seeds among populations. Nested clade phylogeographic analysis of chlorotypes suggests that population genetic structure in C. taliensis has been affected by habitat fragmentation in the past. However, the detection of a moderate nrDNA population subdivision (GST = 0.222; NST = 0.301 provided the evidence of efficient pollen-mediated gene flow among populations and significant phylogeographical structure (NST > GST; P PAL haplotypes indicates that phylogeographical pattern of nrDNA haplotypes might be caused by restricted gene flow with isolation by distance, which was also supported by Mantel’s test of nrDNA haplotypes (r = 0.234, P  Conclusions We found that C. taliensis showed fairly high genetic differentiation resulting from restricted gene flow and habitat fragmentation. This phylogeographical study gives us deep insights into population structure of the species and conservation strategies for germplasm sampling and developing in situ conservation of natural populations.

  17. An Evolutionary-Conserved Function of Mammalian Notch Family Members as Cell Adhesion Molecules

    Science.gov (United States)

    Murata, Akihiko; Yoshino, Miya; Hikosaka, Mari; Okuyama, Kazuki; Zhou, Lan; Sakano, Seiji; Yagita, Hideo; Hayashi, Shin-Ichi

    2014-01-01

    Notch family members were first identified as cell adhesion molecules by cell aggregation assays in Drosophila studies. However, they are generally recognized as signaling molecules, and it was unclear if their adhesion function was restricted to Drosophila. We previously demonstrated that a mouse Notch ligand, Delta-like 1 (Dll1) functioned as a cell adhesion molecule. We here investigated whether this adhesion function was conserved in the diversified mammalian Notch ligands consisted of two families, Delta-like (Dll1, Dll3 and Dll4) and Jagged (Jag1 and Jag2). The forced expression of mouse Dll1, Dll4, Jag1, and Jag2, but not Dll3, on stromal cells induced the rapid and enhanced adhesion of cultured mast cells (MCs). This was attributed to the binding of Notch1 and Notch2 on MCs to each Notch ligand on the stromal cells themselves, and not the activation of Notch signaling. Notch receptor-ligand binding strongly supported the tethering of MCs to stromal cells, the first step of cell adhesion. However, the Jag2-mediated adhesion of MCs was weaker and unlike other ligands appeared to require additional factor(s) in addition to the receptor-ligand binding. Taken together, these results demonstrated that the function of cell adhesion was conserved in mammalian as well as Drosophila Notch family members. Since Notch receptor-ligand interaction plays important roles in a broad spectrum of biological processes ranging from embryogenesis to disorders, our finding will provide a new perspective on these issues from the aspect of cell adhesion. PMID:25255288

  18. Turning strategy into action: implementing a conservation action plan in the Cape Floristic Region

    CSIR Research Space (South Africa)

    Gelderblom, CM

    2003-07-01

    Full Text Available for conservation. These pressures are predicted to intensify, as the region acts as a magnet for settlement and development. This paper thus describes the development of a conservation action plan for the region, arising from the Cape Action Plan...

  19. Evolutionary Origin and Conserved Structural Building Blocks of Riboswitches and Ribosomal RNAs: Riboswitches as Probable Target Sites for Aminoglycosides Interaction

    Directory of Open Access Journals (Sweden)

    Elnaz Mehdizadeh Aghdam

    2014-05-01

    Full Text Available Purpose: Riboswitches, as noncoding RNA sequences, control gene expression through direct ligand binding. Sporadic reports on the structural relation of riboswitches with ribosomal RNAs (rRNA, raises an interest in possible similarity between riboswitches and rRNAs evolutionary origins. Since aminoglycoside antibiotics affect microbial cells through binding to functional sites of the bacterial rRNA, finding any conformational and functional relation between riboswitches/rRNAs is utmost important in both of medicinal and basic research. Methods: Analysis of the riboswitches structures were carried out using bioinformatics and computational tools. The possible functional similarity of riboswitches with rRNAs was evaluated based on the affinity of paromomycin antibiotic (targeting “A site” of 16S rRNA to riboswitches via docking method. Results: There was high structural similarity between riboswitches and rRNAs, but not any particular sequence based similarity between them was found. The building blocks including "hairpin loop containing UUU", "peptidyl transferase center conserved hairpin A loop"," helix 45" and "S2 (G8 hairpin" as high identical rRNA motifs were detected in all kinds of riboswitches. Surprisingly, binding energies of paromomycin with different riboswitches are considerably better than the binding energy of paromomycin with “16S rRNA A site”. Therefore the high affinity of paromomycin to bind riboswitches in comparison with rRNA “A site” suggests a new insight about riboswitches as possible targets for aminoglycoside antibiotics. Conclusion: These findings are considered as a possible supporting evidence for evolutionary origin of riboswitches/rRNAs and also their role in the exertion of antibiotics effects to design new drugs based on the concomitant effects via rRNA/riboswitches.

  20. Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence.

    Science.gov (United States)

    Yeoh, Yun Kit; Dennis, Paul G; Paungfoo-Lonhienne, Chanyarat; Weber, Lui; Brackin, Richard; Ragan, Mark A; Schmidt, Susanne; Hugenholtz, Philip

    2017-08-09

    Culture-independent molecular surveys of plant root microbiomes indicate that soil type generally has a stronger influence on microbial communities than host phylogeny. However, these studies have mostly focussed on model plants and crops. Here, we examine the root microbiomes of multiple plant phyla including lycopods, ferns, gymnosperms, and angiosperms across a soil chronosequence using 16S rRNA gene amplicon profiling. We confirm that soil type is the primary determinant of root-associated bacterial community composition, but also observe a significant correlation with plant phylogeny. A total of 47 bacterial genera are associated with roots relative to bulk soil microbial communities, including well-recognized plant-associated genera such as Bradyrhizobium, Rhizobium, and Burkholderia, and major uncharacterized lineages such as WPS-2, Ellin329, and FW68. We suggest that these taxa collectively constitute an evolutionarily conserved core root microbiome at this site. This lends support to the inference that a core root microbiome has evolved with terrestrial plants over their 400 million year history.Yeoh et al. study root microbiomes of different plant phyla across a tropical soil chronosequence. They confirm that soil type is the primary determinant of root-associated bacterial communities, but also observe a clear correlation with plant phylogeny and define a core root microbiome at this site.

  1. The Mid-Atlantic Regional Wetland Conservation Effects Assessment Project

    Science.gov (United States)

    Megan Lang; Greg McCarty; Mark Walbridge; Patrick Hunt; Tom Ducey; Clinton Church; Jarrod Miller; Laurel Kluber; Ali Sadeghi; Martin Rabenhorst; Amir Sharifi; In-Young Yeo; Andrew Baldwin; Margaret Palmer; Tom Fisher; Dan Fenstermaher; Sanchul Lee; Owen McDonough; Metthea Yepsen; Liza McFarland; Anne Gustafson; Rebecca Fox; Chris Palardy; William Effland; Mari-Vaughn Johnson; Judy Denver; Scott Ator; Joseph Mitchell; Dennis Whigham

    2016-01-01

    Wetlands impart many important ecosystem services, including maintenance of water quality, regulation of the climate and hydrological flows, and enhancement of biodiversity through the provision of food and habitat. The conversion of natural lands to agriculture has led to broad scale historic wetland loss, but current US Department of Agriculture conservation programs...

  2. Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs

    Directory of Open Access Journals (Sweden)

    Nakai Kenta

    2008-04-01

    Full Text Available Abstract Background Interspecies sequence comparison is a powerful tool to extract functional or evolutionary information from the genomes of organisms. A number of studies have compared protein sequences or promoter sequences between mammals, which provided many insights into genomics. However, the correlation between protein conservation and promoter conservation remains controversial. Results We examined promoter conservation as well as protein conservation for 6,901 human and mouse orthologous genes, and observed a very weak correlation between them. We further investigated their relationship by decomposing it based on functional categories, and identified categories with significant tendencies. Remarkably, the 'ribosome' category showed significantly low promoter conservation, despite its high protein conservation, and the 'extracellular matrix' category showed significantly high promoter conservation, in spite of its low protein conservation. Conclusion Our results show the relation of gene function to protein conservation and promoter conservation, and revealed that there seem to be nonparallel components between protein and promoter sequence evolution.

  3. From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors.

    Directory of Open Access Journals (Sweden)

    Ana Zafra Ruano

    2016-05-01

    Full Text Available Src Homology 3 domains are ubiquitous small interaction modules known to act as docking sites and regulatory elements in a wide range of proteins. Prior experimental NMR work on the SH3 domain of Src showed that ligand binding induces long-range dynamic changes consistent with an induced fit mechanism. The identification of the residues that participate in this mechanism produces a chart that allows for the exploration of the regulatory role of such domains in the activity of the encompassing protein. Here we show that a computational approach focusing on the changes in side chain dynamics through ligand binding identifies equivalent long-range effects in the Src SH3 domain. Mutation of a subset of the predicted residues elicits long-range effects on the binding energetics, emphasizing the relevance of these positions in the definition of intramolecular cooperative networks of signal transduction in this domain. We find further support for this mechanism through the analysis of seven other publically available SH3 domain structures of which the sequences represent diverse SH3 classes. By comparing the eight predictions, we find that, in addition to a dynamic pathway that is relatively conserved throughout all SH3 domains, there are dynamic aspects specific to each domain and homologous subgroups. Our work shows for the first time from a structural perspective, which transduction mechanisms are common between a subset of closely related and distal SH3 domains, while at the same time highlighting the differences in signal transduction that make each family member unique. These results resolve the missing link between structural predictions of dynamic changes and the domain sectors recently identified for SH3 domains through sequence analysis.

  4. Are Pharmaceuticals with Evolutionary Conserved Molecular Drug Targets More Potent to Cause Toxic Effects in Non-Target Organisms?

    Science.gov (United States)

    Furuhagen, Sara; Fuchs, Anne; Lundström Belleza, Elin; Breitholtz, Magnus; Gorokhova, Elena

    2014-01-01

    The ubiquitous use of pharmaceuticals has resulted in a continuous discharge into wastewater and pharmaceuticals and their metabolites are found in the environment. Due to their design towards specific drug targets, pharmaceuticals may be therapeutically active already at low environmental concentrations. Several human drug targets are evolutionary conserved in aquatic organisms, raising concerns about effects of these pharmaceuticals in non-target organisms. In this study, we hypothesized that the toxicity of a pharmaceutical towards a non-target invertebrate depends on the presence of the human drug target orthologs in this species. This was tested by assessing toxicity of pharmaceuticals with (miconazole and promethazine) and without (levonorgestrel) identified drug target orthologs in the cladoceran Daphnia magna. The toxicity was evaluated using general toxicity endpoints at individual (immobility, reproduction and development), biochemical (RNA and DNA content) and molecular (gene expression) levels. The results provide evidence for higher toxicity of miconazole and promethazine, i.e. the drugs with identified drug target orthologs. At the individual level, miconazole had the lowest effect concentrations for immobility and reproduction (0.3 and 0.022 mg L−1, respectively) followed by promethazine (1.6 and 0.18 mg L−1, respectively). At the biochemical level, individual RNA content was affected by miconazole and promethazine already at 0.0023 and 0.059 mg L−1, respectively. At the molecular level, gene expression for cuticle protein was significantly suppressed by exposure to both miconazole and promethazine; moreover, daphnids exposed to miconazole had significantly lower vitellogenin expression. Levonorgestrel did not have any effects on any endpoints in the concentrations tested. These results highlight the importance of considering drug target conservation in environmental risk assessments of pharmaceuticals. PMID:25140792

  5. Spt-Ada-Gcn5-Acetyltransferase (SAGA Complex in Plants: Genome Wide Identification, Evolutionary Conservation and Functional Determination.

    Directory of Open Access Journals (Sweden)

    Rakesh Srivastava

    Full Text Available The recruitment of RNA polymerase II on a promoter is assisted by the assembly of basal transcriptional machinery in eukaryotes. The Spt-Ada-Gcn5-Acetyltransferase (SAGA complex plays an important role in transcription regulation in eukaryotes. However, even in the advent of genome sequencing of various plants, SAGA complex has been poorly defined for their components and roles in plant development and physiological functions. Computational analysis of Arabidopsis thaliana and Oryza sativa genomes for SAGA complex resulted in the identification of 17 to 18 potential candidates for SAGA subunits. We have further classified the SAGA complex based on the conserved domains. Phylogenetic analysis revealed that the SAGA complex proteins are evolutionary conserved between plants, yeast and mammals. Functional annotation showed that they participate not only in chromatin remodeling and gene regulation, but also in different biological processes, which could be indirect and possibly mediated via the regulation of gene expression. The in silico expression analysis of the SAGA components in Arabidopsis and O. sativa clearly indicates that its components have a distinct expression profile at different developmental stages. The co-expression analysis of the SAGA components suggests that many of these subunits co-express at different developmental stages, during hormonal interaction and in response to stress conditions. Quantitative real-time PCR analysis of SAGA component genes further confirmed their expression in different plant tissues and stresses. The expression of representative salt, heat and light inducible genes were affected in mutant lines of SAGA subunits in Arabidopsis. Altogether, the present study reveals expedient evidences of involvement of the SAGA complex in plant gene regulation and stress responses.

  6. Conservation and evolutionary divergence in the activity of receptor-regulated smads

    Directory of Open Access Journals (Sweden)

    Sorrentino Gina M

    2012-10-01

    Full Text Available Abstract Background Activity of the Transforming growth factor-β (TGFβ pathway is essential to the establishment of body axes and tissue differentiation in bilaterians. Orthologs for core pathway members have been found in all metazoans, but uncertain homology of the body axes and tissues patterned by these signals raises questions about the activities of these molecules across the metazoan tree. We focus on the principal canonical transduction proteins (R-Smads of the TGFβ pathway, which instruct both axial patterning and tissue differentiation in the developing embryo. We compare the activity of R-Smads from a cnidarian (Nematostella vectensis, an arthropod (Drosophila melanogaster, and a vertebrate (Xenopus laevis in Xenopus embryonic assays. Results Overexpressing NvSmad1/5 ventralized Xenopus embryos when expressed in dorsal blastomeres, similar to the effects of Xenopus Smad1. However, NvSmad1/5 was less potent than XSmad1 in its ability to activate downstream target genes in Xenopus animal cap assays. NvSmad2/3 strongly induced general mesendodermal marker genes, but weakly induced ones involved in specifying the Spemann organizer. NvSmad2/3 was unable to induce a secondary trunk axis in Xenopus embryos, whereas the orthologs from Xenopus (XSmad2 and XSmad3 and Drosophila (dSmad2 were capable of doing so. Replacement of the NvSmad2/3 MH2 domain with the Xenopus XSmad2 MH2 slightly increased its inductive capability, but did not confer an ability to generate a secondary body axis. Conclusions Vertebrate and cnidarian Smad1/5 have similar axial patterning and induction activities, although NvSmad1/5 is less efficient than the vertebrate gene. We conclude that the activities of Smad1/5 orthologs have been largely conserved across Metazoa. NvSmad2/3 efficiently activates general mesendoderm markers, but is unable to induce vertebrate organizer-specific genes or to produce a secondary body axis in Xenopus. Orthologs dSmad2 and XSmad3

  7. Evolutionary Conservation in Biogenesis of β-Barrel Proteins Allows Mitochondria to Assemble a Functional Bacterial Trimeric Autotransporter Protein*

    Science.gov (United States)

    Ulrich, Thomas; Oberhettinger, Philipp; Schütz, Monika; Holzer, Katharina; Ramms, Anne S.; Linke, Dirk; Autenrieth, Ingo B.; Rapaport, Doron

    2014-01-01

    Yersinia adhesin A (YadA) belongs to a class of bacterial adhesins that form trimeric structures. Their mature form contains a passenger domain and a C-terminal β-domain that anchors the protein in the outer membrane (OM). Little is known about how precursors of such proteins cross the periplasm and assemble into the OM. In the present study we took advantage of the evolutionary conservation in the biogenesis of β-barrel proteins between bacteria and mitochondria. We previously observed that upon expression in yeast cells, bacterial β-barrel proteins including the transmembrane domain of YadA assemble into the mitochondrial OM. In the current study we found that when expressed in yeast cells both the monomeric and trimeric forms of full-length YadA were detected in mitochondria but only the trimeric species was fully integrated into the OM. The oligomeric form was exposed on the surface of the organelle in its native conformation and maintained its capacity to adhere to host cells. The co-expression of YadA with a mitochondria-targeted form of the bacterial periplasmic chaperone Skp, but not with SurA or SecB, resulted in enhanced levels of both forms of YadA. Taken together, these results indicate that the proper assembly of trimeric autotransporter can occur also in a system lacking the lipoproteins of the BAM machinery and is specifically enhanced by the chaperone Skp. PMID:25190806

  8. Evolutionary Conservation and Emerging Functional Diversity of the Cytosolic Hsp70:J Protein Chaperone Network of Arabidopsis thaliana.

    Science.gov (United States)

    Verma, Amit K; Diwan, Danish; Raut, Sandeep; Dobriyal, Neha; Brown, Rebecca E; Gowda, Vinita; Hines, Justin K; Sahi, Chandan

    2017-06-07

    Heat shock proteins of 70 kDa (Hsp70s) partner with structurally diverse Hsp40s (J proteins), generating distinct chaperone networks in various cellular compartments that perform myriad housekeeping and stress-associated functions in all organisms. Plants, being sessile, need to constantly maintain their cellular proteostasis in response to external environmental cues. In these situations, the Hsp70:J protein machines may play an important role in fine-tuning cellular protein quality control. Although ubiquitous, the functional specificity and complexity of the plant Hsp70:J protein network has not been studied. Here, we analyzed the J protein network in the cytosol of Arabidopsis thaliana and, using yeast genetics, show that the functional specificities of most plant J proteins in fundamental chaperone functions are conserved across long evolutionary timescales. Detailed phylogenetic and functional analysis revealed that increased number, regulatory differences, and neofunctionalization in J proteins together contribute to the emerging functional diversity and complexity in the Hsp70:J protein network in higher plants. Based on the data presented, we propose that higher plants have orchestrated their "chaperome," especially their J protein complement, according to their specialized cellular and physiological stipulations. Copyright © 2017 Verma et al.

  9. Conservation genetics of evolutionary lineages of the endangered mountain yellow-legged frog, Rana muscosa (Amphibia: Ranidae), in southern California

    Science.gov (United States)

    Schoville, Sean D.; Tustall, Tate S.; Vredenburg, Vance T.; Backlin, Adam R.; Gallegos, Elizabeth; Wood, Dustin A.; Fisher, Robert N.

    2011-01-01

    Severe population declines led to the listing of southern California Rana muscosa (Ranidae) as endangered in 2002. Nine small populations inhabit watersheds in three isolated mountain ranges, the San Gabriel, San Bernardino and San Jacinto. One population from the Dark Canyon tributary in the San Jacinto Mountains has been used to establish a captive breeding population at the San Diego Zoo Institute for Conservation Research. Because these populations may still be declining, it is critical to gather information on how genetic variation is structured in these populations and what historical inter-population connectivity existed between populations. Additionally, it is not clear whether these populations are rapidly losing genetic diversity due to population bottlenecks. Using mitochondrial and microsatellite data, we examine patterns of genetic variation in southern California and one of the last remaining populations of R. muscosa in the southern Sierra Nevada. We find low levels of genetic variation within each population and evidence of genetic bottlenecks. Additionally, substantial population structure is evident, suggesting a high degree of historical isolation within and between mountain ranges. Based on estimates from a multi-population isolation with migration analysis, these populations diversified during glacial episodes of the Pleistocene, with little gene flow during population divergence. Our data demonstrate that unique evolutionary lineages of R. muscosa occupy each mountain range in southern California and should be managed separately. The captive breeding program at Dark Canyon is promising, although mitigating the loss of neutral genetic diversity relative to the natural population might require additional breeding frogs.

  10. Elucidating the evolutionary conserved DNA-binding specificities of WRKY transcription factors by molecular dynamics and in vitro binding assays

    Science.gov (United States)

    Brand, Luise H.; Fischer, Nina M.; Harter, Klaus; Kohlbacher, Oliver; Wanke, Dierk

    2013-01-01

    WRKY transcription factors constitute a large protein family in plants that is involved in the regulation of developmental processes and responses to biotic or abiotic stimuli. The question arises how stimulus-specific responses are mediated given that the highly conserved WRKY DNA-binding domain (DBD) exclusively recognizes the ‘TTGACY’ W-box consensus. We speculated that the W-box consensus might be more degenerate and yet undetected differences in the W-box consensus of WRKYs of different evolutionary descent exist. The phylogenetic analysis of WRKY DBDs suggests that they evolved from an ancestral group IIc-like WRKY early in the eukaryote lineage. A direct descent of group IIc WRKYs supports a monophyletic origin of all other group II and III WRKYs from group I by loss of an N-terminal DBD. Group I WRKYs are of paraphyletic descent and evolved multiple times independently. By homology modeling, molecular dynamics simulations and in vitro DNA–protein interaction-enzyme-linked immunosorbent assay with AtWRKY50 (IIc), AtWRKY33 (I) and AtWRKY11 (IId) DBDs, we revealed differences in DNA-binding specificities. Our data imply that other components are essentially required besides the W-box-specific binding to DNA to facilitate a stimulus-specific WRKY function. PMID:23975197

  11. RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more

    Science.gov (United States)

    Salgado, Heladia; Peralta-Gil, Martin; Gama-Castro, Socorro; Santos-Zavaleta, Alberto; Muñiz-Rascado, Luis; García-Sotelo, Jair S.; Weiss, Verena; Solano-Lira, Hilda; Martínez-Flores, Irma; Medina-Rivera, Alejandra; Salgado-Osorio, Gerardo; Alquicira-Hernández, Shirley; Alquicira-Hernández, Kevin; López-Fuentes, Alejandra; Porrón-Sotelo, Liliana; Huerta, Araceli M.; Bonavides-Martínez, César; Balderas-Martínez, Yalbi I.; Pannier, Lucia; Olvera, Maricela; Labastida, Aurora; Jiménez-Jacinto, Verónica; Vega-Alvarado, Leticia; del Moral-Chávez, Victor; Hernández-Alvarez, Alfredo; Morett, Enrique; Collado-Vides, Julio

    2013-01-01

    This article summarizes our progress with RegulonDB (http://regulondb.ccg.unam.mx/) during the past 2 years. We have kept up-to-date the knowledge from the published literature regarding transcriptional regulation in Escherichia coli K-12. We have maintained and expanded our curation efforts to improve the breadth and quality of the encoded experimental knowledge, and we have implemented criteria for the quality of our computational predictions. Regulatory phrases now provide high-level descriptions of regulatory regions. We expanded the assignment of quality to various sources of evidence, particularly for knowledge generated through high-throughput (HT) technology. Based on our analysis of most relevant methods, we defined rules for determining the quality of evidence when multiple independent sources support an entry. With this latest release of RegulonDB, we present a new highly reliable larger collection of transcription start sites, a result of our experimental HT genome-wide efforts. These improvements, together with several novel enhancements (the tracks display, uploading format and curational guidelines), address the challenges of incorporating HT-generated knowledge into RegulonDB. Information on the evolutionary conservation of regulatory elements is also available now. Altogether, RegulonDB version 8.0 is a much better home for integrating knowledge on gene regulation from the sources of information currently available. PMID:23203884

  12. An Evolutionary Algorithm of the Regional Collaborative Innovation Based on Complex Network

    Directory of Open Access Journals (Sweden)

    Kun Wang

    2016-01-01

    Full Text Available This paper proposed a new perspective to study the evolution of regional collaborative innovation based on complex network theory. The two main conceptions of evolution, “graph with dynamic features” and “network evolution,” have been provided in advance. Afterwards, we illustrate the overall architecture and capability model of the regional collaborative innovation system, which contains several elements and participants. Therefore, we can definitely assume that the regional collaborative innovation system could be regarded as a complex network model. In the proposed evolutionary algorithm, we consider that each node in the network could only connect to less than a certain amount of neighbors, and the extreme value is determined by its importance. Through the derivation, we have created a probability density function as the most important constraint and supporting condition of our simulation experiments. Then, a case study was performed to explore the network topology and validate the effectiveness of our algorithm. All the raw datasets were obtained from the official website of the National Bureau of Statistic of China and some other open sources. Finally, some meaningful recommendations were presented to policy makers, especially based on the experimental results and some common conclusions of complex networks.

  13. Evolutionary conservation in biogenesis of β-barrel proteins allows mitochondria to assemble a functional bacterial trimeric autotransporter protein.

    Science.gov (United States)

    Ulrich, Thomas; Oberhettinger, Philipp; Schütz, Monika; Holzer, Katharina; Ramms, Anne S; Linke, Dirk; Autenrieth, Ingo B; Rapaport, Doron

    2014-10-24

    Yersinia adhesin A (YadA) belongs to a class of bacterial adhesins that form trimeric structures. Their mature form contains a passenger domain and a C-terminal β-domain that anchors the protein in the outer membrane (OM). Little is known about how precursors of such proteins cross the periplasm and assemble into the OM. In the present study we took advantage of the evolutionary conservation in the biogenesis of β-barrel proteins between bacteria and mitochondria. We previously observed that upon expression in yeast cells, bacterial β-barrel proteins including the transmembrane domain of YadA assemble into the mitochondrial OM. In the current study we found that when expressed in yeast cells both the monomeric and trimeric forms of full-length YadA were detected in mitochondria but only the trimeric species was fully integrated into the OM. The oligomeric form was exposed on the surface of the organelle in its native conformation and maintained its capacity to adhere to host cells. The co-expression of YadA with a mitochondria-targeted form of the bacterial periplasmic chaperone Skp, but not with SurA or SecB, resulted in enhanced levels of both forms of YadA. Taken together, these results indicate that the proper assembly of trimeric autotransporter can occur also in a system lacking the lipoproteins of the BAM machinery and is specifically enhanced by the chaperone Skp. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  14. Patterns of evolutionary conservation of ascorbic acid-related genes following whole-genome triplication in Brassica rapa.

    Science.gov (United States)

    Duan, Weike; Song, Xiaoming; Liu, Tongkun; Huang, Zhinan; Ren, Jun; Hou, Xilin; Du, Jianchang; Li, Ying

    2014-12-31

    Ascorbic acid (AsA) is an important antioxidant in plants and an essential vitamin for humans. Extending the study of AsA-related genes from Arabidopsis thaliana to Brassica rapa could shed light on the evolution of AsA in plants and inform crop breeding. In this study, we conducted whole-genome annotation, molecular-evolution and gene-expression analyses of all known AsA-related genes in B. rapa. The nucleobase-ascorbate transporter (NAT) gene family and AsA l-galactose pathway genes were also compared among plant species. Four important insights gained are that: 1) 102 AsA-related gene were identified in B. rapa and they mainly diverged 12-18 Ma accompanied by the Brassica-specific genome triplication event; 2) during their evolution, these AsA-related genes were preferentially retained, consistent with the gene dosage hypothesis; 3) the putative proteins were highly conserved, but their expression patterns varied; and 4) although the number of AsA-related genes is higher in B. rapa than in A. thaliana, the AsA contents and the numbers of expressed genes in leaves of both species are similar, the genes that are not generally expressed may serve as substitutes during emergencies. In summary, this study provides genome-wide insights into evolutionary history and mechanisms of AsA-related genes following whole-genome triplication in B. rapa. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  15. Variability or conservation of hepatitis C virus hypervariable region 1 ...

    Indian Academy of Sciences (India)

    Unknown

    The hypervariable region 1 (HVR1) of the E2 protein of hepatitis C virus (HCV) is highly heterogeneous in its primary sequence and is responsible for significant inter- and intra-individual variation of the infecting virus, which may represent an important pathogenetic mechanism leading to immune escape and persistent ...

  16. Towards conserving regional mammalian species diversity: a case ...

    African Journals Online (AJOL)

    1995-03-03

    Mar 3, 1995 ... teenth degree grid square (= ODS in Lombard 1995) species richness maps based on these two data sets for the region are highly ... different definitions of biodiversity. and to our current limited capabilities of measuring its status ... Species richness has been used as a base dataset for rnonitori ng changes ...

  17. The role of landscape anomalies in regional plant conservation

    Science.gov (United States)

    S. Kelso; C. Hall; G. Maentz

    2001-01-01

    Landscape anomalies are regionally restricted habitats created by unusual geologic, edaphic, or hydrologic factors. Barrens, cliff faces, canyons, hanging gardens, and playas are all examples of landscape anomalies in the arid Southwest. Such sites often harbor an unusual and rich flora, including endemic, disjunct, or relictual plant species. Using examples from our...

  18. FOXP in Tetrapoda: Intrinsically Disordered Regions, Short Linear Motifs and their evolutionary significance

    Directory of Open Access Journals (Sweden)

    Lucas Henriques Viscardi

    2017-03-01

    Full Text Available Abstract The FOXP subfamily is probably the most extensively characterized subfamily of the forkhead superfamily, playing important roles in development and homeostasis in vertebrates. Intrinsically disorder protein regions (IDRs are protein segments that exhibit multiple physical interactions and play critical roles in various biological processes, including regulation and signaling. IDRs in proteins may play an important role in the evolvability of genetic systems. In this study, we analyzed 77 orthologous FOXP genes/proteins from Tetrapoda, regarding protein disorder content and evolutionary rate. We also predicted the number and type of short linear motifs (SLIMs in the IDRs. Similar levels of protein disorder (approximately 70% were found for FOXP1, FOXP2, and FOXP4. However, for FOXP3, which is shorter in length and has a more specific function, the disordered content was lower (30%. Mammals showed higher protein disorders for FOXP1 and FOXP4 than non-mammals. Specific analyses related to linear motifs in the four genes showed also a clear differentiation between FOXPs in mammals and non-mammals. We predicted for the first time the role of IDRs and SLIMs in the FOXP gene family associated with possible adaptive novelties within Tetrapoda. For instance, we found gain and loss of important phosphorylation sites in the Homo sapiens FOXP2 IDR regions, with possible implication for the evolution of human speech.

  19. FOXP in Tetrapoda: Intrinsically Disordered Regions, Short Linear Motifs and their evolutionary significance.

    Science.gov (United States)

    Viscardi, Lucas Henriques; Tovo-Rodrigues, Luciana; Paré, Pamela; Fagundes, Nelson Jurandi Rosa; Salzano, Francisco Mauro; Paixão-Côrtes, Vanessa Rodrigues; Bau, Claiton Henrique Dotto; Bortolini, Maria Cátira

    2017-01-01

    The FOXP subfamily is probably the most extensively characterized subfamily of the forkhead superfamily, playing important roles in development and homeostasis in vertebrates. Intrinsically disorder protein regions (IDRs) are protein segments that exhibit multiple physical interactions and play critical roles in various biological processes, including regulation and signaling. IDRs in proteins may play an important role in the evolvability of genetic systems. In this study, we analyzed 77 orthologous FOXP genes/proteins from Tetrapoda, regarding protein disorder content and evolutionary rate. We also predicted the number and type of short linear motifs (SLIMs) in the IDRs. Similar levels of protein disorder (approximately 70%) were found for FOXP1, FOXP2, and FOXP4. However, for FOXP3, which is shorter in length and has a more specific function, the disordered content was lower (30%). Mammals showed higher protein disorders for FOXP1 and FOXP4 than non-mammals. Specific analyses related to linear motifs in the four genes showed also a clear differentiation between FOXPs in mammals and non-mammals. We predicted for the first time the role of IDRs and SLIMs in the FOXP gene family associated with possible adaptive novelties within Tetrapoda. For instance, we found gain and loss of important phosphorylation sites in the Homo sapiens FOXP2 IDR regions, with possible implication for the evolution of human speech.

  20. Evolutionary toggling of the MAPT 17q21.31 inversion region.

    Science.gov (United States)

    Zody, Michael C; Jiang, Zhaoshi; Fung, Hon-Chung; Antonacci, Francesca; Hillier, LaDeana W; Cardone, Maria Francesca; Graves, Tina A; Kidd, Jeffrey M; Cheng, Ze; Abouelleil, Amr; Chen, Lin; Wallis, John; Glasscock, Jarret; Wilson, Richard K; Reily, Amy Denise; Duckworth, Jaime; Ventura, Mario; Hardy, John; Warren, Wesley C; Eichler, Evan E

    2008-09-01

    Using comparative sequencing approaches, we investigated the evolutionary history of the European-enriched 17q21.31 MAPT inversion polymorphism. We present a detailed, BAC-based sequence assembly of the inverted human H2 haplotype and compare it to the sequence structure and genetic variation of the corresponding 1.5-Mb region for the noninverted H1 human haplotype and that of chimpanzee and orangutan. We found that inversion of the MAPT region is similarly polymorphic in other great ape species, and we present evidence that the inversions occurred independently in chimpanzees and humans. In humans, the inversion breakpoints correspond to core duplications with the LRRC37 gene family. Our analysis favors the H2 configuration and sequence haplotype as the likely great ape and human ancestral state, with inversion recurrences during primate evolution. We show that the H2 architecture has evolved more extensive sequence homology, perhaps explaining its tendency to undergo microdeletion associated with mental retardation in European populations.

  1. A statistically rigorous sampling design to integrate avian monitoring and management within Bird Conservation Regions.

    Science.gov (United States)

    Pavlacky, David C; Lukacs, Paul M; Blakesley, Jennifer A; Skorkowsky, Robert C; Klute, David S; Hahn, Beth A; Dreitz, Victoria J; George, T Luke; Hanni, David J

    2017-01-01

    Monitoring is an essential component of wildlife management and conservation. However, the usefulness of monitoring data is often undermined by the lack of 1) coordination across organizations and regions, 2) meaningful management and conservation objectives, and 3) rigorous sampling designs. Although many improvements to avian monitoring have been discussed, the recommendations have been slow to emerge in large-scale programs. We introduce the Integrated Monitoring in Bird Conservation Regions (IMBCR) program designed to overcome the above limitations. Our objectives are to outline the development of a statistically defensible sampling design to increase the value of large-scale monitoring data and provide example applications to demonstrate the ability of the design to meet multiple conservation and management objectives. We outline the sampling process for the IMBCR program with a focus on the Badlands and Prairies Bird Conservation Region (BCR 17). We provide two examples for the Brewer's sparrow (Spizella breweri) in BCR 17 demonstrating the ability of the design to 1) determine hierarchical population responses to landscape change and 2) estimate hierarchical habitat relationships to predict the response of the Brewer's sparrow to conservation efforts at multiple spatial scales. The collaboration across organizations and regions provided economy of scale by leveraging a common data platform over large spatial scales to promote the efficient use of monitoring resources. We designed the IMBCR program to address the information needs and core conservation and management objectives of the participating partner organizations. Although it has been argued that probabilistic sampling designs are not practical for large-scale monitoring, the IMBCR program provides a precedent for implementing a statistically defensible sampling design from local to bioregional scales. We demonstrate that integrating conservation and management objectives with rigorous statistical

  2. A statistically rigorous sampling design to integrate avian monitoring and management within Bird Conservation Regions.

    Directory of Open Access Journals (Sweden)

    David C Pavlacky

    Full Text Available Monitoring is an essential component of wildlife management and conservation. However, the usefulness of monitoring data is often undermined by the lack of 1 coordination across organizations and regions, 2 meaningful management and conservation objectives, and 3 rigorous sampling designs. Although many improvements to avian monitoring have been discussed, the recommendations have been slow to emerge in large-scale programs. We introduce the Integrated Monitoring in Bird Conservation Regions (IMBCR program designed to overcome the above limitations. Our objectives are to outline the development of a statistically defensible sampling design to increase the value of large-scale monitoring data and provide example applications to demonstrate the ability of the design to meet multiple conservation and management objectives. We outline the sampling process for the IMBCR program with a focus on the Badlands and Prairies Bird Conservation Region (BCR 17. We provide two examples for the Brewer's sparrow (Spizella breweri in BCR 17 demonstrating the ability of the design to 1 determine hierarchical population responses to landscape change and 2 estimate hierarchical habitat relationships to predict the response of the Brewer's sparrow to conservation efforts at multiple spatial scales. The collaboration across organizations and regions provided economy of scale by leveraging a common data platform over large spatial scales to promote the efficient use of monitoring resources. We designed the IMBCR program to address the information needs and core conservation and management objectives of the participating partner organizations. Although it has been argued that probabilistic sampling designs are not practical for large-scale monitoring, the IMBCR program provides a precedent for implementing a statistically defensible sampling design from local to bioregional scales. We demonstrate that integrating conservation and management objectives with rigorous

  3. Species of conservation concern and environmental stressors: Local, regional and global effects [Chapter 6] (Executive Summary)

    Science.gov (United States)

    Steven M. Ostoja; Matthew L. Brooks; Jeanne C. Chambers; Burton K.. Pendleton

    2013-01-01

    Southern Nevada’s unique landscapes and landforms provide habitat for a diversity of plant and wildlife species of conservation concern including many locally and regionally endemic species. The high population density and urbanization of the Las Vegas metropolitan area is the source of many local and regional stressors that affect these species and their habitats:...

  4. Molecular phylogeny of OVOL genes illustrates a conserved C2H2 zinc finger domain coupled by hypervariable unstructured regions.

    Directory of Open Access Journals (Sweden)

    Abhishek Kumar

    Full Text Available OVO-like proteins (OVOL are members of the zinc finger protein family and serve as transcription factors to regulate gene expression in various differentiation processes. Recent studies have shown that OVOL genes are involved in epithelial development and differentiation in a wide variety of organisms; yet there is a lack of comprehensive studies that describe OVOL proteins from an evolutionary perspective. Using comparative genomic analysis, we traced three different OVOL genes (OVOL1-3 in vertebrates. One gene, OVOL3, was duplicated during a whole-genome-duplication event in fish, but only the copy (OVOL3b was retained. From early-branching metazoa to humans, we found that a core domain, comprising a tetrad of C2H2 zinc fingers, is conserved. By domain comparison of the OVOL proteins, we found that they evolved in different metazoan lineages by attaching intrinsically-disordered (ID segments of N/C-terminal extensions of 100 to 1000 amino acids to this conserved core. These ID regions originated independently across different animal lineages giving rise to different types of OVOL genes over the course of metazoan evolution. We illustrated the molecular evolution of metazoan OVOL genes over a period of 700 million years (MY. This study both extends our current understanding of the structure/function relationship of metazoan OVOL genes, and assembles a good platform for further characterization of OVOL genes from diverged organisms.

  5. USING ECO-EVOLUTIONARY INDIVIDUAL-BASED MODELS TO INVESTIGATE SPATIALLY-DEPENDENT PROCESSES IN CONSERVATION GENETICS

    Science.gov (United States)

    Eco-evolutionary population simulation models are powerful new forecasting tools for exploring management strategies for climate change and other dynamic disturbance regimes. Additionally, eco-evo individual-based models (IBMs) are useful for investigating theoretical feedbacks ...

  6. Structural features of DNA are conserved in the promoter region of orthologous genes across different strains of Helicobacter pylori.

    Science.gov (United States)

    Kumar, Aditya; Manivelan, Vasumathi; Bansal, Manju

    2016-09-01

    Promoter regions play a key role in the process of transcription initiation and gene expression, hence promoter identification is an inherent component of the genome annotation process. Identification and characterization of promoters in fully sequenced genomes is a challenging and complex task. An analysis of sequence-dependent DNA structural properties in the promoter region of orthologous and non-orthologous genes can help in characterizing promoters and also provide insights into transcription initiation. Various structural properties, such as duplex stability, protein-induced bendability and intrinsic curvature of promoter sequences have been calculated and compared for 10 different strains of Helicobacter pylori genomes, and it is found that promoter regions in orthologous and non-orthologous genes show distinct trends for these properties, with orthologous genes showing sharper low-stability peak, lower bendability and higher curvature. The average GC content of orthologous genes is higher than that of non-orthologous genes, and relative stability-based promoter annotation tool PromPredict performs better for orthologous genes than non-orthologous genes. The characteristic sequence-dependent structural properties of promoters show significant differences between orthologous and non-orthologous genes. Interestingly, these structural properties of promoters are conserved, but the genes themselves vary in their evolutionary selection rate. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  7. Intestinal Spirochaetes of the Genus Share a Partially Conserved 26 Kilobase Genomic Region with and

    Directory of Open Access Journals (Sweden)

    Yair Motro

    2008-01-01

    Full Text Available Anaerobic intestinal spirochaetes of the genus Brachyspira include both pathogenic and commensal species. The two best-studied members are the pathogenic species B. hyodysenteriae (the aetiological agent of swine dysentery and B. pilosicoli (a cause of intestinal spirochaetosis in humans and other species. Analysis of near-complete genome sequences of these two species identified a highly conserved 26 kilobase (kb region that was shared, against a background of otherwise very little sequence conservation between the two species. PCR amplification was used to identify sets of contiguous genes from this region in the related Brachyspira species B. intermedia, B. innocens, B. murdochii, B. alvinipulli , and B. aalborgi , and demonstrated the presence of at least part of this region in species from throughout the genus. Comparative genomic analysis with other sequenced bacterial species revealed that none of the completely sequenced spirochaete species from different genera contained this conserved cluster of coding sequences. In contrast, Enterococcus faecalis and Escherichia coli contained high gene cluster conservation across the 26 kb region, against an expected background of little sequence conservation between these phylogenetically distinct species. The conserved region in B. hyodysenteriae contained five genes predicted to be associated with amino acid transport and metabolism, four with energy production and conversion, two with nucleotide transport and metabolism, one with ion transport and metabolism, and four with poorly characterised or uncertain function, including an ankyrin repeat unit at the 5’ end. The most likely explanation for the presence of this 26 kb region in the Brachyspira species and in two unrelated enteric bacterial species is that the region has been involved in horizontal gene transfer.

  8. Influence of conservation programs on amphibians using seasonal wetlands in the Prairie Pothole Region

    Science.gov (United States)

    Balas, Caleb J.; Euliss, Ned H.; Mushnet, David M.

    2012-01-01

    Extensive modification of upland habitats surrounding wetlands to facilitate agricultural production has negatively impacted amphibian communities in the Prairie Pothole Region of North America. In attempts to mitigate ecosystem damage associated with extensive landscape alteration, vast tracks of upland croplands have been returned to perennial vegetative cover (i.e., conservation grasslands) under a variety of U.S. Department of Agriculture programs. We evaluated the influence of these conservation grasslands on amphibian occupancy of seasonal wetlands in the Prairie Pothole Region. Using automated call surveys, aquatic funnel traps, and visual encounter surveys, we detected eight amphibian species using wetlands within three land-use categories (farmed, conservation grasslands, and native prairie grasslands) during the summers of 2005 and 2006. Seasonal wetlands within farmlands were used less frequently by amphibians than those within conservation and native prairie grasslands, and wetlands within conservation grasslands were used less frequently than those within native prairie grasslands by all species and life-stages we successfully modeled. Our results suggest that, while not occupied as frequently as wetlands within native prairie, wetlands within conservation grasslands provide important habitat for maintaining amphibian biodiversity in the Prairie Pothole Region

  9. Optimal portfolio design to reduce climate-related conservation uncertainty in the Prairie Pothole Region.

    Science.gov (United States)

    Ando, Amy W; Mallory, Mindy L

    2012-04-24

    Climate change is likely to alter the spatial distributions of species and habitat types but the nature of such change is uncertain. Thus, climate change makes it difficult to implement standard conservation planning paradigms. Previous work has suggested some approaches to cope with such uncertainty but has not harnessed all of the benefits of risk diversification. We adapt Modern Portfolio Theory (MPT) to optimal spatial targeting of conservation activity, using wetland habitat conservation in the Prairie Pothole Region (PPR) as an example. This approach finds the allocations of conservation activity among subregions of the planning area that maximize the expected conservation returns for a given level of uncertainty or minimize uncertainty for a given expected level of returns. We find that using MPT instead of simple diversification in the PPR can achieve a value of the conservation objective per dollar spent that is 15% higher for the same level of risk. MPT-based portfolios can also have 21% less uncertainty over benefits or 6% greater expected benefits than the current portfolio of PPR conservation. Total benefits from conservation investment are higher if returns are defined in terms of benefit-cost ratios rather than benefits alone. MPT-guided diversification can work to reduce the climate-change-induced uncertainty of future ecosystem-service benefits from many land policy and investment initiatives, especially when outcomes are negatively correlated between subregions of a planning area.

  10. Optimal portfolio design to reduce climate-related conservation uncertainty in the Prairie Pothole Region

    Science.gov (United States)

    Ando, Amy W.; Mallory, Mindy L.

    2012-01-01

    Climate change is likely to alter the spatial distributions of species and habitat types but the nature of such change is uncertain. Thus, climate change makes it difficult to implement standard conservation planning paradigms. Previous work has suggested some approaches to cope with such uncertainty but has not harnessed all of the benefits of risk diversification. We adapt Modern Portfolio Theory (MPT) to optimal spatial targeting of conservation activity, using wetland habitat conservation in the Prairie Pothole Region (PPR) as an example. This approach finds the allocations of conservation activity among subregions of the planning area that maximize the expected conservation returns for a given level of uncertainty or minimize uncertainty for a given expected level of returns. We find that using MPT instead of simple diversification in the PPR can achieve a value of the conservation objective per dollar spent that is 15% higher for the same level of risk. MPT-based portfolios can also have 21% less uncertainty over benefits or 6% greater expected benefits than the current portfolio of PPR conservation. Total benefits from conservation investment are higher if returns are defined in terms of benefit–cost ratios rather than benefits alone. MPT-guided diversification can work to reduce the climate-change–induced uncertainty of future ecosystem-service benefits from many land policy and investment initiatives, especially when outcomes are negatively correlated between subregions of a planning area. PMID:22451914

  11. Recovering the evolutionary history of crowned pigeons (Columbidae: Goura): Implications for the biogeography and conservation of New Guinean lowland birds.

    Science.gov (United States)

    Bruxaux, Jade; Gabrielli, Maëva; Ashari, Hidayat; Prŷs-Jones, Robert; Joseph, Leo; Milá, Borja; Besnard, Guillaume; Thébaud, Christophe

    2017-12-01

    Assessing the relative contributions of immigration and diversification into the buildup of species diversity is key to understanding the role of historical processes in driving biogeographical and diversification patterns in species-rich regions. Here, we investigated how colonization, in situ speciation, and extinction history may have generated the present-day distribution and diversity of Goura crowned pigeons (Columbidae), a group of large forest-dwelling pigeons comprising four recognized species that are all endemic to New Guinea. We used a comprehensive geographical and taxonomic sampling based mostly on historical museum samples, and shallow shotgun sequencing, to generate complete mitogenomes, nuclear ribosomal clusters and independent nuclear conserved DNA elements. We used these datasets independently to reconstruct molecular phylogenies. Divergence time estimates were obtained using mitochondrial data only. All analyses revealed similar genetic divisions within the genus Goura and recovered as monophyletic groups the four species currently recognized, providing support for recent taxonomic changes based on differences in plumage characters. These four species are grouped into two pairs of strongly supported sister species, which were previously not recognized as close relatives: Goura sclaterii with Goura cristata, and Goura victoria with Goura scheepmakeri. While the geographical origin of the Goura lineage remains elusive, the crown age of 5.73 Ma is consistent with present-day species diversity being the result of a recent diversification within New Guinea. Although the orogeny of New Guinea's central cordillera must have played a role in driving diversification in Goura, cross-barrier dispersal seems more likely than vicariance to explain the speciation events having led to the four current species. Our results also have important conservation implications. Future assessments of the conservation status of Goura species should consider threat

  12. The methionine-rich low-molecular-weight chloroplast heat-shock protein: evolutionary conservation and accumulation in relation to thermotolerance.

    Science.gov (United States)

    Downs, C; Heckathorn, S; Bryan, J; Coleman, J

    1998-02-01

    The evolutionary conservation of the low-molecular-weight chloroplast-localized heat-shock protein (LMW chlpHsp) in vascular plants was examined using immunological methods. An antibody (Abmet) specific to the LMW chlpHsp was produced using a synthetic 28-residue peptide containing the most conserved elements of its unique "methionine-rich domain" as an antigen. This antibody detected a heat-inducible low-molecular-weight chloroplast protein in plants of six divergent Anthophyta species, including C3, C4, CAM, monocot, and dicot species. Abmet also detected a LMW chlpHsp in species from the Divisions Psilotophyta, Equisetophyta, Polypodiophyta, and Ginkgophyta. A preliminary examination of the relationship between accumulation of the LMW chlpHsp and habitat was also conducted. Seven Anthophyta species originating from both warm- and cool-temperature habitats were grown at 28C and then heat stressed at 40C. A positive qualitative relationship between the accumulation of the LMW chlpHsp and organismal thermotolerance in these species was observed; similar results were obtained separately with four nonAnthophyta species. The strong evolutionary conservation of this LMW Hsp and its localization to the chloroplast, and the correlation between production of this protein and plant thermotolerance, suggest that the LMW chlpHsp plays an important role in adaptation to heat stress.

  13. RECENT ADVANCES IN FUNCTIONAL REGION PREDICTION BY USING STRUCTURAL AND EVOLUTIONARY INFORMATION – REMAINING PROBLEMS AND FUTURE EXTENSIONS

    Directory of Open Access Journals (Sweden)

    Wataru Nemoto

    2013-08-01

    Full Text Available Structural genomics projects have solved many new structures with unknown functions. One strategy to investigate the function of a structure is to computationally find the functionally important residues or regions on it. Therefore, the development of functional region prediction methods has become an important research subject. An effective approach is to use a method employing structural and evolutionary information, such as the evolutionary trace (ET method. ET ranks the residues of a protein structure by calculating the scores for relative evolutionary importance, and locates functionally important sites by identifying spatial clusters of highly ranked residues. After ET was developed, numerous ET-like methods were subsequently reported, and many of them are in practical use, although they require certain conditions. In this mini review, we first introduce the remaining problems and the recent improvements in the methods using structural and evolutionary information. We then summarize the recent developments of the methods. Finally, we conclude by describing possible extensions of the evolution- and structure-based methods.

  14. Identification of evolutionary hotspots based on genetic data from multiple terrestrial and aquatic taxa and gap analysis of hotspots in protected lands encompassed by the South Atlantic Landscape Conservation Cooperative.

    Science.gov (United States)

    Robinson, J.; Snider, M.; Duke, J.; Moyer, G.R.

    2014-01-01

     The southeastern United States is a recognized hotspot of biodiversity for a variety of aquatic taxa, including fish, amphibians, and mollusks. Unfortunately, the great diversity of the area is accompanied by a large proportion of species at risk of extinction . Gap analysis was employed to assess the representation of evolutionary hotspots in protected lands w h ere an evolutionary hotspot was defined as an area with high evolutionary potential and measured by atypical patterns of genetic divergence, genetic diversity, and to a lesser extent genetic similarity across multiple terrestrial or aquatic taxa. A survey of the primary literature produced 16 terrestrial and 14 aquatic genetic datasets for estimation of genetic divergence and diversity. Relative genetic diversity and divergence values for each terrestrial and aquatic dataset were used for interpolation of multispecies genetic surfaces and subsequent visualization using ArcGIS. The multispecies surfaces interpolated from relative divergences and diversity data identified numerous evolutionary hotspots for both terrestrial and aquatic taxa , many of which were afforded some current protection. For instance, 14% of the cells identified as hotspots of aquatic diversity were encompassed by currently protected areas. Additionally, 25% of the highest 1% of terrestrial diversity cells were afforded some level of protection. In contrast, areas of high and low divergence among species, and areas of high variance in diversity were poorly represented in the protected lands. Of particular interest were two areas that were consistently identified by several different measures as important from a conservation perspective. These included an area encompassing the panhandle of Florida and southern Georgia near the Apalachicola National Forest (displaying varying levels of genetic divergence and greater than average levels of genetic diversity) and a large portion of the coastal regions of North and South Carolina

  15. Making the Most of World Natural Heritage—Linking Conservation and Sustainable Regional Development?

    Directory of Open Access Journals (Sweden)

    Katharina Conradin

    2016-03-01

    Full Text Available Today, more than 1000 World Heritage (WH sites are inscribed on UNESCO’s list, 228 of which are natural and mixed heritage sites. Once focused primarily on conservation, World Natural Heritage (WNH sites are increasingly seen as promoters of sustainable regional development. Sustainability-oriented regions, it is assumed, are safeguards for conservation and positively influence local conservation goals. Within UNESCO, discussions regarding the integration of sustainable development in official policies have recently gained momentum. In this article, we investigate the extent to which WNH sites trigger sustainability-oriented approaches in surrounding regions, and how such approaches in turn influence the WNH site and its protection. The results of the study are on the one hand based on a global survey with more than 60% of the WNH sites listed in 2011, and on the other hand on a complementary literature research. Furthermore, we analyze the policy framework necessary to support WNH sites in this endeavor. We conclude that a regional approach to WNH management is necessary to ensure that WNH sites support sustainable regional development effectively, but that the core focus of WNH status must remain environmental conservation.

  16. Analysis of loco-regional and distant recurrences in breast cancer after conservative surgery.

    Science.gov (United States)

    Elsayed, Mostafa; Alhussini, Mahmoud; Basha, Ahmed; Awad, A T

    2016-05-14

    A number of patients treated conservatively for breast cancer will develop loco-regional and distant recurrences. Our aim was to determine how their occurrence may be linked to the evolution of the disease. We analyzed 238 women treated by conservative breast surgery and breast irradiation in a single institution. We evaluated the prognostic factors associated with loco-regional and distant recurrences and the prognostic value of local and regional recurrences on systemic progression. After a median follow-up of 5 year (range 1-10), 16 (6.72%) patients in the breast conservative surgery (BCS) groups had loco-regional recurrence. For distant recurrence, 10 (4.2%) patients had experienced distant recurrence. Lympho-vascular invasion (HR 2.55; 95% CI, 076 to 8.49) and an extensive intraductal component (HR, 2.22; 95% CI, 0.69 to 7.15) and nodal status are risk factors for loco-regional recurrence (LRR) after breast conservative therapy (BCT). Tumor size, nodal status, high histologic grade, and breast cancer diagnosed at a young age (≤35 years) are correlated with higher distant recurrence rates after BCT. Risk factors for LRR after BCS include lympho-vascular invasion, extensive inraductal component, and high nodal status, where as risk factors for distant recurrence include tumor size, nodal status, high histologic grade, and breast cancer diagnosed at a young age (≤35 years).

  17. Highly conserved gene order and numerous novel repetitive elements in genomic regions linked to wing pattern variation in Heliconius butterflies

    Directory of Open Access Journals (Sweden)

    Halder Georg

    2008-07-01

    Full Text Available Abstract Background With over 20 parapatric races differing in their warningly colored wing patterns, the butterfly Heliconius erato provides a fascinating example of an adaptive radiation. Together with matching races of its co-mimic Heliconius melpomene, H. erato also represents a textbook case of Müllerian mimicry, a phenomenon where common warning signals are shared amongst noxious organisms. It is of great interest to identify the specific genes that control the mimetic wing patterns of H. erato and H. melpomene. To this end we have undertaken comparative mapping and targeted genomic sequencing in both species. This paper reports on a comparative analysis of genomic sequences linked to color pattern mimicry genes in Heliconius. Results Scoring AFLP polymorphisms in H. erato broods allowed us to survey loci at approximately 362 kb intervals across the genome. With this strategy we were able to identify markers tightly linked to two color pattern genes: D and Cr, which were then used to screen H. erato BAC libraries in order to identify clones for sequencing. Gene density across 600 kb of BAC sequences appeared relatively low, although the number of predicted open reading frames was typical for an insect. We focused analyses on the D- and Cr-linked H. erato BAC sequences and on the Yb-linked H. melpomene BAC sequence. A comparative analysis between homologous regions of H. erato (Cr-linked BAC and H. melpomene (Yb-linked BAC revealed high levels of sequence conservation and microsynteny between the two species. We found that repeated elements constitute 26% and 20% of BAC sequences from H. erato and H. melpomene respectively. The majority of these repetitive sequences appear to be novel, as they showed no significant similarity to any other available insect sequences. We also observed signs of fine scale conservation of gene order between Heliconius and the moth Bombyx mori, suggesting that lepidopteran genome architecture may be conserved

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

    Science.gov (United States)

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

    2013-01-01

    Premise of the study: 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...

  19. Sustainable Tourism and Natural Resource Conservation in the Polar Regions: An Editorial

    NARCIS (Netherlands)

    Huijbens, Edward; Lamers, M.A.J.

    2017-01-01

    This editorial provides an introduction to the special issue of Resources on Sustainable Tourism and Natural Resource Conservation in the Polar Regions, which proceeds the fifth bi-annual conference of the International Polar Tourism Research Network (IPTRN). The conference and coinciding community

  20. Aligning the diverse: the development of a biodiversity conservation strategy for the Cape Floristic Region

    CSIR Research Space (South Africa)

    Lochner, Paul A

    2003-07-01

    Full Text Available The Cape Action Plan for the Environment (CAPE) sought to develop a long-term strategy and action plan to conserve biodiversity in the Cape Floristic Region (CFR). The high levels of biodiversity in the CFR are matched by complex and fragmented...

  1. A trans-national monarch butterfly population model and implications for regional conservation priorities

    Science.gov (United States)

    Oberhauser, Karen; Wiederholt, Ruscena; Diffendorfer, James E.; Semmens, Darius J.; Ries, Leslie; Thogmartin, Wayne E.; Lopez-Hoffman, Laura; Semmens, Brice

    2017-01-01

    1. The monarch has undergone considerable population declines over the past decade, and the governments of Mexico, Canada, and the United States have agreed to work together to conserve the species.2. Given limited resources, understanding where to focus conservation action is key for widespread species like monarchs. To support planning for continental-scale monarch habitat restoration, we address the question of where restoration efforts are likely to have the largest impacts on monarch butterfly (Danaus plexippus Linn.) population growth rates.3. We present a spatially explicit demographic model simulating the multi-generational annual cycle of the eastern monarch population, and use the model to examine management scenarios, some of which focus on particular regions of North America.4. Improving the monarch habitat in the north central or southern parts of the monarch range yields a slightly greater increase in the population growth rate than restoration in other regions. However, combining restoration efforts across multiple regions yields population growth rates above 1 with smaller simulated improvements in habitat per region than single-region strategies.5. Synthesis and applications: These findings suggest that conservation investment in projects across the full monarch range will be more effective than focusing on one or a few regions, and will require international cooperation across many land use categories.

  2. WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences

    Directory of Open Access Journals (Sweden)

    Pesole Graziano

    2007-02-01

    Full Text Available Abstract Background This work addresses the problem of detecting conserved transcription factor binding sites and in general regulatory regions through the analysis of sequences from homologous genes, an approach that is becoming more and more widely used given the ever increasing amount of genomic data available. Results We present an algorithm that identifies conserved transcription factor binding sites in a given sequence by comparing it to one or more homologs, adapting a framework we previously introduced for the discovery of sites in sequences from co-regulated genes. Differently from the most commonly used methods, the approach we present does not need or compute an alignment of the sequences investigated, nor resorts to descriptors of the binding specificity of known transcription factors. The main novel idea we introduce is a relative measure of conservation, assuming that true functional elements should present a higher level of conservation with respect to the rest of the sequence surrounding them. We present tests where we applied the algorithm to the identification of conserved annotated sites in homologous promoters, as well as in distal regions like enhancers. Conclusion Results of the tests show how the algorithm can provide fast and reliable predictions of conserved transcription factor binding sites regulating the transcription of a gene, with better performances than other available methods for the same task. We also show examples on how the algorithm can be successfully employed when promoter annotations of the genes investigated are missing, or when regulatory sites and regions are located far away from the genes.

  3. Regional Conservation Status of Scleractinian Coral Biodiversity in the Republic of the Marshall Islands

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    Zoe Richards

    2013-07-01

    Full Text Available Preventing the loss of biodiversity is a major challenge in mega-diverse ecosystems such as coral reefs where there is a critical shortage of baseline demographic data. Threatened species assessments play a valuable role in guiding conservation action to manage and mitigate biodiversity loss, but they must be undertaken with precise information at an appropriate spatial scale to provide accurate classifications. Here we explore the regional conservation status of scleractinian corals on isolated Pacific Ocean atolls in the Republic of the Marshall Islands. We compile an integrated regional species list based upon new and historical records, and compare how well the regional threat classifications reflect species level priorities at a global scale. A similar proportion of the 240 species of hard coral recorded in the current survey are classified as Vulnerable at the regional scale as the global scale using the International Union for the Conservation of Nature (IUCN Red List criteria (23% and 20% respectively, however there are distinct differences in the composition of species. When local abundance data is taken into account, a far greater proportion of the regional diversity (up to 80% may face an elevated risk of local extinction. These results suggest coral communities on isolated Pacific coral reefs, which are often predicted to be at low risk, are still vulnerable due to the small and fragmented nature of their populations. This reinforces that to adequately protect biodiversity, ongoing threatened species monitoring and the documentation of species-level changes in abundance and distribution is imperative.

  4. Energy Conservation and Development Plan. Southern Tier Central Region, New York

    Energy Technology Data Exchange (ETDEWEB)

    1979-07-01

    A summary is presented of the work of 40 volunteers working with regional planners to imagine, assess, and prescribe for the development of local energy resources (wind, solar, biomass, and water) and for conservation of all forms of energy. The plan contains a brief summary of the process the citizens followed in formulating the plan, the plans themselves, and appendices which contain more detailed comments by citizens on the possible consequences of the development of each resource. The areas (Chemung, Steuben, and Schuyler counties) experienced severe natural gas curtailments during the winter of 1976-1977. The formulation of an emergency energy conservation plan is also presented.

  5. LA CONSERVACIÓN BIOLÓGICA Y SU PERSPECTIVA EVOLUTIVA Biological Conservation and its Evolutionary Perspective

    Directory of Open Access Journals (Sweden)

    OLGA L MONTENEGRO

    Full Text Available Este artículo revisa tres de las principales causas de amenaza a la diversidad biológica, como son la fragmentación y pérdida del hábitat, así como la invasión de especies exóticas, principalmente en lo que compete a sus implicaciones evolutivas. Los efectos de la fragmentación y/o pérdida del hábitat pueden revisarse a la luz de la sinergia entre factores demográficos y genéticos que moldean cambios evolutivos o que llevan a las poblaciones al vórtice de la extinción. Las invasiones biológicas, aunque han generado pérdidas considerables en la diversidad biológica, ofrecen un escenario interesante para estudiar procesos evolutivos contemporáneos.This paper reviews three of the main threats to biological diversity, such as habitat fragmentation /habitat loss, and invasion of exotic species, mainly from their evolutionary implications. Effects of habitat fragmentation/habitat loss could be addressed by looking at the synergy between demographic and genetic factors that together shape evolutionary changes or otherwise bring populations to extinction vortex. Biological invasions, in spite of their strong negative effects on biological diversity, offer an interesting scenario to study contemporary evolutionary processes.

  6. Position and sequence conservation in Amniota of polymorphic enhancer HS1.2 within the palindrome of IgH 3'Regulatory Region

    Directory of Open Access Journals (Sweden)

    Rocchi Mariano

    2011-03-01

    Full Text Available Abstract Background The Immunoglobulin heavy chain (IgH 3' Regulatory Region (3'RR, located at the 3' of the constant alpha gene, plays a crucial role in immunoglobulin production. In humans, there are 2 copies of the 3'RR, each composed of 4 main elements: 3 enhancers and a 20 bp tandem repeat. The single mouse 3'RR differs from the two human ones for the presence of 4 more regulative elements with the double copy of one enhancer at the border of a palindromic region. Results We compared the 3'RR organization in genomes of vertebrates to depict the evolutionary history of the region and highlight its shared features. We found that in the 8 species in which the whole region was included in a fully assembled contig (mouse, rat, dog, rabbit, panda, orangutan, chimpanzee, and human, the shared elements showed synteny and a highly conserved sequence, thus suggesting a strong evolutionary constraint. In these species, the wide 3'RR (~30 kb in human bears a large palindromic sequence, consisting in two ~3 kb complementary branches spaced by a ~3 kb sequence always including the HS1.2 enhancer. In mouse and rat, HS3 is involved by the palindrome so that one copy of the enhancer is present on each side. A second relevant feature of our present work concerns human polymorphism of the HS1.2 enhancer, associated to immune diseases in our species. We detected a similar polymorphism in all the studied Catarrhini (a primate parvorder. The polymorphism consists of multiple copies of a 40 bp element up to 12 in chimpanzees, 8 in baboons, 6 in macaque, 5 in gibbons, 4 in humans and orangutan, separated by stretches of Cytosine. We show specific binding of this element to nuclear factors. Conclusions The nucleotide sequence of the palindrome is not conserved among evolutionary distant species, suggesting pressures for the maintenance of two self-matching regions driving a three-dimensional structure despite of the inter-specific divergence at sequence level. The

  7. Position and sequence conservation in Amniota of polymorphic enhancer HS1.2 within the palindrome of IgH 3'Regulatory Region.

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    D'Addabbo, Pietro; Scascitelli, Moira; Giambra, Vincenzo; Rocchi, Mariano; Frezza, Domenico

    2011-03-15

    The Immunoglobulin heavy chain (IgH) 3' Regulatory Region (3'RR), located at the 3' of the constant alpha gene, plays a crucial role in immunoglobulin production. In humans, there are 2 copies of the 3'RR, each composed of 4 main elements: 3 enhancers and a 20 bp tandem repeat. The single mouse 3'RR differs from the two human ones for the presence of 4 more regulative elements with the double copy of one enhancer at the border of a palindromic region. We compared the 3'RR organization in genomes of vertebrates to depict the evolutionary history of the region and highlight its shared features. We found that in the 8 species in which the whole region was included in a fully assembled contig (mouse, rat, dog, rabbit, panda, orangutan, chimpanzee, and human), the shared elements showed synteny and a highly conserved sequence, thus suggesting a strong evolutionary constraint. In these species, the wide 3'RR (~30 kb in human) bears a large palindromic sequence, consisting in two ~3 kb complementary branches spaced by a ~3 kb sequence always including the HS1.2 enhancer. In mouse and rat, HS3 is involved by the palindrome so that one copy of the enhancer is present on each side. A second relevant feature of our present work concerns human polymorphism of the HS1.2 enhancer, associated to immune diseases in our species. We detected a similar polymorphism in all the studied Catarrhini (a primate parvorder). The polymorphism consists of multiple copies of a 40 bp element up to 12 in chimpanzees, 8 in baboons, 6 in macaque, 5 in gibbons, 4 in humans and orangutan, separated by stretches of Cytosine. We show specific binding of this element to nuclear factors. The nucleotide sequence of the palindrome is not conserved among evolutionary distant species, suggesting pressures for the maintenance of two self-matching regions driving a three-dimensional structure despite of the inter-specific divergence at sequence level. The information about the conservation of the palindromic

  8. Nucleosome exclusion from the interspecies-conserved central AT-rich region of the Ars insulator.

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    Takagi, Haruna; Inai, Yuta; Watanabe, Shun-ichiro; Tatemoto, Sayuri; Yajima, Mamiko; Akasaka, Koji; Yamamoto, Takashi; Sakamoto, Naoaki

    2012-01-01

    The Ars insulator is a boundary element identified in the upstream region of the arylsulfatase (HpArs) gene in the sea urchin, Hemicentrotus pulcherrimus, and possesses the ability to both block enhancer-promoter communications and protect transgenes from silent chromatin. To understand the molecular mechanism of the Ars insulator, we investigated the correlation between chromatin structure, DNA structure and insulator activity. Nuclease digestion of nuclei isolated from sea urchin embryos revealed the presence of a nuclease-hypersensitive site within the Ars insulator. Analysis of micrococcal nuclease-sensitive sites in the Ars insulator, reconstituted with nucleosomes, showed the exclusion of nucleosomes from the central AT-rich region. Furthermore, the central AT-rich region in naked DNA was sensitive to nucleotide base modification by diethylpyrocarbonate (DEPC). These observations suggest that non-B-DNA structures in the central AT-rich region may inhibit nucleosomal formation, which leads to nuclease hypersensitivity. Furthermore, comparison of nucleotide sequences between the HpArs gene and its ortholog in Strongylocentrotus purpuratus revealed that the central AT-rich region of the Ars insulator is conserved, and this conserved region showed significant enhancer blocking activity. These results suggest that the central AT-rich nucleosome-free region plays an important role in the function of the Ars insulator.

  9. Evolutionary and structural features of the C2, V3 and C3 envelope regions underlying the differences in HIV-1 and HIV-2 biology and infection.

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    Helena Barroso

    Full Text Available BACKGROUND: Unlike in HIV-1 infection, the majority of HIV-2 patients produce broadly reactive neutralizing antibodies, control viral replication and survive as elite controllers. The identification of the molecular, structural and evolutionary footprints underlying these very distinct immunological and clinical outcomes may lead to the development of new strategies for the prevention and treatment of HIV infection. METHODOLOGY/PRINCIPAL FINDINGS: We performed a side-by-side molecular, evolutionary and structural comparison of the C2, V3 and C3 envelope regions from HIV-1 and HIV-2. These regions contain major antigenic targets and are important for receptor binding. In HIV-2, these regions also have immune modulatory properties. We found that these regions are significantly more variable in HIV-1 than in HIV-2. Within each virus, C3 is the most entropic region followed by either C2 (HIV-2 or V3 (HIV-1. The C3 region is well exposed in the HIV-2 envelope and is under strong diversifying selection suggesting that, like in HIV-1, it may harbour neutralizing epitopes. Notably, however, extreme diversification of C2 and C3 seems to be deleterious for HIV-2 and prevent its transmission. Computer modelling simulations showed that in HIV-2 the V3 loop is much less exposed than C2 and C3 and has a retractile conformation due to a physical interaction with both C2 and C3. The concealed and conserved nature of V3 in the HIV-2 is consistent with its lack of immunodominancy in vivo and with its role in preventing immune activation. In contrast, HIV-1 had an extended and accessible V3 loop that is consistent with its immunodominant and neutralizing nature. CONCLUSIONS/SIGNIFICANCE: We identify significant structural and functional constrains to the diversification and evolution of C2, V3 and C3 in the HIV-2 envelope but not in HIV-1. These studies highlight fundamental differences in the biology and infection of HIV-1 and HIV-2 and in their mode of

  10. Effects of Conservation Policies on Forest Cover Change in Giant Panda Habitat Regions, China.

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    Li, Yu; Viña, Andrés; Yang, Wu; Chen, Xiaodong; Zhang, Jindong; Ouyang, Zhiyun; Liang, Zai; Liu, Jianguo

    2013-07-01

    After long periods of deforestation, forest transition has occurred globally, but the causes of forest transition in different countries are highly variable. Conservation policies may play important roles in facilitating forest transition around the world, including China. To restore forests and protect the remaining natural forests, the Chinese government initiated two nationwide conservation policies in the late 1990s -- the Natural Forest Conservation Program (NFCP) and the Grain-To-Green Program (GTGP). While some studies have discussed the environmental and socioeconomic effects of each of these policies independently and others have attributed forest recovery to both policies without rigorous and quantitative analysis, it is necessary to rigorously quantify the outcomes of these two conservation policies simultaneously because the two policies have been implemented at the same time. To fill the knowledge gap, this study quantitatively evaluated the effects of the two conservation policies on forest cover change between 2001 and 2008 in 108 townships located in two important giant panda habitat regions -- the Qinling Mountains region in Shaanxi Province and the Sichuan Giant Panda Sanctuary in Sichuan Province. Forest cover change was evaluated using a land-cover product (MCD12Q1) derived from the Moderate Resolution Imaging Spectroradiometer (MODIS). This product proved to be highly accurate in the study region (overall accuracy was ca. 87%, using 425 ground truth points collected in the field), thus suitable for the forest change analysis performed. Results showed that within the timeframe evaluated, most townships in both regions exhibited either increases or no changes in forest cover. After accounting for a variety of socioeconomic and biophysical attributes, an Ordinary Least Square (OLS) regression model suggests that the two policies had statistically significant positive effects on forest cover change after seven years of implementation, while

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

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    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.

  12. Genetic structure and evolutionary history of three alpine sclerophyllous oaks in East Himalaya-Hengduan Mountains and adjacent regions

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    Li Feng

    2016-11-01

    Full Text Available The East Himalaya-Hengduan Mountains (EH-HM region has a high biodiversity and harbours numerous endemic alpine plants. This is probably the result of combined orographic and climate oscillations occurring since late Tertiary. Here, we determined the genetic structure and evolutionary history of alpine oak species (including Q. spinosa, Q. aquifolioides and Q. rehderiana using both cytoplasmic-nuclear markers and ecological niche models (ENMs, and elucidated the impacts of climate oscillations and environmental heterogeneity on their population demography. Our results indicate there were mixed genetic structure and asymmetric contemporary gene flow within them. The ENMs revealed a similar demographic history for the three species expanded their ranges from the last interglacial (LIG to the last glacial maximum (LGM, which was consistent with effective population sizes changes. Effects of genetic drift and fragmentation of habitats were responsible for the high differentiation and the lack of phylogeographic structure. Our results support that geological and climatic factors since Miocene triggered the differentiation, evolutionary origin and range shifts of the three oak species in the studied area and also emphasize that a multidisciplinary approach combining molecular markers, ENMs and population genetics can yield deep insights into diversification and evolutionary dynamics of species.

  13. Evolutionary history of a keystone pollinator parallels the biome occupancy of angiosperms in the Greater Cape Floristic Region.

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    de Jager, Marinus L; Ellis, Allan G

    2017-02-01

    The Greater Cape Floristic Region (GCFR) in South Africa has been extensively investigated for its phenomenal angiosperm diversity. A key emergent pattern is the occurrence of older plant lineages in the southern Fynbos biome and younger lineages in the northern Succulent Karoo biome. We know practically nothing, however, about the evolutionary history of the animals that pollinate this often highly-specialized flora. In this study, we explore the evolutionary history of an important GCFR fly pollinator, Megapalpus capensis, and ask whether it exhibits broadly congruent genetic structuring and timing of diversification to flowering plants within these biomes. We find that the oldest M. capensis lineages originated in Fynbos during the Miocene, while younger Succulent Karoo lineages diverged in the Pliocene and correspond to the proposed age of this recent biome. A strong signature of population expansion is also recovered for flies in this arid biome, consistent with recent colonization. Our first investigation into the evolutionary history of GCFR pollinators thus supports a recent origin of the SK biome, as inferred from angiosperm phylogenies, and suggests that plants and pollinators may have co-diverged within this remarkable area. Copyright © 2016 Elsevier Inc. All rights reserved.

  14. The research on regional conservation planning of urban historical and cultural areas based on GIS

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    Li, Shangli; Xu, Jian; Li, Qian

    2017-06-01

    With the rapid economic development and the growth of population happening in the urban historical and cultural areas, heritage and historical buildings along with their natural and artificial surrounding environments are suffering constructive destruction. Due to the lack of precise partition of protection region and construction control region in the local cultural relics protection law, traditional regional conservation planning cannot engaged with the urban controllability detailed planning very well. According to the several protection regulations about heritage and historical buildings from latest laws, we choose Baxian Temple area to study on the improvments of traditional regional conservation planning. The technical methods of this study mainly rely on GIS, which can complete the fundamental work of each stage. With the analytic hierarchy process(AHP), the comprehensive architectural value assessments can be calculated according to the investigation results. Based on the calculation results and visual corridor analysis, the precise range of protection region and construction control region can be decided and the specific protection measures can be formulated.

  15. Global conservation model for a mushy region over a moving substrate

    Science.gov (United States)

    Kyselica, J.; Šimkanin, J.

    2018-03-01

    We study solidification over a cool substrate moving with a relative velocity with respect to the rest of the fluid. A mathematical model based on global conservation of solute is presented. The explicit solutions of the governing equations are found and analysed via the asymptotic methods. The assessment of how the boundary-layer flow influences the physical characteristics of the mushy region is given, together with the discussion of a possible connection with the solidification at the inner core boundary.

  16. Aj-rel and Aj-p105, two evolutionary conserved NF-κB homologues in sea cucumber (Apostichopus japonicus) and their involvement in LPS induced immunity.

    Science.gov (United States)

    Wang, Tingting; Sun, Yongxin; Jin, Liji; Thacker, Philip; Li, Shuying; Xu, Yongping

    2013-01-01

    The nuclear factor κB (NF-κB) has been evolutionary conserved from insects to mammals and plays a major regulatory role in the initiation of physiological responses. In this study, we identified and characterized a primitive and functional NF-κB pathway active in the immune defence of the sea cucumber (Apostichopus japonicus). The ancient NF-κB homologues, Aj-rel and Aj-p105, share numerous signature motifs with their vertebrate orthologues, notably the Rel Homology Domain, Rel Protein Signature DNA Binding Motif, Nuclear Localization Signal and the Ankyrin Repeats for Aj-p105. Phylogenetic analyses indicate that these homologues belong to class I and II of NF-κB respectively. We examined the dimerization of Aj-rel and Aj-p105 and our results demonstrated that Aj-rel forms heterdimers with Aj-p105 and the degradation product of Aj-p105, namely Aj-p50. We further observed that LPS stimulation led to the degradation of Aj-p105 and the nuclear translocation of Aj-rel and Aj-p50. Taken together, our data indicate that the NF-κB signaling cascade is active in sea cucumber and plays a crucial role in regulating their immune defence. Our results increase the available information on sea cucumber immunity and provide new information for use in the study of the comparative and evolutionary aspects of immunity. Copyright © 2012 Elsevier Ltd. All rights reserved.

  17. Regional management units for marine turtles: a novel framework for prioritizing conservation and research across multiple scales.

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    Bryan P Wallace

    Full Text Available BACKGROUND: Resolving threats to widely distributed marine megafauna requires definition of the geographic distributions of both the threats as well as the population unit(s of interest. In turn, because individual threats can operate on varying spatial scales, their impacts can affect different segments of a population of the same species. Therefore, integration of multiple tools and techniques--including site-based monitoring, genetic analyses, mark-recapture studies and telemetry--can facilitate robust definitions of population segments at multiple biological and spatial scales to address different management and research challenges. METHODOLOGY/PRINCIPAL FINDINGS: To address these issues for marine turtles, we collated all available studies on marine turtle biogeography, including nesting sites, population abundances and trends, population genetics, and satellite telemetry. We georeferenced this information to generate separate layers for nesting sites, genetic stocks, and core distributions of population segments of all marine turtle species. We then spatially integrated this information from fine- to coarse-spatial scales to develop nested envelope models, or Regional Management Units (RMUs, for marine turtles globally. CONCLUSIONS/SIGNIFICANCE: The RMU framework is a solution to the challenge of how to organize marine turtles into units of protection above the level of nesting populations, but below the level of species, within regional entities that might be on independent evolutionary trajectories. Among many potential applications, RMUs provide a framework for identifying data gaps, assessing high diversity areas for multiple species and genetic stocks, and evaluating conservation status of marine turtles. Furthermore, RMUs allow for identification of geographic barriers to gene flow, and can provide valuable guidance to marine spatial planning initiatives that integrate spatial distributions of protected species and human activities

  18. An evolutionarily conserved intronic region controls the spatiotemporal expression of the transcription factor Sox10

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    Pavan William J

    2008-10-01

    Full Text Available Abstract Background A major challenge lies in understanding the complexities of gene regulation. Mutation of the transcription factor SOX10 is associated with several human diseases. The disease phenotypes reflect the function of SOX10 in diverse tissues including the neural crest, central nervous system and otic vesicle. As expected, the SOX10 expression pattern is complex and highly dynamic, but little is known of the underlying mechanisms regulating its spatiotemporal pattern. SOX10 expression is highly conserved between all vertebrates characterised. Results We have combined in vivo testing of DNA fragments in zebrafish and computational comparative genomics to identify the first regulatory regions of the zebrafish sox10 gene. Both approaches converged on the 3' end of the conserved 1st intron as being critical for spatial patterning of sox10 in the embryo. Importantly, we have defined a minimal region crucial for this function. We show that this region contains numerous binding sites for transcription factors known to be essential in early neural crest induction, including Tcf/Lef, Sox and FoxD3. We show that the identity and relative position of these binding sites are conserved between zebrafish and mammals. A further region, partially required for oligodendrocyte expression, lies in the 5' region of the same intron and contains a putative CSL binding site, consistent with a role for Notch signalling in sox10 regulation. Furthermore, we show that β-catenin, Notch signalling and Sox9 can induce ectopic sox10 expression in early embryos, consistent with regulatory roles predicted from our transgenic and computational results. Conclusion We have thus identified two major sites of sox10 regulation in vertebrates and provided evidence supporting a role for at least three factors in driving sox10 expression in neural crest, otic epithelium and oligodendrocyte domains.

  19. Conserved regions of ribonucleoprotein ribonuclease MRP are involved in interactions with its substrate.

    Science.gov (United States)

    Esakova, Olga; Perederina, Anna; Berezin, Igor; Krasilnikov, Andrey S

    2013-08-01

    Ribonuclease (RNase) MRP is a ubiquitous and essential site-specific eukaryotic endoribonuclease involved in the metabolism of a wide range of RNA molecules. RNase MRP is a ribonucleoprotein with a large catalytic RNA moiety that is closely related to the RNA component of RNase P, and multiple proteins, most of which are shared with RNase P. Here, we report the results of an ultraviolet-cross-linking analysis of interactions between a photoreactive RNase MRP substrate and the Saccharomyces cerevisiae RNase MRP holoenzyme. The results show that the substrate interacts with phylogenetically conserved RNA elements universally found in all enzymes of the RNase P/MRP family, as well as with a phylogenetically conserved RNA region that is unique to RNase MRP, and demonstrate that four RNase MRP protein components, all shared with RNase P, interact with the substrate. Implications for the structural organization of RNase MRP and the roles of its components are discussed.

  20. Hot Spots and Hot Times: Wildlife Road Mortality in a Regional Conservation Corridor

    Science.gov (United States)

    Garrah, Evelyn; Danby, Ryan K.; Eberhardt, Ewen; Cunnington, Glenn M.; Mitchell, Scott

    2015-10-01

    Strategies to reduce wildlife road mortality have become a significant component of many conservation efforts. However, their success depends on knowledge of the temporal and spatial patterns of mortality. We studied these patterns along the 1000 Islands Parkway in Ontario, Canada, a 37 km road that runs adjacent to the St. Lawrence River and bisects the Algonquin-to-Adirondacks international conservation corridor. Characteristics of all vertebrate road kill were recorded during 209 bicycle surveys conducted from 2008 to 2011. We estimate that over 16,700 vertebrates are killed on the road from April to October each year; most are amphibians, but high numbers of birds, mammals, and reptiles were also found, including six reptiles considered at-risk in Canada. Regression tree analysis was used to assess the importance of seasonality, weather, and traffic on road kill magnitude. All taxa except mammals exhibited distinct temporal peaks corresponding to phases in annual life cycles. Variations in weather and traffic were only important outside these peak times. Getis-Ord analysis was used to identify spatial clusters of mortality. Hot spots were found in all years for all taxa, but locations varied annually. A significant spatial association was found between multiyear hot spots and wetlands. The results underscore the notion that multi-species conservation efforts must account for differences in the seasonality of road mortality among species and that multiple years of data are necessary to identify locations where the greatest conservation good can be achieved. This information can be used to inform mitigation strategies with implications for conservation at regional scales.

  1. Modeling and Mapping Golden-winged Warbler Abundance to Improve Regional Conservation Strategies

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    Wayne E. Thogmartin

    2010-12-01

    Full Text Available Conservation planning requires identifying pertinent habitat factors and locating geographic locations where land management may improve habitat conditions for high priority species. I derived habitat models and mapped predicted abundance for the Golden-winged Warbler (Vermivora chrysoptera, a species of high conservation concern, using bird counts, environmental variables, and hierarchical models applied at multiple spatial scales. My aim was to understand habitat associations at multiple spatial scales and create a predictive abundance map for purposes of conservation planning for the Golden-winged Warbler. My models indicated a substantial influence of landscape conditions, including strong positive associations with total forest composition within the landscape. However, many of the associations I observed were counter to reported associations at finer spatial extents; for instance, I found Golden-winged Warblers negatively associated with several measures of edge habitat. No single spatial scale dominated, indicating that this species is responding to factors at multiple spatial scales. I found Golden-winged Warbler abundance was negatively related with Blue-winged Warbler (Vermivora cyanoptera abundance. I also observed a north-south spatial trend suggestive of a regional climate effect that was not previously noted for this species. The map of predicted abundance indicated a large area of concentrated abundance in west-central Wisconsin, with smaller areas of high abundance along the northern periphery of the Prairie Hardwood Transition. This map of predicted abundance compared favorably with independent evaluation data sets and can thus be used to inform regional planning efforts devoted to conserving this species.

  2. The keys to conservative treatment of early-stage squamous cell carcinoma of the tonsillar region.

    Science.gov (United States)

    Laccourreye, O; Castelnau-Marchand, P; Rubin, F; Badoual, C; Halimi, P; Giraud, P

    2017-09-01

    To analyze the medical literature devoted to work-up, epidemiology, local control, survival, complications and sequelae after conservative treatment for early-stage squamous cell carcinoma of the tonsillar region. An analysis of the PubMed (1975-2016) database was performed using the following keywords and associations: "tonsil/tonsillar region/oropharynx" AND "squamous cell carcinoma" AND "early-stage (I-II; T1-2N0M0)" AND "radiation therapy/radiotherapy" OR "conservative surgery/oropharyngectomy/transoral surgery/radical tonsillectomy". The search retrieved 10 retrospective series documenting local control and/or survival in series with more than 50 cases and a minimum 2 years' follow-up after conservative treatment; no prospective studies, meta-analyses and/or Cochrane analyses were found. Magnetic resonance imaging is the key radiological exam for local extension assessment. Human papilloma virus infection (HPV) is a risk factor that must be screened for systematically, since it induces tumoral radio-sensitivity and increases the risk of specific synchronous and metachronous second primaries. Whatever conservative treatment used, local control and survival rates higher than 85% were achieved. Implementing intensity-modulated radiation therapy reduced the incidence and severity of radiation-related complications and sequelae. Transoral surgery yielded very low morbidity/mortality rates, enabled association to ipsilateral neck dissection, and allowed radiation therapy to be reserved for the management of metachronous second primaries. Transoral surgery appeared to be the first-line option in the majority of cases. Lifetime follow-up adapted to HPV status is mandatory. The development of HPV vaccination does not mean that campaigns against smoking and alcohol abuse are of diminished importance. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  3. Challenges of transfrontier conservation areas: Natural resources nationalism, security and regionalism in the southern African development community region

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    Oswell Rusinga

    2012-12-01

    Full Text Available Transfrontier Conservation Areas (TFCAs initiatives in the Southern African Development Community (SADC region offer hope for providing a mechanism for resolving political tensions and conflicts which are not only related to environmental issues but to security concerns as well. The geopolitical implications of TFCAs in the SADC region cannot be overemphasised with regard to international relations and regional integration. The SADS region is characterised by histories of contested military balance of power and geopolitical rivalries which have a potential to degenerate into military confrontation. Although there is a strong belief in multilateral co-operation among SADC member countries, most of them often engage the international community at the bilateral level. Moreover, there is disharmony in constitutional applications of the rule of law, respect of human rights and good governance. However, TFCAs initiatives in Southern Africa have been seen as offering an opportunity to heal the wounds of pre- and post-independence wars of destabilisation through the encouragement of inter-state collaboration and co-operation by giving governments an opportunity for mutual action on issues of common interest.

  4. Phylogeography of the endangered rosewood Dalbergia nigra (Fabaceae): insights into the evolutionary history and conservation of the Brazilian Atlantic Forest

    Science.gov (United States)

    Ribeiro, R A; Lemos-Filho, J P; Ramos, A C S; Lovato, M B

    2011-01-01

    The Brazilian rosewood (Dalbergia nigra) is an endangered tree endemic to the central Brazilian Atlantic Forest, one of the world's most threatened biomes. The population diversity, phylogeographic structure and demographic history of this species were investigated using the variation in the chloroplast DNA (cpDNA) sequences of 185 individuals from 19 populations along the geographical range of the species. Fifteen haplotypes were detected in the analysis of 1297 bp from two non-coding sequences, trnV-trnM and trnL. We identified a strong genetic structure (FST=0.62, Pclimatic changes in the central part of the Atlantic forest, with cycles of forest expansion and contraction, may have led to repeated vicariance events, resulting in the genetic differentiation of these groups. Based on comparisons among the populations of large reserves and small, disturbed fragments of the same phylogeographic group, we also found evidence of recent anthropogenic effects on genetic diversity. The results were also analysed with the aim of contributing to the conservation of D. nigra. We suggest that the three phylogeographic groups could be considered as three distinct management units. Based on the genetic diversity and uniqueness of the populations, we also indicate priority areas for conservation. PMID:20517347

  5. The endocrine system controlling sexual reproduction in animals: Part of the evolutionary ancient but well conserved immune system?

    Science.gov (United States)

    De Loof, Arnold; Schoofs, Liliane; Huybrechts, Roger

    2016-01-15

    Drastic changes in hormone titers, in particular of steroid hormones, are intuitively interpreted as necessary and beneficial for optimal functioning of animals. Peaks in progesterone- and estradiol titers that accompany the estrus cycle in female vertebrates as well as in ecdysteroids at each molt and during metamorphosis of holometabolous insects are prominent examples. A recent analysis of insect metamorphosis yielded the view that, in general, a sharp rise in sex steroid hormone titer signals that somewhere in the body some tissue(s) is undergoing programmed cell death/apoptosis. Increased steroid production is part of this process. Typical examples are ovarian follicle cells in female vertebrates and invertebrates and the prothoracic gland cells, the main production site of ecdysteroids in larval insects. A duality emerges: programmed cell death-apoptosis is deleterious at the cellular level, but it may yield beneficial effects at the organismal level. Reconciling both opposites requires reevaluating the probable evolutionary origin and role of peptidic brain hormones that direct steroid hormone synthesis. Do e.g. Luteinizing Hormone in vertebrates and Prothoracicotropic Hormone (PTTH: acting through the Torso receptor) in insects still retain an ancient role as toxins in the early immune system? Does the functional link of some neuropeptides with Ca(2+)-induced apoptosis make sense in endocrine archeology? The endocrine system as a remnant of the ancient immune system is undoubtedly counterintuitive. Yet, we will argue that such paradigm enables the logical framing of many aspects, the endocrine one inclusive of both male and female reproductive physiology. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. Evolutionary status of dense cores in the NGC 1333 IRAS 4 star-forming region

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    Koumpia, E.; van der Tak, F. F. S.; Kwon, W.; Tobin, J. J.; Fuller, G. A.; Plume, R.

    2016-10-01

    Context. Protostellar evolution after the formation of the protostar is becoming reasonably well characterized, but the evolution from a prestellar core to a protostar is not well known, although the first hydrostatic core (FHSC) must be a pivotal step. Aims: NGC 1333 - IRAS 4C is a potentially very young object that we can directly compare with the nearby Class 0 objects IRAS 4A and IRAS 4B. Observational constraints are provided by spectral imaging from the JCMT Spectral Legacy Survey (330-373 GHz). We present integrated intensity and velocity maps of several species, including CO, H2CO and CH3OH. CARMA observations provide additional information with which we can distinguish IRAS 4C from other evolutionary stages. Methods: We present the observational signatures of the velocity of an observed outflow, the degree of CO depletion, the deuterium fractionation of [DCO+]/[HCO+], and gas kinetic temperatures. Results: We report differences between the three sources in four aspects: a) the kinetic temperature as probed using the H2CO lines is much lower toward IRAS 4C than the other two sources; b) the line profiles of the detected species show strong outflow activity toward IRAS 4A and IRAS 4B, but not toward IRAS 4C; c) the HCN/HNC is <1 toward IRAS 4C, which confirms the cold nature of the source; d) the degree of CO depletion and the deuteration are lowest toward the warmest of the sources, IRAS 4B. Conclusions: IRAS 4C seems to be in a different evolutionary state than the sources IRAS 4A and IRAS 4B. We can probably exclude the FHSC stage becaues of the relatively low Lsmm/Lbol ( 6%), and we investigate the earliest accretion phase of Class 0 stage and the transition between Class 0 to Class I. Our results do not show a consistent scenario for either case; the main problem is the absence of outflow activity and the cold nature of IRAS 4C. The number of FHSC candidates in Perseus is 10 times higher than current models predict, which suggests that the lifespan of

  7. Conservation phylogeography: does historical diversity contribute to regional vulnerability in European tree frogs (Hyla arborea)?

    Science.gov (United States)

    Dufresnes, Christophe; Wassef, Jérôme; Ghali, Karim; Brelsford, Alan; Stöck, Matthias; Lymberakis, Petros; Crnobrnja-Isailovic, Jelka; Perrin, Nicolas

    2013-11-01

    Documenting and preserving the genetic diversity of populations, which conditions their long-term survival, have become a major issue in conservation biology. The loss of diversity often documented in declining populations is usually assumed to result from human disturbances; however, historical biogeographic events, otherwise known to strongly impact diversity, are rarely considered in this context. We apply a multilocus phylogeographic study to investigate the late-Quaternary history of a tree frog (Hyla arborea) with declining populations in the northern and western part of its distribution range. Mitochondrial and nuclear polymorphisms reveal high genetic diversity in the Balkan Peninsula, with a spatial structure moulded by the last glaciations. While two of the main refugial lineages remained limited to the Balkans (Adriatic coast, southern Balkans), a third one expanded to recolonize Northern and Western Europe, loosing much of its diversity in the process. Our findings show that mobile and a priori homogeneous taxa may also display substructure within glacial refugia ('refugia within refugia') and emphasize the importance of the Balkans as a major European biodiversity centre. Moreover, the distribution of diversity roughly coincides with regional conservation situations, consistent with the idea that historically impoverished genetic diversity may interact with anthropogenic disturbances, and increase the vulnerability of populations. Phylogeographic models seem important to fully appreciate the risks of local declines and inform conservation strategies. © 2013 John Wiley & Sons Ltd.

  8. MECP2, a gene associated with Rett syndrome in humans, shows conserved coding regions, independent Alu insertions, and a novel transcript across primate evolution.

    Science.gov (United States)

    Viana, Maria Carolina; Menezes, Albert Nobre; Moreira, Miguel Angelo M; Pissinatti, Alcides; Seuánez, Héctor N

    2015-07-07

    The methyl-CpG Binding Protein two gene (MECP2) encodes a multifunctional protein comprising two isoforms involved in nuclear organization and regulation of splicing and mRNA template activity. This gene is normally expressed in all tissues, with a higher expression level in the brain during neuronal maturation. Loss of MECP2 function is the primary cause of Rett syndrome (RTT) in humans, a dominant, X-linked disorder dramatically affecting neural and motor development. We investigated the molecular evolution of MECP2 in several primate taxa including 36 species in 16 genera of neotropical (platyrrhine) primates. The coding region of the MECP2_e2 isoform showed a high level of evolutionary conservation among humans and other primates, with amino acid substitutions in 14 codons and one in-frame insertion of a single serine codon, between codons 357 and 358, in Ateles paniscus. Most substitutions occurred in noncritical regions of MECP2 and the majority of the algorithms used for analyzing selection did not provide evidence of positive selection. Conversely, we found 48 sites under negative selection in different regions, 23 of which were consistently found by three different algorithms. Similar to an inverted Alu insert found previously in a lesser ape at a parallel location, one Alu insertion of approximately 300 bp in Cebus and Sapajus was found in intron 3. Phylogenetic reconstruction of the intron 3 data provided a topology that was coincident with the consensus arrangement of the primate taxa. RNAseq data in the neotropical primate Callimico goeldii revealed a novel transcript consisting of a noncontinuous region of the human-homologous intron 2 in this species; this transcript accounted for two putative polypeptides. Despite the remarkable evolutionary conservation of MECP2, one in-frame codon insertion was observed in A. paniscus, and one region of intron 3 was affected by a trans-specific Alu retrotransposition in two neotropical primate genera. Moreover

  9. Genetic diversity, evolutionary history and implications for conservation of the lion (Panthera leo) in West and Central Africa

    NARCIS (Netherlands)

    Bertola, L.D.; Hooft, van W.F.; Vrieling, K.; Weerd, de D.R.U.; York, D.S.; Bauer, H.; Prins, H.H.T.; Funston, P.J.; Haes, de H.A.U.; Leirs, H.; Haeringen, van W.A.; Sogbohossou, E.; Tumenta, P.N.; Iongh, de H.H.

    2011-01-01

    Aim In recent decades there has been a marked decline in the numbers of African lions (Panthera leo), especially in West Africa where the species is regionally endangered. Based on the climatological history of western Africa, we hypothesize that West and Central African lions have a unique

  10. Conservation and implications of eukaryote transcriptional regulatory regions across multiple species

    Directory of Open Access Journals (Sweden)

    Deng Minghua

    2008-12-01

    Full Text Available Abstract Background Increasing evidence shows that whole genomes of eukaryotes are almost entirely transcribed into both protein coding genes and an enormous number of non-protein-coding RNAs (ncRNAs. Therefore, revealing the underlying regulatory mechanisms of transcripts becomes imperative. However, for a complete understanding of transcriptional regulatory mechanisms, we need to identify the regions in which they are found. We will call these transcriptional regulation regions, or TRRs, which can be considered functional regions containing a cluster of regulatory elements that cooperatively recruit transcriptional factors for binding and then regulating the expression of transcripts. Results We constructed a hierarchical stochastic language (HSL model for the identification of core TRRs in yeast based on regulatory cooperation among TRR elements. The HSL model trained based on yeast achieved comparable accuracy in predicting TRRs in other species, e.g., fruit fly, human, and rice, thus demonstrating the conservation of TRRs across species. The HSL model was also used to identify the TRRs of genes, such as p53 or OsALYL1, as well as microRNAs. In addition, the ENCODE regions were examined by HSL, and TRRs were found to pervasively locate in the genomes. Conclusion Our findings indicate that 1 the HSL model can be used to accurately predict core TRRs of transcripts across species and 2 identified core TRRs by HSL are proper candidates for the further scrutiny of specific regulatory elements and mechanisms. Meanwhile, the regulatory activity taking place in the abundant numbers of ncRNAs might account for the ubiquitous presence of TRRs across the genome. In addition, we also found that the TRRs of protein coding genes and ncRNAs are similar in structure, with the latter being more conserved than the former.

  11. Local knowledge of the flora of a region: implications in biodiversity conservation

    Directory of Open Access Journals (Sweden)

    Maria da Conceição Pereira

    2016-11-01

    Full Text Available The flora of a region is important in aesthetic, environmental and economic terms. Academic degree holders are fundamental for the sustainable development of a geographically isolated region such as the Azores, the University of Azores (UAc contributing to that goal. We assessed the perception of the UAc students about the origin and the importance of the Azorean flora for conservation, culture and economy, by applying a questionnaire to 309 students in different scientific areas, addressing origin, symbolic importance, economic importance, and environmental functions. Students showed some knowledge about the concepts of endemic, native, introduced and invasive species, but often failed to connect those to specific plant taxa. Most species cited as symbolic were animals, and the plants mentioned were mainly exotic/invasive. Respondents had a sense of the most important crops and forest species, and attributed several functions related to biodiversity and environmental conservation to the flora. Despite the many actions already implemented, more initiatives are required to increase the connection between Azoreans and Azorean flora.

  12. Evolutionary conservation of the signaling proteins upstream of cyclic AMP-dependent kinase and protein kinase C in gastropod mollusks.

    Science.gov (United States)

    Sossin, Wayne S; Abrams, Thomas W

    2009-01-01

    The protein kinase C (PKC) and the cAMP-dependent kinase (protein kinase A; PKA) pathways are known to play important roles in behavioral plasticity and learning in the nervous systems of a wide variety of species across phyla. We briefly review the members of the PKC and PKA family and focus on the evolution of the immediate upstream activators of PKC and PKA i.e., phospholipase C (PLC) and adenylyl cyclase (AC), and their conservation in gastropod mollusks, taking advantage of the recent assembly of the Aplysiacalifornica and Lottia gigantea genomes. The diversity of PLC and AC family members present in mollusks suggests a multitude of possible mechanisms to activate PKA and PKC; we briefly discuss the relevance of these pathways to the known physiological activation of these kinases in Aplysia neurons during plasticity and learning. These multiple mechanisms of activation provide the gastropod nervous system with tremendous flexibility for implementing neuromodulatory responses to both neuronal activity and extracellular signals. Copyright 2009 S. Karger AG, Basel.

  13. Structure of Fusarium poae virus 1 shows conserved and variable elements of partitivirus capsids and evolutionary relationships to picobirnavirus.

    Science.gov (United States)

    Tang, Jinghua; Ochoa, Wendy F; Li, Hua; Havens, Wendy M; Nibert, Max L; Ghabrial, Said A; Baker, Timothy S

    2010-12-01

    Filamentous fungus Fusarium poae is a worldwide cause of the economically important disease Fusarium head blight of cereal grains. The fungus is itself commonly infected with a bisegmented dsRNA virus from the family Partitiviridae. For this study, we determined the structure of partitivirus Fusarium poae virus 1 (FpV1) to a resolution of 5.6Å or better by electron cryomicroscopy and three-dimensional image reconstruction. The main structural features of FpV1 are consistent with those of two other fungal partitiviruses for which high-resolution structures have been recently reported. These shared features include a 120-subunit T=1 capsid comprising 60 quasisymmetrical capsid protein dimers with both shell and protruding domains. Distinguishing features are evident throughout the FpV1 capsid, however, consistent with its more massive subunits and its greater phylogenetic divergence relative to the other two structurally characterized partitiviruses. These results broaden our understanding of conserved and variable elements of fungal partitivirus structure, as well as that of vertebrate picobirnavirus, and support the suggestion that a phylogenetic subcluster of partitiviruses closely related to FpV1 should constitute a separate taxonomic genus. Copyright © 2010 Elsevier Inc. All rights reserved.

  14. Visions of the past and dreams of the future in the Orient: the Irano-Turanian region from classical botany to evolutionary studies.

    Science.gov (United States)

    Manafzadeh, Sara; Staedler, Yannick M; Conti, Elena

    2017-08-01

    Ever since the 19th century, the immense arid lands of the Orient, now called the Irano-Turanian (IT) floristic region, attracted the interest of European naturalists with their tremendous plant biodiversity. Covering approximately 30% of the surface of Eurasia (16000000 km 2 ), the IT region is one of the largest floristic regions of the world. The IT region represents one of the hotspots of evolutionary and biological diversity in the Old World, and serves as a source of xerophytic taxa for neighbouring regions. Moreover, it is the cradle of the numerous species domesticated in the Fertile Crescent. Over the last 200 years, naturalists outlined different borders for the IT region. Yet, the delimitation and evolutionary history of this area remain one of the least well-understood fields of global biogeography, even though it is crucial to explaining the distribution of life in Eurasia. No comprehensive review of the biogeographical delimitations nor of the role of geological and climatic changes in the evolution of the IT region is currently available. After considering the key role of floristic regions in biogeography, we review the history of evolving concepts about the borders and composition of the IT region over the past 200 years and outline a tentative circumscription for it. We also summarise current knowledge on the geological and climatic history of the IT region. We then use this knowledge to generate specific evolutionary hypotheses to explain how different geological, palaeoclimatic, and ecological factors contributed to range expansion and contraction, thus shaping patterns of speciation in the IT region over time and space. Both historical and ecological biogeography should be applied to understand better the floristic diversification of the region. This will ultimately require evolutionary comparative analyses based on integrative phylogenetic, geological, climatic, ecological, and species distribution studies on the region. Furthermore, an

  15. Phylogenetic and regulatory region analysis of Wnt5 genes reveals conservation of a regulatory module with putative implication in pancreas development

    Directory of Open Access Journals (Sweden)

    Arhondakis Stilianos

    2010-08-01

    Full Text Available Abstract Background Wnt5 genes belong to the large Wnt family, encoding proteins implicated into several tumorigenic and developmental processes. Phylogenetic analyses showed that Wnt5 gene has been duplicated at the divergence time of gnathostomata from agnatha. Interestingly, experimental data for some species indicated that only one of the two Wnt5 paralogs participates in the development of the endocrine pancreas. The purpose of this paper is to reexamine the phylogenetic history of the Wnt5 developmental regulators and investigate the functional shift between paralogs through comparative genomics. Results In this study, the phylogeny of Wnt5 genes was investigated in species belonging to protostomia and deuterostomia. Furthermore, an in silico regulatory region analysis of Wnt5 paralogs was conducted, limited to those species with insulin producing cells and pancreas, covering the evolutionary distance from agnatha to gnathostomata. Our results confirmed the Wnt5 gene duplication and additionally revealed that this duplication event included also the upstream region. Moreover, within this latter region, a conserved module was detected to which a complex of transcription factors, known to be implicated in embryonic pancreas formation, bind. Conclusions Results and observations presented in this study, allow us to conclude that during evolution, the Wnt5 gene has been duplicated in early vertebrates, and that some paralogs conserved a module within their regulatory region, functionally related to embryonic development of pancreas. Interestingly, our results allowed advancing a possible explanation on why the Wnt5 orthologs do not share the same function during pancreas development. As a final remark, we suggest that an in silico comparative analysis of regulatory regions, especially when associated to published experimental data, represents a powerful approach for explaining shift of roles among paralogs. Reviewers This article was reviewed

  16. Phylogenetic and regulatory region analysis of Wnt5 genes reveals conservation of a regulatory module with putative implication in pancreas development.

    Science.gov (United States)

    Kapasa, Maria; Arhondakis, Stilianos; Kossida, Sophia

    2010-08-04

    Wnt5 genes belong to the large Wnt family, encoding proteins implicated into several tumorigenic and developmental processes. Phylogenetic analyses showed that Wnt5 gene has been duplicated at the divergence time of gnathostomata from agnatha. Interestingly, experimental data for some species indicated that only one of the two Wnt5 paralogs participates in the development of the endocrine pancreas. The purpose of this paper is to reexamine the phylogenetic history of the Wnt5 developmental regulators and investigate the functional shift between paralogs through comparative genomics. In this study, the phylogeny of Wnt5 genes was investigated in species belonging to protostomia and deuterostomia. Furthermore, an in silico regulatory region analysis of Wnt5 paralogs was conducted, limited to those species with insulin producing cells and pancreas, covering the evolutionary distance from agnatha to gnathostomata. Our results confirmed the Wnt5 gene duplication and additionally revealed that this duplication event included also the upstream region. Moreover, within this latter region, a conserved module was detected to which a complex of transcription factors, known to be implicated in embryonic pancreas formation, bind. Results and observations presented in this study, allow us to conclude that during evolution, the Wnt5 gene has been duplicated in early vertebrates, and that some paralogs conserved a module within their regulatory region, functionally related to embryonic development of pancreas. Interestingly, our results allowed advancing a possible explanation on why the Wnt5 orthologs do not share the same function during pancreas development. As a final remark, we suggest that an in silico comparative analysis of regulatory regions, especially when associated to published experimental data, represents a powerful approach for explaining shift of roles among paralogs.

  17. Molecular Characterization and Expression Profiling of Brachypodium distachyon L. Cystatin Genes Reveal High Evolutionary Conservation and Functional Divergence in Response to Abiotic Stress

    Directory of Open Access Journals (Sweden)

    Saminathan Subburaj

    2017-05-01

    Full Text Available Cystatin is a class of proteins mainly involved in cysteine protease inhibition and plant growth and development, as well as tolerance under various abiotic stresses. In this study, we performed the first comprehensive analysis of the molecular characterization and expression profiling in response to various abiotic stresses of the cystatin gene family in Brachypodium distachyon, a novel model plant for Triticum species with huge genomes. Comprehensive searches of the Brachypodium genome database identified 25 B. distachyon cystatin (BdC genes that are distributed unevenly on chromosomes; of these, nine and two were involved in tandem and segmental duplication events, respectively. All BdC genes had similar exon/intron structural organization, with three conserved motifs similar to those from other plant species, indicating their high evolutionary conservation. Expression profiling of 10 typical BdC genes revealed ubiquitous expression in different organs at varying expression levels. BdC gene expression in seedling leaves was particularly highly induced by various abiotic stresses, including the plant hormone abscisic acid and various environmental cues (cold, H2O2, CdCl2, salt, and drought. Interestingly, most BdC genes were significantly upregulated under multiple abiotic stresses, including BdC15 under all stresses, BdC7-2 and BdC10 under five stresses, and BdC7-1, BdC2-1, BdC14, and BdC12 under four stresses. The putative metabolic pathways of cytastin genes in response to various abiotic stresses mainly involve the aberrant protein degradation pathway and reactive oxygen species (ROS-triggered programmed cell death signaling pathways. These observations provide a better understanding of the structural and functional characteristics of the plant cystatin gene family.

  18. Conservation status and regional habitat priorities for the Orinoco crocodile: Past, present, and future.

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    Sergio A Balaguera-Reina

    Full Text Available Conservation of large predator species has historically been a challenge because they often overlap in resource utilization with humans; furthermore, there is a general lack of in-depth knowledge of their ecology and natural history. We assessed the conservation status of the Orinoco crocodile (Crocodylus intermedius, defining regional habitat priorities/crocodile conservation units (RHP/CCU and regional research priorities (RRP for this species. We also estimated a species distribution model (SDM to define current suitable areas where the species might inhabit and/or that might be successfully colonized. The SDM area obtained with a suitable habitat probability ≥ 0.5 was 23,621 km2. Out of 2,562 km2 are included within protected areas in both Colombia (1,643 km2 and Venezuela (919 km2, which represents only 10.8% of C. intermedius' potential range. Areas such as Laguna de Chigüichigüe (flood plain lagoon exhibited an increase in population abundance. In contrast, localities such as the Cojedes and Manapire Rivers reported a significant reduction in relative abundance values. In Colombia, disparity in previous survey methods prevented accurate estimation of population trends. Only one study in this country described an increase over a 13 years span in the Ele, Lipa, and Cravo Norte River populations based on nest surveys. We defined 34 critical areas (16 in Colombia, 17 in Venezuela, and one covering both countries where we need to preserve/research/monitor and/or generate management actions, 10 RHP/CCU (six from Venezuela and four from Colombia and 24 RRP (11 from Venezuela, 12 from Colombia, and one in both countries. Caño Guaritico (Creek and the Capanaparo River in Venezuela and the Ele, Lipa, Cravo Norte River System and the Guayabero River in Colombia were defined as areas with the most optimal conditions for long-term preservation and maintenance of C. intermedius populations. We conclude that the conservation status of this species

  19. Conservation status and regional habitat priorities for the Orinoco crocodile: Past, present, and future.

    Science.gov (United States)

    Balaguera-Reina, Sergio A; Espinosa-Blanco, Ariel S; Morales-Betancourt, Mónica A; Seijas, Andrés E; Lasso, Carlos A; Antelo, Rafael; Densmore, Llewellyn D

    2017-01-01

    Conservation of large predator species has historically been a challenge because they often overlap in resource utilization with humans; furthermore, there is a general lack of in-depth knowledge of their ecology and natural history. We assessed the conservation status of the Orinoco crocodile (Crocodylus intermedius), defining regional habitat priorities/crocodile conservation units (RHP/CCU) and regional research priorities (RRP) for this species. We also estimated a species distribution model (SDM) to define current suitable areas where the species might inhabit and/or that might be successfully colonized. The SDM area obtained with a suitable habitat probability ≥ 0.5 was 23,621 km2. Out of 2,562 km2 are included within protected areas in both Colombia (1,643 km2) and Venezuela (919 km2), which represents only 10.8% of C. intermedius' potential range. Areas such as Laguna de Chigüichigüe (flood plain lagoon) exhibited an increase in population abundance. In contrast, localities such as the Cojedes and Manapire Rivers reported a significant reduction in relative abundance values. In Colombia, disparity in previous survey methods prevented accurate estimation of population trends. Only one study in this country described an increase over a 13 years span in the Ele, Lipa, and Cravo Norte River populations based on nest surveys. We defined 34 critical areas (16 in Colombia, 17 in Venezuela, and one covering both countries) where we need to preserve/research/monitor and/or generate management actions, 10 RHP/CCU (six from Venezuela and four from Colombia) and 24 RRP (11 from Venezuela, 12 from Colombia, and one in both countries). Caño Guaritico (Creek) and the Capanaparo River in Venezuela and the Ele, Lipa, Cravo Norte River System and the Guayabero River in Colombia were defined as areas with the most optimal conditions for long-term preservation and maintenance of C. intermedius populations. We conclude that the conservation status of this species is still

  20. Unusual evolutionary conservation and frequent DNA segment exchange in class I genes of the major histocompatibility complex.

    OpenAIRE

    Hayashida, H; Miyata, T.

    1983-01-01

    From comparisons of homologous DNA sequences for many different genes, it was shown that the silent positions of protein-encoding regions and introns evolve at high and remarkably similar rates for different genes. In addition, both silent positions and introns behave like clocks; they accumulated base substitutions at approximately constant rates with respect to geological time. The rates of evolution were estimated to be 5.5 X 10(-9), 3.7 X 10(-9), and 5.3 X 10(-9) per site per year for sil...

  1. Evolutionary Conserved Function of Barley and Arabidopsis 3-KETOACYL-CoA SYNTHASES in Providing Wax Signals for Germination of Powdery Mildew Fungi1[C][W

    Science.gov (United States)

    Weidenbach, Denise; Jansen, Marcus; Franke, Rochus B.; Hensel, Goetz; Weissgerber, Wiebke; Ulferts, Sylvia; Jansen, Irina; Schreiber, Lukas; Korzun, Viktor; Pontzen, Rolf; Kumlehn, Jochen; Pillen, Klaus; Schaffrath, Ulrich

    2014-01-01

    For plant pathogenic fungi, such as powdery mildews, that survive only on a limited number of host plant species, it is a matter of vital importance that their spores sense that they landed on the right spot to initiate germination as quickly as possible. We investigated a barley (Hordeum vulgare) mutant with reduced epicuticular leaf waxes on which spores of adapted and nonadapted powdery mildew fungi showed reduced germination. The barley gene responsible for the mutant wax phenotype was cloned in a forward genetic screen and identified to encode a 3-KETOACYL-CoA SYNTHASE (HvKCS6), a protein participating in fatty acid elongation and required for synthesis of epicuticular waxes. Gas chromatography-mass spectrometry analysis revealed that the mutant has significantly fewer aliphatic wax constituents with a chain length above C-24. Complementation of the mutant restored wild-type wax and overcame germination penalty, indicating that wax constituents less present on the mutant are a crucial clue for spore germination. Investigation of Arabidopsis (Arabidopsis thaliana) transgenic plants with sense silencing of Arabidopsis REQUIRED FOR CUTICULAR WAX PRODUCTION1, the HvKCS6 ortholog, revealed the same germination phenotype against adapted and nonadapted powdery mildew fungi. Our findings hint to an evolutionary conserved mechanism for sensing of plant surfaces among distantly related powdery mildews that is based on KCS6-derived wax components. Perception of such a signal must have been evolved before the monocot-dicot split took place approximately 150 million years ago. PMID:25201879

  2. Northwest Climate Science Center: Integrating Regional Research, Conservation and Natural Resource Management

    Science.gov (United States)

    Mote, P.; Bisbal, G.

    2012-12-01

    The Northwest Climate Science Center (NW CSC) was established in 2010, among the first three of eight regional Climate Science Centers created by the Department of the Interior (DOI). The NW CSC is supported by an academic consortium (Oregon State University, University of Idaho, and the University of Washington), which has the capacity to generate and coordinate decision-relevant science related to climate, thus serving stakeholders across the Pacific Northwest region. The NW CSC has overlapping boundaries with three Landscape Conservation Cooperatives (LCCs): the Great Northern, the Great Basin, and the North Pacific. Collaboration between the NW CSC and these three LCCs addresses the highest priority regional climate science needs of Northwest natural and cultural resource managers. Early in 2012, the NW CSC released its first Strategic Plan for the period 2012-2015. The plan offers a practical blueprint for operation and describes five core services that the NW CSC provides to the Northwest community. These core services emphasize (a) bringing together the regional resource management and science communities to calibrate priorities and ensure efficient integration of climate science resources and tools when addressing practical issues of regional significance; (b) developing and implementing a stakeholder-driven science agenda which highlights the NW CSC's regional leadership in generating scenarios of the future environment of the NW; (c) supporting and training graduate students at the three consortium universities, including through an annual 'Climate science boot camp'; (d) providing a platform for effective climate-change-related communication among scientists, resource managers, and the general public; and (e) national leadership in data management and climate scenario development.

  3. Diversity and distribution of aquatic insects in Southern Brazil wetlands: implications for biodiversity conservation in a Neotropical region

    Directory of Open Access Journals (Sweden)

    Leonardo Maltchik

    2012-03-01

    Full Text Available The selection of priority areas is an enormous challenge for biodiversity conservation. Some biogeographic methods have been used to identify the priority areas to conservation, and panbiogeography is one of them. This study aimed at the utilization of panbiogeographic tools, to identify the distribution patterns of aquatic insect genera, in wetland systems of an extensive area in the Neotropical region (~280 000km², and to compare the distribution of the biogeographic units identified by the aquatic insects, with the conservation units of Southern Brazil. We analyzed the distribution pattern of 82 genera distributed in four orders of aquatic insects (Diptera, Odonata, Ephemeroptera and Trichoptera in Southern Brazil wetlands. Therefore, 32 biogeographic nodes corresponded to the priority areas for conservation of the aquatic insect diversity. Among this total, 13 were located in the Atlantic Rainforest, 16 in the Pampa and three amongst both biomes. The distribution of nodes showed that only 15% of the dispersion centers of insects were inserted in conservation units. The four priority areas pointed by node cluster criterion must be considered in further inclusions of areas for biodiversity conservation in Southern Brazil wetlands, since such areas present species from differrent ancestral biota. The inclusion of such areas into the conservation units would be a strong way to conserve the aquatic biodiversity in this region.

  4. Conserving Prairie Pothole Region wetlands and surrounding grasslands: evaluating effects on amphibians

    Science.gov (United States)

    Mushet, David M.; Neau, Jordan L.

    2014-01-01

    The maintenance of viable and genetically diverse populations of amphibians in the Prairie Pothole Region of the United States depends on upland as well as wetland over-wintering and landscape level habitat features.Prairie pothole wetlands provide important amphibian breeding habitat while grasslands surrounding these wetlands provide foraging habitat for adults, overwintering habitat for some species, and important connectivity among breeding wetlands.Grasslands surrounding wetlands were found to be especially important for wood frogs and northern leopard frogs, while croplands dominated habitat utilized by Great Plains toads and Woodhouse’s toads.Habitat suitability mapping highlighted (1) the influence of deep-water overwintering wetlands on suitable habitat for four of five anuran species encountered; (2) the lack of overlap between areas of core habitat for both the northern leopard frog and wood frog compared to the core habitat for both toad species; and (3) the importance of conservation programs in providing grassland components of northern leopard frog and wood frog habitat.Currently, there are approximately 7.2 million acres (2.9 million hectares, ha) of habitat in the PPR identified as suitable for amphibians. WRP and CRP wetland and grassland habitats accounted for approximately 1.9 million acres (0.75 million ha) or 26 percent of this total area.Continued loss of amphibian habitat resulting from an ongoing trend of returning PPR conservation lands to crop production, will likely have significant negative effects on the region’s ability to maintain amphibian biodiversity. Conversely, increases in conservation wetlands and surrounding grasslands on the PPR landscape have great potential to positively influence the region’s amphibian populations.

  5. FOXP in Tetrapoda: Intrinsically Disordered Regions, Short Linear Motifs and their evolutionary significance

    OpenAIRE

    Viscardi, Lucas Henriques; Tovo-Rodrigues, Luciana; Par?, Pamela; Fagundes, Nelson Jurandi Rosa; Salzano, Francisco Mauro; Paix?o-C?rtes, Vanessa Rodrigues; Bau, Claiton Henrique Dotto; Bortolini, Maria C?tira

    2017-01-01

    Abstract The FOXP subfamily is probably the most extensively characterized subfamily of the forkhead superfamily, playing important roles in development and homeostasis in vertebrates. Intrinsically disorder protein regions (IDRs) are protein segments that exhibit multiple physical interactions and play critical roles in various biological processes, including regulation and signaling. IDRs in proteins may play an important role in the evolvability of genetic systems. In this study, we analyz...

  6. Functional analysis of COP1 and SPA orthologs from Physcomitrella and rice during photomorphogenesis of transgenic Arabidopsis reveals distinct evolutionary conservation.

    Science.gov (United States)

    Ranjan, Aashish; Dickopf, Stephen; Ullrich, Kristian K; Rensing, Stefan A; Hoecker, Ute

    2014-07-01

    Plants have evolved light sensing mechanisms to optimally adapt their growth and development to the ambient light environment. The COP1/SPA complex is a key negative regulator of light signaling in the well-studied dicot Arabidopsis thaliana. COP1 and members of the four SPA proteins are part of an E3 ubiquitin ligase that acts in darkness to ubiquitinate several transcription factors involved in light responses, thereby targeting them for degradation by the proteasome. While COP1 is also found in humans, SPA proteins appear specific to plants. Here, we have functionally addressed evolutionary conservation of COP1 and SPA orthologs from the moss Physcomitrella, the monocot rice and the dicot Arabidopsis. To this end, we analyzed the activities of COP1- and SPA-like proteins from Physcomitrella patens and rice when expressed in Arabidopsis. Expression of rice COP1 and Physcomitrella COP1 protein sequences predominantly complemented all phenotypic aspects of the viable, hypomorphic cop1-4 mutant and the null, seedling-lethal cop1-5 mutant of Arabidopsis: rice COP1 fully rescued the constitutive-photomorphogenesis phenotype in darkness and the leaf expansion defect of cop1 mutants, while it partially restored normal photoperiodic flowering in cop1. Physcomitrella COP1 partially restored normal seedling growth and flowering time, while it fully restored normal leaf expansion in the cop1 mutants. In contrast, expression of a SPA ortholog from Physcomitrella (PpSPAb) in Arabidopsis spa mutants did not rescue any facet of the spa mutant phenotype, suggesting that the PpSPAb protein is not functionally conserved or that the Arabidopsis function evolved after the split of mosses and seed plants. The SPA1 ortholog from rice (OsSPA1) rescued the spa mutant phenotype in dark-grown seedlings, but did not complement any spa mutant phenotype in light-grown seedlings or in adult plants. Our results show that COP1 protein sequences from Physcomitrella, rice and Arabidopsis have

  7. Functional analysis of COP1 and SPA orthologs from Physcomitrella and rice during photomorphogenesis of transgenic Arabidopsis reveals distinct evolutionary conservation

    Science.gov (United States)

    2014-01-01

    Background Plants have evolved light sensing mechanisms to optimally adapt their growth and development to the ambient light environment. The COP1/SPA complex is a key negative regulator of light signaling in the well-studied dicot Arabidopsis thaliana. COP1 and members of the four SPA proteins are part of an E3 ubiquitin ligase that acts in darkness to ubiquitinate several transcription factors involved in light responses, thereby targeting them for degradation by the proteasome. While COP1 is also found in humans, SPA proteins appear specific to plants. Here, we have functionally addressed evolutionary conservation of COP1 and SPA orthologs from the moss Physcomitrella, the monocot rice and the dicot Arabidopsis. Results To this end, we analyzed the activities of COP1- and SPA-like proteins from Physcomitrella patens and rice when expressed in Arabidopsis. Expression of rice COP1 and Physcomitrella COP1 protein sequences predominantly complemented all phenotypic aspects of the viable, hypomorphic cop1-4 mutant and the null, seedling-lethal cop1-5 mutant of Arabidopsis: rice COP1 fully rescued the constitutive-photomorphogenesis phenotype in darkness and the leaf expansion defect of cop1 mutants, while it partially restored normal photoperiodic flowering in cop1. Physcomitrella COP1 partially restored normal seedling growth and flowering time, while it fully restored normal leaf expansion in the cop1 mutants. In contrast, expression of a SPA ortholog from Physcomitrella (PpSPAb) in Arabidopsis spa mutants did not rescue any facet of the spa mutant phenotype, suggesting that the PpSPAb protein is not functionally conserved or that the Arabidopsis function evolved after the split of mosses and seed plants. The SPA1 ortholog from rice (OsSPA1) rescued the spa mutant phenotype in dark-grown seedlings, but did not complement any spa mutant phenotype in light-grown seedlings or in adult plants. Conclusion Our results show that COP1 protein sequences from Physcomitrella

  8. Local-Regional Recurrence of Triple Negative Breast Cancer after Breast-Conserving Surgery and Radiation

    Science.gov (United States)

    Freedman, Gary M.; Anderson, Penny R.; Li, Tianyu; Nicolaou, Nicos

    2010-01-01

    Purpose To study results of radiation on the local control of triple receptor negative breast cancer (negative estrogen (ER), progesterone (PR) and HER-2/neu receptors). Materials and Methods Conservative surgery and radiation were used in 753 patients with T1–T2 breast cancer. Three groups were defined by receptor status: ER or PR (+) group 1; ER and PR (−) but HER-2 (+) group 2; and triple negative (TN) group 3. Factors analyzed were age, menopause, race, stage, tumor size, node status, presentation, grade, extensive in-situ disease, margins, and systemic therapy. The primary endpoint was 5-year local-regional recurrence (LRR) isolated or total with distant metastases. Results ER and PR negative patients were statistically significantly more likely to be black, T2, have tumors detectable on both mammogram and physical exam, grade 3, and receive chemotherapy. There were no significant differences in ER and PR negative patients by Her-2 status. There was a significant difference in rates of first distant metastases (3%, 12% and 7% for groups 1, 2 and 3, respectively, p=0.009). However, the isolated 5-year LRR was not significantly different (2.3%, 4.6%, and 3.2%, respectively, p=0.36) between the 3 groups.. Conclusions Patients with TN breast cancer are not at significantly increased risk for isolated LRR at 5-years so remain appropriate candidates for breast conservation. PMID:19156929

  9. Conserved DNA motifs in the type II-A CRISPR leader region.

    Science.gov (United States)

    Van Orden, Mason J; Klein, Peter; Babu, Kesavan; Najar, Fares Z; Rajan, Rakhi

    2017-01-01

    The Clustered Regularly Interspaced Short Palindromic Repeats associated (CRISPR-Cas) systems consist of RNA-protein complexes that provide bacteria and archaea with sequence-specific immunity against bacteriophages, plasmids, and other mobile genetic elements. Bacteria and archaea become immune to phage or plasmid infections by inserting short pieces of the intruder DNA (spacer) site-specifically into the leader-repeat junction in a process called adaptation. Previous studies have shown that parts of the leader region, especially the 3' end of the leader, are indispensable for adaptation. However, a comprehensive analysis of leader ends remains absent. Here, we have analyzed the leader, repeat, and Cas proteins from 167 type II-A CRISPR loci. Our results indicate two distinct conserved DNA motifs at the 3' leader end: ATTTGAG (noted previously in the CRISPR1 locus of Streptococcus thermophilus DGCC7710) and a newly defined CTRCGAG, associated with the CRISPR3 locus of S. thermophilus DGCC7710. A third group with a very short CG DNA conservation at the 3' leader end is observed mostly in lactobacilli. Analysis of the repeats and Cas proteins revealed clustering of these CRISPR components that mirrors the leader motif clustering, in agreement with the coevolution of CRISPR-Cas components. Based on our analysis of the type II-A CRISPR loci, we implicate leader end sequences that could confer site-specificity for the adaptation-machinery in the different subsets of type II-A CRISPR loci.

  10. Exploring Conservation Options in the Broad-Leaved Korean Pine Mixed Forest of the Changbai Mountain Region

    Directory of Open Access Journals (Sweden)

    Lin Ma

    2015-05-01

    Full Text Available The broad-leaved Korean pine (Pinus koraiensis mixed forest (BKPF is one of the most biodiverse zonal communities in the northern temperate zone. Changbai Mountain in northeastern China contains one of the largest BKPFs in the region. The government of China has established a network of 23 nature reserves to protect the BKPF and the species that depend on it for habitat, including the endangered Siberian tiger (Panthera tigris altaica. This study used the conservation planning software C-Plan to calculate the irreplaceability value of each unit to assess how efficiently and comprehensively the existing conservation network supports biodiversity and to identify gap areas that, if integrated into the network, would expand its protection capability. Results show a number of high-conservation-value planning units concentrated along certain ridges. The existing conservation network is structured such that the habitats of only 24 species (out of a total of 75 achieve established conservation targets. Of the other 51 species, 20 achieve less than 50% of their conservation targets. However, expanding the network to include high-conservation-value gap areas could achieve conservation targets for 64 species and could provide different degrees of protection to the other 11 species. Using C-Plan software can guide decision-making to expand the conservation network in this most precious of mountainous ecological zones.

  11. Large-scale sequence analysis of hemagglutinin of influenza A virus identifies conserved regions suitable for targeting an anti-viral response.

    Science.gov (United States)

    Sahini, Leepakshi; Tempczyk-Russell, Anna; Agarwal, Ritu

    2010-02-17

    Influenza A viral surface protein, hemagglutinin, is the major target of neutralizing antibody response and hence a main constituent of all vaccine formulations. But due to its marked evolutionary variability, vaccines have to be reformulated so as to include the hemagglutinin protein from the emerging new viral strain. With the constant fear of a pandemic, there is critical need for the development of anti-viral strategies that can provide wider protection against any Influenza A pathogen. An anti-viral approach that is directed against the conserved regions of the hemaggutinin protein has a potential to protect against any current and new Influenza A virus and provide a solution to this ever-present threat to public health. Influenza A human hemagglutinin protein sequences available in the NCBI database, corresponding to H1, H2, H3 and H5 subtypes, were used to identify highly invariable regions of the protein. Nine such regions were identified and analyzed for structural properties like surface exposure, hydrophilicity and residue type to evaluate their suitability for targeting an anti-peptide antibody/anti-viral response. This study has identified nine conserved regions in the hemagglutinin protein, five of which have the structural characteristics suitable for an anti-viral/anti-peptide response. This is a critical step in the design of efficient anti-peptide antibodies as novel anti-viral agents against any Influenza A pathogen. In addition, these anti-peptide antibodies will provide broadly cross-reactive immunological reagents and aid the rapid development of vaccines against new and emerging Influenza A strains.

  12. Identification and characterization of conserved and variable regions of lime witches' broom phytoplasma genome.

    Science.gov (United States)

    Siampour, Majid; Izadpanah, Keramatollah; Marzachi, Cristina; Salehi Abarkoohi, Mohammad

    2015-09-01

    Several segments (∼20  kbp) of the lime witches' broom (LWB) phytoplasma genome (16SrII group) were sequenced and analysed. A 5.7  kbp segment (LWB-C) included conserved genes whose phylogenetic tree was consistent with that generated using 16S rRNA genes. Another 6.4  kbp LWB phytoplasma genome segment (LWB-NC) was structurally similar to the putative mobile unit or sequence variable mosaic genomic region of phytoplasmas, although it represented a new arrangement of genes or pseudogenes such as phage-related protein genes and tra5 insertion sequences. Sequence- and phylogenetic-based evidence suggested that LWB-NC is a genomic region which includes horizontally transferred genes and could be regarded as a hot region to incorporate more foreign genes into the genome of LWB phytoplasma. The presence of phylogenetically related fragments of retroelements was also verified in the LWB phytoplasma genome. Putative intragenomic retrotransposition or retrohoming of these elements might have been determinant in shaping and manipulating the LWB phytoplasma genome. Altogether, the results of this study suggested that the genome of LWB phytoplasma is colonized by a variety of genes that have been acquired through horizontal gene transfer events, which may have further affected the genome through intragenomic mobility and insertion at cognate or incognate sites. Some of these genes are expected to have been involved in the development of features specific to LWB phytoplasma.

  13. Illicit crops and armed conflict as constraints on biodiversity conservation in the Andes region.

    Science.gov (United States)

    Fjeldså, Jon; Alvarez, María D; Lazcano, Juan Mario; León, Blanca

    2005-05-01

    Coca, once grown for local consumption in the Andes, is now produced for external markets, often in areas with armed conflict. Internationally financed eradication campaigns force traffickers and growers to constantly relocate, making drug-related activities a principal cause of forest loss. The impact on biodiversity is known only in general terms, and this article presents the first regional analysis to identify areas of special concern, using bird data as proxy. The aim of conserving all species may be significantly constrained in the Santa Marta and Perijá mountains, Darién, some parts of the Central Andes in Colombia, and between the middle Marañón and middle Huallaga valleys in Peru. Solutions to the problem must address the root causes: international drug markets, long-lasting armed conflict, and lack of alternative income for the rural poor.

  14. Agricultural conservation practices and wetland ecosystem services in the wetland-rich Piedmont–Coastal Plain region

    Science.gov (United States)

    Diane De Steven; Richard Lowrance

    2011-01-01

    In the eastern U.S. Coastal Plain and Piedmont region, diverse inland wetlands (riverine, depressional, wet flats) have been impacted by or converted to agriculture. Farm Bill conservation practices that restore or enhance wetlands can return their ecological functions and services to the agricultural landscape. We review the extent of regional knowledge regarding the...

  15. Importance of regional variation in conservation planning: A rangewide example of the Greater Sage-Grouse

    Science.gov (United States)

    Doherty, Kevin E.; Evans, Jeffrey S.; Coates, Peter S.; Juliusson, Lara; Fedy, Bradley C.

    2016-01-01

    We developed rangewide population and habitat models for Greater Sage-Grouse (Centrocercus urophasianus) that account for regional variation in habitat selection and relative densities of birds for use in conservation planning and risk assessments. We developed a probabilistic model of occupied breeding habitat by statistically linking habitat characteristics within 4 miles of an occupied lek using a nonlinear machine learning technique (Random Forests). Habitat characteristics used were quantified in GIS and represent standard abiotic and biotic variables related to sage-grouse biology. Statistical model fit was high (mean correctly classified = 82.0%, range = 75.4–88.0%) as were cross-validation statistics (mean = 80.9%, range = 75.1–85.8%). We also developed a spatially explicit model to quantify the relative density of breeding birds across each Greater Sage-Grouse management zone. The models demonstrate distinct clustering of relative abundance of sage-grouse populations across all management zones. On average, approximately half of the breeding population is predicted to be within 10% of the occupied range. We also found that 80% of sage-grouse populations were contained in 25–34% of the occupied range within each management zone. Our rangewide population and habitat models account for regional variation in habitat selection and the relative densities of birds, and thus, they can serve as a consistent and common currency to assess how sage-grouse habitat and populations overlap with conservation actions or threats over the entire sage-grouse range. We also quantified differences in functional habitat responses and disturbance thresholds across the Western Association of Fish and Wildlife Agencies (WAFWA) management zones using statistical relationships identified during habitat modeling. Even for a species as specialized as Greater Sage-Grouse, our results show that ecological context matters in both the strength of habitat selection (i

  16. Fire mosaics and reptile conservation in a fire-prone region.

    Science.gov (United States)

    Nimmo, D G; Kelly, L T; Spence-Bailey, L M; Watson, S J; Taylor, R S; Clarke, M F; Bennett, A F

    2013-04-01

    Fire influences the distribution of fauna in terrestrial biomes throughout the world. Use of fire to achieve a mosaic of vegetation in different stages of succession after burning (i.e., patch-mosaic burning) is a dominant conservation practice in many regions. Despite this, knowledge of how the spatial attributes of vegetation mosaics created by fire affect fauna is extremely scarce, and it is unclear what kind of mosaic land managers should aim to achieve. We selected 28 landscapes (each 12.6 km(2) ) that varied in the spatial extent and diversity of vegetation succession after fire in a 104,000 km(2) area in the semiarid region of southeastern Australia. We surveyed for reptiles at 280 sites nested within the 28 landscapes. The landscape-level occurrence of 9 of the 22 species modeled was associated with the spatial extent of vegetation age classes created by fire. Biogeographic context and the extent of a vegetation type influenced 7 and 4 species, respectively. No species were associated with the diversity of vegetation ages within a landscape. Negative relations between reptile occurrence and both extent of recently burned vegetation (≤10 years postfire, n = 6) and long unburned vegetation (>35 years postfire, n = 4) suggested that a coarse-grained mosaic of areas (e.g. >1000 ha) of midsuccessional vegetation (11-35 years postfire) may support the fire-sensitive reptile species we modeled. This age class coincides with a peak in spinifex cover, a keystone structure for reptiles in semiarid and arid Australia. Maintaining over the long term a coarse-grained mosaic of large areas of midsuccessional vegetation in mallee ecosystems will need to be balanced against the short-term negative effects of large fires on many reptile species and a documented preference by species from other taxonomic groups, particularly birds, for older vegetation. © 2012 Society for Conservation Biology.

  17. Developmental plasticity in Protea as an evolutionary response to environmental clines in the Cape Floristic Region.

    Science.gov (United States)

    Carlson, Jane E; Holsinger, Kent E

    2012-01-01

    Local adaptation along steep environmental gradients likely contributes to plant diversity in the Cape Region of South Africa, yet existing analyses of trait divergence are limited to static measurements of functional traits rather than trajectories of individual development. We explore whether five taxa of evergreen shrubs (Protea section Exsertae) differ in their developmental trajectories and capacity for plasticity using two environmentally-distinct common gardens in South Africa. We measured seedlings in the summer-dry season and winter-wet season of each of two consecutive years to characterize ontogeny and plasticity within years, as same-age leaf cohorts mature, and between years, i.e., from leaf one cohort to the next. We compared patterns of development between gardens to assess whether trait trajectories are programmed versus plastic and examined whether developmental differences covaried with characteristics of a seedling's home environment. We detected plasticity in developmental trajectories for leaf area, stomatal size, stomatal pore index, and to a limited extent specific leaf area, but not for stomatal density. We showed that the species growing in the harshest environments exhibits both the smallest increase in leaf area between years and the least change in SLA and photosynthetic rates as leaves age within years. These results show that within this clade, species have diverged in developmental trajectories and plasticity as well as in mean trait values. Some of these differences may be associated with adaptation to cold and drought stress within an environmentally-complex region.

  18. Developmental plasticity in Protea as an evolutionary response to environmental clines in the Cape Floristic Region.

    Directory of Open Access Journals (Sweden)

    Jane E Carlson

    Full Text Available Local adaptation along steep environmental gradients likely contributes to plant diversity in the Cape Region of South Africa, yet existing analyses of trait divergence are limited to static measurements of functional traits rather than trajectories of individual development. We explore whether five taxa of evergreen shrubs (Protea section Exsertae differ in their developmental trajectories and capacity for plasticity using two environmentally-distinct common gardens in South Africa. We measured seedlings in the summer-dry season and winter-wet season of each of two consecutive years to characterize ontogeny and plasticity within years, as same-age leaf cohorts mature, and between years, i.e., from leaf one cohort to the next. We compared patterns of development between gardens to assess whether trait trajectories are programmed versus plastic and examined whether developmental differences covaried with characteristics of a seedling's home environment. We detected plasticity in developmental trajectories for leaf area, stomatal size, stomatal pore index, and to a limited extent specific leaf area, but not for stomatal density. We showed that the species growing in the harshest environments exhibits both the smallest increase in leaf area between years and the least change in SLA and photosynthetic rates as leaves age within years. These results show that within this clade, species have diverged in developmental trajectories and plasticity as well as in mean trait values. Some of these differences may be associated with adaptation to cold and drought stress within an environmentally-complex region.

  19. Functional analyses of a conserved region in glucosyltransferases of Streptococcus mutans.

    Science.gov (United States)

    Chia, J S; Yang, C S; Chen, J Y

    1998-10-01

    Streptococcus mutans glucosyltransferases (GTFs; GtfB, -C, and -D) synthesize water-soluble and -insoluble glucan polymers from sucrose. We have identified previously a conserved region of 19 amino acids (aa) (Gtf-P1; aa 409 to 427 of GtfB and aa 435 to 453 of GtfC) which is functionally important for both enzymatic activity and bacterial adherence. Monoclonal antibodies directed against Gtf-P1 selectively inhibited insoluble glucan synthesis by GtfB and -C but had no effect on soluble glucan synthesis by GtfD, suggesting that despite an apparent near identity of sequence, corresponding residues may function differently in these enzymes. To test this hypothesis, we used different strategies of mutagenesis to analyze amino acid residues of GtfB and GtfC in Gtf-P1. In-frame insertion of 6 amino acids preceding, or deletion of 14 amino acids within, this conserved region abolished the enzymatic activities of both GtfB and GtfC. Substitution of several residues in combination by random mutagenesis resulted in GtfB, but not GtfC, enzymes exhibiting decreased glucan synthesis and reduced rates of sucrose hydrolysis. Amino acid substitutions of Asp residues in GtfB or GtfC were found to be more critical for enzymatic activity than at other positions of this region. Interestingly, single mutation at Asp411 or Asp413 of GtfB resulted in enzymes retaining about 20% of wild-type activity, whereas mutagenesis of the corresponding Asp at position 437 or 439 in GtfC resulted in complete loss of enzymatic activity. Furthermore, single amino acid substitution of a Val residue between the two Asp residues enhanced the sucrase- and glucan-synthesizing activities of GtfB and GtfC. These results confirmed the report from another laboratory that Asp residues in the Gtf-P1 region are essential for enzymatic catalysis and provide new evidence that identical residues may function differently in closely related Gtf enzymes.

  20. Mechanisms of aquatic species invasions across the South Atlantic Landscape Conservation Cooperative region

    Science.gov (United States)

    Benson, Amy J.; Stith, Bradley M.; Engel, Victor C.

    2016-12-15

    Invasive species are a global issue, and the southeastern United States is not immune to the problems they present. Therefore, various analyses using modeling and exploratory statistics were performed on the U.S. Geological Survey Nonindigenous Aquatic Species (NAS) Database with the primary objective of determining the most appropriate use of presence-only data as related to invasive species in the South Atlantic Landscape Conservation Cooperative (SALCC) region. A hierarchical model approach showed that a relatively small amount of high-quality data from planned surveys can be used to leverage the information in presence-only observations, having a broad spatial coverage and high biases of observer detection and in site selection. Because a variety of sampling protocols can be used in planned surveys, this approach to the analysis of presence-only data is widely applicable. An important part of the management of natural landscapes is the preservation of designated protected areas. When the hydrologic connection was considered in this analysis, the number of potential invaders that could spread to each protected area within the SALCC region was greatly increased, with a mean exceeding 30 species and the maximum reaching 57 species. Nearly all protected areas are hydrologically connected to at least 20 nonindigenous aquatic species. To examine possible factors which may contribute to nonindigenous aquatic species richness in the SALCC region, a set of exploratory statistics was employed. The best statistical model that included a combination of three anthropogenic variables (densities of housing, roads, and reservoirs) and two environmental variables (elevation range and longitude) explained approximately 62 percent of the variation in introduced species richness. Highest nonindigenous aquatic species richness occurred in the more upland, mountainous regions, where elevation range favored reservoirs and attracted urban centers. Lastly, patterns seen in a diffusion

  1. Identification of conserved regions and residues within Hedgehog acyltransferase critical for palmitoylation of Sonic Hedgehog.

    Directory of Open Access Journals (Sweden)

    John A Buglino

    2010-06-01

    Full Text Available Sonic hedgehog (Shh is a palmitoylated protein that plays key roles in mammalian development and human cancers. Palmitoylation of Shh is required for effective long and short range Shh-mediated signaling. Attachment of palmitate to Shh is catalyzed by Hedgehog acyltransferase (Hhat, a member of the membrane bound O-acyl transferase (MBOAT family of multipass membrane proteins. The extremely hydrophobic composition of MBOAT proteins has limited their biochemical characterization. Except for mutagenesis of two conserved residues, there has been no structure-function analysis of Hhat, and the regions of the protein required for Shh palmitoylation are unknown.Here we undertake a systematic approach to identify residues within Hhat that are required for protein stability and/or enzymatic activity. We also identify a second, novel MBOAT homology region (residues 196-234 that is required for Hhat activity. In total, ten deletion mutants and eleven point mutants were generated and analyzed. Truncations at the N- and C-termini of Hhat yielded inactive proteins with reduced stability. Four Hhat mutants with deletions within predicted loop regions and five point mutants retained stability but lost palmitoylation activity. We purified two point mutants, W378A and H379A, with defective Hhat activity. Kinetic analyses revealed alterations in apparent K(m and V(max for Shh and/or palmitoyl CoA, changes that likely explain the catalytic defects observed for these mutants.This study has pinpointed specific regions and multiple residues that regulate Hhat stability and catalysis. Our findings should be applicable to other MBOAT proteins that mediate lipid modification of Wnt proteins and ghrelin, and should serve as a model for understanding how secreted morphogens are modified by palmitoyl acyltransferases.

  2. Conserving the Greater Sage-grouse: A social-ecological systems case study from the California-Nevada region

    Science.gov (United States)

    Duvall, Alison L; Metcalf, Alexander L.; Coates, Peter S.

    2016-01-01

    The Endangered Species Act (ESA) continues to serve as one of the most powerful and contested federal legislative mandates for conservation. In the midst of heated debates, researchers, policy makers, and conservation practitioners champion the importance of cooperative conservation and social-ecological systems approaches, which forge partnerships at multiple levels and scales to address complex ecosystem challenges. However, few real-world examples exist to demonstrate how multifaceted collaborations among stakeholders who share a common goal of conserving at-risk species may be nested within a systems framework to achieve social and ecological goals. Here, we present a case study of Greater Sage-grouse (Centrocercus urophasianus) conservation efforts in the “Bi-State” region of California and Nevada, United States. Using key-informant interviews, we explored dimensions and drivers of this landscape-scale conservation effort. Three themes emerged from the interviews, including 1) ESA action was transformed into opportunity for system-wide conservation; 2) a diverse, locally based partnership anchored collaboration and engagement across multiple levels and scales; and 3) best-available science combined with local knowledge led to “certainty of effectiveness and implementation”—the criteria used by the US Fish and Wildlife Service to evaluate conservation efforts when making listing decisions. Ultimately, collaborative conservation through multistakeholder engagement at various levels and scales led to proactive planning and implementation of conservation measures and precluded the need for an ESA listing of the Bi-State population of Greater Sage-grouse. This article presents a potent example of how a systems approach integrating policy, management, and learning can be used to successfully overcome the conflict-laden and “wicked” challenges that surround at-risk species conservation.

  3. Identifying regional landscapes for conservation planning: a case study from KwaZulu-Natal, South Africa

    CSIR Research Space (South Africa)

    Fairbanks, DHK

    2000-08-30

    Full Text Available The application of landscape ecology in conservation biology has rarely occurred in the context of defined landscapes. Conservation planning has focussed on representation of species diversity patterns and assumed that ecosystems, landscapes...

  4. The evolutionary rates of HCV estimated with subtype 1a and 1b sequences over the ORF length and in different genomic regions.

    Directory of Open Access Journals (Sweden)

    Manqiong Yuan

    Full Text Available Considerable progress has been made in the HCV evolutionary analysis, since the software BEAST was released. However, prior information, especially the prior evolutionary rate, which plays a critical role in BEAST analysis, is always difficult to ascertain due to various uncertainties. Providing a proper prior HCV evolutionary rate is thus of great importance.176 full-length sequences of HCV subtype 1a and 144 of 1b were assembled by taking into consideration the balance of the sampling dates and the even dispersion in phylogenetic trees. According to the HCV genomic organization and biological functions, each dataset was partitioned into nine genomic regions and two routinely amplified regions. A uniform prior rate was applied to the BEAST analysis for each region and also the entire ORF. All the obtained posterior rates for 1a are of a magnitude of 10(-3 substitutions/site/year and in a bell-shaped distribution. Significantly lower rates were estimated for 1b and some of the rate distribution curves resulted in a one-sided truncation, particularly under the exponential model. This indicates that some of the rates for subtype 1b are less accurate, so they were adjusted by including more sequences to improve the temporal structure.Among the various HCV subtypes and genomic regions, the evolutionary patterns are dissimilar. Therefore, an applied estimation of the HCV epidemic history requires the proper selection of the rate priors, which should match the actual dataset so that they can fit for the subtype, the genomic region and even the length. By referencing the findings here, future evolutionary analysis of the HCV subtype 1a and 1b datasets may become more accurate and hence prove useful for tracing their patterns.

  5. Conserved DNA motifs in the type II-A CRISPR leader region

    Science.gov (United States)

    Babu, Kesavan; Najar, Fares Z.

    2017-01-01

    The Clustered Regularly Interspaced Short Palindromic Repeats associated (CRISPR-Cas) systems consist of RNA-protein complexes that provide bacteria and archaea with sequence-specific immunity against bacteriophages, plasmids, and other mobile genetic elements. Bacteria and archaea become immune to phage or plasmid infections by inserting short pieces of the intruder DNA (spacer) site-specifically into the leader-repeat junction in a process called adaptation. Previous studies have shown that parts of the leader region, especially the 3′ end of the leader, are indispensable for adaptation. However, a comprehensive analysis of leader ends remains absent. Here, we have analyzed the leader, repeat, and Cas proteins from 167 type II-A CRISPR loci. Our results indicate two distinct conserved DNA motifs at the 3′ leader end: ATTTGAG (noted previously in the CRISPR1 locus of Streptococcus thermophilus DGCC7710) and a newly defined CTRCGAG, associated with the CRISPR3 locus of S. thermophilus DGCC7710. A third group with a very short CG DNA conservation at the 3′ leader end is observed mostly in lactobacilli. Analysis of the repeats and Cas proteins revealed clustering of these CRISPR components that mirrors the leader motif clustering, in agreement with the coevolution of CRISPR-Cas components. Based on our analysis of the type II-A CRISPR loci, we implicate leader end sequences that could confer site-specificity for the adaptation-machinery in the different subsets of type II-A CRISPR loci. PMID:28392985

  6. Conserved DNA motifs in the type II-A CRISPR leader region

    Directory of Open Access Journals (Sweden)

    Mason J. Van Orden

    2017-04-01

    Full Text Available The Clustered Regularly Interspaced Short Palindromic Repeats associated (CRISPR-Cas systems consist of RNA-protein complexes that provide bacteria and archaea with sequence-specific immunity against bacteriophages, plasmids, and other mobile genetic elements. Bacteria and archaea become immune to phage or plasmid infections by inserting short pieces of the intruder DNA (spacer site-specifically into the leader-repeat junction in a process called adaptation. Previous studies have shown that parts of the leader region, especially the 3′ end of the leader, are indispensable for adaptation. However, a comprehensive analysis of leader ends remains absent. Here, we have analyzed the leader, repeat, and Cas proteins from 167 type II-A CRISPR loci. Our results indicate two distinct conserved DNA motifs at the 3′ leader end: ATTTGAG (noted previously in the CRISPR1 locus of Streptococcus thermophilus DGCC7710 and a newly defined CTRCGAG, associated with the CRISPR3 locus of S. thermophilus DGCC7710. A third group with a very short CG DNA conservation at the 3′ leader end is observed mostly in lactobacilli. Analysis of the repeats and Cas proteins revealed clustering of these CRISPR components that mirrors the leader motif clustering, in agreement with the coevolution of CRISPR-Cas components. Based on our analysis of the type II-A CRISPR loci, we implicate leader end sequences that could confer site-specificity for the adaptation-machinery in the different subsets of type II-A CRISPR loci.

  7. An analytical review of Halffter's Mexican transition zone, and its relevance for evolutionary biogeography, ecology and biogeographical regionalization.

    Science.gov (United States)

    Halffter, Gonzalo; Morrone, Juan J

    2017-01-25

    The Mexican transition zone (MTZ) is the complex area where the Neotropical and Nearctic biotas overlap, including south-western United States, Mexico and a large part of Central America extending to the Nicaraguan lowlands. In a strict sense, it corresponds to the mountain highlands of Mexico, Guatemala, Honduras, El Salvador and Nicaragua. We review Halffter's theory explaining the biotic evolution of the MTZ, including the description and discussion of the distributional patterns and cenocrons recognized within it. Distributional patterns are generalizations that help analyse and compare distributions of different taxa. Cenocrons correspond to sets of taxa that share the same biogeographic history, constituting identifiable subsets within the transitional biota by their common biotic origin and evolutionary history. The heuristic value of distributional patterns and cenocrons lies in their application to formulate hypotheses on biotic assembly in the geographical-ecological space, to analyse the ecological response to anthropic impact, to analyse altitudinal patterns and to undertake time-slicing in cladistic biogeography. Three case studies are analysed with some detail: the Neotropical genus Canthon and the tribe Phanaeini and the Holarctic/Nearctic subfamily Geotrupinae. The Paleoamerican and Mexican Plateau cenocrons define the approximate boundaries of the MTZ, whereas the Mountain Mesoamerican, Nearctic and Typical Neotropical cenocrons correspond to the more conventional boundaries of the Nearctic and Neotropical regions. The biotic assembly of the MTZ is summarized into five stages: in the Jurassic-Cretaceous, the Paleoamerican cenocron (later diversified into five varieties) extended in Mexico; in the Late Cretaceous-Palaeocene, the Mexican Plateau cenocron dispersed from South America; in the Oligocene-Miocene, the Mountain Mesoamerican cenocron dispersed from the Central American Nucleus; in the Miocene-Pliocene, the Nearctic cenocron dispersed from

  8. Genome-wide analyses in bacteria show small-RNA enrichment for long and conserved intergenic regions.

    Science.gov (United States)

    Tsai, Chen-Hsun; Liao, Rick; Chou, Brendan; Palumbo, Michael; Contreras, Lydia M

    2015-01-01

    Interest in finding small RNAs (sRNAs) in bacteria has significantly increased in recent years due to their regulatory functions. Development of high-throughput methods and more sophisticated computational algorithms has allowed rapid identification of sRNA candidates in different species. However, given their various sizes (50 to 500 nucleotides [nt]) and their potential genomic locations in the 5' and 3' untranslated regions as well as in intergenic regions, identification and validation of true sRNAs have been challenging. In addition, the evolution of bacterial sRNAs across different species continues to be puzzling, given that they can exert similar functions with various sequences and structures. In this study, we analyzed the enrichment patterns of sRNAs in 13 well-annotated bacterial species using existing transcriptome and experimental data. All intergenic regions were analyzed by WU-BLAST to examine conservation levels relative to species within or outside their genus. In total, more than 900 validated bacterial sRNAs and 23,000 intergenic regions were analyzed. The results indicate that sRNAs are enriched in intergenic regions, which are longer and more conserved than the average intergenic regions in the corresponding bacterial genome. We also found that sRNA-coding regions have different conservation levels relative to their flanking regions. This work provides a way to analyze how noncoding RNAs are distributed in bacterial genomes and also shows conserved features of intergenic regions that encode sRNAs. These results also provide insight into the functions of regions surrounding sRNAs and into optimization of RNA search algorithms. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  9. Recommendations for the conservation and management of humpback dolphins Sousa chinensis in the Algoa Bay region, South Africa

    Directory of Open Access Journals (Sweden)

    L. Karczmarski

    1998-02-01

    Full Text Available The natural history of humpback dolphins Sousa chinensis inhabiting the Algoa Bay region. Eastern Cape, South Africa, was investigated by means of land- and sea-based surveys undertaken between May 1991 and May 1994. This article reviews the findings which are relevant to the conservation of humpback dolphins and provides recommendations for both the conservation and management of this species in Eastern Cape waters. In general, humpback dolphins appear to be typical coastal dolphins which occur in small numbers, have low population growth and depend on restricted inshore resources. Establishment of protected areas where human impact could be limited or controlled seems to be the most effective conservation/management approach. Habitats critical for humpback dolphins in Eastern Cape waters (inshore rocky reefs and the dolphin's core areas in the Algoa Bay region have been identified. It is recommended that a conservation and management zone (marine sanctuary in the Algoa Bay region be established and a suitable site for it is identified. Given adequate legislation and proper management, this area could be used for the development of ecotourism, including dolphin-watch operations, which would further stimulate interest in coastal conservation.

  10. Potent influenza A virus entry inhibitors targeting a conserved region of hemagglutinin.

    Science.gov (United States)

    Lin, Dongguo; Luo, Yinzhu; Yang, Guang; Li, Fangfang; Xie, Xiangkun; Chen, Daiwei; He, Lifang; Wang, Jingyu; Ye, Chunfeng; Lu, Shengsheng; Lv, Lin; Liu, Shuwen; He, Jian

    2017-11-15

    Influenza A viruses (IAVs) induce acute respiratory disease and cause significant morbidity and mortality throughout the world. With the emergence of drug-resistant viral strains, new and effective anti-IAV drugs with different modes of action are urgently needed. In this study, by conjugating cholesterol to the N-terminus of the short peptide KKWK, a lipopeptide named S-KKWK was created. The anti-IAV test indicated that S-KKWK and its derivatives displayed potent antiviral activities against a broad variety of influenza A viral strains including oseltamivir-resistant strains and clinically relevant isolates with IC 50 values ranging from 0.7 to 3.0µM. An extensive mechanistic study showed that these peptides functioned as viral "entry blockers" by inhibiting the conformational rearrangements of HA2 subunit, thereby interrupting the fusion of virus-host cell membranes. Significantly, a computer-aided docking simulation and protein sequence alignment identified conserved residues in the stem region of HA2 as the possible binding site of S-KKWK, which may be employed as a potential drug target for designing anti-IAVs with a broad-spectrum of activity. By targeting this region, a potent anti-IAV agent was subsequently created. In addition, the anti-IAV activity of S-KKWK was assessed by experiments with influenza A virus-infected mice, in which S-KKWK reduced the mortality of infected animals and extended survival time significantly. Overall, in addition to providing a strategy for designing broad-spectrum anti-IAV agents, these results indicate that S-KKWK and its derivatives are prospective candidates for potent antivirals. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. Transcribed-ultra conserved region expression is associated with outcome in high-risk neuroblastoma

    Directory of Open Access Journals (Sweden)

    Garaventa Alberto

    2009-12-01

    Full Text Available Abstract Background Neuroblastoma is the most common, pediatric, extra-cranial, malignant solid tumor. Despite multimodal therapeutic protocols, outcome for children with a high-risk clinical phenotype remains poor, with long-term survival still less than 40%. Hereby, we evaluated the potential of non-coding RNA expression to predict outcome in high-risk, stage 4 neuroblastoma. Methods We analyzed expression of 481 Ultra Conserved Regions (UCRs by reverse transcription-quantitative real-time PCR and of 723 microRNAs by microarrays in 34 high-risk, stage 4 neuroblastoma patients. Results First, the comparison of 8 short- versus 12 long-term survivors showed that 54 UCRs were significantly (P P P P Conclusions Our pilot study suggests that a deregulation of the microRNA/T-UCR network may play an important role in the pathogenesis of neuroblastoma. After further validation on a larger independent set of samples, such findings may be applied as the first T-UCR prognostic signature for high-risk neuroblastoma patients.

  12. Prey preferences of the snow leopard (Panthera uncia: regional diet specificity holds global significance for conservation.

    Directory of Open Access Journals (Sweden)

    Salvador Lyngdoh

    Full Text Available The endangered snow leopard is a large felid that is distributed over 1.83 million km(2 globally. Throughout its range it relies on a limited number of prey species in some of the most inhospitable landscapes on the planet where high rates of human persecution exist for both predator and prey. We reviewed 14 published and 11 unpublished studies pertaining to snow leopard diet throughout its range. We calculated prey consumption in terms of frequency of occurrence and biomass consumed based on 1696 analysed scats from throughout the snow leopard's range. Prey biomass consumed was calculated based on the Ackerman's linear correction factor. We identified four distinct physiographic and snow leopard prey type zones, using cluster analysis that had unique prey assemblages and had key prey characteristics which supported snow leopard occurrence there. Levin's index showed the snow leopard had a specialized dietary niche breadth. The main prey of the snow leopard were Siberian ibex (Capra sibrica, blue sheep (Pseudois nayaur, Himalayan tahr (Hemitragus jemlahicus, argali (Ovis ammon and marmots (Marmota spp. The significantly preferred prey species of snow leopard weighed 55±5 kg, while the preferred prey weight range of snow leopard was 36-76 kg with a significant preference for Siberian ibex and blue sheep. Our meta-analysis identified critical dietary resources for snow leopards throughout their distribution and illustrates the importance of understanding regional variation in species ecology; particularly prey species that have global implications for conservation.

  13. Prey preferences of the snow leopard (Panthera uncia): regional diet specificity holds global significance for conservation.

    Science.gov (United States)

    Lyngdoh, Salvador; Shrotriya, Shivam; Goyal, Surendra P; Clements, Hayley; Hayward, Matthew W; Habib, Bilal

    2014-01-01

    The endangered snow leopard is a large felid that is distributed over 1.83 million km(2) globally. Throughout its range it relies on a limited number of prey species in some of the most inhospitable landscapes on the planet where high rates of human persecution exist for both predator and prey. We reviewed 14 published and 11 unpublished studies pertaining to snow leopard diet throughout its range. We calculated prey consumption in terms of frequency of occurrence and biomass consumed based on 1696 analysed scats from throughout the snow leopard's range. Prey biomass consumed was calculated based on the Ackerman's linear correction factor. We identified four distinct physiographic and snow leopard prey type zones, using cluster analysis that had unique prey assemblages and had key prey characteristics which supported snow leopard occurrence there. Levin's index showed the snow leopard had a specialized dietary niche breadth. The main prey of the snow leopard were Siberian ibex (Capra sibrica), blue sheep (Pseudois nayaur), Himalayan tahr (Hemitragus jemlahicus), argali (Ovis ammon) and marmots (Marmota spp). The significantly preferred prey species of snow leopard weighed 55±5 kg, while the preferred prey weight range of snow leopard was 36-76 kg with a significant preference for Siberian ibex and blue sheep. Our meta-analysis identified critical dietary resources for snow leopards throughout their distribution and illustrates the importance of understanding regional variation in species ecology; particularly prey species that have global implications for conservation.

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

    OpenAIRE

    Ricketts, T. H.

    2001-01-01

    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...

  15. Remembering the evolutionary Freud.

    Science.gov (United States)

    Young, Allan

    2006-03-01

    Throughout his career as a writer, Sigmund Freud maintained an interest in the evolutionary origins of the human mind and its neurotic and psychotic disorders. In common with many writers then and now, he believed that the evolutionary past is conserved in the mind and the brain. Today the "evolutionary Freud" is nearly forgotten. Even among Freudians, he is regarded to be a red herring, relevant only to the extent that he diverts attention from the enduring achievements of the authentic Freud. There are three ways to explain these attitudes. First, the evolutionary Freud's key work is the "Overview of the Transference Neurosis" (1915). But it was published at an inopportune moment, forty years after the author's death, during the so-called "Freud wars." Second, Freud eventually lost interest in the "Overview" and the prospect of a comprehensive evolutionary theory of psychopathology. The publication of The Ego and the Id (1923), introducing Freud's structural theory of the psyche, marked the point of no return. Finally, Freud's evolutionary theory is simply not credible. It is based on just-so stories and a thoroughly discredited evolutionary mechanism, Lamarckian use-inheritance. Explanations one and two are probably correct but also uninteresting. Explanation number three assumes that there is a fundamental difference between Freud's evolutionary narratives (not credible) and the evolutionary accounts of psychopathology that currently circulate in psychiatry and mainstream journals (credible). The assumption is mistaken but worth investigating.

  16. Effects of island area on plant species distribution and conservation implications in the Thousand Island Lake region

    OpenAIRE

    Que Sun; Jianbo Lu; Jianguo Wu; Fengfeng Zhang

    2008-01-01

    Numerous human activities have resulted in landscape fragmentation, and dam construction is one of them that often leads to drastic changes in biodiversity and ecosystem functioning on local and regional scales. In this study, we investigated how island area size affected the distribution of plant species in the Thousand Island Lake region. Also, we compared several conservation scenarios for maximizing plant species diversity. We found 56 tree species and 79 shrub species in 74 islands that ...

  17. Estimation of Farm-Forward Regional Economic Impacts for the North Plains Groundwater Conservation District in Texas

    OpenAIRE

    Guerrero, Bridget L.; Dudensing, Rebekka M.; McCorkle, Dean A.; Hanselka, Daniel D.; Hudson, Darren; Amosson, Stephen H.

    2012-01-01

    Impacts of alternative agricultural water conservation strategies are being evaluated in the Texas Panhandle. Stakeholders have expressed concern that all effects need to be accounted for including the regional economy. A methodology was developed to evaluate the effects on the backward and forward-linked processing sectors and differentiated results are presented.

  18. Species of conservation concern and environmental stressors: Local regional and global effects [Chapter 6

    Science.gov (United States)

    Steven M. Ostoja; Mathew L. Brooks; Jeanne C. Chambers; Burton K. Pendleton

    2013-01-01

    Species conservation has traditionally been based on individual species within the context of their requisite habitat, which is generally defined as the communities and ecosystems deemed necessary for their persistence. Conservation decisions are hampered by the fact that environmental stressors that potentially threaten the persistence of species can operate at...

  19. Microcollinearity in an ethylene receptor coding gene region of the Coffea canephora genome is extensively conserved with Vitis vinifera and other distant dicotyledonous sequenced genomes.

    Science.gov (United States)

    Guyot, Romain; de la Mare, Marion; Viader, Véronique; Hamon, Perla; Coriton, Olivier; Bustamante-Porras, José; Poncet, Valérie; Campa, Claudine; Hamon, Serge; de Kochko, Alexandre

    2009-02-25

    Coffea canephora, also called Robusta, belongs to the Rubiaceae, the fourth largest angiosperm family. This diploid species (2x = 2n = 22) has a fairly small genome size of approximately 690 Mb and despite its extreme economic importance, particularly for developing countries, knowledge on the genome composition, structure and evolution remain very limited. Here, we report the 160 kb of the first C. canephora Bacterial Artificial Chromosome (BAC) clone ever sequenced and its fine analysis. This clone contains the CcEIN4 gene, encoding an ethylene receptor, and twenty other predicted genes showing a high gene density of one gene per 7.8 kb. Most of them display perfect matches with C. canephora expressed sequence tags or show transcriptional activities through PCR amplifications on cDNA libraries. Twenty-three transposable elements, mainly Class II transposon derivatives, were identified at this locus. Most of these Class II elements are Miniature Inverted-repeat Transposable Elements (MITE) known to be closely associated with plant genes. This BAC composition gives a pattern similar to those found in gene rich regions of Solanum lycopersicum and Medicago truncatula genomes indicating that the CcEIN4 regions may belong to a gene rich region in the C. canephora genome. Comparative sequence analysis indicated an extensive conservation between C. canephora and most of the reference dicotyledonous genomes studied in this work, such as tomato (S. lycopersicum), grapevine (V. vinifera), barrel medic M. truncatula, black cottonwood (Populus trichocarpa) and Arabidopsis thaliana. The higher degree of microcollinearity was found between C. canephora and V. vinifera, which belong respectively to the Asterids and Rosids, two clades that diverged more than 114 million years ago. This study provides a first glimpse of C. canephora genome composition and evolution. Our data revealed a remarkable conservation of the microcollinearity between C. canephora and V. vinifera and a high

  20. RNA expression in a cartilaginous fish cell line reveals ancient 3' noncoding regions highly conserved in vertebrates.

    Science.gov (United States)

    Forest, David; Nishikawa, Ryuhei; Kobayashi, Hiroshi; Parton, Angela; Bayne, Christopher J; Barnes, David W

    2007-01-23

    We have established a cartilaginous fish cell line [Squalus acanthias embryo cell line (SAE)], a mesenchymal stem cell line derived from the embryo of an elasmobranch, the spiny dogfish shark S. acanthias. Elasmobranchs (sharks and rays) first appeared >400 million years ago, and existing species provide useful models for comparative vertebrate cell biology, physiology, and genomics. Comparative vertebrate genomics among evolutionarily distant organisms can provide sequence conservation information that facilitates identification of critical coding and noncoding regions. Although these genomic analyses are informative, experimental verification of functions of genomic sequences depends heavily on cell culture approaches. Using ESTs defining mRNAs derived from the SAE cell line, we identified lengthy and highly conserved gene-specific nucleotide sequences in the noncoding 3' UTRs of eight genes involved in the regulation of cell growth and proliferation. Conserved noncoding 3' mRNA regions detected by using the shark nucleotide sequences as a starting point were found in a range of other vertebrate orders, including bony fish, birds, amphibians, and mammals. Nucleotide identity of shark and human in these regions was remarkably well conserved. Our results indicate that highly conserved gene sequences dating from the appearance of jawed vertebrates and representing potential cis-regulatory elements can be identified through the use of cartilaginous fish as a baseline. Because the expression of genes in the SAE cell line was prerequisite for their identification, this cartilaginous fish culture system also provides a physiologically valid tool to test functional hypotheses on the role of these ancient conserved sequences in comparative cell biology.

  1. Management of the Regional Lymph Nodes Following Breast-Conservation Therapy for Early-Stage Breast Cancer: An Evolving Paradigm

    Energy Technology Data Exchange (ETDEWEB)

    Warren, Laura E.G. [Harvard Radiation Oncology Program, Boston, Massachusetts (United States); Punglia, Rinaa S.; Wong, Julia S. [Department of Radiation Oncology, Brigham and Women' s Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts (United States); Bellon, Jennifer R., E-mail: jbellon@lroc.harvard.edu [Department of Radiation Oncology, Brigham and Women' s Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts (United States)

    2014-11-15

    Radiation therapy to the breast following breast conservation surgery has been the standard of care since randomized trials demonstrated equivalent survival compared to mastectomy and improved local control and survival compared to breast conservation surgery alone. Recent controversies regarding adjuvant radiation therapy have included the potential role of additional radiation to the regional lymph nodes. This review summarizes the evolution of regional nodal management focusing on 2 topics: first, the changing paradigm with regard to surgical evaluation of the axilla; second, the role for regional lymph node irradiation and optimal design of treatment fields. Contemporary data reaffirm prior studies showing that complete axillary dissection may not provide additional benefit relative to sentinel lymph node biopsy in select patient populations. Preliminary data also suggest that directed nodal radiation therapy to the supraclavicular and internal mammary lymph nodes may prove beneficial; publication of several studies are awaited to confirm these results and to help define subgroups with the greatest likelihood of benefit.

  2. Ranked Conservation Opportunity Areas for Region 7 (ECO_RES.RANKED_OAS)

    Science.gov (United States)

    The RANKED_OAS are all the Conservation Opportunity Areas identified by MoRAP that have subsequently been ranked by patch size, landform representation, and the targeted land cover class (highest rank for conservation management = 1 [LFRANK_NOR]). The OAs designate areas with potential for forest or grassland conservation because they are areas of natural or semi-natural land cover that are at least 75 meters away from roads and away from patch edges. The OAs were modeled by creating distance grids using the National Land Cover Database and the Census Bureau's TIGER roads files.

  3. Ranked Conservation Opportunity Areas for Region 7 (ECO_RES.RANKED_OAS)

    Data.gov (United States)

    U.S. Environmental Protection Agency — The RANKED_OAS are all the Conservation Opportunity Areas identified by MoRAP that have subsequently been ranked by patch size, landform representation, and the...

  4. DisoMCS: Accurately Predicting Protein Intrinsically Disordered Regions Using a Multi-Class Conservative Score Approach.

    Directory of Open Access Journals (Sweden)

    Zhiheng Wang

    Full Text Available The precise prediction of protein intrinsically disordered regions, which play a crucial role in biological procedures, is a necessary prerequisite to further the understanding of the principles and mechanisms of protein function. Here, we propose a novel predictor, DisoMCS, which is a more accurate predictor of protein intrinsically disordered regions. The DisoMCS bases on an original multi-class conservative score (MCS obtained by sequence-order/disorder alignment. Initially, near-disorder regions are defined on fragments located at both the terminus of an ordered region connecting a disordered region. Then the multi-class conservative score is generated by sequence alignment against a known structure database and represented as order, near-disorder and disorder conservative scores. The MCS of each amino acid has three elements: order, near-disorder and disorder profiles. Finally, the MCS is exploited as features to identify disordered regions in sequences. DisoMCS utilizes a non-redundant data set as the training set, MCS and predicted secondary structure as features, and a conditional random field as the classification algorithm. In predicted near-disorder regions a residue is determined as an order or a disorder according to the optimized decision threshold. DisoMCS was evaluated by cross-validation, large-scale prediction, independent tests and CASP (Critical Assessment of Techniques for Protein Structure Prediction tests. All results confirmed that DisoMCS was very competitive in terms of accuracy of prediction when compared with well-established publicly available disordered region predictors. It also indicated our approach was more accurate when a query has higher homologous with the knowledge database.The DisoMCS is available at http://cal.tongji.edu.cn/disorder/.

  5. Income level and regional policies, underlying factors associated with unwarranted variations in conservative breast cancer surgery in Spain

    Directory of Open Access Journals (Sweden)

    Peiró-Moreno Salvador

    2011-04-01

    Full Text Available Abstract Background Geographical variations in medical practice are expected to be small when the evidence about the effectiveness and safety of a particular technology is abundant. This would be the case of the prescription of conservative surgery in breast cancer patients. In these cases, when variation is larger than expected by need, socioeconomic factors have been argued as an explanation. Objectives: Using an ecologic design, our study aims at describing the variability in the use of surgical conservative versus non-conservative treatment. Additionally, it seeks to establish whether the socioeconomic status of the healthcare area influences the use of one or the other technique. Methods 81,868 mastectomies performed between 2002 and 2006 in 180 healthcare areas were studied. Standardized utilization rates of breast cancer conservative (CS and non-conservative (NCS procedures were estimated as well as the variation among areas, using small area statistics. Concentration curves and dominance tests were estimated to determine the impact of income and instruction levels in the healthcare area on surgery rates. Multilevel analyses were performed to determine the influence of regional policies. Results Variation in the use of CS was massive (4-fold factor between the highest and the lowest rate and larger than in the case of NCS (2-fold, whichever the age group. Healthcare areas with higher economic and instruction levels showed highest rates of CS, regardless of the age group, while areas with lower economic and educational levels yielded higher rates of NCS interventions. Living in a particular Autonomous Community (AC, explained a substantial part of the CS residual variance (up to a 60.5% in women 50 to 70. Conclusion The place where a woman lives -income level and regional policies- explain the unexpectedly high variation found in utilization rates of conservative breast cancer surgery.

  6. Quantifying the National Significance of Local Areas for Regional Conservation Planning: North Carolina’s Mountain Treasures

    Directory of Open Access Journals (Sweden)

    R. Travis Belote

    2017-05-01

    Full Text Available Conservation scientists recognize that additional protected areas are needed to maintain biological diversity and ecological processes. As regional conservation planners embark on recommending additional areas for protection in formal ecological reserves, it is important to evaluate candidate lands for their role in building a resilient protected areas system of the future. Here, we evaluate North Carolina’s Mountain Treasures with respect to their (1 ecological integrity, (2 role in connecting existing core protected areas, (3 potential to diversify the ecosystem representation of reserves, and (4 role in maintaining hotspots of biologically-rich areas that are not well protected. Mountain Treasures represent a citizen inventory of roadless areas and serve as candidates for elevated levels of conservation protection on U.S. federal lands. We compared Mountain Treasures to other candidate lands throughout the country to evaluate their potential national significance. While the Mountain Treasures tended to be more impacted by human modifications than other roadless areas, they are as important as other roadless areas with respect to their role in connecting existing protected areas and diversifying representation of ecosystems in conservation reserves. However, Mountain Treasures tended to have a much higher biodiversity priority index than other roadless areas leading to an overall higher composite score compared to other roadless areas. Our analysis serves as an example of how using broad-scale datasets can help conservation planners assess the national significance of local areas.

  7. Improving spatial prioritisation for remote marine regions: optimising biodiversity conservation and sustainable development trade-offs

    Science.gov (United States)

    Moore, Cordelia H.; Radford, Ben T.; Possingham, Hugh P.; Heyward, Andrew J.; Stewart, Romola R.; Watts, Matthew E.; Prescott, Jim; Newman, Stephen J.; Harvey, Euan S.; Fisher, Rebecca; Bryce, Clay W.; Lowe, Ryan J.; Berry, Oliver; Espinosa-Gayosso, Alexis; Sporer, Errol; Saunders, Thor

    2016-08-01

    Creating large conservation zones in remote areas, with less intense stakeholder overlap and limited environmental information, requires periodic review to ensure zonation mitigates primary threats and fill gaps in representation, while achieving conservation targets. Follow-up reviews can utilise improved methods and data, potentially identifying new planning options yielding a desirable balance between stakeholder interests. This research explored a marine zoning system in north-west Australia-a biodiverse area with poorly documented biota. Although remote, it is economically significant (i.e. petroleum extraction and fishing). Stakeholder engagement was used to source the best available biodiversity and socio-economic data and advanced spatial analyses produced 765 high resolution data layers, including 674 species distributions representing 119 families. Gap analysis revealed the current proposed zoning system as inadequate, with 98.2% of species below the Convention on Biological Diversity 10% representation targets. A systematic conservation planning algorithm Maxan provided zoning options to meet representation targets while balancing this with industry interests. Resulting scenarios revealed that conservation targets could be met with minimal impacts on petroleum and fishing industries, with estimated losses of 4.9% and 7.2% respectively. The approach addressed important knowledge gaps and provided a powerful and transparent method to reconcile industry interests with marine conservation.

  8. 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.

  9. Structure-sequence based analysis for identification of conserved regions in proteins

    Science.gov (United States)

    Zemla, Adam T; Zhou, Carol E; Lam, Marisa W; Smith, Jason R; Pardes, Elizabeth

    2013-05-28

    Disclosed are computational methods, and associated hardware and software products for scoring conservation in a protein structure based on a computationally identified family or cluster of protein structures. A method of computationally identifying a family or cluster of protein structures in also disclosed herein.

  10. Conservation Status of the Family Orchidaceae in Spain Based on European, National, and Regional Catalogues of Protected Species

    Directory of Open Access Journals (Sweden)

    Daniel de la Torre Llorente

    2018-01-01

    Full Text Available This report reviews the European, National, and Regional catalogues of protected species, focusing specifically on the Orchidaceae family to determine which species seem to be well-protected and where they are protected. Moreover, this examination highlights which species appear to be underprotected and therefore need to be included in some catalogues of protection or be catalogued under some category of protection. The national and regional catalogues that should be implemented are shown, as well as what species should be included within them. This report should be a helpful guideline for environmental policies about orchid’s conservation in Spain, at least at the regional and national level. Around 76% of the Spanish orchid flora are listed with any figure of protection or included in any red list, either nationally (about 12–17% or regionally (72%.

  11. Rice pseudomolecule-anchored cross-species DNA sequence alignments indicate regional genomic variation in expressed sequence conservation

    Directory of Open Access Journals (Sweden)

    Thomas Howard

    2007-08-01

    Full Text Available Abstract Background Various methods have been developed to explore inter-genomic relationships among plant species. Here, we present a sequence similarity analysis based upon comparison of transcript-assembly and methylation-filtered databases from five plant species and physically anchored rice coding sequences. Results A comparison of the frequency of sequence alignments, determined by MegaBLAST, between rice coding sequences in TIGR pseudomolecules and annotations vs 4.0 and comprehensive transcript-assembly and methylation-filtered databases from Lolium perenne (ryegrass, Zea mays (maize, Hordeum vulgare (barley, Glycine max (soybean and Arabidopsis thaliana (thale cress was undertaken. Each rice pseudomolecule was divided into 10 segments, each containing 10% of the functionally annotated, expressed genes. This indicated a correlation between relative segment position in the rice genome and numbers of alignments with all the queried monocot and dicot plant databases. Colour-coded moving windows of 100 functionally annotated, expressed genes along each pseudomolecule were used to generate 'heat-maps'. These revealed consistent intra- and inter-pseudomolecule variation in the relative concentrations of significant alignments with the tested plant databases. Analysis of the annotations and derived putative expression patterns of rice genes from 'hot-spots' and 'cold-spots' within the heat maps indicated possible functional differences. A similar comparison relating to ancestral duplications of the rice genome indicated that duplications were often associated with 'hot-spots'. Conclusion Physical positions of expressed genes in the rice genome are correlated with the degree of conservation of similar sequences in the transcriptomes of other plant species. This relative conservation is associated with the distribution of different sized gene families and segmentally duplicated loci and may have functional and evolutionary implications.

  12. Dynamic sediment discharge in the Hekou-Longmen region of Yellow River and soil and water conservation implications.

    Science.gov (United States)

    Gao, Peng; Deng, Jingcheng; Chai, Xueke; Mu, Xingmin; Zhao, Guangju; Shao, Hongbo; Sun, Wenyi

    2017-02-01

    The middle reaches of the Yellow River Basin transport the vast majority of sediment (>85% of the basin's total available sediment load), which has had profound effects on the characteristics of the middle and lower reaches of the Yellow River. Since the late 1950s, soil and water conservation measures have been extensively implemented in the Loess Plateau, China, especially since the 1970s. This has resulted in sediment discharge changing significantly. In this study, data from 22 catchments in the region of the Loess Plateau from Hekou to Longmen in the middle reaches of the Yellow River were analyzed to investigate the responses of the sediment regime to climate change and human activities. The non-parametric Mann-Kendall test and the Pettitt test were used to identify trends and shifts in sediment discharge. All 22 catchments had a significantly decreasing trend (Pwater conservation and environmental rehabilitation campaigns, have played a more prominent role in the changes in sediment regimes. In order to reduce soil erosion and sediment yield, more attention should be paid to proper and rational soil and water conservation and eco-restoration in this region. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. Conserved residues within the HIV-1 Vpu transmembrane-proximal hinge region modulate BST2 binding and antagonism.

    Science.gov (United States)

    Lukhele, Sabelo; Cohen, Éric A

    2017-03-14

    BST2 inhibits HIV-1 release by tethering nascent virions to the surface of infected cells. HIV-1 Vpu overcomes this restriction by removing BST2 from viral budding sites via BST2 intracellular trapping and sequestration, surface downregulation and/or displacement mechanisms. Vpu is composed of a short luminal tail, a transmembrane domain (TMD) and a cytoplasmic hinge region that is followed by two helices. BST2 counteraction relies on the ability of Vpu to physically bind BST2 through TMD interactions and recruit the clathrin-dependent trafficking machinery via a canonical acidic di-leucine signalling motif within the helix-2 of Vpu. The highly conserved Vpu transmembrane-proximal hinge region encompasses residues that resemble an acidic leucine-based trafficking motif, whose functional roles are currently ill-defined. In this study, we investigated the contribution of these residues towards Vpu-mediated BST2 antagonism. We show that while these conserved residues have no intrinsic activity on the cellular distribution of Vpu in the absence of BST2, they regulate the ability of Vpu to bind to BST2 and, consequently, govern both BST2-dependent trafficking properties of the protein as well as its co-localization with BST2. Moreover, these residues, particularly a glutamic acid residue positioned immediately following the TMD, are a determinant not only for efficient targeting of BST2, but also binding and degradation of CD4, another host membrane protein targeted by Vpu. Mechanistically, our data are consistent with a role of these residues in the maintenance of the Vpu TMD conformational configuration such that interactions with membrane-associated host targets are favoured. Altogether, this work demonstrates an important regulatory role of the transmembrane-proximal Vpu hinge region residues towards enabling the protein to efficiently engage its target host proteins. Thus, this highly conserved, cytosolic Vpu hinge region may represent an attractive target for the

  14. Comparative genetic structure in pines: evolutionary and conservation consequences Estructura genética comparada en pinos: consecuencias evolutivas y para la conservación

    OpenAIRE

    PATRICIA DELGADO; ARGELIA CUENCA; Escalante, Ana E.; FRANCISCO MOLINA-FREANER; DANIEL PIÑERO

    2002-01-01

    Pines have been the focus of several studies that estimate population genetic parameters using both allozymes and chloroplast single sequence repeats (SSRs). Also, the genus has also been recently studied using molecular systematics so that we now have a more clear understanding of their evolutionary history. With this background we studied comparatively the genetic structure in pines. Expected heterozygosity is particularly constant with a 99 % confidence interval between 0.19 and 0.23 in sp...

  15. Molecular studies of Callithrix pygmaea (Primates, Platyrrhini based on transferrin intronic and ND1 regions: implications for taxonomy and conservation

    Directory of Open Access Journals (Sweden)

    Tagliaro Claudia Helena

    2000-01-01

    Full Text Available Traditional classifications of Platyrrhini monkeys, based mainly on morphological features, are being contested by recent molecular data. The subfamily Callitrichinae (Platyrrhini, Primates consists of a diverse group of species, many of them considered endangered. Our analysis of two DNA regions, a mtDNA gene (ND1 and a nuclear gene (intronic regions of the transferrin gene, suggests that Callithrix pygmaea may have sufficient variability to justify the existence of subspecies or even separate species. Phylogenetic dendrograms based on the ND1 region show that this species is more closely related to Amazonian than to Atlantic forest marmosets. These results reopen the discussion about diversity and conservation programs based exclusively on traditional classifications.

  16. Conservation of Repeats at the Mammalian KCNQ1OT1-CDKN1C Region Suggests a Role in Genomic Imprinting

    Directory of Open Access Journals (Sweden)

    Marcos De Donato

    2017-06-01

    Full Text Available KCNQ1OT1 is located in the region with the highest number of genes showing genomic imprinting, but the mechanisms controlling the genes under its influence have not been fully elucidated. Therefore, we conducted a comparative analysis of the KCNQ1/KCNQ1OT1-CDKN1C region to study its conservation across the best assembled eutherian mammalian genomes sequenced to date and analyzed potential elements that may be implicated in the control of genomic imprinting in this region. The genomic features in these regions from human, mouse, cattle, and dog show a higher number of genes and CpG islands (detected using cpgplot from EMBOSS, but lower number of repetitive elements (including short interspersed nuclear elements and long interspersed nuclear elements, compared with their whole chromosomes (detected by RepeatMasker. The KCNQ1OT1-CDKN1C region contains the highest number of conserved noncoding sequences (CNS among mammals, where we found 16 regions containing about 38 different highly conserved repetitive elements (using mVista, such as LINE1 elements: L1M4, L1MB7, HAL1, L1M4a, L1Med, and an LTR element: MLT1H. From these elements, we found 74 CNS showing high sequence identity (>70% between human, cattle, and mouse, from which we identified 13 motifs (using Multiple Em for Motif Elicitation/Motif Alignment and Search Tool with a significant probability of occurrence, 3 of which were the most frequent and were used to find transcription factor–binding sites. We detected several transcription factors (using JASPAR suite from the families SOX, FOX, and GATA. A phylogenetic analysis of these CNS from human, marmoset, mouse, rat, cattle, dog, horse, and elephant shows branches with high levels of support and very similar phylogenetic relationships among these groups, confirming previous reports. Our results suggest that functional DNA elements identified by comparative genomics in a region densely populated with imprinted mammalian genes may be

  17. 75 FR 31463 - Comal County Regional Habitat Conservation Plan, Comal County, TX

    Science.gov (United States)

    2010-06-03

    ... agreed to undertake to minimize and mitigate the effects of incidental take of federally listed species... measures the Applicant has agreed to undertake to minimize the potential for and mitigate the potential..., Acting Regional Director, Southwest Region, Albuquerque, New Mexico. BILLING CODE 4310-55-P ...

  18. Using regional bird density distribution models to evaluate protected area networks and inform conservation planning

    Science.gov (United States)

    John D. Alexander; Jaime L. Stephens; Sam Veloz; Leo Salas; Josée S. Rousseau; C. John Ralph; Daniel A. Sarr

    2017-01-01

    As data about populations of indicator species become available, proactive strategies that improve representation of biological diversity within protected area networks should consider finer-scaled evaluations, especially in regions identified as important through course-scale analyses. We use density distribution models derived from a robust regional bird...

  19. The non-conserved region of MRP is involved in the virulence of Streptococcus suis serotype 2.

    Science.gov (United States)

    Li, Quan; Fu, Yang; Ma, Caifeng; He, Yanan; Yu, Yanfei; Du, Dechao; Yao, Huochun; Lu, Chengping; Zhang, Wei

    2017-10-03

    Muramidase-released protein (MRP) of Streptococcus suis serotype 2 (SS2) is an important epidemic virulence marker with an unclear role in bacterial infection. To investigate the biologic functions of MRP, 3 mutants named Δmrp, Δmrp domain 1 (Δmrp-d1), and Δmrp domain 2 (Δmrp-d2) were constructed to assess the phenotypic changes between the parental strain and the mutant strains. The results indicated that MRP domain 1 (MRP-D1, the non-conserved region of MRP from a virulent strain, a.a. 242-596) played a critical role in adherence of SS2 to host cells, compared with MRP domain 1* (MRP-D1*, the non-conserved region of MRP from a low virulent strain, a.a. 239-598) or MRP domain 2 (MRP-D2, the conserved region of MRP, a.a. 848-1222). We found that MRP-D1 but not MRP-D2, could bind specifically to fibronectin (FN), factor H (FH), fibrinogen (FG), and immunoglobulin G (IgG). Additionally, we confirmed that mrp-d1 mutation significantly inhibited bacteremia and brain invasion in a mouse infection model. The mrp-d1 mutation also attenuated the intracellular survival of SS2 in RAW246.7 macrophages, shortened the growth ability in pig blood and decreased the virulence of SS2 in BALB/c mice. Furthermore, antiserum against MRP-D1 was found to dramatically impede SS2 survival in pig blood. Finally, immunization with recombinant MRP-D1 efficiently enhanced murine viability after SS2 challenge, indicating its potential use in vaccination strategies. Collectively, these results indicated that MRP-D1 is involved in SS2 virulence and eloquently demonstrate the function of MRP in pathogenesis of infection.

  20. Strong genetic structure among coral populations within a conservation priority region, the Bird's Head Seascape (Papua, Indonesia

    Directory of Open Access Journals (Sweden)

    Craig John Starger

    2015-11-01

    Full Text Available Marine Protected Areas (MPAs are widely considered to be one of the best strategies available for protecting species diversity and ecosystem processes in marine environments. While data on connectivity and genetic structure of marine populations are critical to designing appropriately sized and spaced networks of MPAs, such data are rarely available. This study examines genetic structure in reef-building corals from Papua and West Papua, Indonesia, one of the most biodiverse and least disturbed coral reef regions in the world. We focused on two common reef-building corals, Pocillopora damicornis (Linnaeus 1758 and Seriatopora hystrix (family: Pocilloporidae, from three regions under different management regimes: Teluk Cenderawasih, Raja Ampat, and southwest Papua. Analyses of molecular variance, assignment tests, and genetical bandwidth mapping based on microsatellite variation revealed significant genetic structure in both species, although there were no clear regional filters to gene flow among regions. Overall, P. damicornis populations were less structured (FST = 0.139, p < 0.00001 than S. hystrix (FST = 0.357, p < 0.00001. Despite occurring in one of the most pristine marine habitats in Indonesia, populations of both species showed evidence of recent declines. Furthermore, exclusion of individual populations from connectivity analyses resulted in marked increases in self-recruitment. Maintaining connectivity within and among regions of Eastern Indonesia will require coral conservation on the local scales and regional networks of MPAs. 

  1. Diversity and distribution of aquatic insects in Southern Brazil wetlands: implications for biodiversity conservation in a Neotropical region

    Directory of Open Access Journals (Sweden)

    Leonardo Maltchik

    2012-03-01

    Full Text Available The selection of priority areas is an enormous challenge for biodiversity conservation. Some biogeographic methods have been used to identify the priority areas to conservation, and panbiogeography is one of them. This study aimed at the utilization of panbiogeographic tools, to identify the distribution patterns of aquatic insect genera, in wetland systems of an extensive area in the Neotropical region (~280 000km², and to compare the distribution of the biogeographic units identified by the aquatic insects, with the conservation units of Southern Brazil. We analyzed the distribution pattern of 82 genera distributed in four orders of aquatic insects (Diptera, Odonata, Ephemeroptera and Trichoptera in Southern Brazil wetlands. Therefore, 32 biogeographic nodes corresponded to the priority areas for conservation of the aquatic insect diversity. Among this total, 13 were located in the Atlantic Rainforest, 16 in the Pampa and three amongst both biomes. The distribution of nodes showed that only 15% of the dispersion centers of insects were inserted in conservation units. The four priority areas pointed by node cluster criterion must be considered in further inclusions of areas for biodiversity conservation in Southern Brazil wetlands, since such areas present species from differrent ancestral biota. The inclusion of such areas into the conservation units would be a strong way to conserve the aquatic biodiversity in this region.La selección de áreas prioritarias es un enorme desafío para la conservación de la biodiversidad. Métodos biogeográficos se han utilizado para identificar áreas prioritarias para la conservación, como la panbiogeografía. Este estudio tuvo como objetivo el empleo de herramientas panbiogeográficas, para identificar los patrones de distribución de los géneros de insectos acuáticos, en los sistemas de humedales de una extensa área de la región Neotropical (~280 000km², y así comparar la distribución de las

  2. Use of biodiversity hotspots for conservation of Marine Molluscs: a regional approach

    Directory of Open Access Journals (Sweden)

    D. BEDULLI

    2002-12-01

    Full Text Available A method to define biodiversity hot spots as regards marine molluscs is proposed. Species richness of Italian marine molluscs is analysed by means of data collected by members of the Italian Malacological Society. Data are ordered in the database ‘Census of Italian Marine Molluscs’ available on the Internet. The Census contains about 20.000 records concerning 901 species sampled in 663 localities around all the Italian coasts. The records are divided into 59 lots; for each lot we formulate an index of species richness not related to the sampling effort. This index shows a positive correlation with the environmental diversity and with the proportion of hard substrates on the sea bottom. In the lots we assess the distribution of species worth of protection (according to literature and of most rare species. Combining these data with the distribution of lots with higher values of species richness index, we identify hot spots available for conservation.

  3. Intelligent irrigation performance: evaluation and quantifying its ability for conserving water in arid region

    Science.gov (United States)

    Al-Ghobari, Hussein M.; Mohammad, Fawzi S.

    2011-12-01

    Intelligent irrigation technologies have been developed in recent years to apply irrigation to turf and landscape plants. These technologies are an evapotranspiration (ET)-based irrigation controller, which calculates ET for local microclimate. Then, the controller creates a program for loading and communicating automatically with drip or sprinkler system controllers. The main objective of this study was to evaluate the effectiveness of the new ET sensors in ability to irrigate agricultural crops and to conserve water use for crop in arid climatic conditions. This paper presents the case for water conservation using intelligent irrigation system (IIS) application technology. The IIS for automating irrigation scheduling was implemented and tested with sprinkle and drip irrigation systems to irrigate wheat and tomato crops. Another irrigation scheduling system was also installed and operated as another treatment, which is based on weather data that retrieved from an automatic weather station. This irrigation control system was running in parallel to the former system (IIS) to be control experiments for comparison purposes. However, this article discusses the implementation of IIS, its installation, testing and calibration of various components. The experiments conducted for one growing season 2009-2010 and the results were represented and discussed herein. Data from all plots were analyzed, which were including soil water status, water consumption, and crop yield. The initial results indicate that up to 25% water saving by intelligent irrigation compared to control method, while maintaining competing yield. Results show that the crop evapotranspiration values for control experiments were higher than that of ET-System in consistent trend during whole growth season. The analysis points out that the values of the two treatments were somewhat close to each other's only in the initial development stages. Generally, the ET-System, with some modification was precise in

  4. Evolutionary Nephrology.

    Science.gov (United States)

    Chevalier, Robert L

    2017-05-01

    Progressive kidney disease follows nephron loss, hyperfiltration, and incomplete repair, a process described as "maladaptive." In the past 20 years, a new discipline has emerged that expands research horizons: evolutionary medicine. In contrast to physiologic (homeostatic) adaptation, evolutionary adaptation is the result of reproductive success that reflects natural selection. Evolutionary explanations for physiologically maladaptive responses can emerge from mismatch of the phenotype with environment or evolutionary tradeoffs. Evolutionary adaptation to a terrestrial environment resulted in a vulnerable energy-consuming renal tubule and a hypoxic, hyperosmolar microenvironment. Natural selection favors successful energy investment strategy: energy is allocated to maintenance of nephron integrity through reproductive years, but this declines with increasing senescence after ~40 years of age. Risk factors for chronic kidney disease include restricted fetal growth or preterm birth (life history tradeoff resulting in fewer nephrons), evolutionary selection for APOL1 mutations (that provide resistance to trypanosome infection, a tradeoff), and modern life experience (Western diet mismatch leading to diabetes and hypertension). Current advances in genomics, epigenetics, and developmental biology have revealed proximate causes of kidney disease, but attempts to slow kidney disease remain elusive. Evolutionary medicine provides a complementary approach by addressing ultimate causes of kidney disease. Marked variation in nephron number at birth, nephron heterogeneity, and changing susceptibility to kidney injury throughout life history are the result of evolutionary processes. Combined application of molecular genetics, evolutionary developmental biology (evo-devo), developmental programming and life history theory may yield new strategies for prevention and treatment of chronic kidney disease.

  5. Effects of Long-term Conservation Tillage on Soil Nutrients in Sloping Fields in Regions Characterized by Water and Wind Erosion

    OpenAIRE

    Chunjian Tan; Xue Cao; Shuai Yuan; Weiyu Wang; Yongzhong Feng; Bo Qiao

    2015-01-01

    Conservation tillage is commonly used in regions affected by water and wind erosion. To understand the effects of conservation tillage on soil nutrients and yield, a long-term experiment was set up in a region affected by water and wind erosion on the Loess Plateau. The treatments used were traditional tillage (CK), no tillage (NT), straw mulching (SM), plastic-film mulching (PM), ridging and plastic-film mulching (RPM) and intercropping (In). Our results demonstrate that the available nutrie...

  6. Diversity, natural history and conservation of amphibians and reptiles from the San Vito Region, southwestern Costa Rica.

    Science.gov (United States)

    Santos-Barrera, Georgina; Pacheco, Jesus; Mendoza-Quijano, Fernando; Bolaños, Federico; Cháves, Gerardo; Daily, Gretchen C; Ehrlich, Paul R; Ceballos, Gerardo

    2008-06-01

    We present an inventory of the amphibians and reptiles of the San Vito de Coto Brus region, including the Las Cruces Biological Station, in southern Costa Rica, which is the result of a survey of the herpetofauna occurring in mountain forest fragments, pastures, coffee plantations, and other disturbed areas. We found 67 species, included 26 species of amphibians and of 41 of reptiles. We describe the distribution patterns of the community on the basis of the life zones, elevation, fragmentation, and degree of anthropogenic impact. We also provide some nouvelle data on the systematics of some select taxa, their geographical ranges, microhabitats, activity, and other relevant ecological and natural history features. Finally, we comment on the present conservation status of the herpetofauna in the region. Previous literature and collection records indicate a higher number of species occurring in this area, which suggests that some declines have occurred, especially of amphibians, in last decades.

  7. On the evolutionary conservation of hydrogen bonds made by buried polar amino acids: the hidden joists, braces and trusses of protein architecture.

    Science.gov (United States)

    Worth, Catherine L; Blundell, Tom L

    2010-05-31

    The hydrogen bond patterns between mainchain atoms in protein structures not only give rise to regular secondary structures but also satisfy mainchain hydrogen bond potential. However, not all mainchain atoms can be satisfied through hydrogen bond interactions that arise in regular secondary structures; in some locations sidechain-to-mainchain hydrogen bonds are required to provide polar group satisfaction. Buried polar residues that are hydrogen-bonded to mainchain amide atoms tend to be highly conserved within protein families, confirming that mainchain architecture is a critical restraint on the evolution of proteins. We have investigated the stabilizing roles of buried polar sidechains on the backbones of protein structures by performing an analysis of solvent inaccessible residues that are entirely conserved within protein families and superfamilies and hydrogen bonded to an equivalent mainchain atom in each family member. We show that polar and sometimes charged sidechains form hydrogen bonds to mainchain atoms in the cores of proteins in a manner that has been conserved in evolution. Although particular motifs have previously been identified where buried polar residues have conserved roles in stabilizing protein structure, for example in helix capping, we demonstrate that such interactions occur in a range of architectures and highlight those polar amino acid types that fulfil these roles. We show that these buried polar residues often span elements of secondary structure and provide stabilizing interactions of the overall protein architecture. Conservation of buried polar residues and the hydrogen-bond interactions that they form implies an important role for maintaining protein structure, contributing strong restraints on amino acid substitutions during divergent protein evolution. Our analysis sheds light on the important stabilizing roles of these residues in protein architecture and provides further insight into factors influencing the evolution of

  8. On the evolutionary conservation of hydrogen bonds made by buried polar amino acids: the hidden joists, braces and trusses of protein architecture

    Directory of Open Access Journals (Sweden)

    Worth Catherine L

    2010-05-01

    Full Text Available Abstract Background The hydrogen bond patterns between mainchain atoms in protein structures not only give rise to regular secondary structures but also satisfy mainchain hydrogen bond potential. However, not all mainchain atoms can be satisfied through hydrogen bond interactions that arise in regular secondary structures; in some locations sidechain-to-mainchain hydrogen bonds are required to provide polar group satisfaction. Buried polar residues that are hydrogen-bonded to mainchain amide atoms tend to be highly conserved within protein families, confirming that mainchain architecture is a critical restraint on the evolution of proteins. We have investigated the stabilizing roles of buried polar sidechains on the backbones of protein structures by performing an analysis of solvent inaccessible residues that are entirely conserved within protein families and superfamilies and hydrogen bonded to an equivalent mainchain atom in each family member. Results We show that polar and sometimes charged sidechains form hydrogen bonds to mainchain atoms in the cores of proteins in a manner that has been conserved in evolution. Although particular motifs have previously been identified where buried polar residues have conserved roles in stabilizing protein structure, for example in helix capping, we demonstrate that such interactions occur in a range of architectures and highlight those polar amino acid types that fulfil these roles. We show that these buried polar residues often span elements of secondary structure and provide stabilizing interactions of the overall protein architecture. Conclusions Conservation of buried polar residues and the hydrogen-bond interactions that they form implies an important role for maintaining protein structure, contributing strong restraints on amino acid substitutions during divergent protein evolution. Our analysis sheds light on the important stabilizing roles of these residues in protein architecture and provides

  9. On farm conservation of Musa diversity in the great lakes region of ...

    African Journals Online (AJOL)

    Banana (Musa spp.) cultivar diversity in the Great Lakes region of East Africa has been on the decline for the last several decades. A number of abiotic, biotic and socio-economic factors are thought to be responsible for this decline. In spite of low variation with respect to stress resistance, a number of farmers have ...

  10. Analysing biodiversity and conservation knowledge products to support regional environmental assessments

    Science.gov (United States)

    Brooks, Thomas M.; Akçakaya, H. Resit; Burgess, Neil D.; Butchart, Stuart H. M.; Hilton-Taylor, Craig; Hoffmann, Michael; Juffe-Bignoli, Diego; Kingston, Naomi; Macsharry, Brian; Parr, Mike; Perianin, Laurence; Regan, Eugenie C.; Rodrigues, Ana S. L.; Rondinini, Carlo; Shennan-Farpon, Yara; Young, Bruce E.

    2016-02-01

    Two processes for regional environmental assessment are currently underway: the Global Environment Outlook (GEO) and Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES). Both face constraints of data, time, capacity, and resources. To support these assessments, we disaggregate three global knowledge products according to their regions and subregions. These products are: The IUCN Red List of Threatened Species, Key Biodiversity Areas (specifically Important Bird & Biodiversity Areas [IBAs], and Alliance for Zero Extinction [AZE] sites), and Protected Planet. We present fourteen Data citations: numbers of species occurring and percentages threatened; numbers of endemics and percentages threatened; downscaled Red List Indices for mammals, birds, and amphibians; numbers, mean sizes, and percentage coverages of IBAs and AZE sites; percentage coverage of land and sea by protected areas; and trends in percentages of IBAs and AZE sites wholly covered by protected areas. These data will inform the regional/subregional assessment chapters on the status of biodiversity, drivers of its decline, and institutional responses, and greatly facilitate comparability and consistency between the different regional/subregional assessments.

  11. Analysing biodiversity and conservation knowledge products to support regional environmental assessments

    Science.gov (United States)

    Brooks, Thomas M.; Akçakaya, H. Resit; Burgess, Neil D.; Butchart, Stuart H.M.; Hilton-Taylor, Craig; Hoffmann, Michael; Juffe-Bignoli, Diego; Kingston, Naomi; MacSharry, Brian; Parr, Mike; Perianin, Laurence; Regan, Eugenie C.; Rodrigues, Ana S.L.; Rondinini, Carlo; Shennan-Farpon, Yara; Young, Bruce E.

    2016-01-01

    Two processes for regional environmental assessment are currently underway: the Global Environment Outlook (GEO) and Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES). Both face constraints of data, time, capacity, and resources. To support these assessments, we disaggregate three global knowledge products according to their regions and subregions. These products are: The IUCN Red List of Threatened Species, Key Biodiversity Areas (specifically Important Bird & Biodiversity Areas [IBAs], and Alliance for Zero Extinction [AZE] sites), and Protected Planet. We present fourteen Data citations: numbers of species occurring and percentages threatened; numbers of endemics and percentages threatened; downscaled Red List Indices for mammals, birds, and amphibians; numbers, mean sizes, and percentage coverages of IBAs and AZE sites; percentage coverage of land and sea by protected areas; and trends in percentages of IBAs and AZE sites wholly covered by protected areas. These data will inform the regional/subregional assessment chapters on the status of biodiversity, drivers of its decline, and institutional responses, and greatly facilitate comparability and consistency between the different regional/subregional assessments. PMID:26881749

  12. Conservation of indigenous knowledge of medicinal plants of Western Himalayan region Rawalakot, Azad Kashmir, Pakistan.

    Science.gov (United States)

    Hussain, Sajjad; Murtaza, Ghulam; Mehmood, Ansar; Qureshi, Rizwana Aleem

    2017-05-01

    The aim of present was to document indigenous knowledge of medicinal plants traditionally used by inhabitants of Rawalakot Azad Kashmir and to screen selected medicinal plants for their antibacterial potential. Several field surveys were conducted to document indigenous knowledge of medicinal plants through interviews from local inhabitants during 2010-2013. During the study, 58 plant species, belonging to 37 families, were identified and their medicinal uses were recorded. Ethnobotanical data indicates that inhabitants of Rawalakot use medicinal plant mainly for the treatment of stomach, liver and sexual disorders. Usually fresh plant materials were used for medicinal preparations and administrated orally. Among all the species studied, three most frequently used medicinal plants Achillea millefolium, Berberis lycium and Zanthoxylum armatum were screened for their antibacterial potential by using disc diffusion method. The crude aqueous, petroleum ether and ethanolic extracts were found to be very active against selected bacterial strains. The present study contributes significantly to the medicinal plant knowledge and shows that medicinal plant knowledge is deteriorating among younger generations. Therefore, further research is needed to document indigenous knowledge, to find conservation status of medicinal plant species and to find antimicrobial compounds for more sophisticated usage of medicinal plants in future.

  13. Conserved immunogenic region of a major core protein (p24) of human and simian immunodeficiency viruses.

    Science.gov (United States)

    Koito, A; Hattori, T; Matsushita, S; Maeda, Y; Nozaki, C; Sagawa, K; Takatsuki, K

    1988-12-01

    A murine monoclonal antibody (MoAb), VAK 4, has been known to specifically react with a major core protein (p24) as well as with its precursor (p55-57) and intermediate precursor (p40) of human immunodeficiency virus strain IIIB (HTLV-IIIB). Radioimmunoprecipitation assays revealed that VAK 4 MoAb precipitated a major core protein and its precursors from a variety of strains of HIV and also from simian immunodeficiency virus (SIV), although the molecular weights of the precursor proteins in each viral strain were slightly different. A protein synthesized by transfected Escherichia coli containing amino acid sequences corresponding to residues 121-436 of the HTLV-IIIB gag gene was reactive with VAK 4 MoAb, but the protein carrying only residues 121-309 was not reactive, suggesting that the epitope recognized by VAK 4 MoAb resides at the carboxyl terminus of p24 protein. A competitive enzyme-linked immunosorbent assay showed that patient sera containing anticore protein antibody inhibited the binding of VAK 4 to HTLV-IIIB. These findings suggested that VAK 4 MoAb recognized an immunogenic and conserved epitope belonging to a major core protein of HIV-related viruses.

  14. Gcn4 misregulation reveals a direct role for the evolutionary conserved EKC/KEOPS in the t6A modification of tRNAs

    OpenAIRE

    Daugeron, Marie-Claire; Lenstra, Tineke L.; Frizzarin, Martina; El Yacoubi, Basma; Liu, Xipeng; Baudin-Baillieu, Agnès; Lijnzaad, Philip; Decourty, Laurence; Saveanu, Cosmin; Jacquier, Alain; Frank C P Holstege; de Crécy-Lagard, Valérie; van Tilbeurgh, Herman; Libri, Domenico

    2011-01-01

    International audience; The EKC/KEOPS complex is universally conserved in Archaea and Eukarya and has been implicated in several cellular processes, including transcription, telomere homeostasis and genomic instability. However, the molecular function of the complex has remained elusive so far. We analyzed the transcriptome of EKC/KEOPS mutants and observed a specific profile that is highly enriched in targets of the Gcn4p transcriptional activator. GCN4 expression was found to be activated a...

  15. Additionality in Conservation Easements Programs: Grassland Easements in the Prairie Pothole Region

    OpenAIRE

    Savage, Jeffrey; Claassen, Roger; Breneman, Vincent E.; Loesch, Chuck; Williams, Ryan

    2014-01-01

    Conversion of native sod (grassland) to cropland in the Prairie Pothole Region (PPR) is threatening important breeding habitats for migratory birds. About 50 percent of North American ducks are produced in the grasslands of the PPR, even though this habitat accounts for only ten percent of duck breeding territory. Once lost, native grassland habitats are difficult to reconstruct. To protect these habitats, the U.S. Fish and Wildlife Service (FWS) holds permanent easements prohibiting grasslan...

  16. Partial characterization of immunoglobulin light chains of carcharhine sharks: evidence for phylogenetic conservation of variable region and divergence of constant region structure.

    Science.gov (United States)

    Marchalonis, J J; Schluter, S F; Rosenshein, I L; Wang, A C

    1988-01-01

    Isolated light chains of IgM-type immunoglobulins of carcharhine sharks were analyzed by serological and biochemical means. When analyzed by isoelectric focusing analysis, light chains of the tiger shark (Galecerdo cuvieri), the galapagos shark (Carcharhinus galapagensis) and the sandbar shark (Carcharhinus plumbeus) showed a broad, but patterned, spectrum of bands ranging from pI 5.0 to 7.7 in which discrete families were observed. Serologically, light chains of the galapagos shark cross-reacted with rabbit antibodies against mouse immunoglobulin and a synthetic peptide corresponding to the J segment of T cell receptor beta chain. The latter cross-reaction is shared among light chains and T cell receptors. Although there was considerable heterogeneity in isoelectric focusing analysis, the light chains were homogeneous on the basis of apparent mass (23 kDa) and those of tiger shark and galapagos shark had relatively homogeneous dominant N-terminal sequences representing the first framework. The N-terminal sequences of these two shark light chains, were strongly homologous to one another and showed 75% identity to certain V kappa sequences of man and dog. Homology was also shown to V lambda sequences, but the degree of identity was approximately 50%. Following cleavage of the tiger shark light chain with o-iodosobenzoic acid which cleaves at tryptophanyl residues, a constant region peptide was isolated by gel filtration. It was possible to identify the homolog of this peptide within the constant regions of mammalian kappa and lambda chain, but the relationship to C kappa chain was stronger. The degree of identity among the corresponding C region peptides of mammalian, avian and elasmobranch species was much less than that observed for the framework 1 sequence of the light chain variable region. These data support the concept that variable and J region sequence have been conserved in the evolution of placoderm-derived vertebrates, but that constant regions show much

  17. In silico study of rotavirus VP7 surface accessible conserved regions for antiviral drug/vaccine design.

    Directory of Open Access Journals (Sweden)

    Ambarnil Ghosh

    Full Text Available BACKGROUND: Rotaviral diarrhoea kills about half a million children annually in developing countries and accounts for one third of diarrhea related hospitalizations. Drugs and vaccines against the rotavirus are handicapped, as in all viral diseases, by the rapid mutational changes that take place in the DNA and protein sequences rendering most of these ineffective. As of now only two vaccines are licensed and approved by the WHO (World Health Organization, but display reduced efficiencies in the underdeveloped countries where the disease is more prevalent. We approached this issue by trying to identify regions of surface exposed conserved segments on the surface glycoproteins of the virion, which may then be targeted by specific peptide vaccines. We had developed a bioinformatics protocol for these kinds of problems with reference to the influenza neuraminidase protein, which we have refined and expanded to analyze the rotavirus issue. RESULTS: Our analysis of 433 VP7 (Viral Protein 7 from rotavirus surface protein sequences across 17 subtypes encompassing mammalian hosts using a 20D Graphical Representation and Numerical Characterization method, identified four possible highly conserved peptide segments. Solvent accessibility prediction servers were used to identify that these are predominantly surface situated. These regions analyzed through selected epitope prediction servers for their epitopic properties towards possible T-cell and B-cell activation showed good results as epitopic candidates (only dry lab confirmation. CONCLUSIONS: The main reasons for the development of alternative vaccine strategies for the rotavirus are the failure of current vaccines and high production costs that inhibit their application in developing countries. We expect that it would be possible to use the protein surface exposed regions identified in our study as targets for peptide vaccines and drug designs for stable immunity against divergent strains of the

  18. In silico study of rotavirus VP7 surface accessible conserved regions for antiviral drug/vaccine design.

    Science.gov (United States)

    Ghosh, Ambarnil; Chattopadhyay, Shiladitya; Chawla-Sarkar, Mamta; Nandy, Papiya; Nandy, Ashesh

    2012-01-01

    Rotaviral diarrhoea kills about half a million children annually in developing countries and accounts for one third of diarrhea related hospitalizations. Drugs and vaccines against the rotavirus are handicapped, as in all viral diseases, by the rapid mutational changes that take place in the DNA and protein sequences rendering most of these ineffective. As of now only two vaccines are licensed and approved by the WHO (World Health Organization), but display reduced efficiencies in the underdeveloped countries where the disease is more prevalent. We approached this issue by trying to identify regions of surface exposed conserved segments on the surface glycoproteins of the virion, which may then be targeted by specific peptide vaccines. We had developed a bioinformatics protocol for these kinds of problems with reference to the influenza neuraminidase protein, which we have refined and expanded to analyze the rotavirus issue. Our analysis of 433 VP7 (Viral Protein 7 from rotavirus) surface protein sequences across 17 subtypes encompassing mammalian hosts using a 20D Graphical Representation and Numerical Characterization method, identified four possible highly conserved peptide segments. Solvent accessibility prediction servers were used to identify that these are predominantly surface situated. These regions analyzed through selected epitope prediction servers for their epitopic properties towards possible T-cell and B-cell activation showed good results as epitopic candidates (only dry lab confirmation). The main reasons for the development of alternative vaccine strategies for the rotavirus are the failure of current vaccines and high production costs that inhibit their application in developing countries. We expect that it would be possible to use the protein surface exposed regions identified in our study as targets for peptide vaccines and drug designs for stable immunity against divergent strains of the rotavirus. Though this study is fully dependent on

  19. Harmonizing outdoor recreation and bird conservation targets in protected areas: Applying available monitoring data to facilitate collaborative management at the regional scale.

    Science.gov (United States)

    Pouwels, Rogier; Sierdsema, Henk; Foppen, Ruud P B; Henkens, René J H G; Opdam, Paul F M; van Eupen, Michiel

    2017-08-01

    In protected areas managers have to achieve conservation targets while providing opportunities for outdoor recreation. This dual mandate causes conflicts in choosing between management options. Furthermore, the persistence of a protected species within the management unit often depends on how conservation areas elsewhere in the region are managed. We present an assessment procedure to guide groups of managers in aligning outdoor recreation and bird conservation targets for a regional scale protected area in the Netherlands. We used existing bird monitoring data and simulated visitor densities to statistically model the impact of outdoor recreation on bird densities. The models were used to extrapolate the local impacts for other parts of the area, but also to assess the impact on conservation targets at the regional level that were determined by the national government. The assessment shows impacts of outdoor recreation on Nightjar (Caprimulgus europaeus), Stonechat (Saxicola torquata) and Woodlark (Lullula arborea), reducing the regional population by up to 28 percent. The Woodlark population size was reduced below the level of the politically determined conservation target. The output of the regression models provides information that connects implications of local management to regional scale conservation targets. The spatial maps of bird densities can help in deciding where reducing visitor disturbance is expected to result in increasing bird populations, or where alternative measures, such as improving the habitat conditions, could be effective. We suggest that by using our assessment procedure collaborative decision making is facilitated. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Barcoding Chrysomelidae: a resource for taxonomy and biodiversity conservation in the Mediterranean Region.

    Science.gov (United States)

    Magoga, Giulia; Sassi, Davide; Daccordi, Mauro; Leonardi, Carlo; Mirzaei, Mostafa; Regalin, Renato; Lozzia, Giuseppe; Montagna, Matteo

    2016-01-01

    The Mediterranean Region is one of the world's biodiversity hot-spots, which is also characterized by high level of endemism. Approximately 2100 species of leaf beetle (Coleoptera; Chrysomelidae) are known from this area, a number that increases year after year and represents 5/6% of the known species. These features, associated with the urgent need to develop a DNA-based species identification approach for a broad spectrum of leaf beetle species, prompted us to develop a database of nucleotide sequences, with a solid taxonomic background, for all the Chrysomelidae Latreille, 1802 sensu latu inhabiting the Mediterranean region. The Mediterranean Chrysomelidae Barcoding project, which has started in 2009, involves more than fifty entomologists and molecular biologists from different European countries. Numerous collecting campaigns have been organized during the first seven years of the project, which led to the collection of more than 5000 leaf beetle specimens. In addition, during these collecting campaigns two new allochthonous species for Europe, namely Ophraella communa LeSage, 1986 and Colasposoma dauricum Mannerheim, 1849, were intercepted and some species new to science were discovered (e.g., Pachybrachis sassii Montagna, 2011 and Pachybrachis holerorum Montagna et al., 2013). DNA was extracted from 1006 specimens (~13% of the species inhabiting the Mediterranean region) and a total of 910 cox1 gene sequences were obtained (PCR amplification efficiency of 93.8%). Here we report the list of the barcoded subfamilies, genera and the number of species for which cox1 gene sequences were obtained; the metadata associated with each specimen and a list of problematic species for which marker amplification failed. In addition, the nucleotide divergence within and between species and genera was estimated and values of intraspecific nucleotide divergence greater than the average have been discussed. Cryptocephalus quadripunctatus G. A. Olivier, 1808, Cryptocephalus

  1. Role of forest conservation in lessening land degradation in a temperate region: the Monarch Butterfly Biosphere Reserve, Mexico.

    Science.gov (United States)

    Manzo-Delgado, Lilia; López-García, José; Alcántara-Ayala, Irasema

    2014-06-01

    With international concern about the rates of deforestation worldwide, particular attention has been paid to Latin America. Forest conservation programmes in Mexico include Payment for Environmental Services (PES), a scheme that has been successfully introduced in the Monarch Butterfly Biosphere Reserve. To seek further evidence of the role of PES in lessening land degradation processes in a temperate region, the conservation state of the Cerro Prieto ejido within the Reserve was assessed by an analysis of changes in vegetation cover and land-use between 1971 and 2013. There were no changes in the total forest surface area, but the relative proportions of the different classes of cover density had changed. In 1971, closed and semi-closed forest occupied 247.81 ha and 5.38 ha, 82.33% and 1.79% of the total area of the ejido, respectively. By 2013, closed forest had decreased to 230.38 ha (76.54% of the ejido), and semi-closed cover was 17.23 ha (5.72% of the ejido), suggesting that some semi-closed forest had achieved closed status. The final balance between forest losses and recovery was: 29.63 ha were lost, whereas 13.72 ha were recovered. Losses were mainly linked to a sanitation harvest programme to control the bark beetle Scolytus mundus. Ecotourism associated with forest conservation in the Cerro Prieto ejido has been considered by inhabitants as a focal alternative for economic development. Consequently, it is essential to develop a well-planned and solidly structured approach based on social cohesion to foster a community-led sustainable development at local level. Copyright © 2013 Elsevier Ltd. All rights reserved.

  2. The Jumonji gene family in Crassostrea gigas suggests evolutionary conservation of Jmj-C histone demethylases orthologues in the oyster gametogenesis and development.

    Science.gov (United States)

    Fellous, Alexandre; Favrel, Pascal; Guo, Ximing; Riviere, Guillaume

    2014-03-15

    Jumonji (Jmj) proteins are histone demethylases, which control the identity of stem cells. Jmj genes were characterized from plants to mammals where they have been implicated in the epigenetic regulation of development. Despite the Pacific oyster Crassostrea gigas representing one of the most important aquaculture resources worldwide, the molecular mechanisms governing the embryogenesis and reproduction of this lophotrochozoan species remain poorly understood. However, annotations in the C. gigas EST library suggested the presence of putative Jumonji genes, raising the question of the conservation of this family of histone demethylases in the oyster. Using Primer walking, 5'-RACE PCR and in silico analyses, we characterized nine Jumonji orthologues in the oyster, called Cg-Jmj, bearing conserved domains critical for putative histone demethylase activity. Phylogenic analyses revealed that oyster Jumonji cluster into two distinct groups: 'single-domain Jmj' and 'multi-domain Jmj', and define 8 subgroups corresponding to each cognate orthologues in metazoans. RT-qPCR investigations showed specific regulations of Cg-Jmj mRNAs during the early development and along the reproduction cycle. Furthermore, in situ and in toto hybridizations indicate that oyster Jumonji genes are transcribed mostly within the gonad in adult oysters whereas they display a ubiquitous expression during embryonic and larval development. Our study demonstrates the presence of nine Jumonji orthologues in the oyster C. gigas. Their domain conservation and their expression profile suggest an implication during reproduction and development, questioning about the epigenetic regulation by histone methylation in lophotrochozoans. Copyright © 2013 Elsevier B.V. All rights reserved.

  3. Regional summer cooling from agricultural management practices that conserve soil carbon in the northern North American Great Plains

    Science.gov (United States)

    Stoy, Paul; Bromley, Gabriel; Gerken, Tobias; Tang, Angela; Morgan, Mallory; Wood, David; Ahmed, Selena; Bauer, Brad; Brookshire, Jack; Haggerty, Julia; Jarchow, Meghann; Miller, Perry; Peyton, Brent; Rashford, Ben; Spangler, Lee; Swanson, David; Taylor, Suzi; Poulter, Ben

    2017-04-01

    Conserving soil carbon resources while transitioning to a C negative economy is imperative for meeting global climate targets, and can also have critical but under-investigated regional effects. Parts of the North American northern Great Plains have experienced a remarkable 6 W m-2 decrease in summertime radiative forcing since the 1970s. Extreme temperature events now occur less frequently, maximum temperatures have decreased by some 2 ˚ C, and precipitation has increased by 10 mm per decade in some areas. This regional trend toward a cooler and wetter summer climate has coincided with changes in agricultural management. Namely, the practice of keeping fields fallow during summer (hereafter 'summerfallow') has declined by some 23 Mha from the 1970s until the present in the Canadian Prairie Provinces and across the U.S., an area of similar size to the United Kingdom. In addition to potential climate impacts, replacing summerfallow with no-till cropping systems results in lesser soil carbon losses - or even gains - and usually confers economic benefits. In other words, replacing summerfallow with no-till cropping may have resulted in a 'win-win-win' scenario for regional climate, soil carbon conservation, and farm-scale economics. The interaction between carbon, climate, and the economy in this region - and the precise domain that has experienced cooling - are still unknown, which limits our ability to forecast coupled carbon, climate, and human dynamics. Here, we use eddy covariance measurements to demonstrate that summerfallow results in carbon losses during the growing season of the same magnitude as carbon uptake by winter and spring wheat, on the order of 100 - 200 g C m-2 per growing season. We use eddy covariance energy flux measurements to model atmospheric boundary layer and lifted condensation level heights to demonstrate that observed regional changes in near-surface humidity (of up to 7%) are necessary to simulate observed increases in convective

  4. Mitigation and Compensation under EU Nature Conservation Law in the Flemish Region: Beyond the Deadlock for Development Projects?

    Directory of Open Access Journals (Sweden)

    Hendrik Schoukens

    2014-05-01

    Full Text Available For years, the predicament of many of the European protected habitats and species in the Flemish Region, as in many other Member States, passed relatively unnoticed. The lack of proper rules and clear implementation rules fuelled the impression amongst project developers and planning authorities that the impacts of project developments on biodiversity did not really warrant closer assessment. However, in the past ten years, strict national case law has significantly altered this view. Faced with tighter judicial scrutiny, the Habitats and Birds Directives were seen as an important obstacle to project development. Hence mitigation and compensation have now come up as novel approaches to better align spatial aspirations with the conservation of nature. In reality, mitigation was often used as a cover-up for projects that would not fit the strict requirements enshrined in the derogatory clauses. Interestingly, the Belgian Council of State showed itself quite cautious in reasserting the lax view of some planning authorities on mitigation and compensation. In reviewing the legality of several new approaches to mitigation and compensation, the Belgian Council of State, which was initially very cautious in quashing decisions that would actually jeopardise major infrastructure developments, has rendered some compelling rulings on the specific application of mitigation and compensatory measures in a spatial planning context. By letting the objectives of EU nature conservation law prevail in the face of economic interests, the recent case law of the Belgian Council of State can be seen as a remarkable example of judicial environmental activism.

  5. Conserved regions of the DMD 3' UTR regulate translation and mRNA abundance in cultured myotubes.

    Science.gov (United States)

    Larsen, C Aaron; Howard, Michael T

    2014-08-01

    Duchenne muscular dystrophy (DMD), a severe muscle-wasting disease, is caused by mutations in the DMD gene, which encodes for the protein dystrophin. Its regulation is of therapeutic interest as even small changes in expression of functional dystrophin can significantly impact the severity of DMD. While tissue-specific distribution and transcriptional regulation of several DMD mRNA isoforms has been well characterized, the post-transcriptional regulation of dystrophin synthesis is not well understood. Here, we utilize qRTPCR and a quantitative dual-luciferase reporter assay to examine the effects of isoform specific DMD 5' UTRs and the highly conserved DMD 3' UTR on mRNA abundance and translational control of gene expression in C2C12 cells. The 5' UTRs were shown to initiate translation with low efficiency in both myoblasts and myotubes. Whereas, two large highly conserved elements in the 3' UTR, which overlap the previously described Lemaire A and D regions, increase mRNA levels and enhance translation upon differentiation of myoblasts into myotubes. The results presented here implicate an important role for DMD UTRs in dystrophin expression and delineate the cis-acting elements required for the myotube-specific regulation of steady-state mRNA levels and translational enhancer activity found in the DMD 3' UTR. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. Conserved regions of the DMD 3’ UTR regulate translation and mRNA abundance in cultured myotubes

    Science.gov (United States)

    Larsen, C. Aaron; Howard, Michael T.

    2014-01-01

    Duchenne muscular dystrophy (DMD), a severe muscle-wasting disease, is caused by mutations in the DMD gene, which encodes for the protein dystrophin. Its regulation is of therapeutic interest as even small changes in expression of functional dystrophin can significantly impact the severity of DMD. While tissue-specific distribution and transcriptional regulation of several DMD mRNA isoforms has been well characterized, the post-transcriptional regulation of dystrophin synthesis is not well understood. Here, we utilize qRTPCR and a quantitative dual-luciferase reporter assay to examine the effects of isoform specific DMD 5’ UTRs and the highly conserved DMD 3’ UTR on mRNA abundance and translational control of gene expression in C2C12 cells. The 5’ UTRs were shown to initiate translation with low efficiency in both myoblasts and myotubes. Whereas, two large highly conserved elements in the 3’ UTR, which overlap the previously described Lemaire A and D regions, increase mRNA levels and enhance translation upon differentiation of myoblasts into myotubes. The results presented here implicate an important role for DMD UTRs in dystrophin expression and delineate the cis-acting elements required for the myotube-specific regulation of steady-state mRNA levels and translational enhancer activity found in the DMD 3’ UTR. PMID:24928536

  7. Rice Cellulose SynthaseA8 Plant-Conserved Region Is a Coiled-Coil at the Catalytic Core Entrance

    Energy Technology Data Exchange (ETDEWEB)

    Rushton, Phillip S.; Olek, Anna T.; Makowski, Lee; Badger, John; Steussy, C. Nicklaus; Carpita, Nicholas C.; Stauffacher, Cynthia V. (NEU); (Purdue)

    2016-11-22

    The crystallographic structure of a rice (Oryza sativa) cellulose synthase, OsCesA8, plant-conserved region (P-CR), one of two unique domains in the catalytic domain of plant CesAs, was solved to 2.4 Å resolution. Two antiparallel α-helices form a coiled-coil domain linked by a large extended connector loop containing a conserved trio of aromatic residues. The P-CR structure was fit into a molecular envelope for the P-CR domain derived from small-angle X-ray scattering data. The P-CR structure and molecular envelope, combined with a homology-based chain trace of the CesA8 catalytic core, were modeled into a previously determined CesA8 small-angle X-ray scattering molecular envelope to produce a detailed topological model of the CesA8 catalytic domain. The predicted position for the P-CR domain from the molecular docking models places the P-CR connector loop into a hydrophobic pocket of the catalytic core, with the coiled-coil aligned near the entrance of the substrate UDP-glucose into the active site. In this configuration, the P-CR coiled-coil alone is unlikely to regulate substrate access to the active site, but it could interact with other domains of CesA, accessory proteins, or other CesA catalytic domains to control substrate delivery.

  8. Evolutionary Nephrology

    Directory of Open Access Journals (Sweden)

    Robert L. Chevalier

    2017-05-01

    Full Text Available Progressive kidney disease follows nephron loss, hyperfiltration, and incomplete repair, a process described as “maladaptive.” In the past 20 years, a new discipline has emerged that expands research horizons: evolutionary medicine. In contrast to physiologic (homeostatic adaptation, evolutionary adaptation is the result of reproductive success that reflects natural selection. Evolutionary explanations for physiologically maladaptive responses can emerge from mismatch of the phenotype with environment or from evolutionary tradeoffs. Evolutionary adaptation to a terrestrial environment resulted in a vulnerable energy-consuming renal tubule and a hypoxic, hyperosmolar microenvironment. Natural selection favors successful energy investment strategy: energy is allocated to maintenance of nephron integrity through reproductive years, but this declines with increasing senescence after ∼40 years of age. Risk factors for chronic kidney disease include restricted fetal growth or preterm birth (life history tradeoff resulting in fewer nephrons, evolutionary selection for APOL1 mutations (which provide resistance to trypanosome infection, a tradeoff, and modern life experience (Western diet mismatch leading to diabetes and hypertension. Current advances in genomics, epigenetics, and developmental biology have revealed proximate causes of kidney disease, but attempts to slow kidney disease remain elusive. Evolutionary medicine provides a complementary approach by addressing ultimate causes of kidney disease. Marked variation in nephron number at birth, nephron heterogeneity, and changing susceptibility to kidney injury throughout the life history are the result of evolutionary processes. Combined application of molecular genetics, evolutionary developmental biology (evo-devo, developmental programming, and life history theory may yield new strategies for prevention and treatment of chronic kidney disease.

  9. Liberal-Conservative Synthesis: the Experience of Creating the Concept of Evolutionary Modernization of Russia in the Second half of the 19th Century

    Directory of Open Access Journals (Sweden)

    Maxim N. Krot

    2015-06-01

    Full Text Available The article is devoted to consideration of the liberal-conservative conception of Russia formed in the second half of the 19th century by a number of Russian public figures and statesmen, the most prominent of which were B.N. Chicherin, K.D. Cavelin and A.D. Gradovsky. The author reveals the main stages of modernization of the social and political system in Russia suggested by the liberals. The author deals with the concrete projects of changes and reforms, characterizes the methods of achieving these aims. The article reveals the essence of the liberal-conservative "anticonstitutionalism" of the 60s and the first half of the 70s of the 19th century, identifies the main arguments, used by the representatives of this social thought trend for proving their opinion. One issue is considered separately: the draft of the administrative reform by K.D. Kavelin, having offered a wide reorganization of the supreme bodies of state administration and the nature of their formation in order to prepare the basis for establishing of representative government in Russia in the future. The article characterizes the situation in Russia at the turn of 1870 - 1880s, under the circumstances of which there is a gradual transition of liberal conservatives to the idea of immediate creation of representative bodies in Russia. The author analyzes in detail the following: the main arguments and motivations, having induced them to introducing the requirements as well as the projects themselves, devoted to the establishment of elected representative bodies that were supposed to be integrated into the existing government management, complementing and improving it. In the article special attention is drawn to the harmonious combination of liberal - reformational and conservative-preserving principles that, according to its authors, on the one hand, must have promoted the evolution of social and political relations in the country, have avoided their stagnation and degradation

  10. Covalent protein modification with ISG15 via a conserved cysteine in the hinge region.

    Directory of Open Access Journals (Sweden)

    Veronika N Bade

    Full Text Available The ubiquitin-like protein ISG15 (interferon-stimulated gene of 15 kDa is strongly induced by type I interferons and displays antiviral activity. As other ubiquitin-like proteins (Ubls, ISG15 is post-translationally conjugated to substrate proteins by an isopeptide bond between the C-terminal glycine of ISG15 and the side chains of lysine residues in the substrates (ISGylation. ISG15 consists of two ubiquitin-like domains that are separated by a hinge region. In many orthologs, this region contains a single highly reactive cysteine residue. Several hundred potential substrates for ISGylation have been identified but only a few of them have been rigorously verified. In order to investigate the modification of several ISG15 substrates, we have purified ISG15 conjugates from cell extracts by metal-chelate affinity purification and immunoprecipitations. We found that the levels of proteins modified by human ISG15 can be decreased by the addition of reducing agents. With the help of thiol blocking reagents, a mutational analysis and miRNA mediated knock-down of ISG15 expression, we revealed that this modification occurs in living cells via a disulphide bridge between the substrates and Cys78 in the hinge region of ISG15. While the ISG15 activating enzyme UBE1L is conjugated by ISG15 in the classical way, we show that the ubiquitin conjugating enzyme Ubc13 can either be classically conjugated by ISG15 or can form a disulphide bridge with ISG15 at the active site cysteine 87. The latter modification would interfere with its function as ubiquitin conjugating enzyme. However, we found no evidence for an ISG15 modification of the dynamin-like GTPases MxA and hGBP1. These findings indicate that the analysis of potential substrates for ISG15 conjugation must be performed with great care to distinguish between the two types of modification since many assays such as immunoprecipitation or metal-chelate affinity purification are performed with little or no

  11. A System Dynamics Model to Conserve Arid Region Water Resources through Aquifer Storage and Recovery in Conjunction with a Dam

    Directory of Open Access Journals (Sweden)

    Amir Niazi

    2014-08-01

    Full Text Available Groundwater depletion poses a significant threat in arid and semi-arid areas where rivers are usually ephemeral and groundwater is the major source of water. The present study investigated whether an effective water resources management strategy, capable of minimizing evaporative water losses and groundwater depletion while providing water for expanded agricultural activities, can be achieved through aquifer storage and recovery (ASR implemented in conjunction with water storage in an ephemeral river. A regional development modeling framework, including both ASR and a dam design developed through system dynamics modeling, was validated using a case study for the Sirik region of Iran. The system dynamics model of groundwater flow and the comprehensive system dynamics model developed in this study showed that ASR was a beneficial strategy for the region’s farmers and the groundwater system, since the rate of groundwater depletion declined significantly (from 14.5 meters per 40 years to three meters over the same period. Furthermore, evaporation from the reservoir decreased by 50 million cubic meters over the simulation period. It was concluded that the proposed system dynamics model is an effective tool in helping to conserve water resources and reduce depletion in arid regions and semi-arid areas.

  12. Desalination as Groundwater Conservation: The Cost of Protecting Cultural and Environmental Resources in Chile's Region II

    Science.gov (United States)

    Edwards, E. C.; Cristi, O.; Libecap, G. D.

    2012-12-01

    of the empirical work, the theoretical development provides an important perspective into groundwater management and the important role of understanding the physical system in water marketing. Worldwide, subsidized and scarce water is allocated to farmers for social and political reasons. The losses from this type of allocation are often ignored or marginalized. The Chilean case demonstrates that the losses due to economically inefficient allocation are real, because the alternative is greater consumption of other resources (fossil fuels in this case), not conservation. The Chilean case also demonstrates the difficulty of adequately defining water rights for efficient markets due to the physical properties of hydrologic systems. Because groundwater and surface water systems are linked and water is partially recycled, water markets may over allocate water to consumptive users or those with preferable extraction locations. This paper provides a theoretical exposition of how water rights that fail incorporate important properties of the physical system may lead to inefficient water markets.

  13. Characteristics of water erosion and conservation practice in arid regions of Central Asia: Xinjiang Province, China as an example

    Directory of Open Access Journals (Sweden)

    Wentai Zhang

    2015-06-01

    Full Text Available Located in the inland arid area of Central Asia and northwest China, Xinjiang has recently received heightened concerns over soil water erosion, which is highly related with the sustainable utilization of barren soil and limited water resources. Data from the national soil erosion survey of China (1985–2011 and Xinjiang statistical yearbook (2000–2010 was used to analyze the trend, intensity, and serious soil water erosion regions. Results showed that the water erosion area in Xinjiang was 87.6×103 km2 in 2011, mainly distributed in the Ili river valley and the northern and southern Tian Mountain. Soil erosion gradient was generally slight and the average erosion modulus was 2184 t/(km2 a. During the last 26 years, the water erosion area in Xinjiang decreased by 23.2%, whereas the intensity was still increasing. The driving factors from large to small impact included: population boom and human activities>vegetation degradation>rainfall and climate change>topography and soil erodibility>tectonics movement. Soil water erosion resulted in eco-environmental and socioeconomic losses, such as destroying farmland and grassland, triggering floods, sedimentation of reservoirs, damaging transportation and irrigation facilities, and aggravating poverty. A landscape ecological design approach is suggested for integrated control of soil erosion. Currently, an average of 2.07×103 km2 of formerly eroded area is conserved each year. This study highlighted the importance and longevity of soil and water conservation efforts in Xinjiang, and offered some suggestions on ecological restoration and combating desertification in arid regions of Central Asia.

  14. In Silico Design and Experimental Validation of siRNAs Targeting Conserved Regions of Multiple Hepatitis C Virus Genotypes.

    Science.gov (United States)

    ElHefnawi, Mahmoud; Kim, TaeKyu; Kamar, Mona A; Min, Saehong; Hassan, Nafisa M; El-Ahwany, Eman; Kim, Heeyoung; Zada, Suher; Amer, Marwa; Windisch, Marc P

    2016-01-01

    RNA interference (RNAi) is a post-transcriptional gene silencing mechanism that mediates the sequence-specific degradation of targeted RNA and thus provides a tremendous opportunity for development of oligonucleotide-based drugs. Here, we report on the design and validation of small interfering RNAs (siRNAs) targeting highly conserved regions of the hepatitis C virus (HCV) genome. To aim for therapeutic applications by optimizing the RNAi efficacy and reducing potential side effects, we considered different factors such as target RNA variations, thermodynamics and accessibility of the siRNA and target RNA, and off-target effects. This aim was achieved using an in silico design and selection protocol complemented by an automated MysiRNA-Designer pipeline. The protocol included the design and filtration of siRNAs targeting highly conserved and accessible regions within the HCV internal ribosome entry site, and adjacent core sequences of the viral genome with high-ranking efficacy scores. Off-target analysis excluded siRNAs with potential binding to human mRNAs. Under this strict selection process, two siRNAs (HCV353 and HCV258) were selected based on their predicted high specificity and potency. These siRNAs were tested for antiviral efficacy in HCV genotype 1 and 2 replicon cell lines. Both in silico-designed siRNAs efficiently inhibited HCV RNA replication, even at low concentrations and for short exposure times (24h); they also exceeded the antiviral potencies of reference siRNAs targeting HCV. Furthermore, HCV353 and HCV258 siRNAs also inhibited replication of patient-derived HCV genotype 4 isolates in infected Huh-7 cells. Prolonged treatment of HCV replicon cells with HCV353 did not result in the appearance of escape mutant viruses. Taken together, these results reveal the accuracy and strength of our integrated siRNA design and selection protocols. These protocols could be used to design highly potent and specific RNAi-based therapeutic oligonucleotide

  15. Energy conservation programs of Pemex exploration and production, south region; Programas de ahorro de energia en Pemex exploracion y produccion, region sur

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez Milla, Guillermo; Garcia Juarez, Francisco; Alarcon Aleman, Jose Mauricio [Instituto de Investigaciones Electricas, Cuernavaca (Mexico)

    1998-12-31

    The technological developments of energy economizing equipment constitute a powerful tool for the conservation and saving of the electric energy in new or existing installations. Petroleos Mexicanos (PEMEX) Exploration and Production initiated in 1997 a program for energy economizing in the South region, for which the Instituto de Investigaciones Electricas, through its Unit for the Use of Energy, collaborated performing energy assessments in 115 buildings of the above mentioned region. This paper describes the employed methodology to carry on the energy assessment, which consisted in an analysis of each building and different options for energy economizing were presented, which was accompanied with cost-benefit studies. The results obtained show that the air conditioning equipment and lighting represent the most important loads permanently connected, therefore the study was concentrated in these two loads [Espanol] Los desarrollos tecnologicos de equipos ahorradores de energia constituyen una poderosa herramienta para la conservacion y el ahorro de energia electrica en instalaciones nuevas o existentes. Petroleos Mexicanos (PEMEX) Exploracion y Produccion inicio en 1997 un programa para el ahorro de energia en la region sur, para lo cual el Instituto de Investigaciones Electricas, a traves de la Unidad de Uso de Energia, colaboro realizando diagnosticos energeticos en 115 edificios de dicha region. En este documento se describe la metodologia utilizada para realizar el diagnostico energetico, el cual consistio en un analisis de cada edificio y se presentaron diversas opciones para ahorrar energia, lo cual se acompano de estudios de costo-beneficio. Los resultados obtenidos muestran que los equipos de aire acondicionado e iluminacion representan la parte mas importante de las cargas conectadas permanentemente, por lo que el estudio se concentro en estas dos cargas

  16. A novel bioinformatics pipeline to discover genes related to arbuscular mycorrhizal symbiosis based on their evolutionary conservation pattern among higher plants.

    Science.gov (United States)

    Favre, Patrick; Bapaume, Laure; Bossolini, Eligio; Delorenzi, Mauro; Falquet, Laurent; Reinhardt, Didier

    2014-12-03

    Genes involved in arbuscular mycorrhizal (AM) symbiosis have been identified primarily by mutant screens, followed by identification of the mutated genes (forward genetics). In addition, a number of AM-related genes has been identified by their AM-related expression patterns, and their function has subsequently been elucidated by knock-down or knock-out approaches (reverse genetics). However, genes that are members of functionally redundant gene families, or genes that have a vital function and therefore result in lethal mutant phenotypes, are difficult to identify. If such genes are constitutively expressed and therefore escape differential expression analyses, they remain elusive. The goal of this study was to systematically search for AM-related genes with a bioinformatics strategy that is insensitive to these problems. The central element of our approach is based on the fact that many AM-related genes are conserved only among AM-competent species. Our approach involves genome-wide comparisons at the proteome level of AM-competent host species with non-mycorrhizal species. Using a clustering method we first established orthologous/paralogous relationships and subsequently identified protein clusters that contain members only of the AM-competent species. Proteins of these clusters were then analyzed in an extended set of 16 plant species and ranked based on their relatedness among AM-competent monocot and dicot species, relative to non-mycorrhizal species. In addition, we combined the information on the protein-coding sequence with gene expression data and with promoter analysis. As a result we present a list of yet uncharacterized proteins that show a strongly AM-related pattern of sequence conservation, indicating that the respective genes may have been under selection for a function in AM. Among the top candidates are three genes that encode a small family of similar receptor-like kinases that are related to the S-locus receptor kinases involved in sporophytic

  17. Multiple Identified Neurons and Peripheral Nerves Innervating the Prothoracic Defense Glands in Stick Insects Reveal Evolutionary Conserved and Novel Elements of a Chemical Defense System

    Directory of Open Access Journals (Sweden)

    Johannes Strauß

    2017-11-01

    Full Text Available The defense glands in the dorsal prothorax are an important autapomorphic trait of stick insects (Phasmatodea. Here, we study the functional anatomy and neuronal innervation of the defense glands in Anisomorpha paromalus (Westwood, 1859 (Pseudophasmatinae, a species which sprays its defense secretions when disturbed or attacked. We use a neuroanatomical approach to identify the nerves innervating the gland muscles and the motoneurons with axons in the different nerves. The defense gland is innervated by nerves originating from two segments, the subesophageal ganglion (SOG, and the prothoracic ganglion. Axonal tracing confirms the gland innervation via the anterior subesophageal nerve, and two intersegmental nerves, the posterior subesophageal nerve, and the anterior prothoracic nerve. Axonal tracing of individual nerves reveals eight identified neuron types in the subesophageal or prothoracic ganglion. The strongest innervating nerve of the gland is the anterior subesophageal nerve, which also supplies dorsal longitudinal thorax muscles (neck muscles by separate nerve branches. Tracing of individual nerve branches reveals different sets of motoneurons innervating the defense gland (one ipsilateral and one contralateral subesophageal neuron or the neck muscle (ventral median neurons. The ipsilateral and contralateral subesophageal neurons have no homologs in related taxa like locusts and crickets, and thus evolved within stick insects with the differentiation of the defense glands. The overall innervation pattern suggests that the longitudinal gland muscles derived from dorsal longitudinal neck muscles. In sum, the innervating nerves for dorsal longitudinal muscles are conserved in stick insects, while the neuronal control system was specialized with conserved motoneurons for the persisting neck muscles, and evolutionarily novel subesophageal and prothoracic motoneurons innervating the defense gland.

  18. Tissue-specific DNA methylation is conserved across human, mouse, and rat, and driven by primary sequence conservation.

    Science.gov (United States)

    Zhou, Jia; Sears, Renee L; Xing, Xiaoyun; Zhang, Bo; Li, Daofeng; Rockweiler, Nicole B; Jang, Hyo Sik; Choudhary, Mayank N K; Lee, Hyung Joo; Lowdon, Rebecca F; Arand, Jason; Tabers, Brianne; Gu, C Charles; Cicero, Theodore J; Wang, Ting

    2017-09-12

    Uncovering mechanisms of epigenome evolution is an essential step towards understanding the evolution of different cellular phenotypes. While studies have confirmed DNA methylation as a conserved epigenetic mechanism in mammalian development, little is known about the conservation of tissue-specific genome-wide DNA methylation patterns. Using a comparative epigenomics approach, we identified and compared the tissue-specific DNA methylation patterns of rat against those of mouse and human across three shared tissue types. We confirmed that tissue-specific differentially methylated regions are strongly associated with tissue-specific regulatory elements. Comparisons between species revealed that at a minimum 11-37% of tissue-specific DNA methylation patterns are conserved, a phenomenon that we define as epigenetic conservation. Conserved DNA methylation is accompanied by conservation of other epigenetic marks including histone modifications. Although a significant amount of locus-specific methylation is epigenetically conserved, the majority of tissue-specific DNA methylation is not conserved across the species and tissue types that we investigated. Examination of the genetic underpinning of epigenetic conservation suggests that primary sequence conservation is a driving force behind epigenetic conservation. In contrast, evolutionary dynamics of tissue-specific DNA methylation are best explained by the maintenance or turnover of binding sites for important transcription factors. Our study extends the limited literature of comparative epigenomics and suggests a new paradigm for epigenetic conservation without genetic conservation through analysis of transcription factor binding sites.

  19. Examples of geodiversity - biodiversity relationships from Brabant's sand regions, in nature conservation and restoration

    Science.gov (United States)

    van den Ancker, Hanneke; Heskes, Erik; Jungerius, Pieter Dirk; Maes, Bert; Harthoorn, Jaap

    2014-05-01

    The Dutch province of Noord-Brabant is dominated by sand landscapes of aeolian and riverine origin dating from Pleistocene and Holocene times. Brabant's geological history is governed by its position on the fringe of a geological basin with re-activated faults and a Weichselian polar dune desert, a history that makes the region unique in Europe. Some areas have assemblages of geomorphology and soils that have remained relatively untouched up to the present day. In these more pristine areas, the morphological, geological and soil development is a governing factor for the small-scale vegetation differences and biodiversity. Examples of these relationships will be shown, such as loam forests, wetlands caused by 'wijst' - a feature that is special for Brabant, in which the higher grounds are wetter than the lower grounds - active drift sands, and dry and wet heathlands with 'vennen' - small ponds in different gradations of paludization. Many of these areas are Natura-2000 habitats. The geodiversity-biodiversity relationships will be part of the proposal for a European Geopark in Brabant. Measures to restore biodiversity are only sustainable if geodiversity is part of the nature restoration plan e.g. the history of the local landscape, geology, geomorphology and soils. Even if the areas have undergone a drastic transformation. Two examples will be given of nature restoration projects based on geodiversity-biodiversity relationships. The first example is the restoration of an active drift sand, such as still occur in The Netherlands but are extremely rare in the rest of Europe. Over the last decades they have also stabilized in The Netherlands due to high nitrogen deposition. The other example concerns a nature restoration project in a stream valley. These stream valleys originally had a high and small-scale geodiversity that was completely destroyed by stream regulation for agriculture production. This was the first project to study the former and present-day geo

  20. Revisiting Coleoptera a + T-rich region: structural conservation, phylogenetic and phylogeographic approaches in mitochondrial control region of bioluminescent Elateridae species (Coleoptera).

    Science.gov (United States)

    Amaral, Danilo T; Mitani, Yasuo; Oliveira, Gabriela; Ohmiya, Yoshihiro; Viviani, Vadim R

    2017-09-01

    The control region (CR) or A + T-rich region in Coleoptera mt genome is poorly characterized, including the Elateroidea bioluminescent species. Here, we provided the first attempt to characterize and compare the structure and organization of the CR of different species within Elateridae. We also revisited some sequenced Coleoptera CR and observed consensus T-stretches, non-conserved sequences near the stem-loop and unusual inner tRNAs-like sequences. All these features are probably involved in the replication start of the mt genome. The phylogenetic relationships in Elateridae bioluminescent groups using partial sequence of CR showed the monophyly of Pyrearinus pumilus group and Pyrearinus as a polyphyletic genus, corroborating our previous results. The wider genetic variation obtained by CR analysis could separate two different lineages that occur within P. termitilluminans populations. In Elateridae, the CR exhibited high polymorphism within and between populations, which was also observed in other Coleoptera species, suggesting that the CR could be described as a suitable molecular marker to be applied in phylogenetic and phylogeographic studies.

  1. Comparative analyses of coding and noncoding DNA regions indicate that Acropora (Anthozoa: Scleractina) possesses a similar evolutionary tempo of nuclear vs. mitochondrial genomes as in plants.

    Science.gov (United States)

    Chen, I-Ping; Tang, Chung-Yu; Chiou, Chih-Yung; Hsu, Jia-Ho; Wei, Nuwei Vivian; Wallace, Carden C; Muir, Paul; Wu, Henry; Chen, Chaolun Allen

    2009-01-01

    Evidence suggests that the mitochondrial (mt)DNA of anthozoans is evolving at a slower tempo than their nuclear DNA; however, parallel surveys of nuclear and mitochondrial variations and calibrated rates of both synonymous and nonsynonymous substitutions across taxa are needed in order to support this scenario. We examined species of the scleractinian coral genus Acropora, including previously unstudied species, for molecular variations in protein-coding genes and noncoding regions of both nuclear and mt genomes. DNA sequences of a calmodulin (CaM)-encoding gene region containing three exons, two introns and a 411-bp mt intergenic spacer (IGS) spanning the cytochrome b (cytb) and NADH 2 genes, were obtained from 49 Acropora species. The molecular evolutionary rates of coding and noncoding regions in nuclear and mt genomes were compared in conjunction with published data, including mt cytochrome b, the control region, and nuclear Pax-C introns. Direct sequencing of the mtIGS revealed an average interspecific variation comparable to that seen in published data for mt cytb. The average interspecific variation of the nuclear genome was two to five times greater than that of the mt genome. Based on the calibration of the closure of Panama Isthmus (3.0 mya) and closure of the Tethy Seaway (12 mya), synonymous substitution rates ranged from 0.367% to 1.467% Ma(-1) for nuclear CaM, which is about 4.8 times faster than those of mt cytb (0.076-0.303% Ma(-1)). This is similar to the findings in plant genomes that the nuclear genome is evolving at least five times faster than those of mitochondrial counterparts.

  2. Expression analysis of Egr-1 ortholog in metamorphic brain of honeybee (Apis mellifera L.): Possible evolutionary conservation of roles of Egr in eye development in vertebrates and insects.

    Science.gov (United States)

    Ugajin, Atsushi; Watanabe, Takayuki; Uchiyama, Hironobu; Sasaki, Tetsuhiko; Yajima, Shunsuke; Ono, Masato

    2016-09-16

    Specific genes quickly transcribed after extracellular stimuli without de novo protein synthesis are known as immediate early genes (IEGs) and are thought to contribute to learning and memory processes in the mature nervous system of vertebrates. A recent study revealed that the homolog of Early growth response protein-1 (Egr-1), which is one of the best-characterized vertebrate IEGs, shared similar properties as a neural activity-dependent gene in the adult brain of insects. With regard to the roles of vertebrate Egr-1 in neural development, the contribution to the development and growth of visual systems has been reported. However, in insects, the expression dynamics of the Egr-1 homologous gene during neural development remains poorly understood. Our expression analysis demonstrated that AmEgr, a honeybee homolog of Egr-1, was transiently upregulated in the developing brain during the early to mid pupal stages. In situ hybridization and 5-bromo-2'-deoxyuridine (BrdU) immunohistochemistry revealed that AmEgr was mainly expressed in post-mitotic cells in optic lobes, the primary visual center of the insect brain. These findings suggest the evolutionarily conserved role of Egr homologs in the development of visual systems in vertebrates and insects. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. Historical ecology meets conservation and evolutionary genetics: a secondary contact zone between Carabus violaceus (Coleoptera, Carabidae populations inhabiting ancient and recent woodlands in north-western Germany

    Directory of Open Access Journals (Sweden)

    Andrea Matern

    2011-05-01

    Full Text Available Only very few cases have documented that an increase in connectivity after a period of fragmentation in ecological time has had an effect on the distribution, genetic structure and morphology of stenotopic species. In this study we present an example of clinal variability in a woodland ground beetle as a result of changes in the connectivity of a landscape during the last two centuries. The study area hosts both the nominate form C. violaceus s. str. and the subspecies C. v. purpurascens, which is ranked as a distinct species by some authors. We studied 12 Carabus violaceus populations from a 30 km transect of ancient and recent forests in north-western Germany. We analyzed three polymorphic enzyme loci, classified the elytron sculpture and measured the shape of the aedeagus tip of the specimens. C. violaceus showed secondary gradients both in allozyme markers and morphometric characters in our study area. A genetic differentiation of 16% between the populations is high but lies within the range of intraspecific variability in habitat specialists of the genus Carabus. Populations had no significant deficit of heterozygotes. We found many hybrid populations in terms of morphological properties. This study highlights the conservation value of ancient woodland and the consequences of landscape connectivity and defragmentation on the genetic setting of a ground beetle. Moreover, it shows that differences in the external shape of male genitalia do not prevent gene flow within the genus Carabus. Thus, the establishment of species status should not exclusively be based on this property.

  4. Bayesian phylogeny analysis of vertebrate serpins illustrates evolutionary conservation of the intron and indels based six groups classification system from lampreys for ∼500 MY

    Directory of Open Access Journals (Sweden)

    Abhishek Kumar

    2015-06-01

    Full Text Available The serpin superfamily is characterized by proteins that fold into a conserved tertiary structure and exploits a sophisticated and irreversible suicide-mechanism of inhibition. Vertebrate serpins are classified into six groups (V1–V6, based on three independent biological features—genomic organization, diagnostic amino acid sites and rare indels. However, this classification system was based on the limited number of mammalian genomes available. In this study, several non-mammalian genomes are used to validate this classification system using the powerful Bayesian phylogenetic method. This method supports the intron and indel based vertebrate classification and proves that serpins have been maintained from lampreys to humans for about 500 MY. Lampreys have fewer than 10 serpins, which expand into 36 serpins in humans. The two expanding groups V1 and V2 have SERPINB1/SERPINB6 and SERPINA8/SERPIND1 as the ancestral serpins, respectively. Large clusters of serpins are formed by local duplications of these serpins in tetrapod genomes. Interestingly, the ancestral HCII/SERPIND1 locus (nested within PIK4CA possesses group V4 serpin (A2APL1, homolog of α2-AP/SERPINF2 of lampreys; hence, pointing to the fact that group V4 might have originated from group V2. Additionally in this study, details of the phylogenetic history and genomic characteristics of vertebrate serpins are revisited.

  5. Gcn4 misregulation reveals a direct role for the evolutionary conserved EKC/KEOPS in the t6A modification of tRNAs.

    Science.gov (United States)

    Daugeron, Marie-Claire; Lenstra, Tineke L; Frizzarin, Martina; El Yacoubi, Basma; Liu, Xipeng; Baudin-Baillieu, Agnès; Lijnzaad, Philip; Decourty, Laurence; Saveanu, Cosmin; Jacquier, Alain; Holstege, Frank C P; de Crécy-Lagard, Valérie; van Tilbeurgh, Herman; Libri, Domenico

    2011-08-01

    The EKC/KEOPS complex is universally conserved in Archaea and Eukarya and has been implicated in several cellular processes, including transcription, telomere homeostasis and genomic instability. However, the molecular function of the complex has remained elusive so far. We analyzed the transcriptome of EKC/KEOPS mutants and observed a specific profile that is highly enriched in targets of the Gcn4p transcriptional activator. GCN4 expression was found to be activated at the translational level in mutants via the defective recognition of the inhibitory upstream ORFs (uORFs) present in its leader. We show that EKC/KEOPS mutants are defective for the N6-threonylcarbamoyl adenosine modification at position 37 (t(6)A(37)) of tRNAs decoding ANN codons, which affects initiation at the inhibitory uORFs and provokes Gcn4 de-repression. Structural modeling reveals similarities between Kae1 and bacterial enzymes involved in carbamoylation reactions analogous to t(6)A(37) formation, supporting a direct role for the EKC in tRNA modification. These findings are further supported by strong genetic interactions of EKC mutants with a translation initiation factor and with threonine biosynthesis genes. Overall, our data provide a novel twist to understanding the primary function of the EKC/KEOPS and its impact on several essential cellular functions like transcription and telomere homeostasis.

  6. The impacts of conservation agriculture on crop yield in China depend on specific practices, crops and cropping regions

    Directory of Open Access Journals (Sweden)

    Chengyan Zheng

    2014-10-01

    Full Text Available For smooth and wide application of conservation agriculture (CA, remaining uncertainties about its impacts on crop yield need to be reduced. Based on previous field experiments in China, a meta-analysis was performed to quantify the actual impacts of CA practices (NT: no/reduced-tillage only, CTSR: conventional tillage with straw retention, NTSR: NT with straw retention on crop yields as compared to conventional tillage without straw retention (CT. Although CA practices increased crop yield by 4.6% on average, there were large variations in their impacts. For each CA practice, CTSR and NTSR significantly increased crop yield by 4.9% and 6.3%, respectively, compared to CT. However, no significant effect was found for NT. Among ecological areas, significant positive effects of CA practices were found in areas with an annual precipitation below 600 mm. Similar effects were found in areas with annual mean air temperature above 5 °C. For cropping regions, CA increased crop yield by 6.4% and 5.5% compared to CT in Northwest and South China, respectively, whereas no significant effects were found in the North China and Northeast China regions. Among crops, the positive effects of CA practices were significantly higher in maize (7.5% and rice (4.1% than in wheat (2.9%. NT likely decreased wheat yield. Our results indicate that there are great differences in the impacts of CA practices on crop yield, owing to regional variation in climate and crop types. CA will most likely increase maize yield but reduce wheat yield. It is strongly recommended to apply CA with crop straw retention in maize cropping areas and seasons with a warm and dry climate pattern.

  7. Useful parasites: the evolutionary biology and biotechnology ...

    Indian Academy of Sciences (India)

    , transposable elements have long been considered as 'parasitic' or 'selfish'. Today, we ... research niche and deserve to be included into the agenda of molecular ecologists, evolutionary geneticists, conservation biologists and plant breeders.

  8. Quantifying the Effects of Conservation Practices on Soil, Water, and Nutrients in the Loess Mesa Ravine Region of the Loess Plateau, China

    Science.gov (United States)

    Xu, Xiang-Zhou; Li, Mei-Juan; Liu, Bin; Kuang, Shang-Fu; Xu, Shi-Guo

    2012-05-01

    A large number of soil and water conservation programs have been implemented on the Loess Plateau of China since the 1950s. To comprehensively assess the merits and demerits of the conservation practices is of great importance in further supervising the conservation strategy for the Loess Plateau. This study calculates the impact factors of conservation practices on soil, water, and nutrients during the period 1954-2004 in the Nanxiaohegou Catchment, a representative catchment in the Loess Mesa Ravine Region of the Loess Plateau, China. Brief conclusions could be drawn as follows: (1) Soil erosion and nutrient loss had been greatly mitigated through various conservation practices. About half of the total transported water and 94.8 % of the total transported soil and nutrients, had been locally retained in the selected catchment. The soil retained from small watersheds do not only form large-scale fertile farmland but also safeguard the Yellow River against overflow. (2) Check dam was the most appropriate conservation practice on the Loess Plateau. In the selected catchment, more than 90 % of the retained soil and water were accomplished by the dam farmland, although the dam farmland occupied only 2.3 % of the total area of all conservation measures. Retention abilities of the characteristic conservation practices were in the following order: dam farmland > terrace farmland > forest land and grassland. (3) The conservation practices were more powerful in retaining sediment than in reducing runoff from the Loess Plateau, and the negative effects of the conservation practices on reducing water to the Yellow River were relatively slight.

  9. In Silico Design and Experimental Validation of siRNAs Targeting Conserved Regions of Multiple Hepatitis C Virus Genotypes.

    Directory of Open Access Journals (Sweden)

    Mahmoud ElHefnawi

    Full Text Available RNA interference (RNAi is a post-transcriptional gene silencing mechanism that mediates the sequence-specific degradation of targeted RNA and thus provides a tremendous opportunity for development of oligonucleotide-based drugs. Here, we report on the design and validation of small interfering RNAs (siRNAs targeting highly conserved regions of the hepatitis C virus (HCV genome. To aim for therapeutic applications by optimizing the RNAi efficacy and reducing potential side effects, we considered different factors such as target RNA variations, thermodynamics and accessibility of the siRNA and target RNA, and off-target effects. This aim was achieved using an in silico design and selection protocol complemented by an automated MysiRNA-Designer pipeline. The protocol included the design and filtration of siRNAs targeting highly conserved and accessible regions within the HCV internal ribosome entry site, and adjacent core sequences of the viral genome with high-ranking efficacy scores. Off-target analysis excluded siRNAs with potential binding to human mRNAs. Under this strict selection process, two siRNAs (HCV353 and HCV258 were selected based on their predicted high specificity and potency. These siRNAs were tested for antiviral efficacy in HCV genotype 1 and 2 replicon cell lines. Both in silico-designed siRNAs efficiently inhibited HCV RNA replication, even at low concentrations and for short exposure times (24h; they also exceeded the antiviral potencies of reference siRNAs targeting HCV. Furthermore, HCV353 and HCV258 siRNAs also inhibited replication of patient-derived HCV genotype 4 isolates in infected Huh-7 cells. Prolonged treatment of HCV replicon cells with HCV353 did not result in the appearance of escape mutant viruses. Taken together, these results reveal the accuracy and strength of our integrated siRNA design and selection protocols. These protocols could be used to design highly potent and specific RNAi-based therapeutic

  10. Evolutionary Awareness

    Directory of Open Access Journals (Sweden)

    Gregory Gorelik

    2014-10-01

    Full Text Available In this article, we advance the concept of “evolutionary awareness,” a metacognitive framework that examines human thought and emotion from a naturalistic, evolutionary perspective. We begin by discussing the evolution and current functioning of the moral foundations on which our framework rests. Next, we discuss the possible applications of such an evolutionarily-informed ethical framework to several domains of human behavior, namely: sexual maturation, mate attraction, intrasexual competition, culture, and the separation between various academic disciplines. Finally, we discuss ways in which an evolutionary awareness can inform our cross-generational activities—which we refer to as “intergenerational extended phenotypes”—by helping us to construct a better future for ourselves, for other sentient beings, and for our environment.

  11. Evolutionary macroecology

    Directory of Open Access Journals (Sweden)

    José Alexandre F. Diniz-Filho

    2013-10-01

    Full Text Available Macroecology focuses on ecological questions at broad spatial and temporal scales, providing a statistical description of patterns in species abundance, distribution and diversity. More recently, historical components of these patterns have begun to be investigated more deeply. We tentatively refer to the practice of explicitly taking species history into account, both analytically and conceptually, as ‘evolutionary macroecology’. We discuss how the evolutionary dimension can be incorporated into macroecology through two orthogonal and complementary data types: fossils and phylogenies. Research traditions dealing with these data have developed more‐or‐less independently over the last 20–30 years, but merging them will help elucidate the historical components of diversity gradients and the evolutionary dynamics of species’ traits. Here we highlight conceptual and methodological advances in merging these two research traditions and review the viewpoints and toolboxes that can, in combination, help address patterns and unveil processes at temporal and spatial macro‐scales.

  12. Evolutionary Expectations

    DEFF Research Database (Denmark)

    Nash, Ulrik William

    2014-01-01

    cognitive bounds will perceive business opportunities identically. In addition, because cues provide information about latent causal structures of the environment, changes in causality must be accompanied by changes in cognitive representations if adaptation is to be maintained. The concept of evolutionary......, they are correlated among people who share environments because these individuals satisfice within their cognitive bounds by using cues in order of validity, as opposed to using cues arbitrarily. Any difference in expectations thereby arise from differences in cognitive ability, because two individuals with identical......The concept of evolutionary expectations descends from cue learning psychology, synthesizing ideas on rational expectations with ideas on bounded rationality, to provide support for these ideas simultaneously. Evolutionary expectations are rational, but within cognitive bounds. Moreover...

  13. [Evolutionary medicine].

    Science.gov (United States)

    Wjst, M

    2013-12-01

    Evolutionary medicine allows new insights into long standing medical problems. Are we "really stoneagers on the fast lane"? This insight might have enormous consequences and will allow new answers that could never been provided by traditional anthropology. Only now this is made possible using data from molecular medicine and systems biology. Thereby evolutionary medicine takes a leap from a merely theoretical discipline to practical fields - reproductive, nutritional and preventive medicine, as well as microbiology, immunology and psychiatry. Evolutionary medicine is not another "just so story" but a serious candidate for the medical curriculum providing a universal understanding of health and disease based on our biological origin. © Georg Thieme Verlag KG Stuttgart · New York.

  14. Incorporating evolutionary processes into population viability models.

    Science.gov (United States)

    Pierson, Jennifer C; Beissinger, Steven R; Bragg, Jason G; Coates, David J; Oostermeijer, J Gerard B; Sunnucks, Paul; Schumaker, Nathan H; Trotter, Meredith V; Young, Andrew G

    2015-06-01

    We examined how ecological and evolutionary (eco-evo) processes in population dynamics could be better integrated into population viability analysis (PVA). Complementary advances in computation and population genomics can be combined into an eco-evo PVA to offer powerful new approaches to understand the influence of evolutionary processes on population persistence. We developed the mechanistic basis of an eco-evo PVA using individual-based models with individual-level genotype tracking and dynamic genotype-phenotype mapping to model emergent population-level effects, such as local adaptation and genetic rescue. We then outline how genomics can allow or improve parameter estimation for PVA models by providing genotypic information at large numbers of loci for neutral and functional genome regions. As climate change and other threatening processes increase in rate and scale, eco-evo PVAs will become essential research tools to evaluate the effects of adaptive potential, evolutionary rescue, and locally adapted traits on persistence. © 2014 Society for Conservation Biology.

  15. Teaching evolutionary biology

    Directory of Open Access Journals (Sweden)

    Rosana Tidon

    2004-01-01

    Full Text Available Evolutionary Biology integrates several disciplines of Biology in a complex and interactive manner, where a deep understanding of the subject demands knowledge in diverse areas. Since this knowledge is often inaccessible to the majority of specialized professionals, including the teachers, we present some reflections in order to stimulate discussions aimed at the improvement of the conditions of education in this area. We examine the profile of evolutionary teaching in Brazil, based on questionnaires distributed to teachers in Secondary Education in the Federal District, on data provided by the "National Institute for Educational Studies and Research", and on information collected from teachers working in various regions of this country. Issues related to biological misconceptions, curriculum and didactic material are discussed, and some proposals are presented with the objective of aiding discussions aimed at the improvement of the teaching of evolutionary biology.

  16. A practical study for Treatment and Conservation a group of Silver Coins from Dhamar Regional Museum, Dhamar, Yemen.

    Directory of Open Access Journals (Sweden)

    Mohamed M. Megahed

    2014-04-01

    Full Text Available A big group of silver coins{35 coins} was discovered in Banawa excavation , Dhamar , season 2002, and now it is situated in Dhamar Regional Museum ,Yemen. They were covered with a thin grey and black corrosion layers that disfigured them and hid their figures and inscriptions , also Some coins miss parts and others lost their circular.The aims of this work are identified the metallic composition of the coins , investigate the nature of corrosion grown during the long-term burial and identify its products that will help us to understand the corrosive factors and the degradation mechanisms , cleaning the group of coins from the superficial dirt and the corrosion products in order to discover as much as possible the surface topography, and to reveal the surfaces details , finally to establish them against further deterioration .To achieve that samples from the coins were examined by Metallographic Microscope {ME} , Scanning Electron Microscope {SEM}, the corrosion products were analyzed by X-ray diffraction{XRD} , and X-ray fluorescence { XRF} was used to determine the coins metallic constituents. Chemical cleaning was chosen for treating the coins and they were isolated to preserve them against further attack. After treatment and conservation, the coins figures and inscriptions that could be identified showed that this group of coins dates back to Umayyad period , exactly the reign of caliph Abd al-Malik ibn Marwan{ 65- 86 A.H}{685-705A.D} and his descendants till 106 A.H. 

  17. ChIP-seq Identification of Weakly Conserved Heart Enhancers

    Energy Technology Data Exchange (ETDEWEB)

    Blow, Matthew J.; McCulley, David J.; Li, Zirong; Zhang, Tao; Akiyama, Jennifer A.; Holt, Amy; Plajzer-Frick, Ingrid; Shoukry, Malak; Wright, Crystal; Chen, Feng; Afzal, Veena; Bristow, James; Ren, Bing; Black, Brian L.; Rubin, Edward M.; Visel, Axel; Pennacchio, Len A.

    2010-07-01

    Accurate control of tissue-specific gene expression plays a pivotal role in heart development, but few cardiac transcriptional enhancers have thus far been identified. Extreme non-coding sequence conservation successfully predicts enhancers active in many tissues, but fails to identify substantial numbers of heart enhancers. Here we used ChIP-seq with the enhancer-associated protein p300 from mouse embryonic day 11.5 heart tissue to identify over three thousand candidate heart enhancers genome-wide. Compared to other tissues studied at this time-point, most candidate heart enhancers are less deeply conserved in vertebrate evolution. Nevertheless, the testing of 130 candidate regions in a transgenic mouse assay revealed that most of them reproducibly function as enhancers active in the heart, irrespective of their degree of evolutionary constraint. These results provide evidence for a large population of poorly conserved heart enhancers and suggest that the evolutionary constraint of embryonic enhancers can vary depending on tissue type.

  18. Evolutionary Conservation of pou5f3 Genomic Organization and Its Dynamic Distribution during Embryogenesis and in Adult Gonads in Japanese Flounder Paralichthys olivaceus

    Directory of Open Access Journals (Sweden)

    Jinning Gao

    2017-01-01

    Full Text Available Octamer-binding transcription factor 4 (Oct4 is a member of POU (Pit-Oct-Unc transcription factor family Class V that plays a crucial role in maintaining the pluripotency and self-renewal of stem cells. Though it has been deeply investigated in mammals, its lower vertebrate homologue, especially in the marine fish, is poorly studied. In this study, we isolated the full-length sequence of Paralichthys olivaceus pou5f3 (Popou5f3, and we found that it is homologous to mammalian Oct4. We identified two transcript variants with different lengths of 3′-untranslated regions (UTRs generated by alternative polyadenylation (APA. Quantitative real-time RT-PCR (qRT-PCR, in situ hybridization (ISH and immunohistochemistry (IHC were implemented to characterize the spatial and temporal expression pattern of Popou5f3 during early development and in adult tissues. Our results show that Popou5f3 is maternally inherited, abundantly expressed at the blastula and early gastrula stages, then greatly diminishes at the end of gastrulation. It is hardly detectable from the heart-beating stage onward. We found that Popou5f3 expression is restricted to the adult gonads, and continuously expresses during oogenesis while its dynamics are downregulated during spermatogenesis. Additionally, numerous cis-regulatory elements (CRE on both sides of the flanking regions show potential roles in regulating the expression of Popou5f3. Taken together, these findings could further our understanding of the functions and evolution of pou5f3 in lower vertebrates, and also provides fundamental information for stem cell tracing and genetic manipulation in Paralichthys olivaceus.

  19. Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty

    Directory of Open Access Journals (Sweden)

    Green Eric D

    2009-07-01

    Full Text Available Abstract Background Large-scale genome rearrangements brought about by chromosome breaks underlie numerous inherited diseases, initiate or promote many cancers and are also associated with karyotype diversification during species evolution. Recent research has shown that these breakpoints are nonrandomly distributed throughout the mammalian genome and many, termed "evolutionary breakpoints" (EB, are specific genomic locations that are "reused" during karyotypic evolution. When the phylogenetic trajectory of orthologous chromosome segments is considered, many of these EB are coincident with ancient centromere activity as well as new centromere formation. While EB have been characterized as repeat-rich regions, it has not been determined whether specific sequences have been retained during evolution that would indicate previous centromere activity or a propensity for new centromere formation. Likewise, the conservation of specific sequence motifs or classes at EBs among divergent mammalian taxa has not been determined. Results To define conserved sequence features of EBs associated with centromere evolution, we performed comparative sequence analysis of more than 4.8 Mb within the tammar wallaby, Macropus eugenii, derived from centromeric regions (CEN, euchromatic regions (EU, and an evolutionary breakpoint (EB that has undergone convergent breakpoint reuse and past centromere activity in marsupials. We found a dramatic enrichment for long interspersed nucleotide elements (LINE1s and endogenous retroviruses (ERVs and a depletion of short interspersed nucleotide elements (SINEs shared between CEN and EBs. We analyzed the orthologous human EB (14q32.33, known to be associated with translocations in many cancers including multiple myelomas and plasma cell leukemias, and found a conserved distribution of similar repetitive elements. Conclusion Our data indicate that EBs tracked within the class Mammalia harbor sequence features retained since the

  20. Investigating the timing of origin and evolutionary processes shaping regional species diversity: Insights from simulated data and neotropical butterfly diversification rates.

    Science.gov (United States)

    Matos-Maraví, Pável

    2016-07-01

    Different diversification scenarios have been proposed to explain the origin of extant biodiversity. However, most existing meta-analyses of time-calibrated phylogenies rely on approaches that do not quantitatively test alternative diversification processes. Here, I highlight the shortcomings of using species divergence ranks, which is a method widely used in meta-analyses. Divergence ranks consist of categorizing cladogenetic events to certain periods of time, typically to either Pleistocene or to pre-Pleistocene ages. This approach has been claimed to shed light on the origin of most extant species and the timing and dynamics of diversification in any biogeographical region. However, interpretations drawn from such method often confound two fundamental questions in macroevolutionary studies, tempo (timing of evolutionary rate shifts) and mode ("how" and "why" of speciation). By using simulated phylogenies under four diversification scenarios, constant-rate, diversity-dependence, high extinction, and high speciation rates in the Pleistocene, I showed that interpretations based on species divergence ranks might have been seriously misleading. Future meta-analyses of dated phylogenies need to be aware of the impacts of incomplete taxonomic sampling, tree topology, and divergence time uncertainties, as well as they might be benefited by including quantitative tests of alternative diversification models that acknowledge extinction and diversity dependence. © 2016 The Author(s).

  1. Conserved POU/OCT- and GATA-binding sites in 5'-flanking promoter region of mammalian WNT8B orthologs.

    Science.gov (United States)

    Katoh, Masuko; Katoh, Masaru

    2007-05-01

    WNT family members are secreted-type glycoproteins regulating cell fate, planar cell polarity, cell adhesion, and cell movement. WNT signals are context-dependently transduced to the canonical pathway for the transcriptional up-regulation of MYC, CCND1, FGF20, JAG1, WISP1 and DKK1 genes, and also to the non-canonical pathway for the activation of RHOA, JNK, PKC, NFAT and NLK signaling cascades. We cloned and characterized the wild-type human WNT8B, while another group the aberrant human WNT8B with Gly230Ala and Arg284Leu amino-acid substitutions. Although WNT8B is undetectable in normal adult tissues by using Northern blot analyses, WNT8B is expressed in gastric cancer, pancreatic cancer, colorectal cancer, breast cancer, and embryonal tumors. Here, comparative integromics on WNT8B orthologs were investigated by using bioinformatics (Techint) and human intelligence (Humint). Cow Wnt8b gene was identified within NW_001494361.1 genome sequence. Predicted sequence XM_582222.3 was an artificial cow Wnt8b with aberrant prediction for the first exon. Cow Wnt8b complete coding sequence was found to encode a 350-amino-acid protein, which showed 96.9% total-amino-acid identity with human WNT8B. Comparative proteomics revealed that N-terminal signal peptide, 22 Cys residues, two Asn-linked glycosylation sites, Gly230, and Arg284 of human WNT8B were conserved among mammalian WNT8B orthologs. Comparative genomics revealed that POU/OCT- and GATA-binding sites in the 5'-flanking promoter region were conserved among human, chimpanzee, cow, mouse, and rat WNT8B orthologs. In silico expression analyses revealed that human WNT8B was expressed in embryoid body derived from embryonic stem (ES) cells, hepatocyte progenitors derived from ES cells, fetal brain, diffuse-type gastric cancer, colorectal cancer, prostate cancer, and ovarian fibrotheoma. Based on the expression profiles of POU and GATA family transcription factors, it was revealed that WNT8B expression in hepatocyte

  2. High Conservation of Tetanus and Botulinum Neurotoxins Cleavage Sites on Human SNARE Proteins Suggests That These Pathogens Exerted Little or No Evolutionary Pressure on Humans

    Science.gov (United States)

    Carle, Stefan; Barth, Holger; Montecucco, Cesare

    2017-01-01

    The Genome Aggregation Database presently contains >120,000 human genomes. We searched in this database for the presence of mutations at the sites of tetanus (TeNT) and botulinum neurotoxins (BoNTs) cleavages of the three SNARE proteins: VAMP, SNAP-25 and Syntaxin. These mutations could account for some of the BoNT/A resistant patients. At the same time, this approach was aimed at testing the possibility that TeNT and BoNT may have acted as selective agents in the development of resistance to tetanus or botulism. We found that mutations of the SNARE proteins are very rare and concentrated outside the SNARE motif required for the formation of the SNARE complex involved in neuroexocytosis. No changes were found at the BoNT cleavage sites of VAMP and syntaxins and only one very rare mutation was found in the essential C-terminus region of SNAP-25, where Arg198 was replaced with a Cys residue. This is the P1’ cleavage site for BoNT/A and the P1 cleavage site for BoNT/C. We found that the Arg198Cys mutation renders SNAP-25 resistant to BoNT/A. Nonetheless, its low frequency (1.8 × 10−5) indicates that mutations of SNAP-25 at the BoNT/A cleavage site are unlikely to account for the existence of BoNT/A resistant patients. More in general, the present findings indicate that tetanus and botulinum neurotoxins have not acted as selective agents during human evolution as it appears to have been the case for tetanus in rats and chicken. PMID:29257047

  3. High Conservation of Tetanus and Botulinum Neurotoxins Cleavage Sites on Human SNARE Proteins Suggests That These Pathogens Exerted Little or No Evolutionary Pressure on Humans

    Directory of Open Access Journals (Sweden)

    Stefan Carle

    2017-12-01

    Full Text Available The Genome Aggregation Database presently contains >120,000 human genomes. We searched in this database for the presence of mutations at the sites of tetanus (TeNT and botulinum neurotoxins (BoNTs cleavages of the three SNARE proteins: VAMP, SNAP-25 and Syntaxin. These mutations could account for some of the BoNT/A resistant patients. At the same time, this approach was aimed at testing the possibility that TeNT and BoNT may have acted as selective agents in the development of resistance to tetanus or botulism. We found that mutations of the SNARE proteins are very rare and concentrated outside the SNARE motif required for the formation of the SNARE complex involved in neuroexocytosis. No changes were found at the BoNT cleavage sites of VAMP and syntaxins and only one very rare mutation was found in the essential C-terminus region of SNAP-25, where Arg198 was replaced with a Cys residue. This is the P1’ cleavage site for BoNT/A and the P1 cleavage site for BoNT/C. We found that the Arg198Cys mutation renders SNAP-25 resistant to BoNT/A. Nonetheless, its low frequency (1.8 × 10−5 indicates that mutations of SNAP-25 at the BoNT/A cleavage site are unlikely to account for the existence of BoNT/A resistant patients. More in general, the present findings indicate that tetanus and botulinum neurotoxins have not acted as selective agents during human evolution as it appears to have been the case for tetanus in rats and chicken.

  4. Developing Spatially Explicit Habitat Models for Grassland Bird Conservation Planning in the Prairie Pothole Region of North Dakota

    Science.gov (United States)

    Neal D. Niemuth; Michael E. Estey; Charles R. Loesch

    2005-01-01

    Conservation planning for birds is increasingly focused on landscapes. However, little spatially explicit information is available to guide landscape-level conservation planning for many species of birds. We used georeferenced 1995 Breeding Bird Survey (BBS) data in conjunction with land-cover information to develop a spatially explicit habitat model predicting the...

  5. Evolutionary paths of streptococcal and staphylococcal superantigens

    Directory of Open Access Journals (Sweden)

    Okumura Kayo

    2012-08-01

    Full Text Available Abstract Background Streptococcus pyogenes (GAS harbors several superantigens (SAgs in the prophage region of its genome, although speG and smez are not located in this region. The diversity of SAgs is thought to arise during horizontal transfer, but their evolutionary pathways have not yet been determined. We recently completed sequencing the entire genome of S. dysgalactiae subsp. equisimilis (SDSE, the closest relative of GAS. Although speG is the only SAg gene of SDSE, speG was present in only 50% of clinical SDSE strains and smez in none. In this study, we analyzed the evolutionary paths of streptococcal and staphylococcal SAgs. Results We compared the sequences of the 12–60 kb speG regions of nine SDSE strains, five speG+ and four speG–. We found that the synteny of this region was highly conserved, whether or not the speG gene was present. Synteny analyses based on genome-wide comparisons of GAS and SDSE indicated that speG is the direct descendant of a common ancestor of streptococcal SAgs, whereas smez was deleted from SDSE after SDSE and GAS split from a common ancestor. Cumulative nucleotide skew analysis of SDSE genomes suggested that speG was located outside segments of steeper slopes than the stable region in the genome, whereas the region flanking smez was unstable, as expected from the results of GAS. We also detected a previously undescribed staphylococcal SAg gene, selW, and a staphylococcal SAg -like gene, ssl, in the core genomes of all Staphylococcus aureus strains sequenced. Amino acid substitution analyses, based on dN/dS window analysis of the products encoded by speG, selW and ssl suggested that all three genes have been subjected to strong positive selection. Evolutionary analysis based on the Bayesian Markov chain Monte Carlo method showed that each clade included at least one direct descendant. Conclusions Our findings reveal a plausible model for the comprehensive evolutionary pathway of streptococcal and

  6. Regional Extinctions and Quaternary Shifts in the Geographic Range of Lestodelphys halli, the Southernmost Living Marsupial: Clues for Its Conservation

    Science.gov (United States)

    Formoso, Anahí E.; Martin, Gabriel M.; Teta, Pablo; Carbajo, Aníbal E.; Sauthier, Daniel E. Udrizar; Pardiñas, Ulyses F. J.

    2015-01-01

    The Patagonian opossum (Lestodelphys halli), the southernmost living marsupial, inhabits dry and open environments, mainly in the Patagonian steppe (between ~32°S and ~49°S). Its rich fossil record shows its occurrence further north in Central Argentina during the Quaternary. The paleoenvironmental meaning of the past distribution of L. halli has been mostly addressed in a subjective framework without an explicit connection with the climatic “space” currently occupied by this animal. Here, we assessed the potential distribution of this species and the changes occurred in its geographic range during late Pleistocene-Holocene times and linked the results obtained with conservation issues. To this end, we generated three potential distribution models with fossil records and three with current ones, using MaxEnt software. These models showed a decrease in the suitable habitat conditions for the species, highlighting a range shift from Central-Eastern to South-Western Argentina. Our results support that the presence of L. halli in the Pampean region during the Pleistocene-Holocene can be related to precipitation and temperature variables and that its current presence in Patagonia is more related to temperature and dominant soils. The models obtained suggest that the species has been experiencing a reduction in its geographic range since the middle Holocene, a process that is in accordance with a general increase in moisture and temperature in Central Argentina. Considering the findings of our work and the future scenario of global warming projected for Patagonia, we might expect a harsh impact on the distribution range of this opossum in the near future. PMID:26203650

  7. Incorporating evolutionary principles into environmental management and policy

    DEFF Research Database (Denmark)

    Lankau, Richard; Jørgensen, Peter Søgaard; Harris, David J.

    2011-01-01

    in conservation biology, and the necessary next step for the field is to consider ways in which conservation policy makers and managers can proactively manipulate evolutionary processes to achieve their goals. In this review, we aim to illustrate the potential conservation benefits of an increased understanding......As policymakers and managers work to mitigate the effects of rapid anthropogenic environmental changes, they need to consider organisms’ responses. In light of recent evidence that evolution can be quite rapid, this now includes evolutionary responses. Evolutionary principles have a long history...... of evolutionary history and prescriptive manipulation of three basic evolutionary factors: selection, variation, and gene flow. For each, we review and propose ways that policy makers and managers can use evolutionary thinking to preserve threatened species, combat pest species, or reduce undesirable evolutionary...

  8. Conservation of Sand Dune Vegetation in Coastal areas of the Valencian Region (Spain); Estado de conservacion de la vegetacion dunar en las costas de la comunidad Valenciana

    Energy Technology Data Exchange (ETDEWEB)

    Albertos, B.; San Miguel, E.; Draper, I.; Garilleti, R.; Lara, F.; Varela, J. M.

    2010-07-01

    The state of conservation of the coastal dune vegetation in Valencia region has been assessed within a survey of the vegetal communities present in these systems.The conservation status has been evaluated through a qualitative scale which integrates criteria such as dune extension, structure and diversity of the vegetal communities, level of ruderalization, presence of invasive species, and floristic rarity. Special attention has been paid to the usual aggressions to this type of ecosystem and the situation of the most aggressive invasive plants. (Author) 15 refs.

  9. Loco-regional control after neo-adjuvant chemotherapy and conservative treatment for locally advanced breast cancer patients.

    Science.gov (United States)

    Levy, Antonin; Borget, Isabelle; Bahri, Manel; Arnedos, Monica; Rivin, Eleonor; Vielh, Philippe; Balleyguier, Corinne; Rimareix, Françoise; Bourgier, Céline

    2014-01-01

    Breast-conserving treatment (BCT) has been validated for breast cancer patients receiving adjuvant chemotherapy. Our objective was to evaluate the difference in loco-regional recurrence (LRR) rates between BCT and mastectomy in patients receiving radiation therapy after neo-adjuvant chemotherapy (NCT). A retrospective data base was used to identify all patients with breast cancer undergoing NCT from 2002 to 2007. Patients with initial metastatic disease were excluded from this analysis. LRR was compared between those undergoing BCT and mastectomy. Individual variables associated with LRR were evaluated. Two hundred eighty-four patients were included, 111 (39%) underwent BCT and 173 (61%) mastectomy. Almost all patients (99%) in both groups received postoperative radiation. Pathologic complete response was seen in 37 patients, of which 28 underwent BCT (p loco-regional control rate was 91% (95% CI: 86-94%). The 10-year LRR rate was similar in the BCT group (9.2% [95% CI: 4.9-16.7%]) and in the mastectomy group (10.7% [95% CI: 5.9-15.2%]; p = 0.8). Ten-year overall survival (OS) rates (63% [95% CI: 46-79%] in the BCT group; 60% [95% CI: 47-73%] in the mastectomy group, p = 0.8) were not statistically different between the two patient populations. Multivariate analysis showed that AJCC stage ≥ III (HR: 2.6; 95% CI: 1.2-5.8; p = 0.02), negative PR (HR: 6; 95% CI: 1.2-30.6, p = 0.03), and number of positive lymph nodes ≥3 (HR: 2.5; 95% CI: 1.1-5.9; p = 0.03) were independent predictors of LRR. Ten-year OS was similar in the BCT and in the mastectomy group (p = 0.1). The rate of LRR was low and did not significantly differ between the BCT and the mastectomy group after NCT. Randomized trials assessing whether mastectomy can be safely omitted in selected breast cancer patients (nonstage III tumors or those which do not require adjuvant hormone suppression) which respond to NCT are required. © 2014 Wiley Periodicals, Inc.

  10. Review of the Diversity, Ecology, and Conservation of Elasmobranchs in the Azores Region, Mid-North Atlantic

    Directory of Open Access Journals (Sweden)

    Diya Das

    2017-11-01

    Full Text Available A vulnerable species group, such as, the elasmobranchs, in a data-deficient context presents a complicated management problem. Evidence suggests that the Azores islands, a remote archipelago on the Mid-Atlantic Ridge, serve essential functions in the life-history of species across taxa. The diversity of marine resources within its EEZ are exploited by local to international fleets, and the full extent of fishing pressure can often be underestimated. Although sharks and rays appear to be of minor importance in the fishery, the possibilities of illegal, unreported, and unregulated fishing raises concerns about these threatened species. However, this group has failed to attract management attention, visible in the lack of regional studies focused on biodiversity, ecology, or threats of elasmobranchs. Our work attempts to review and update the information on elasmobranchs of the Azores and identify potential threats, mainly by the local fisheries. We aim to highlight knowledge gaps that require further research and conservation actions. We (1 update the annotated checklist of elasmobranch species, (2 compare species distribution across a biogeographically similar section of the North Atlantic, and (3 analyze the interaction of elasmobranch species with local fisheries. We confirm 61 chondrichthyan species for the Azores (39 sharks, 17 rays, and 5 chimaeras, adding 19 species to the previous annotated checklist of 1997. The Azores elasmobranch species assemblage most resembles Madeira, the neighboring Macaronesian archipelago. Biogeographic affinities between the chosen regions of the North Atlantic are reflected in the taxonomic structure of families. Although underestimated in the local fisheries, elasmobranchs constitute a regular but highly variable portion of total landings. Misreporting and misidentification is perhaps the greatest concern in the local fisheries records, further aggravated by few existing catch regulations for elasmobranchs

  11. Evolutionary institutionalism.

    Science.gov (United States)

    Fürstenberg, Dr Kai

    Institutions are hard to define and hard to study. Long prominent in political science have been two theories: Rational Choice Institutionalism (RCI) and Historical Institutionalism (HI). Arising from the life sciences is now a third: Evolutionary Institutionalism (EI). Comparative strengths and weaknesses of these three theories warrant review, and the value-to-be-added by expanding the third beyond Darwinian evolutionary theory deserves consideration. Should evolutionary institutionalism expand to accommodate new understanding in ecology, such as might apply to the emergence of stability, and in genetics, such as might apply to political behavior? Core arguments are reviewed for each theory with more detailed exposition of the third, EI. Particular attention is paid to EI's gene-institution analogy; to variation, selection, and retention of institutional traits; to endogeneity and exogeneity; to agency and structure; and to ecosystem effects, institutional stability, and empirical limitations in behavioral genetics. RCI, HI, and EI are distinct but complementary. Institutional change, while amenable to rational-choice analysis and, retrospectively, to criticaljuncture and path-dependency analysis, is also, and importantly, ecological. Stability, like change, is an emergent property of institutions, which tend to stabilize after change in a manner analogous to allopatric speciation. EI is more than metaphorically biological in that institutional behaviors are driven by human behaviors whose evolution long preceded the appearance of institutions themselves.

  12. Exporting conservation

    OpenAIRE

    LTRA-12

    2012-01-01

    Metadata only record Soil degradation represents a major threat to food security, particularly in mountainous regions of Southeast Asia, where rainfall can wash away inches of topsoil. This article presents conservation agriculture as a potential solution, focusing on the work that North Carolina Agricultural and Technical State University conducts in Southeast Asia in conjunction with regional partners as part of the Sustainable Agriculture and Natural Resource Management (SANREM) collabo...

  13. Spatial Analysis of Conservation Priorities Based on Ecosystem Services in the Atlantic Forest Region of Misiones, Argentina

    Directory of Open Access Journals (Sweden)

    Matthew L. Clark

    2012-08-01

    Full Text Available Understanding the spatial pattern of ecosystem services is important for effective environmental policy and decision-making. In this study, we use a geospatial decision-support tool (Marxan to identify conservation priorities for habitat and a suite of ecosystem services (storage carbon, soil retention and water yield in the Upper Paraná Atlantic Forest from Misiones, Argentina—an area of global conservation priority. Using these results, we then evaluate the efficiency of existing protected areas in conserving both habitat and ecosystem services. Selected areas for conserving habitat had an overlap of carbon and soil ecosystem services. Yet, selected areas for water yield did not have this overlap. Furthermore, selected areas with relatively high overlap of ecosystem services tended to be inside protected areas; however, other important areas for ecosystem services (i.e., central highlands do not have legal protection, revealing the importance of enforcing existing environmental regulations in these areas.

  14. Loco-regional morbidity after breast conservation and axillary lymph node dissection for early breast cancer with or without regional nodes radiotherapy, perspectives in modern breast cancer treatment: the Skagen Trial 1 is active

    DEFF Research Database (Denmark)

    Nielsen, Hanne Melgaard; Friis, Rasmus Blechingberg; Linnet, Søren

    2017-01-01

    BACKGROUND: Axillary lymph node dissection (ALND) and adjuvant radiotherapy (RT) in early breast cancer are associated with a risk of morbidity, including lymphedema and impaired shoulder mobility. The aim of this study was to evaluate loco-regional morbidity after breast conserving surgery (BCS...

  15. Ranching and conservation in the Santa Cruz River Region, Sonora: Milpillas Case Study (Ganaderia y Conservacion en la Region del Rio Santa Cruz, Sonora: El Caso del Grupo Milpillas)

    Science.gov (United States)

    Joaquin Murrieta-Saldivar

    2006-01-01

    The Sonoran Institute (SI) is a non-profit organization working with people toward common conservation goals. Two objectives guide the work of the Sonoran Institute in the Santa Cruz River Region in Sonora, Mexico: to establish projects with community participation that can result in tangible and long-lasting benefits to the environment, and to ensure success by...

  16. Red states, blue states, and divorce: understanding the impact of conservative Protestantism on regional variation in divorce rates.

    Science.gov (United States)

    Glass, Jennifer; Levchak, Philip

    2014-01-01

    Why do states with larger proportions of religious conservatives have higher divorce rates than states with lower proportions of religious conservatives? This project examines whether earlier transitions to marriage and parenthood among conservative Protestants (known risk factors for divorce) contribute to this paradox while attending to other plausible explanations. County-level demographic information from all 50 states is combined from a variety of public data sources and merged with individual records from the National Surveys of Family Growth to estimate both aggregated county and multilevel individual models of divorce. Results show that individual religious conservatism is positively related to individual divorce risk, solely through the earlier transitions to adulthood and lower incomes of conservative Protestants. However, the proportion of conservative Protestants in a county is also independently and positively associated with both the divorce rate in that county and an individual's likelihood of divorcing. The earlier family formation and lower levels of educational attainment and income in counties with a higher proportion of conservative Protestants can explain a substantial portion of this association. Little support is found for alternative explanations of the association between religious conservatism and divorce rates, including the relative popularity of marriage versus cohabitation across counties.

  17. A pilot study to investigate the role of the 26S proteasome in radiotherapy resistance and loco-regional recurrence following breast conserving therapy for early breast cancer.

    Science.gov (United States)

    Elfadl, Dalia; Hodgkinson, Victoria C; Long, Ervine D; Scaife, Lucy; Drew, Philip J; Lind, Michael J; Cawkwell, Lynn

    2011-08-01

    Breast conserving therapy is a currently accepted method for managing patients with early stage breast cancer. However, approximately 7% of patients may develop loco-regional tumour recurrence within 5 years. We previously reported that expression of the 26S proteasome may be associated with radio-resistance. Here we aimed to analyse the 26S proteasome in a pilot series of early breast cancers and correlate the findings with loco-regional recurrence. Fourteen patients with early breast cancer who developed loco-regional recurrence within 4 years of completing breast conserving therapy were selected according to strict criteria and compared with those from 14 patients who were disease-free at 10 years. Decreased expression of the 26S proteasome was significantly associated with radio-resistance, manifested as the development of a loco-regional recurrence within 4 years of breast conserving therapy (p = 0.018). This small pilot study provides further suggestion that the 26S proteasome may be associated with response to radiotherapy. Copyright © 2011 Elsevier Ltd. All rights reserved.

  18. Remarkable evolutionary conservation of SOX14 orthologues

    Indian Academy of Sciences (India)

    SOX14 Bos taurus, 7. SOX14 Mus musculus, 8. SOX14 Rattus norvegicus,. 9. SOX14 Monodelphis domestica, 10. SOX14 Ornithorinchus anatinus, 11. SOX14. Gallus gallus, 12. SOX14 Xenopus tropicalis, 13. SOX14 Danio rerio, 14. SOX14. Oreochromis aureus, 15. SOX14 Takifugu rubripes, 16. SOX21 Homo sapiens, 17.

  19. Remarkable evolutionary conservation of SOX14 orthologues

    Indian Academy of Sciences (India)

    cluded SOX14/Sox14 genes of human (Homo sapiens), chim- panzee (Pan troglodytes), macaca (Macaca mulatta), dog. (Canis familiaris), horse (Equus cabalus), mouse (Mus mus- culus), opposum (Monodelphis domestica), platypus (Or- nithorinchus anatinus), chicken (Gallus gallus), frog (Xeno- pus tropicalis), zebrafish ...

  20. Evolutionary conservation of the mature oocyte proteome

    Directory of Open Access Journals (Sweden)

    Tamar Lotan

    2014-06-01

    Significance: The current study provides the first proteomic profile of an oocyte of a cnidarian organism the starlet sea anemone N. vectensis and gives new insights on the ancient origin of an oocyte proteome template. The comparative analysis with a chordate oocyte suggests that the oocyte proteome predates the divergence of the cnidarian and bilaterian lineages. In addition, the data generated in the study will serve as a valuable resource for further developmental and evolutional studies.

  1. Remarkable evolutionary conservation of SOX14 orthologues

    Indian Academy of Sciences (India)

    PCR based approach was used to identify Sox14 of goat, cow and rat, while nucleotide and amino acid sequence alignments and mapping were performed using information currently available in public database. Comparative sequence analysis revealed remarkable identity among Sox14 orthologues and helped us to ...

  2. 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.

  3. Functionality of intergenic transcription: an evolutionary comparison.

    Directory of Open Access Journals (Sweden)

    Philipp Khaitovich

    2006-10-01

    Full Text Available Although a large proportion of human transcription occurs outside the boundaries of known genes, the functional significance of this transcription remains unknown. We have compared the expression patterns of known genes as well as intergenic transcripts within the ENCODE regions between humans and chimpanzees in brain, heart, testis, and lymphoblastoid cell lines. We find that intergenic transcripts show patterns of tissue-specific conservation of their expression, which are comparable to exonic transcripts of known genes. This suggests that intergenic transcripts are subject to functional constraints that restrict their rate of evolutionary change as well as putative positive selection to an extent comparable to that of classical protein-coding genes. In brain and testis, we find that part of this intergenic transcription is caused by widespread use of alternative promoters. Further, we find that about half of the expression differences between humans and chimpanzees are due to intergenic transcripts.

  4. Evolutionary rate variation and RNA secondary structure prediction

    DEFF Research Database (Denmark)

    Knudsen, B; Andersen, E S; Damgaard, Christian Kroun

    2004-01-01

    of approach. Determining these rates can be hard to do reliably without a large and accurate initial alignment, which ideally also has structural annotation. Hence, one must often apply rates extracted from other RNA families with trusted alignments and structures. Here, we investigate this problem......Predicting RNA secondary structure using evolutionary history can be carried out by using an alignment of related RNA sequences with conserved structure. Accurately determining evolutionary substitution rates for base pairs and single stranded nucleotides is a concern for methods based on this type....... In addition we obtained an alignment of the 5' HIV-1 region that is more consistent with the structure than that currently in the database. We added randomized noise to the original values of the rates to investigate the stability of predictions to rate matrix deviations. We find that changes within a fairly...

  5. Diversity, natural history and conservation of amphibians and reptiles from the San Vito Region, southwestern Costa Rica

    Directory of Open Access Journals (Sweden)

    Georgina Santos-Barrera

    2008-06-01

    Full Text Available We present an inventory of the amphibians and reptiles of the San Vito de Coto Brus region, including the Las Cruces Biological Station, in southern Costa Rica, which is the result of a survey of the herpetofauna occurring in mountain forest fragments, pastures, coffee plantations, and other disturbed areas. We found 67 species, included 26 species of amphibians and of 41of reptiles. We describe the distribution patterns of the community on the basis of the life zones, elevation, fragmentation, and degree of anthropogenic impact. We also provide some nouvelle data on the systematics of some select taxa, their geographical ranges, microhabitats, activity, and other relevant ecological and natural history features. Finally, we comment on the present conservation status of the herpetofauna in the region. Previous literature and collection records indicate a higher number of species occurring in this area, which suggests that some declines have occurred, especially of amphibians, in last decades. Rev. Biol. Trop. 56 (2: 755-778. Epub 2008 June 30.En este artículo se presenta un inventario de los anfibios y reptiles de la región de San Vito de Coto Brus incluyendo la Estación de Biología Las Cruces, en el sur de Costa Rica. Se llevó a cabo una evaluación de las poblaciones de anfibios y reptiles presentes en los parches de bosque, potreros, cafetales y otras áreas perturbadas de la región. Como resultado de esta evaluación se registraron 26 especies de anfibios y 41 de reptiles lo que suma un total de 67 especies. Asimismo se describen los patrones generales de distribución de las especies basándose en los tipos de vegetación así como en la altitud, fragmentación y grado de perturbación antrópica en el área. Se proporcionan algunos datos sobre la sistemática de las especies, su distribución geográfica, el microhábitat que ocupan, su actividad y otros datos ecológicos y biológicos relevantes. Finalmente, se presenta una breve

  6. EvoTol: a protein-sequence based evolutionary intolerance framework for disease-gene prioritization

    OpenAIRE

    Rackham, Owen?J.?L.; Shihab, Hashem A.; Johnson, Michael R.; Petretto, Enrico

    2014-01-01

    Methods to interpret personal genome sequences are increasingly required. Here, we report a novel framework (EvoTol) to identify disease-causing genes using patient sequence data from within protein coding-regions. EvoTol quantifies a gene's intolerance to mutation using evolutionary conservation of protein sequences and can incorporate tissue-specific gene expression data. We apply this framework to the analysis of whole-exome sequence data in epilepsy and congenital heart disease, and demon...

  7. Evolutionary psychology and intelligence research.

    Science.gov (United States)

    Kanazawa, Satoshi

    2010-01-01

    This article seeks to unify two subfields of psychology that have hitherto stood separately: evolutionary psychology and intelligence research/differential psychology. I suggest that general intelligence may simultaneously be an evolved adaptation and an individual-difference variable. Tooby and Cosmides's (1990a) notion of random quantitative variation on a monomorphic design allows us to incorporate heritable individual differences in evolved adaptations. The Savanna-IQ Interaction Hypothesis, which is one consequence of the integration of evolutionary psychology and intelligence research, can potentially explain why less intelligent individuals enjoy TV more, why liberals are more intelligent than conservatives, and why night owls are more intelligent than morning larks, among many other findings. The general approach proposed here will allow us to integrate evolutionary psychology with any other aspect of differential psychology. Copyright 2010 APA, all rights reserved.

  8. Global loss of avian evolutionary uniqueness in urban areas.

    Science.gov (United States)

    Ibáñez-Álamo, Juan Diego; Rubio, Enrique; Benedetti, Yanina; Morelli, Federico

    2017-08-01

    Urbanization, one of the most important anthropogenic impacts on Earth, is rapidly expanding worldwide. This expansion of urban land-covered areas is known to significantly reduce different components of biodiversity. However, the global evidence for this effect is mainly focused on a single diversity measure (species richness) with a few local or regional studies also supporting reductions in functional diversity. We have used birds, an important ecological group that has been used as surrogate for other animals, to investigate the hypothesis that urbanization reduces the global taxonomical and/or evolutionary diversity. We have also explored whether there is evidence supporting that urban bird communities are evolutionarily homogenized worldwide in comparison with nonurban ones by means of using evolutionary distinctiveness (how unique are the species) of bird communities. To our knowledge, this is the first attempt to quantify the effect of urbanization in more than one single diversity measure as well as the first time to look for associations between urbanization and phylogenetic diversity at a large spatial scale. Our findings show a strong and globally consistent reduction in taxonomic diversity in urban areas, which is also synchronized with the evolutionary homogenization of urban bird communities. Despite our general patterns, we found some regional differences in the intensity of the effect of cities on bird species richness or evolutionary distinctiveness, suggesting that conservation efforts should be adapted locally. Our findings might be useful for conservationists and policymakers to minimize the impact of urban development on Earth's biodiversity and help design more realistic conservation strategies. © 2016 The Authors. Global Change Biology Published by John Wiley & Sons Ltd.

  9. Evolutionary principles and their practical application.

    Science.gov (United States)

    Hendry, Andrew P; Kinnison, Michael T; Heino, Mikko; Day, Troy; Smith, Thomas B; Fitt, Gary; Bergstrom, Carl T; Oakeshott, John; Jørgensen, Peter S; Zalucki, Myron P; Gilchrist, George; Southerton, Simon; Sih, Andrew; Strauss, Sharon; Denison, Robert F; Carroll, Scott P

    2011-03-01

    Evolutionary principles are now routinely incorporated into medicine and agriculture. Examples include the design of treatments that slow the evolution of resistance by weeds, pests, and pathogens, and the design of breeding programs that maximize crop yield or quality. Evolutionary principles are also increasingly incorporated into conservation biology, natural resource management, and environmental science. Examples include the protection of small and isolated populations from inbreeding depression, the identification of key traits involved in adaptation to climate change, the design of harvesting regimes that minimize unwanted life-history evolution, and the setting of conservation priorities based on populations, species, or communities that harbor the greatest evolutionary diversity and potential. The adoption of evolutionary principles has proceeded somewhat independently in these different fields, even though the underlying fundamental concepts are the same. We explore these fundamental concepts under four main themes: variation, selection, connectivity, and eco-evolutionary dynamics. Within each theme, we present several key evolutionary principles and illustrate their use in addressing applied problems. We hope that the resulting primer of evolutionary concepts and their practical utility helps to advance a unified multidisciplinary field of applied evolutionary biology.

  10. NemaFootPrinter: a web based software for the identification of conserved non-coding genome sequence regions between C. elegans and C. briggsae

    Directory of Open Access Journals (Sweden)

    Morandi Paolo

    2005-12-01

    Full Text Available Abstract Background NemaFootPrinter (Nematode Transcription Factor Scan Through Philogenetic Footprinting is a web-based software for interactive identification of conserved, non-exonic DNA segments in the genomes of C. elegans and C. briggsae. It has been implemented according to the following project specifications: a Automated identification of orthologous gene pairs. b Interactive selection of the boundaries of the genes to be compared. c Pairwise sequence comparison with a range of different methods. d Identification of putative transcription factor binding sites on conserved, non-exonic DNA segments. Results Starting from a C. elegans or C. briggsae gene name or identifier, the software identifies the putative ortholog (if any, based on information derived from public nematode genome annotation databases. The investigator can then retrieve the genome DNA sequences of the two orthologous genes; visualize graphically the genes' intron/exon structure and the surrounding DNA regions; select, through an interactive graphical user interface, subsequences of the two gene regions. Using a bioinformatics toolbox (Blast2seq, Dotmatcher, Ssearch and connection to the rVista database the investigator is able at the end of the procedure to identify and analyze significant sequences similarities, detecting the presence of transcription factor binding sites corresponding to the conserved segments. The software automatically masks exons. Discussion This software is intended as a practical and intuitive tool for the researchers interested in the identification of non-exonic conserved sequence segments between C. elegans and C. briggsae. These sequences may contain regulatory transcriptional elements since they are conserved between two related, but rapidly evolving genomes. This software also highlights the power of genome annotation databases when they are conceived as an open resource and the possibilities offered by seamless integration of different web

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

    Science.gov (United States)

    Chakravorty, S; Sarkar, S; Gachhui, R

    2015-01-01

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

  12. Global priorities for conservation across multiple dimensions of mammalian diversity.

    Science.gov (United States)

    Brum, Fernanda T; Graham, Catherine H; Costa, Gabriel C; Hedges, S Blair; Penone, Caterina; Radeloff, Volker C; Rondinini, Carlo; Loyola, Rafael; Davidson, Ana D

    2017-07-18

    Conservation priorities that are based on species distribution, endemism, and vulnerability may underrepresent biologically unique species as well as their functional roles and evolutionary histories. To ensure that priorities are biologically comprehensive, multiple dimensions of diversity must be considered. Further, understanding how the different dimensions relate to one another spatially is important for conservation prioritization, but the relationship remains poorly understood. Here, we use spatial conservation planning to (i) identify and compare priority regions for global mammal conservation across three key dimensions of biodiversity-taxonomic, phylogenetic, and traits-and (ii) determine the overlap of these regions with the locations of threatened species and existing protected areas. We show that priority areas for mammal conservation exhibit low overlap across the three dimensions, highlighting the need for an integrative approach for biodiversity conservation. Additionally, currently protected areas poorly represent the three dimensions of mammalian biodiversity. We identify areas of high conservation priority among and across the dimensions that should receive special attention for expanding the global protected area network. These high-priority areas, combined with areas of high priority for other taxonomic groups and with social, economic, and political considerations, provide a biological foundation for future conservation planning efforts.

  13. The Political Economy of Conservation at Mount Elgon, Uganda: Between Local Deprivation, Regional Sustainability, and Global Public Goods

    Directory of Open Access Journals (Sweden)

    Paul Vedeld

    2016-01-01

    Full Text Available This paper presents a case study from Mount Elgon National Park, Uganda, examining and deepening an understanding of direct incomes and costs of conservation for local people close to protected areas. In the early 1990s, collaborative arrangements were introduced to Mount Elgon National Park to improve people-park relations and enhance rural livelihoods after a period of violent evictions and severe resource access restrictions. In areas with such arrangements – including resource access agreements, Taungya farming, and beekeeping schemes – we observe a marginal increase in annual incomes for involved households. Other incomes accrue from tourism revenue sharing schemes, a community revolving fund, and payments for carbon sequestration. However, these incomes are economically marginal (1.2% of household income, unevenly distributed and instrumentally used to reward compliance with park regulations. They do not necessarily accrue to those incurring costs due to eviction and exclusion, crop raiding, resource access restrictions and conflicts. By contrast, costs constitute at least 20.5 % of total household incomes, making it difficult to see how conservation, poverty alleviation and development can be locally reconciled if local populations continue to bear the economic brunt of conservation. We recommend a shift in policy towards donor and state responsibility for compensating costs on a relevant scale. Such a shift would be an important step towards a more substantive rights-based model of conservation, and would enhance the legitimacy of protected area management in the context of both extreme poverty and natural resource dependence.

  14. Local conservation scores without a priori assumptions on neutral substitution rates

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    Hagenauer Joachim

    2008-04-01

    Full Text Available Abstract Background Comparative genomics aims to detect signals of evolutionary conservation as an indicator of functional constraint. Surprisingly, results of the ENCODE project revealed that about half of the experimentally verified functional elements found in non-coding DNA were classified as unconstrained by computational predictions. Following this observation, it has been hypothesized that this may be partly explained by biased estimates on neutral evolutionary rates used by existing sequence conservation metrics. All methods we are aware of rely on a comparison with the neutral rate and conservation is estimated by measuring the deviation of a particular genomic region from this rate. Consequently, it is a reasonable assumption that inaccurate neutral rate estimates may lead to biased conservation and constraint estimates. Results We propose a conservation signal that is produced by local Maximum Likelihood estimation of evolutionary parameters using an optimized sliding window and present a Kullback-Leibler projection that allows multiple different estimated parameters to be transformed into a conservation measure. This conservation measure does not rely on assumptions about neutral evolutionary substitution rates and little a priori assumptions on the properties of the conserved regions are imposed. We show the accuracy of our approach (KuLCons on synthetic data and compare it to the scores generated by state-of-the-art methods (phastCons, GERP, SCONE in an ENCODE region. We find that KuLCons is most often in agreement with the conservation/constraint signatures detected by GERP and SCONE while qualitatively very different patterns from phastCons are observed. Opposed to standard methods KuLCons can be extended to more complex evolutionary models, e.g. taking insertion and deletion events into account and corresponding results show that scores obtained under this model can diverge significantly from scores using the simpler model

  15. Bird diversity in the Serra do Aracá region, northwestern Brazilian Amazon: preliminary check-list with considerations on biogeography and conservation

    Directory of Open Access Journals (Sweden)

    Sérgio Henrique Borges

    2014-08-01

    Full Text Available We inventoried the birds from Serra do Aracá region, state of Amazonas. The region encompasses a high diversity of vegetation types, including white sand forests and campinas, terra firme and flooded forests, montane forests and tepuis. We recorded 416 bird taxa in 69 families through captures with mist nets, tape recording of bird voices, and collection of voucher specimens. A large proportion of them (61% were recorded in a single vegetation type. Qualitative estimates suggest that approximately 580 bird species occur in the region. The avifauna of the Aracá region has a mixed biogeographic composition, with species typical of both margins of the Rio Negro occurring sympatrically. Additionally, species whose distributions are restricted to three areas of endemism for Amazonian birds (Imeri, Guiana and Pantepui were recorded in the region. Rare landscapes in the Brazilian Amazon are found in the Serra do Aracá region. Additionally, we recorded endemic and rare birds, highlighting the value of the region for conservation. The Serra do Aracá State Park officially protects montane forests, terra firme forests and tepuis. We suggest that the large extension of white sand campinas and igapó forests at the southern portion of Serra do Aracá should be also preserved in order to improve the representation of the rich natural heritage of the region.

  16. Effects of Long-term Conservation Tillage on Soil Nutrients in Sloping Fields in Regions Characterized by Water and Wind Erosion

    Science.gov (United States)

    Tan, Chunjian; Cao, Xue; Yuan, Shuai; Wang, Weiyu; Feng, Yongzhong; Qiao, Bo

    2015-12-01

    Conservation tillage is commonly used in regions affected by water and wind erosion. To understand the effects of conservation tillage on soil nutrients and yield, a long-term experiment was set up in a region affected by water and wind erosion on the Loess Plateau. The treatments used were traditional tillage (CK), no tillage (NT), straw mulching (SM), plastic-film mulching (PM), ridging and plastic-film mulching (RPM) and intercropping (In). Our results demonstrate that the available nutrients in soils subjected to non-traditional tillage treatments decreased during the first several years and then remained stable over the last several years of the experiment. The soil organic matter and total nitrogen content increased gradually over 6 years in all treatments except CK. The nutrient content of soils subjected to conservative tillage methods, such as NT and SM, were significantly higher than those in soils under the CK treatment. Straw mulching and film mulching effectively reduced an observed decrease in soybean yield. Over the final 6 years of the experiment, soybean yields followed the trend RPM > PM > SM > NT > CK > In. This trend has implications for controlling soil erosion and preventing non-point source pollution in sloping fields by sacrificing some food production.

  17. Culture Development Planning in the Special Region of Yogyakarta (Management Planning of Cultural Heritage in Kotagede District based on Community Empowerment Conservation Model

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    Eko Suryanti

    2014-09-01

    Full Text Available The Special Region of Yogyakarta is a cultural rich city with excellent cultural resources. Yogyakarta should manage their assets with long-term planning to keep the sustainability. There is a very unique planning process due to a combination of political, technocratic, participatory, top down and bottom up approaches. This planning process is comprehensive or integrated because its involved many actor from multisectoral, multidisciplinary, multi regulatory, and multi planning documents, etc. Local wisdoms have been coloring the planning documents. This study describe and analyze the cultural development planning in Yogyakarta especially on the Management Planning in Kotagede Cultural Heritage District. We used qualitative descriptive approach methods and Miles and Huberman analysis methods. Participation of community and Non Governmental Organization (NGO in conservation planning of cultural heritage in this area is very significant in simplify the government task because people have been more literate in planning, have database of cultural assets, and capable of making their own decisions for the future of the region. Participatory rural appraisal (PRA dan Rapid Rural Appraisal (RRA were integrated in the planning process of Kotagede Heritage District management, thus it becomes a model of cultural heritage with community empowerment-based conservation. Keywords: culture development planning, comprehensive planning, heritage cultural district, community empowerment-based conservation.

  18. Connecting Asian Heritage Conservation to the Idea of Performative Regionalism: A Case of Community-Enhancing Design Interventions in the Historical Art District of Liulichang Beijing

    Directory of Open Access Journals (Sweden)

    Diana Thamrin

    2015-02-01

    Full Text Available The active and sometimes ruthless modernisation in Asia has triggered an urgent need to secure the protection and continuation of its rich heritage and diverse regional attributes. However, as in the case of China, the Asian perspective of conservation is different from the West in terms of the nature or ways of design interventions produced and its purposes. This phenomenon has frequently triggered criticisms from heritage conservation professionals. Hence, the objective of this paper is to explore the interventions done on Asian heritage sites, taking the Liulichang Art District in Beijing as the case study, and analyze the positive influence they have brought. The paper starts by distinguishing the Asian concept and values of authenticity in conservation that differ from the West and how these principles have been applied in Liulichang, a famous ancient street known for the selling and practice of classical Chinese arts, mostly for Chinese painting. Using the phenomenological method of analysis, the paper further elaborates on the importance of community building in learning and appreciating the art of Chinese painting and discusses the positive impact made by the design interventions in Liulichang, particularly in terms of community engagement and creation of novel ways to accommodate traditional cultural practices of Chinese painting. Results reflect that the Asian perspective of conservation do not always follow the principle of minimum intervention favoured by the West, but how contemporary interventions could be merged into the heritage site to revive regional communities and cultural activities, connecting Asian architectural conservation with the design approach coined by Barbara Allen (2005 as Performative Regionalism, hence developing the idea and practice of this approach as a result of the discussion. Rather than merely following textual or scientific procedures like in the West, this approach requires a more experiential way of

  19. Evolutionary developmental psychology

    National Research Council Canada - National Science Library

    King, Ashley C; Bjorklund, David F

    2010-01-01

    The field of evolutionary developmental psychology can potentially broaden the horizons of mainstream evolutionary psychology by combining the principles of Darwinian evolution by natural selection...

  20. Assessment of soil erosion and conservation on agricultural sloping lands using plot data in the semi-arid hilly loess region of China

    Directory of Open Access Journals (Sweden)

    T.X. Zhu

    2014-11-01

    New hydrological insights for the region: The results revealed that runoff per unit area slightly increased with slope angle on SSP, but reached a maximum at 15° and then decreased with slope angle on LSP. Soil loss per unit area increased with slope angle on both SSP and LSP. An average of 36.4% less runoff but only 3.6% less soil loss per unit area was produced on LSP than on SSP. The S factor calculated using the slope factor equations in USLE/RUSLE was significantly greater than that estimated from the measured soil loss on the plots. Rainstorms with recurrence intervals greater than 2 years were responsible for more than two thirds of the total soil and water loss. The effectiveness in reducing surface runoff by five types of conservation practices was mixed. However, all the conservation practices yielded much less soil loss than cropland.

  1. Threats, conservation strategies, and prognosis for suckers (Catostomidae) in North America: insights from regional case studies of a diverse family of non-game fishes

    Science.gov (United States)

    Cooke, Steven J.; Bunt, Christopher M.; Hamilton, Steven J.; Jennings, Cecil A.; Pearson, Micheal P.; Cooperman, Michael S.; Markle, Douglas F.

    2005-01-01

    Catostomid fishes are a diverse family of 76+ freshwater species that are distributed across North America in many different habitats. This group of fish is facing a variety of impacts and conservation issues that are somewhat unique relative to more economically valuable and heavily managed fish species. Here, we present a brief series of case studies to highlight the threats such as migration barriers, flow regulation, environmental contamination, habitat degradation, exploitation and impacts from introduced (non-native) species that are facing catostomids in different regions. Collectively, the case studies reveal that individual species usually are not threatened by a single, isolated factor. Instead, species in general face numerous stressors that threaten multiple stages of their life history. Several factors have retarded sucker conservation including widespread inabilities of field workers to distinguish some species, lack of basic natural history and ecological knowledge of life history, and the misconception that suckers are tolerant of degraded conditions and are of little social or ecological value. Without a specific constituent group lobbying for conservation of non-game fishes, all such species, including members of the catostomid family, will continue to face serious risks because of neglect, ignorance, and misunderstanding. We suggest that conservation strategies should incorporate research and education/outreach components. Other conservation strategies that would be effective for protecting suckers include freshwater protected areas for critical habitat, restoration of degraded habitat, and design of catostomid-friendly fish bypass facilities. We believe that the plight of the catostomids is representative of the threats facing many other non-game freshwater fishes with diverse life-history strategies globally.

  2. Some assembly required: evolutionary and systems perspectives on the mammalian reproductive system.

    Science.gov (United States)

    Mordhorst, Bethany R; Wilson, Miranda L; Conant, Gavin C

    2016-01-01

    In this review, we discuss the way that insights from evolutionary theory and systems biology shed light on form and function in mammalian reproductive systems. In the first part of the review, we contrast the rapid evolution seen in some reproductive genes with the generally conservative nature of development. We discuss directional selection and coevolution as potential drivers of rapid evolution in sperm and egg proteins. Such rapid change is very different from the highly conservative nature of later embryo development. However, it is not unique, as some regions of the sex chromosomes also show elevated rates of evolutionary change. To explain these contradictory trends, we argue that it is not reproductive functions per se that induce rapid evolution. Rather, it is the fact that biotic interactions, such as speciation events and sexual conflict, have no evolutionary endpoint and hence can drive continuous evolutionary changes. Returning to the question of sex chromosome evolution, we discuss the way that recent advances in evolutionary genomics and systems biology and, in particular, the development of a theory of gene balance provide a better understanding of the evolutionary patterns seen on these chromosomes. We end the review with a discussion of a surprising and incompletely understood phenomenon observed in early embryos: namely the Warburg effect, whereby glucose is fermented to lactate and alanine rather than respired to carbon dioxide. We argue that evolutionary insights, from both yeasts and tumor cells, help to explain the Warburg effect, and that new metabolic modeling approaches are useful in assessing the potential sources of the effect.

  3. A computational method for identification of vaccine targets from protein regions of conserved human leukocyte antigen binding

    DEFF Research Database (Denmark)

    Olsen, Lars Rønn; Simon, Christian; Kudahl, Ulrich J.

    2015-01-01

    Background: Computational methods for T cell-based vaccine target discovery focus on selection of highly conserved peptides identified across pathogen variants, followed by prediction of their binding of human leukocyte antigen molecules. However, experimental studies have shown that T cells often...... the number of potential vaccine targets compared to the number of targets discovered using the traditional approach where low-frequency peptides are excluded. Conclusions: We developed a webserver with an intuitive visualization scheme for summarizing the T cell-based antigenic potential of any given protein...

  4. ADAPTIF CONSERVATION (ACM MODEL IN INCREASING FAMILY SUPPORT AND COMPLIANCE TREATMENT IN PATIENT WITH PULONARY TUBERCULOSIS IN SURABAYA CITY REGION

    Directory of Open Access Journals (Sweden)

    Siti Nur Kholifah

    2017-04-01

    Full Text Available Introduction: Tuberculosis (TB in Indonesia is still health problem and the prevalence rate is high. Discontinuing medication and lack of family support are the causalities. Numbers of strategies to overcome are seemingly not succeeded. Roles and responsibilities of family nursing are crucial to improve participation, motivation of individual, family and community in prevention, including pulmonary tuberculosis. Unfortunately, models of pulmonary tuberculosis currently unavailable. The combination of adaptation and conservation in complementarily improving family support and compliance in medication is introduced in this study. Method: This research intended to analyze Adaptive Conservation Model (ACM in extending family support and treatment compliance. Modeling steps including model analysis, expert validation, field trial, implementation and recommending the output model. Research subject involves 15 families who implement family Assistance and supervision in Medication (ASM and other 15 families with ACM. Result: The study revealed ACM is better than ASM on the case of family support and medication compliances. It supports the role of environment as influential factor on individual health belief, values and decision making. Therefore, it is advised to apply ACM in enhancing family support and compliance of pulmonary TB patients. Discussion: Social and family supports to ACM group obtained by developing interaction through communication. Family interaction necessary to improve family support to pulmonary tuberculosis patients. And social support plays as motivator to maintain compliance on medication

  5. 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.

  6. Conserved and species-specific alternative splicing in mammalian genomes

    Directory of Open Access Journals (Sweden)

    Favorov Alexander V

    2007-12-01

    Full Text Available Abstract Background Alternative splicing has been shown to be one of the major evolutionary mechanisms for protein diversification and proteome expansion, since a considerable fraction of alternative splicing events appears to be species- or lineage-specific. However, most studies were restricted to the analysis of cassette exons in pairs of genomes and did not analyze functionality of the alternative variants. Results We analyzed conservation of human alternative splice sites and cassette exons in the mouse and dog genomes. Alternative exons, especially minor-isofom ones, were shown to be less conserved than constitutive exons. Frame-shifting alternatives in the protein-coding regions are less conserved than frame-preserving ones. Similarly, the conservation of alternative sites is highest for evenly used alternatives, and higher when the distance between the sites is divisible by three. The rate of alternative-exon and site loss in mouse is slightly higher than in dog, consistent with faster evolution of the former. The evolutionary dynamics of alternative sites was shown to be consistent with the model of random activation of cryptic sites. Conclusion Consistent with other studies, our results show that minor cassette exons are less conserved than major-alternative and constitutive exons. However, our study provides evidence that this is caused not only by exon birth, but also lineage-specific loss of alternative exons and sites, and it depends on exon functionality.

  7. Conservation and promotion of the geological heritage in the «Ile-de-France» region (France): Establishment of a decision support-tool based on inventory

    Science.gov (United States)

    Auberger, Elise; Gély, Jean-Pierre; De Wever, Patrick; Merle, Didier

    2017-04-01

    Based on an initiative by the "Regional Commission of Geological Patrimony" (CRPG), the French state and the regional government of Ile-de-France co-financed the setting up of an inventory with the aim of safeguarding geological sites of patrimonial interest. This project forms part of larger scale policies, at the national and European level. Geological studies in the Paris region began as early as the 18th century, in the fields of cartography and paleontology. Later on, prominent scientists like G. Cuvier, A. Brongniart and A. d'Orbigny established the first concepts in sedimentology and stratigraphy through the description of Cenozoic fossil sites that rank amongst the richest in the world and geological formations in the Paris Basin. Eventually, later on, five historical stratotypes were established in the Ile-de-France region. Yet, at present, this geological heritage is constantly threatened by expanding urbanisation. To conserve this diverse geological patrimony, we have set up a protocol composed of 4 main actions: i) The exhaustive and objective referencing of geological sites in Ile-de-France. This information is centralised in a database, which currently comprises 639 sites (mainly of anthropic nature such as quarries) ii) The pre-selection of sites (298 out of the initial 639) based on sufficient accessibility and potential geological interest. iii) The use of a method of description and hierarchisation - following the guidelines of the National Geological Heritage Inventory Program (INPG) - on the pre-selected sites. iv) Establishment of a schedule specifying actions of geo-conservation which will take into account the patrimonial value of the sites, but also their threats, their juridical status and the socio-economic context of the region. The purpose of this program is to conserve a collection of geological sites that reflect the totality of the regional geology in Ile-de-France. The results of this study will be released to the general public and

  8. The high-resolution structure of activated opsin reveals a conserved solvent network in the transmembrane region essential for activation

    Science.gov (United States)

    Blankenship, Elise; Vahedi-Faridi, Ardeschir; Lodowski, David T.

    2015-01-01

    Rhodopsin, a light-activated G protein coupled receptor (GPCR), has been the subject of numerous biochemical and structural investigations, serving as a model receptor for GPCRs and their activation. Herein we present the 2.3 Å resolution structure of native-source rhodopsin stabilized in a conformation competent for G protein binding. An extensive water-mediated hydrogen bond network linking the chromophore binding site to the site of G protein binding is observed, providing connections to conserved motifs essential for GPCR activation. Comparison of this extensive solvent mediated hydrogen-bonding network to the positions of ordered solvent in earlier crystallographic structures of rhodopsin photointermediates reveals both static structural and dynamic functional water-protein interactions present during the activation process. When taken with observations that solvent occupies similar positions in the structures of other GPCRs, these analyses strongly support an integral role for this dynamic ordered water network in both rhodopsin and GPCR activation. PMID:26526852

  9. Correlation of microsynteny conservation and disease gene distribution in mammalian genomes

    Directory of Open Access Journals (Sweden)

    Li Xiting

    2009-11-01

    Full Text Available Abstract Background With the completion of the whole genome sequence for many organisms, investigations into genomic structure have revealed that gene distribution is variable, and that genes with similar function or expression are located within clusters. This clustering suggests that there are evolutionary constraints that determine genome architecture. However, as most of the evidence for constraints on genome evolution comes from studies on yeast, it is unclear how much of this prior work can be extrapolated to mammalian genomes. Therefore, in this work we wished to examine the constraints on regions of the mammalian genome containing conserved gene clusters. Results We first identified regions of the mouse genome with microsynteny conservation by comparing gene arrangement in the mouse genome to the human, rat, and dog genomes. We then asked if any particular gene types were found preferentially in conserved regions. We found a significant correlation between conserved microsynteny and the density of mouse orthologs of human disease genes, suggesting that disease genes are clustered in genomic regions of increased microsynteny conservation. Conclusion The correlation between microsynteny conservation and disease gene locations indicates that regions of the mouse genome with microsynteny conservation may contain undiscovered human disease genes. This study not only demonstrates that gene function constrains mammalian genome organization, but also identifies regions of the mouse genome that can be experimentally examined to produce mouse models of human disease.

  10. A perennial ryegrass CBF gene cluster is located in a region predicted by conserved synteny between Poaceae species.

    Science.gov (United States)

    Tamura, K; Yamada, T

    2007-01-01

    CBF/DREB1 proteins are the most important regulators of the cold temperature signaling pathway in many plants. CBF genes are candidates for low-temperature tolerance QTL in wheat and barley. Ten novel putative CBF cDNAs of perennial ryegrass (Lolium perenne L.) have been isolated from cold-treated leaf tissue. Their primary structures contain some conserved motifs, characteristic of the gene class. Phylogenetic analysis revealed that LpCBF genes were attributable to the HvCBF3-, and HvCBF4-subgroups following the previously proposed classification of barley CBF genes. RT-PCR analysis revealed that the expression of LpCBF genes was rapidly induced in response to low temperature and that the expression pattern under the low-temperature conditions for a long period was different between the various LpCBF genes. Five of the ten LpCBF genes were assigned to the genetic linkage map using the p150/112 reference mapping population. LpCBFIb, LpCBFII, LpCBFIIIb and LpCBFIIIc were mapped on LG5 forming a cluster within 2.2 cM, while LpCBFVb was located on LG1. Based on comparative genetic studies, conserved synteny for CBF gene family was observed between the Triticeae cereals and perennial ryegrass. Information on the perennial ryegrass CBF genes at both the molecular and genetic level obtained in this study would be useful for the further study on the role of CBF genes and low-temperature tolerance in grasses.

  11. Conserved microstructure of the Brassica B Genome of Brassica nigra in relation to homologous regions of Arabidopsis thaliana, B. rapa and B. oleracea

    Science.gov (United States)

    2013-01-01

    Background The Brassica B genome is known to carry several important traits, yet there has been limited analyses of its underlying genome structure, especially in comparison to the closely related A and C genomes. A bacterial artificial chromosome (BAC) library of Brassica nigra was developed and screened with 17 genes from a 222 kb region of A. thaliana that had been well characterised in both the Brassica A and C genomes. Results Fingerprinting of 483 apparently non-redundant clones defined physical contigs for the corresponding regions in B. nigra. The target region is duplicated in A. thaliana and six homologous contigs were found in B. nigra resulting from the whole genome triplication event shared by the Brassiceae tribe. BACs representative of each region were sequenced to elucidate the level of microscale rearrangements across the Brassica species divide. Conclusions Although the B genome species separated from the A/C lineage some 6 Mya, comparisons between the three paleopolyploid Brassica genomes revealed extensive conservation of gene content and sequence identity. The level of fractionation or gene loss varied across genomes and genomic regions; however, the greatest loss of genes was observed to be common to all three genomes. One large-scale chromosomal rearrangement differentiated the B genome suggesting such events could contribute to the lack of recombination observed between B genome species and those of the closely related A/C lineage. PMID:23586706

  12. Evolutionary Information Theory

    Directory of Open Access Journals (Sweden)

    Mark Burgin

    2013-04-01

    Full Text Available Evolutionary information theory is a constructive approach that studies information in the context of evolutionary processes, which are ubiquitous in nature and society. In this paper, we develop foundations of evolutionary information theory, building several measures of evolutionary information and obtaining their properties. These measures are based on mathematical models of evolutionary computations, machines and automata. To measure evolutionary information in an invariant form, we construct and study universal evolutionary machines and automata, which form the base for evolutionary information theory. The first class of measures introduced and studied in this paper is evolutionary information size of symbolic objects relative to classes of automata or machines. In particular, it is proved that there is an invariant and optimal evolutionary information size relative to different classes of evolutionary machines. As a rule, different classes of algorithms or automata determine different information size for the same object. The more powerful classes of algorithms or automata decrease the information size of an object in comparison with the information size of an object relative to weaker4 classes of algorithms or machines. The second class of measures for evolutionary information in symbolic objects is studied by introduction of the quantity of evolutionary information about symbolic objects relative to a class of automata or machines. To give an example of applications, we briefly describe a possibility of modeling physical evolution with evolutionary machines to demonstrate applicability of evolutionary information theory to all material processes. At the end of the paper, directions for future research are suggested.

  13. Results of the global conservation assessment of the freshwater crabs (Brachyura, Pseudothelphusidae and Trichodactylidae: The Neotropical region, with an update on diversity

    Directory of Open Access Journals (Sweden)

    Neil Cumberlidge

    2014-11-01

    Full Text Available The freshwater crabs of the Neotropics comprise 311 species in two families (Pseudothelphusidae and Trichodactylidae and one or both of these families are found in all of the countries in the Neotropical region (except for Chile and some of the Caribbean islands. Colombia (102 species, 81% endemic and Mexico (67 species, 95% endemic are the biodiversity hotspots of freshwater crab species richness and country-level endemism for this region. The results of the IUCN Red List conservation assessments show that 34% of pseudothelphusids and 10% of trichodactylids have an elevated risk of extinction, 29% of pseudothelphusids and 75% of trichodactylids are not at-risk (Least Concern, and although none are actually extinct, 56% of pseudothelphusids and 17% of trichodactylids are too poorly known to assess (Data Deficient. Colombia (14 species, Venezuela (7 species, Mexico (6 species, and Ecuador (5 species are the countries with the highest number of threatened species of Neotropical freshwater crabs. The majority of threatened species are restricted-range semiterrestrial endemics living in habitats subjected to deforestation, alteration of drainage patterns, and pollution. This underlines the need to prioritize and develop conservation measures before species decline to levels from which they cannot recover. These results represent a baseline that can be used to design strategies to save threatened Neotropical species of freshwater crabs.

  14. The alpha helix 1 from the first conserved region of HIV1 gp120 is reconstructed in the short NQ21 peptide.

    Science.gov (United States)

    Khrustalev, Vladislav Victorovich; Khrustaleva, Tatyana Aleksandrovna; Kahanouskaya, Ekaterina Yurievna; Rudnichenko, Yulia Anatolyevna; Bandarenka, Hanna Vitalyevna; Arutyunyan, Alexander Migranovich; Girel, Kseniya Victorovna; Khinevich, Nadia Vladimirovna; Ksenofontov, Alexander Leonidovich; Kordyukova, Larisa Valentinovna

    2018-01-15

    Investigations of short peptides that can be used in the next phase of synthetic HIV1 vaccine development are an urgent goal, as well as investigations of peptides that can be used in immunological tests with the aim to check the titer of antibodies against the alpha helix 1 from the first conserved region of HIV1 gp120 that are known to cause antibody-dependent cellular cytotoxicity (ADCC). The aim of this work was to study the structure of the NQ21 peptide corresponding to the less mutable part of the first conserved region of HIV1 gp120 (residues 94-114). The NQ21 peptide and its conjugate with biotin (biotin-NQ21) are absolutely alpha-helical in phosphate buffer solutions at pH = 6.8, 7.4 and 8.0, as well as in the dried form, according to the results of surface-enhanced Raman scattering (SERS) spectroscopy. Results of the native gel electrophoresis and thermal analysis under the control of spectrofluorometer and near UV circular dichroism (CD) showed that the peptide exists in form of octamers and tetramers at pH = 7.4, that is important information for further vaccine development. Strong signal of interacting Trp residues in oligomers in the far UV CD obscures the signal from secondary structure, but becomes less intensive during the heating. Copyright © 2017 Elsevier Inc. All rights reserved.

  15. Thermal environment analysis and energy conservation research of rural residence in cold regions of China based on BIM platform

    Science.gov (United States)

    Dong, J. Y.; Cheng, W.; Ma, C. P.; Xin, L. S.; Tan, Y. T.

    2017-06-01

    In order to study the issue of rural residential energy consumption in cold regions of China, modeled an architecture prototype based on BIM platform according to the affecting factors of rural residential thermal environment, and imported the virtual model which contains building information into energy analysis tools and chose the appropriate building orientation. By analyzing the energy consumption of the residential buildings with different enclosure structure forms, we designed the optimal energy-saving residence form. There is a certain application value of this method for researching the energy consumption and energy-saving design for the rural residence in cold regions of China.

  16. Analysis of the cat eye syndrome critical region in humans and the region of conserved synteny in mice: a search for candidate genes at or near the human chromosome 22 pericentromere.

    Science.gov (United States)

    Footz, T K; Brinkman-Mills, P; Banting, G S; Maier, S A; Riazi, M A; Bridgland, L; Hu, S; Birren, B; Minoshima, S; Shimizu, N; Pan, H; Nguyen, T; Fang, F; Fu, Y; Ray, L; Wu, H; Shaull, S; Phan, S; Yao, Z; Chen, F; Huan, A; Hu, P; Wang, Q; Loh, P; Qi, S; Roe, B A; McDermid, H E

    2001-06-01

    We have sequenced a 1.1-Mb region of human chromosome 22q containing the dosage-sensitive gene(s) responsible for cat eye syndrome (CES) as well as the 450-kb homologous region on mouse chromosome 6. Fourteen putative genes were identified within or adjacent to the human CES critical region (CESCR), including three known genes (IL-17R, ATP6E, and BID) and nine novel genes, based on EST identity. Two putative genes (CECR3 and CECR9) were identified, in the absence of EST hits, by comparing segments of human and mouse genomic sequence around two solitary amplified exons, thus showing the utility of comparative genomic sequence analysis in identifying transcripts. Of the 14 genes, 10 were confirmed to be present in the mouse genomic sequence in the same order and orientation as in human. Absent from the mouse region of conserved synteny are CECR1, a promising CES candidate gene from the center of the contig, neighboring CECR4, and CECR7 and CECR8, which are located in the gene-poor proximal 400 kb of the contig. This latter proximal region, located approximately 1 Mb from the centromere, shows abundant duplicated gene fragments typical of pericentromeric DNA. The margin of this region also delineates the boundary of conserved synteny between the CESCR and mouse chromosome 6. Because the proximal CESCR appears abundant in duplicated segments and, therefore, is likely to be gene poor, we consider the putative genes identified in the distal CESCR to represent the majority of candidate genes for involvement in CES.

  17. G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae.

    Science.gov (United States)

    Capra, John A; Paeschke, Katrin; Singh, Mona; Zakian, Virginia A

    2010-07-22

    G-quadruplex DNA is a four-stranded DNA structure formed by non-Watson-Crick base pairing between stacked sets of four guanines. Many possible functions have been proposed for this structure, but its in vivo role in the cell is still largely unresolved. We carried out a genome-wide survey of the evolutionary conservation of regions with the potential to form G-quadruplex DNA structures (G4 DNA motifs) across seven yeast species. We found that G4 DNA motifs were significantly more conserved than expected by chance, and the nucleotide-level conservation patterns suggested that the motif conservation was the result of the formation of G4 DNA structures. We characterized the association of conserved and non-conserved G4 DNA motifs in Saccharomyces cerevisiae with more than 40 known genome features and gene classes. Our comprehensive, integrated evolutionary and functional analysis confirmed the previously observed associations of G4 DNA motifs with promoter regions and the rDNA, and it identified several previously unrecognized associations of G4 DNA motifs with genomic features, such as mitotic and meiotic double-strand break sites (DSBs). Conserved G4 DNA motifs maintained strong associations with promoters and the rDNA, but not with DSBs. We also performed the first analysis of G4 DNA motifs in the mitochondria, and surprisingly found a tenfold higher concentration of the motifs in the AT-rich yeast mitochondrial DNA than in nuclear DNA. The evolutionary conservation of the G4 DNA motif and its association with specific genome features supports the hypothesis that G4 DNA has in vivo functions that are under evolutionary constraint.

  18. G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    John A Capra

    2010-07-01

    Full Text Available G-quadruplex DNA is a four-stranded DNA structure formed by non-Watson-Crick base pairing between stacked sets of four guanines. Many possible functions have been proposed for this structure, but its in vivo role in the cell is still largely unresolved. We carried out a genome-wide survey of the evolutionary conservation of regions with the potential to form G-quadruplex DNA structures (G4 DNA motifs across seven yeast species. We found that G4 DNA motifs were significantly more conserved than expected by chance, and the nucleotide-level conservation patterns suggested that the motif conservation was the result of the formation of G4 DNA structures. We characterized the association of conserved and non-conserved G4 DNA motifs in Saccharomyces cerevisiae with more than 40 known genome features and gene classes. Our comprehensive, integrated evolutionary and functional analysis confirmed the previously observed associations of G4 DNA motifs with promoter regions and the rDNA, and it identified several previously unrecognized associations of G4 DNA motifs with genomic features, such as mitotic and meiotic double-strand break sites (DSBs. Conserved G4 DNA motifs maintained strong associations with promoters and the rDNA, but not with DSBs. We also performed the first analysis of G4 DNA motifs in the mitochondria, and surprisingly found a tenfold higher concentration of the motifs in the AT-rich yeast mitochondrial DNA than in nuclear DNA. The evolutionary conservation of the G4 DNA motif and its association with specific genome features supports the hypothesis that G4 DNA has in vivo functions that are under evolutionary constraint.

  19. Control regions for chromosome replication are conserved with respect to both sequence and location between Escherichia coli strains

    DEFF Research Database (Denmark)

    Frimodt-Møller, Jakob; Charbon, Godefroid; Krogfelt, Karen Angeliki

    2015-01-01

    In Escherichia coli, chromosome replication is initiated from oriC by the DnaA initiator protein associated with ATP. Three non-coding regions contribute to the activity of DnaA. The datA locus is instrumental in conversion of DnaAATP to DnaAADP (DDAH; datA dependent DnaAATP hydrolysis) whereas Dna...

  20. Conservation in the first internal transcribed spacer (ITS1) region of Hematodinium perezi (genotype III) from Callinectes sapidus .

    Science.gov (United States)

    Pagenkopp Lohan, Katrina M; Small, Hamish J; Shields, Jeffrey D; Place, Allen R; Reece, Kimberly S

    2013-03-13

    Hematodinium spp. infections have been reported from blue crabs Callinectes sapidus in high-salinity waters of the USA from New Jersey to Texas. Recently, H. perezi (genotype III) has been proposed as the parasite species and genotype infecting blue crabs from Virginia; however, it is unknown whether this same genotype is present in blue crabs from other locations. To address this question, we collected 317 blue crabs from Massachusetts, Virginia, Georgia, Florida, Louisiana, and Texas to test for the presence of H. perezi (III) using a specific PCR assay targeting the first internal transcribed spacer (ITS1) region of the ribosomal RNA gene complex. To examine the genetic variation within H. perezi (III), ITS1 region sequences from the parasite in blue crabs from multiple locations were compared to each other and to those of H. perezi (III) found in alternate hosts from Virginia. In total, 34 distinct ITS1 sequence variants of the parasite were identified from blue crabs alone, and 38 distinct variants were identified when alternate hosts were included. However, a single ITS1 sequence variant appeared in all geographic regions and hosts, and also in blue crabs sampled from a previous study. The high similarity among all the ITS1 region sequences examined (>98%) and the observation of a single variant found throughout a large geographic range, strongly suggests that a single species and genotype of Hematodinium, specifically H. perezi (III), infects blue crabs from Virginia to Texas and multiple alternate host species in Virginia.

  1. A single conserved basic residue in the potassium channel filter region controls KCNQ1 insensitivity toward scorpion toxins.

    Science.gov (United States)

    Chen, Zongyun; Hu, Youtian; Wang, Bin; Cao, Zhijian; Li, Wenxin; Wu, Yingliang

    2015-09-01

    Although many studies concerning the sensitivity mechanism of scorpion toxin-potassium channel interactions have been reported, few have explored the biochemical insensitivity mechanisms of potassium channel receptors toward natural scorpion toxin peptides, such as the KCNQ1 channel. Here, by sequence alignment analyses of the human KCNQ1 channel and scorpion potassium channel MmKv2, which is completely insensitive to scorpion toxins, we proposed that the insensitivity mechanism of KCNQ1 toward natural scorpion toxins might involve two functional regions, the turret and filter regions. Based on this observation, a series of KCNQ1 mutants were constructed to study molecular mechanisms of the KCNQ1 channel insensitivity toward natural scorpion toxins. Electrophysiological studies of chimera channels showed that the channel filter region controls KCNQ1 insensitivity toward the classical scorpion toxin ChTX. Interestingly, further residue mutant experiments showed that a single basic residue in the filter region determined the insensitivity of KCNQ1 channels toward scorpion toxins. Our present work showed that amino acid residue diversification at common sites controls the sensitivity and insensitivity of potassium channels toward scorpion toxins. The unique insensitivity mechanism of KCNQ1 toward natural scorpion toxins will accelerate the rational design of potent peptide inhibitors toward this channel.

  2. Simple Shared Motifs (SSM in conserved region of promoters: a new approach to identify co-regulation patterns

    Directory of Open Access Journals (Sweden)

    Théret Nathalie

    2011-09-01

    Full Text Available Abstract Background Regulation of gene expression plays a pivotal role in cellular functions. However, understanding the dynamics of transcription remains a challenging task. A host of computational approaches have been developed to identify regulatory motifs, mainly based on the recognition of DNA sequences for transcription factor binding sites. Recent integration of additional data from genomic analyses or phylogenetic footprinting has significantly improved these methods. Results Here, we propose a different approach based on the compilation of Simple Shared Motifs (SSM, groups of sequences defined by their length and similarity and present in conserved sequences of gene promoters. We developed an original algorithm to search and count SSM in pairs of genes. An exceptional number of SSM is considered as a common regulatory pattern. The SSM approach is applied to a sample set of genes and validated using functional gene-set enrichment analyses. We demonstrate that the SSM approach selects genes that are over-represented in specific biological categories (Ontology and Pathways and are enriched in co-expressed genes. Finally we show that genes co-expressed in the same tissue or involved in the same biological pathway have increased SSM values. Conclusions Using unbiased clustering of genes, Simple Shared Motifs analysis constitutes an original contribution to provide a clearer definition of expression networks.

  3. Regional estimates of ecological services derived from U.S. Department of Agriculture conservation programs in the Mississippi Alluvial Valley

    Science.gov (United States)

    Faulkner, Stephen P.; Baldwin, Michael J.; Barrow, Wylie C.; Waddle, Hardin; Keeland, Bobby D.; Walls, Susan C.; James, Dale; Moorman, Tom

    2010-01-01

    The Mississippi Alluvial Valley (MAV) is the Nation?s largest floodplain and this once predominantly forested ecosystem provided significant habitat for a diverse flora and fauna, sequestered carbon in trees and soil, and stored floodwater, sediments, and nutrients within the floodplain. This landscape has been substantially altered by the conversion of nearly 75% of the riparian forests, predominantly to agricultural cropland, with significant loss and degradation of important ecosystem services. Large-scale efforts have been employed to restore the forest and wetland resources and the U.S. Department of Agriculture (USDA) Wetlands Reserve Program (WRP) and Conservation Reserve Program (CRP) represent some of the most extensive restoration programs in the MAV. The objective of the WRP is to restore and protect the functions and values of wetlands in agricultural landscapes with an emphasis on habitat for migratory birds and wetland-dependent wildlife, protection and improvement of water quality, flood attenuation, ground water recharge, protection of native flora and fauna, and educational and scientific scholarship.

  4. Conserved genetic regions across angiosperms as tools to develop single-copy nuclear markers in gymnosperms: an example using cycads.

    Science.gov (United States)

    Salas-Leiva, Dayana E; Meerow, Alan W; Francisco-Ortega, Javier; Calonje, Michael; Griffith, M Patrick; Stevenson, Dennis W; Nakamura, Kyoko

    2014-07-01

    Several individuals of the Caribbean Zamia clade and other cycad genera were used to identify single-copy nuclear genes for phylogeographic and phylogenetic studies in Cycadales. Two strategies were employed to select target loci: (i) a tblastX search of Arabidopsis conserved ortholog sequence (COS) set and (ii) a tblastX search of Arabidopsis-Populus-Vitis-Oryza Shared Single-Copy genes (APVO SSC) against the EST Zamia databases in GenBank. From the first strategy, 30 loci were selected, and from the second, 16 loci. In both cases, the matching GenBank accessions of Zamia were used as a query for retrieving highly similar sequences from Cycas, Picea, Pinus species or Ginkgo biloba. After retrieving and aligning all the sequences in each locus, intron predictions were completed to assist in primer design. PCR was carried out in three rounds to detect paralogous loci. A total of 29 loci were successfully amplified as a single band of which 20 were likely single-copy loci. These loci showed different diversity and divergence levels. A preliminary screening allowed us to select 8 promising loci (40S, ATG2, BG, GroES, GTP, LiSH, PEX4 and TR) for the Zamia pumila complex and 4 loci (COS26, GroES, GTP and HTS) for all other cycad genera. Published 2014. This article is a U.S. Government work and is in the public domain in the U.S.A.

  5. Advances in universal influenza virus vaccine design and antibody mediated therapies based on conserved regions of the hemagglutinin.

    Science.gov (United States)

    Krammer, Florian; Palese, Peter; Steel, John

    2015-01-01

    The threat of novel influenza viruses emerging into the human population from animal reservoirs, as well as the short duration of protection conferred by licensed vaccines against human seasonal strains has spurred research efforts to improve upon current vaccines and develop novel therapeutics against influenza viruses. In recent years these efforts have resulted in the identification of novel, highly conserved epitopes for neutralizing antibodies on the influenza virus hemagglutinin protein, which are present in both the stalk and globular head domains of the molecule. The existence of such epitopes may allow for generation of novel therapeutic antibodies, in addition to serving as attractive targets of novel vaccine design. The aims of developing improved vaccines include eliciting broader protection from drifted strains, inducing long-lived immunity against seasonal strains, and allowing for the rational design of vaccines that can be stockpiled for use as pre-pandemic vaccines. In addition, an increased focus on influenza virus vaccine research has prompted an improved understanding of how the immune system responds to influenza virus infection.

  6. Molecular Dynamics Simulations of the STAS Domains of Rat Prestin and Human Pendrin Reveal Conformational Motions in Conserved Flexible Regions

    Directory of Open Access Journals (Sweden)

    Alok K. Sharma

    2014-02-01

    Full Text Available Background: Molecular dynamics (MD simulations provide valuable information on the conformational changes that accompany time-dependent motions in proteins. The reported crystal structure of rat prestin (PDB 3LLO is remarkable for an α1-α2 inter-helical angle that differs substantially from those observed in bacterial STAS domains of SulP anion transporters and anti-sigma factor antagonists. However, NMR data on the rat prestin STAS domain in solution suggests dynamic features at or near the α1-α2 helical region (Pasqualetto et al JMB, 2010. We therefore performed a 100 ns 300K MD simulation study comparing the STAS domains of rat prestin and (modeled human pendrin, to explore possible conformational flexibility in the region of the α1 and α2 helices. Methods: The conformation of the loop missing in the crystal structure of rat prestin STAS (11 amino acids between helix α1 and strand β3 was built using Modeller. MD simulations were performed with GROMACSv4.6 using GROMOS96 53a6 all-atom force field. Results: A subset of secondary structured elements of the STAS domains exhibits significant conformational changes during the simulation time course. The conformationally perturbed segments include the majority of loop regions, as well as the α1 and α2 helices. A significant decrease in the α1-α2 inter-helical angle observed across the simulation trajectory leads to closer helical packing at their C-termini. The end-simulation conformations of the prestin and pendrin STAS domains, including their decreased α1-α2 inter-helical angles, resemble more closely the packing of corresponding helices in the STAS structures of bacterial SulP transporters Rv1739c and ychM, as well as those of the anti-sigma factor antagonists. Several structural segments of the modeled human pendrin STAS domain exhibit larger atomic motions and greater conformational deviations than the corresponding regions of rat prestin, predicting that the human pendrin STAS

  7. When theory trumps ideology: Lessons from evolutionary psychology.

    Science.gov (United States)

    Tybur, Joshua M; Navarrete, Carlos David

    2015-01-01

    Evolutionary psychologists are personally liberal, just as social psychologists are. Yet their research has rarely been perceived as liberally biased--if anything, it has been erroneously perceived as motivated by conservative political agendas. Taking a closer look at evolutionary psychologists might offer the broader social psychology community guidance in neutralizing some of the biases Duarte et al. discuss.

  8. Diversity, natural history and conservation of amphibians and reptiles from the San Vito Region, southwestern Costa Rica

    OpenAIRE

    Santos Barrera, Georgina; Pacheco, Jesus; Mendoza Quijano, Fernando; Bolaños, Federico; Cháves, Gerardo; C. Daily, Gretchen; R. Eirlich, Paul; Ceballos, Gerardo

    2007-01-01

    We present an inventory of the amphibians and reptiles of the San Vito de Coto Brus region, including the Las Cruces Biological Station, in southern Costa Rica, which is the result of a survey of the herpetofauna occurring in mountain forest fragments, pastures, coffee plantations, and other disturbed areas. We found 67 species, included 26 species of amphibians and of 41 of reptiles. We describe the distribution patterns of the community on the basis of the life zones, elevation, fragmentati...

  9. Characteristics of water erosion and conservation practice in arid regions of Central Asia: Xinjiang Province, China as an example

    OpenAIRE

    Zhang, Wentai; Zhou, Jianqin; Feng, Guanglong; Weindorf, David C.; Hu, Guiqing; Sheng, Jiandong

    2015-01-01

    Located in the inland arid area of Central Asia and northwest China, Xinjiang has recently received heightened concerns over soil water erosion, which is highly related with the sustainable utilization of barren soil and limited water resources. Data from the national soil erosion survey of China (1985–2011) and Xinjiang statistical yearbook (2000–2010) was used to analyze the trend, intensity, and serious soil water erosion regions. Results showed that the water erosion area in Xinjiang was ...

  10. Preferential Targeting of Conserved Gag Regions after Vaccination with a Heterologous DNA Prime-Modified Vaccinia Virus Ankara Boost HIV-1 Vaccine Regimen.

    Science.gov (United States)

    Bauer, Asli; Podola, Lilli; Mann, Philipp; Missanga, Marco; Haule, Antelmo; Sudi, Lwitiho; Nilsson, Charlotta; Kaluwa, Bahati; Lueer, Cornelia; Mwakatima, Maria; Munseri, Patricia J; Maboko, Leonard; Robb, Merlin L; Tovanabutra, Sodsai; Kijak, Gustavo; Marovich, Mary; McCormack, Sheena; Joseph, Sarah; Lyamuya, Eligius; Wahren, Britta; Sandström, Eric; Biberfeld, Gunnel; Hoelscher, Michael; Bakari, Muhammad; Kroidl, Arne; Geldmacher, Christof

    2017-09-15

    Prime-boost vaccination strategies against HIV-1 often include multiple variants for a given immunogen for better coverage of the extensive viral diversity. To study the immunologic effects of this approach, we characterized breadth, phenotype, function, and specificity of Gag-specific T cells induced by a DNA-prime modified vaccinia virus Ankara (MVA)-boost vaccination strategy, which uses mismatched Gag immunogens in the TamoVac 01 phase IIa trial. Healthy Tanzanian volunteers received three injections of the DNA-SMI vaccine encoding a subtype B and AB-recombinant Gagp37 and two vaccinations with MVA-CMDR encoding subtype A Gagp55 Gag-specific T-cell responses were studied in 42 vaccinees using fresh peripheral blood mononuclear cells. After the first MVA-CMDR boost, vaccine-induced gamma interferon-positive (IFN-γ+) Gag-specific T-cell responses were dominated by CD4+ T cells (P viruses. While including multiple variants for a given immunogen in prime-boost vaccination strategies is one approach that aims to improve coverage for global virus variants, the immunologic consequences of this strategy have been poorly defined so far. It is unclear whether inclusion of multiple variants in prime-boost vaccination strategies improves recognition of variant viruses by T cells and by which mechanisms this would be achieved, either by improved cross-recognition of multiple variants for a given antigenic region or through preferential targeting of antigenic regions more conserved between prime and boost. Engineering vaccines to induce adaptive immune responses that preferentially target conserved antigenic regions of viral vulnerability might facilitate better immune control after preventive and therapeutic vaccination for HIV and for other variable viruses. Copyright © 2017 American Society for Microbiology.

  11. Mutations within a conserved region of the hepatitis C virus E2 glycoprotein that influence virus-receptor interactions and sensitivity to neutralizing antibodies.

    Science.gov (United States)

    Dhillon, Simrat; Witteveldt, Jeroen; Gatherer, Derek; Owsianka, Ania M; Zeisel, Mirjam B; Zahid, Muhammad N; Rychłowska, Malgorzata; Foung, Steven K H; Baumert, Thomas F; Angus, Allan G N; Patel, Arvind H

    2010-06-01

    Cell culture-adaptive mutations within the hepatitis C virus (HCV) E2 glycoprotein have been widely reported. We identify here a single mutation (N415D) in E2 that arose during long-term passaging of HCV strain JFH1-infected cells. This mutation was located within E2 residues 412 to 423, a highly conserved region that is recognized by several broadly neutralizing antibodies, including the mouse monoclonal antibody (MAb) AP33. Introduction of N415D into the wild-type (WT) JFH1 genome increased the affinity of E2 to the CD81 receptor and made the virus less sensitive to neutralization by an antiserum to another essential entry factor, SR-BI. Unlike JFH1(WT), the JFH1(N415D) was not neutralized by AP33. In contrast, it was highly sensitive to neutralization by patient-derived antibodies, suggesting an increased availability of other neutralizing epitopes on the virus particle. We included in this analysis viruses carrying four other single mutations located within this conserved E2 region: T416A, N417S, and I422L were cell culture-adaptive mutations reported previously, while G418D was generated here by growing JFH1(WT) under MAb AP33 selective pressure. MAb AP33 neutralized JFH1(T416A) and JFH1(I422L) more efficiently than the WT virus, while neutralization of JFH1(N417S) and JFH1(G418D) was abrogated. The properties of all of these viruses in terms of receptor reactivity and neutralization by human antibodies were similar to JFH1(N415D), highlighting the importance of the E2 412-423 region in virus entry.

  12. Interactive effects of climate change with nutrients, mercury, and freshwater acidification on key taxa in the North Atlantic Landscape Conservation Cooperative region

    Science.gov (United States)

    Pinkney, Alfred E.; Driscoll, Charles T.; Evers, David C.; Hooper, Michael J.; Horan, Jeffrey; Jones, Jess W.; Lazarus, Rebecca S.; Marshall, Harold G.; Milliken, Andrew; Rattner, Barnett A.; Schmerfeld, John J.; Sparling, Donald W.

    2015-01-01

    The North Atlantic Landscape Conservation Cooperative LCC (NA LCC) is a public–private partnership that provides information to support conservation decisions that may be affected by global climate change (GCC) and other threats. The NA LCC region extends from southeast Virginia to the Canadian Maritime Provinces. Within this region, the US National Climate Assessment documented increases in air temperature, total precipitation, frequency of heavy precipitation events, and rising sea level, and predicted more drastic changes. Here, we synthesize literature on the effects of GCC interacting with selected contaminant, nutrient, and environmental processes to adversely affect natural resources within this region. Using a case study approach, we focused on 3 stressors with sufficient NA LCC region-specific information for an informed discussion. We describe GCC interactions with a contaminant (Hg) and 2 complex environmental phenomena—freshwater acidification and eutrophication. We also prepared taxa case studies on GCC- and GCC-contaminant/nutrient/process effects on amphibians and freshwater mussels. Several avian species of high conservation concern have blood Hg concentrations that have been associated with reduced nesting success. Freshwater acidification has adversely affected terrestrial and aquatic ecosystems in the Adirondacks and other areas of the region that are slowly recovering due to decreased emissions of N and sulfur oxides. Eutrophication in many estuaries within the region is projected to increase from greater storm runoff and less denitrification in riparian wetlands. Estuarine hypoxia may be exacerbated by increased stratification. Elevated water temperature favors algal species that produce harmful algal blooms (HABs). In several of the region's estuaries, HABs have been associated with bird die-offs. In the NA LCC region, amphibian populations appear to be declining. Some species may be adversely affected by GCC through higher temperatures

  13. Interactive effects of climate change with nutrients, mercury, and freshwater acidification on key taxa in the North Atlantic Landscape Conservation Cooperative region.

    Science.gov (United States)

    Pinkney, Alfred E; Driscoll, Charles T; Evers, David C; Hooper, Michael J; Horan, Jeffrey; Jones, Jess W; Lazarus, Rebecca S; Marshall, Harold G; Milliken, Andrew; Rattner, Barnett A; Schmerfeld, John; Sparling, Donald W

    2015-07-01

    The North Atlantic Landscape Conservation Cooperative LCC (NA LCC) is a public-private partnership that provides information to support conservation decisions that may be affected by global climate change (GCC) and other threats. The NA LCC region extends from southeast Virginia to the Canadian Maritime Provinces. Within this region, the US National Climate Assessment documented increases in air temperature, total precipitation, frequency of heavy precipitation events, and rising sea level, and predicted more drastic changes. Here, we synthesize literature on the effects of GCC interacting with selected contaminant, nutrient, and environmental processes to adversely affect natural resources within this region. Using a case study approach, we focused on 3 stressors with sufficient NA LCC region-specific information for an informed discussion. We describe GCC interactions with a contaminant (Hg) and 2 complex environmental phenomena-freshwater acidification and eutrophication. We also prepared taxa case studies on GCC- and GCC-contaminant/nutrient/process effects on amphibians and freshwater mussels. Several avian species of high conservation concern have blood Hg concentrations that have been associated with reduced nesting success. Freshwater acidification has adversely affected terrestrial and aquatic ecosystems in the Adirondacks and other areas of the region that are slowly recovering due to decreased emissions of N and sulfur oxides. Eutrophication in many estuaries within the region is projected to increase from greater storm runoff and less denitrification in riparian wetlands. Estuarine hypoxia may be exacerbated by increased stratification. Elevated water temperature favors algal species that produce harmful algal blooms (HABs). In several of the region's estuaries, HABs have been associated with bird die-offs. In the NA LCC region, amphibian populations appear to be declining. Some species may be adversely affected by GCC through higher temperatures and

  14. Confronting and resolving competing values behind conservation objectives.

    Science.gov (United States)

    Karp, Daniel S; Mendenhall, Chase D; Callaway, Elizabeth; Frishkoff, Luke O; Kareiva, Peter M; Ehrlich, Paul R; Daily, Gretchen C

    2015-09-01

    Diverse motivations for preserving nature both inspire and hinder its conservation. Optimal conservation strategies may differ radically depending on the objective. For example, creating nature reserves may prevent extinctions through protecting severely threatened species, whereas incentivizing farmland hedgerows may benefit people through bolstering pest-eating or pollinating species. Win-win interventions that satisfy multiple objectives are alluring, but can also be elusive. To achieve better outcomes, we developed and implemented a practical typology of nature conservation framed around seven common conservation objectives. Using an intensively studied bird assemblage in southern Costa Rica as a case study, we applied the typology in the context of biodiversity's most pervasive threat: habitat conversion. We found that rural habitats in a varied tropical landscape, comprising small farms, villages, forest fragments, and forest reserves, provided biodiversity-driven processes that benefit people, such as pollination, seed dispersal, and pest consumption. However, species valued for their rarity, endemism, and evolutionary distinctness declined in farmland. Conserving tropical forest on farmland increased species that international tourists value, but not species discussed in Costa Rican newspapers. Despite these observed trade-offs, our analyses also revealed promising synergies. For example, we found that maintaining forest cover surrounding farms in our study region would likely enhance most conservation objectives at minimal expense to others. Overall, our typology provides a framework for resolving the competing objectives of modern conservation.

  15. A practical study for Treatment and Conservation a group of Silver Coins from Dhamar Regional Museum, Dhamar, Yemen.

    OpenAIRE

    Mohamed M. Megahed

    2014-01-01

    A big group of silver coins{35 coins} was discovered in Banawa excavation , Dhamar , season 2002, and now it is situated in Dhamar Regional Museum ,Yemen. They were covered with a thin grey and black corrosion layers that disfigured them and hid their figures and inscriptions , also Some coins miss parts and others lost their circular.The aims of this work are identified the metallic composition of the coins , investigate the nature of corrosion grown during the long-term burial and identify ...

  16. The Commercial Districts by Lombardia Region and Municipality of Milan to sustain commercial services in the conservation areas

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    Luca Tamini

    2009-12-01

    Full Text Available Commerce plays a social protection role and can give quality to a city and a community or subtract from it and attribute meaning and character to places or render them banal in a standardised landscape. Intervention to improve shops and businesses open to the public can support more general urban regeneration processes and may be implemented through public policies. The Lombardy Region has recently organised a competition for funding of projects which improve commercial activities and public establishments in geographical areas identified as business districts (urban or more regional. The organiser of the project which involves businesses and the local context they are set in is the municipality, which, however, is obliged to apply in partnership with at least that association which represents most of the businesses operating in commerce. The mix of commerce, crafts and innovative service industries is a specific trait of the Milan metropolitan area which is described as a possible area in which to activate urban regeneration processes.

  17. Aligning science and policy to achieve evolutionarily enlightened conservation.

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    Cook, Carly N; Sgrò, Carla M

    2017-06-01

    There is increasing recognition among conservation scientists that long-term conservation outcomes could be improved through better integration of evolutionary theory into management practices. Despite concerns that the importance of key concepts emerging from evolutionary theory (i.e., evolutionary principles and processes) are not being recognized by managers, there has been little effort to determine the level of integration of evolutionary theory into conservation policy and practice. We assessed conservation policy at 3 scales (international, national, and provincial) on 3 continents to quantify the degree to which key evolutionary concepts, such as genetic diversity and gene flow, are being incorporated into conservation practice. We also evaluated the availability of clear guidance within the applied evolutionary biology literature as to how managers can change their management practices to achieve better conservation outcomes. Despite widespread recognition of the importance of maintaining genetic diversity, conservation policies provide little guidance about how this can be achieved in practice and other relevant evolutionary concepts, such as inbreeding depression, are mentioned rarely. In some cases the poor integration of evolutionary concepts into management reflects a lack of decision-support tools in the literature. Where these tools are available, such as risk-assessment frameworks, they are not being adopted by conservation policy makers, suggesting that the availability of a strong evidence base is not the only barrier to evolutionarily enlightened management. We believe there is a clear need for more engagement by evolutionary biologists with policy makers to develop practical guidelines that will help managers make changes to conservation practice. There is also an urgent need for more research to better understand the barriers to and opportunities for incorporating evolutionary theory into conservation practice. © 2016 Society for Conservation

  18. Understanding the distribution of marine megafauna in the English channel region: identifying key habitats for conservation within the busiest seaway on earth.

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    McClellan, Catherine M; Brereton, Tom; Dell'Amico, Florence; Johns, David G; Cucknell, Anna-C; Patrick, Samantha C; Penrose, Rod; Ridoux, Vincent; Solandt, Jean-Luc; Stephan, Eric; Votier, Stephen C; Williams, Ruth; Godley, Brendan J

    2014-01-01

    The temperate waters of the North-Eastern Atlantic have a long history of maritime resource richness and, as a result, the European Union is endeavouring to maintain regional productivity and biodiversity. At the intersection of these aims lies potential conflict, signalling the need for integrated, cross-border management approaches. This paper focuses on the marine megafauna of the region. This guild of consumers was formerly abundant, but is now depleted and protected under various national and international legislative structures. We present a meta-analysis of available megafauna datasets using presence-only distribution models to characterise suitable habitat and identify spatially-important regions within the English Channel and southern bight of the North Sea. The integration of studies from dedicated and opportunistic observer programmes in the United Kingdom and France provide a valuable perspective on the spatial and seasonal distribution of various taxonomic groups, including large pelagic fishes and sharks, marine mammals, seabirds and marine turtles. The Western English Channel emerged as a hotspot of biodiversity for megafauna, while species richness was low in the Eastern English Channel. Spatial conservation planning is complicated by the highly mobile nature of marine megafauna, however they are important components of the marine environment and understanding their distribution is a first crucial step toward their inclusion into marine ecosystem management.

  19. ROCC, a conserved region in cohesin's Mcd1 subunit, is essential for the proper regulation of the maintenance of cohesion and establishment of condensation

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    Eng, Thomas; Guacci, Vincent; Koshland, Doug

    2014-01-01

    Cohesin helps orchestrate higher-order chromosome structure, thereby promoting sister chromatid cohesion, chromosome condensation, DNA repair, and transcriptional regulation. To elucidate how cohesin facilitates these diverse processes, we mutagenized Mcd1p, the kleisin regulatory subunit of budding yeast cohesin. In the linker region of Mcd1p, we identified a novel evolutionarily conserved 10–amino acid cluster, termed the regulation of cohesion and condensation (ROCC) box. We show that ROCC promotes cohesion maintenance by protecting a second activity of cohesin that is distinct from its stable binding to chromosomes. The existence of this second activity is incompatible with the simple embrace mechanism of cohesion. In addition, we show that the ROCC box is required for the establishment of condensation. We provide evidence that ROCC controls cohesion maintenance and condensation establishment through differential functional interactions with Pds5p and Wpl1p. PMID:24966169

  20. The non-random clustering of non-synonymous substitutions and its relationship to evolutionary rate

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    Stone Eric A

    2011-08-01

    Full Text Available Abstract Background Protein sequences are subject to a mosaic of constraint. Changes to functional domains and buried residues, for example, are more apt to disrupt protein structure and function than are changes to residues participating in loops or exposed to solvent. Regions of constraint on the tertiary structure of a protein often result in loose segmentation of its primary structure into stretches of slowly- and rapidly-evolving amino acids. This clustering can be exploited, and existing methods have done so by relying on local sequence conservation as a signature of selection to help identify functionally important regions within proteins. We invert this paradigm by leveraging the regional nature of protein structure and function to both illuminate and make use of genome-wide patterns of local sequence conservation. Results Our hypothesis is that the regional nature of structural and functional constraints will assert a positive autocorrelation on the evolutionary rates of neighboring sites, which, in a pairwise comparison of orthologous proteins, will manifest itself as the clustering of non-synonymous changes across the amino acid sequence. We introduce a dispersion ratio statistic to test this and related hypotheses. Using genome-wide interspecific comparisons of orthologous protein pairs, we reveal a strong log-linear relationship between the degree of clustering and the intensity of constraint. We further demonstrate how this relationship varies with the evolutionary distance between the species being compared. We provide some evidence that proteins with a history of positive selection deviate from genome-wide trends. Conclusions We find a significant association between the evolutionary rate of a protein and the degree to which non-synonymous changes cluster along its primary sequence. We show that clustering is a non-redundant predictor of evolutionary rate, and we speculate that conflicting signals of clustering and constraint may

  1. The C-terminal 18 Amino Acid Region of Dengue Virus NS5 Regulates its Subcellular Localization and Contains a Conserved Arginine Residue Essential for Infectious Virus Production.

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    Moon Y F Tay

    2016-09-01

    Full Text Available Dengue virus NS5 is the most highly conserved amongst the viral non-structural proteins and is responsible for capping, methylation and replication of the flavivirus RNA genome. Interactions of NS5 with host proteins also modulate host immune responses. Although replication occurs in the cytoplasm, an unusual characteristic of DENV2 NS5 is that it localizes to the nucleus during infection with no clear role in replication or pathogenesis. We examined NS5 of DENV1 and 2, which exhibit the most prominent difference in nuclear localization, employing a combination of functional and structural analyses. Extensive gene swapping between DENV1 and 2 NS5 identified that the C-terminal 18 residues (Cter18 alone was sufficient to direct the protein to the cytoplasm or nucleus, respectively. The low micromolar binding affinity between NS5 Cter18 and the nuclear import receptor importin-alpha (Impα, allowed their molecular complex to be purified, crystallised and visualized at 2.2 Å resolution using x-ray crystallography. Structure-guided mutational analysis of this region in GFP-NS5 clones of DENV1 or 2 and in a DENV2 infectious clone reveal residues important for NS5 subcellular localization. Notably, the trans conformation adopted by Pro-884 allows proper presentation for binding Impα and mutating this proline to Thr, as present in DENV1 NS5, results in mislocalizaion of NS5 to the cytoplasm without compromising virus fitness. In contrast, a single mutation to alanine at NS5 position R888, a residue conserved in all flaviviruses, resulted in a completely non-viable virus, and the R888K mutation led to a severely attenuated phentoype, even though NS5 was located in the nucleus. R888 forms a hydrogen bond with Y838 that is also conserved in all flaviviruses. Our data suggests an evolutionarily conserved function for NS5 Cter18, possibly in RNA interactions that are critical for replication, that is independent of its role in subcellular localization.

  2. Coupled social and ecological outcomes of agricultural intensification in Costa Rica and the future of biodiversity conservation in tropical agricultural regions

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    Sanfiorenzo, A. R.; Waits, L.; Finegan, B.; Shaver, I.; Chain Guadarrama, A.; Cleary, K.; Santiago-Garcia, R.; Hormel, L.; Vierling, L. A.; Bosque-Perez, N.; DeClerck, F.; Fagan, M. E.; Sibelet, N.

    2016-12-01

    Tropical ecosystem conversion to agriculture has caused widespread habitat loss and created fragmented landscapes composed of remnant forest patches embedded in a matrix of agricultural land uses. Non-traditional agricultural export (NTAE) crops such as pineapple are rapidly replacing multiuse landscapes characterized by a diverse matrix of pasture and smallholder crops with intensive, large-scale, monoculture plantations. Using an interdisciplinary approach, we examine the coupled social and ecological implications of agricultural intensification Guided by frameworks from political economy, landscape ecology and landscape genetics we: (1) describe the social and economic implications of pineapple expansion, specifically the concentration of land, labor and financial resources, (2) quantify pineapple cultivation's spatial characteristics, and (3) assess the effects of pineapple expansion on surrounding forest ecosystems, on the agricultural matrix and on biodiversity conservation. Our results indicate that pineapple production concentrates land, labor, and financial resources, which has a homogenizing effect on the agricultural economy in the study region. This constrains farm-based livelihoods, with larger implications for food security and agricultural diversity. Landscape ecology and genetics analyses further reveal how pineapple production simplifies and homogenizes the agricultural matrix between forest patches, which increase the genetic structure and reduce the genetic diversity of Symphonia globulifera a forest understory tree species. To offset the effects of agricultural intensification on social and environmental systems, we recommend developing landscape level land use planning capacity. Furthermore, agricultural and conservation policy reform is needed to promote landscape heterogeneity and economic diversity within the agricultural sector. Our interdisciplinary research provides a detailed examination of the social and ecological impacts of

  3. A comparison among root soil-conservation effects for nine herbs at the cold region highway in north-eastern China

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    Xu, W.; Wang, X.; Zhang, Y.; Liu, Y.

    2014-12-01

    High soil-conservation herbs are very important for slope vegetation restoration of a highway in serious sandstorm regions. In this study, nine common herbs in northeast China were selected and compared to study soil-conservation effects by using an undisturbed-soil trough scouring method for soil anti-scourability enhancement and hydrostatic collapse method for soil anti-erodibility. Further, principal components analysis was used to identify significant root features that affected soil erosion resistance. Results indicated that different herbs had distinct enhancement effects on soil erosion resistance. Soil anti-scourability enhancement index decreased with increases of soil depth, slope gradient and rainfall amount. Relationship between soil anti-erodibility enhancement index ( S) and immersion time ( t) is a cubic spline in each different herb type ( R 2 ≥ 0.88). Herb root features such as micro-aggregates, organic matter, net leaf weight, thick root length, fine root length and biomass contributed a leading role in soil erosion resistance enhancement effect, and all their common factor variances were more than 0.81. Descending order of soil erosion resistance enhancement effect in soil anti-scourability for nine herbs is Poa pratensis, Medicago sativa, Viola philippica, Rudbeckia hirta, Clematis heracleifolia, Kalimeris indica, Cosmos bipinnata, Hemerocallis fulva and Sedum elatinoides, while the sequence of soil anti-erodibility is M. sativa, S. elatinoides, P. pratensis, R. hirta, H. fulva, V. philippica, C. heracleifolia, C. bipinnata and K. indica. Therefore, we concluded that P. pratensis and M. sativa were the most suitable herbs for resisting soil erosion and recommended to be widely planted for road vegetation recovery in this region.

  4. Delta-associated molluscan life and death assemblages in the northern Adriatic Sea: Implications for paleoecology, regional diversity and conservation.

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    Weber, Kristina; Zuschin, Martin

    2013-01-15

    Life-death (LD) studies of shelly macrofauna are important to evaluate how well a fossil assemblage can reflect the original living community, but can also serve as a proxy for recent ecological shifts in marine habitats and in practice this has to be distinguished using taphonomic preservation pattern and estimates of time-averaging. It remains to be rigorously evaluated, however, how to distinguish between sources of LD disagreement. In addition, death assemblages (DAs) also preserve important information on regional diversity which is not available from single censuses of the life assemblages (LAs). The northern Adriatic Sea is an ecosystem under anthropogenic pressure, and we studied the distribution and abundance of living and dead bivalve and gastropod species in the physically stressful environments (tidal flat and shallow sublittoral soft bottoms) associated with the delta of the Isonzo River (Gulf of Trieste). Specifically we evaluated the fidelity of richness, evenness, abundance, habitat discrimination and beta diversity. A total of 10,740 molluscs from fifteen tidal flat and fourteen sublittoral sites were analyzed for species composition and distribution of living and dead molluscs. Of 78 recorded species, only eleven were numerically abundant. There were many more dead than living individuals and rarefied species richness in the DA was higher at all spatial scales, but the differences are lower in habitats and in the region than at individual stations. Evenness was always higher in death assemblages, and probably due to temporally more variable LAs the differences are stronger in the sublittoral habitats. Distinct assemblages characterized intertidal and sublittoral habitats, and the distribution and abundance of empty shells generally corresponded to that of the living species. Death assemblages have lower beta diversity than life assemblages, but empty shells capture compositional differences between habitats to a higher degree than living shells

  5. Comparative phylogeography and population genetics within Buteo lineatus reveals evidence of distinct evolutionary lineages

    Science.gov (United States)

    Hull, J.M.; Strobel, Bradley N.; Boal, C.W.; Hull, A.C.; Dykstra, C.R.; Irish, A.M.; Fish, A.M.; Ernest, H.B.

    2008-01-01

    Traditional subspecies classifications may suggest phylogenetic relationships that are discordant with evolutionary history and mislead evolutionary inference. To more accurately describe evolutionary relationships and inform conservation efforts, we investigated the genetic relationships and demographic histories of Buteo lineatus subspecies in eastern and western North America using 21 nuclear microsatellite loci and 375-base pairs of mitochondrial control region sequence. Frequency based analyses of mitochondrial sequence data support significant population distinction between eastern (B. l. lineatus/alleni/texanus) and western (B. l. elegans) subspecies of B. lineatus. This distinction was further supported by frequency and Bayesian analyses of the microsatellite data. We found evidence of differing demographic histories between regions; among eastern sites, mitochondrial data suggested that rapid population expansion occurred following the end of the last glacial maximum, with B. l. texanus population expansion preceding that of B. l. lineatus/alleni. No evidence of post-glacial population expansion was detected among western samples (B. l. elegans). Rather, microsatellite data suggest that the western population has experienced a recent bottleneck, presumably associated with extensive anthropogenic habitat loss during the 19th and 20th centuries. Our data indicate that eastern and western populations of B. lineatus are genetically distinct lineages, have experienced very different demographic histories, and suggest management as separate conservation units may be warranted. ?? 2008 Elsevier Inc. All rights reserved.

  6. The Phylogeographical Pattern and Conservation of the Chinese Cobra (Naja atra) across Its Range Based on Mitochondrial Control Region Sequences

    Science.gov (United States)

    Lin, Long-Hui; Hua, Lei; Qu, Yan-Fu; Gao, Jian-Fang; Ji, Xiang

    2014-01-01

    The vulnerable Chinese cobra (Naja atra) ranges from southeastern China south of the Yangtze River to northern Vietnam and Laos. Large mountain ranges and water bodies may influence the pattern of genetic diversity of this species. We sequenced the mitochondrial DNA control region (1029 bp) using 285 individuals collected from 23 localities across the species' range and obtained 18 sequences unique to Taiwan from GenBank for phylogenetic and population analysis. Two distinct clades were identified, one including haplotypes from the two westernmost localities (Hekou and Miyi) and the other including haplotypes from all sampling sites except Miyi. A strong population structure was found (Φst = 0.76, P<0.0001) with high haplotype diversity (h = 1.00) and low nucleotide diversity (π = 0.0049). The Luoxiao and Nanling Mountains act as historical geographical barriers limiting gene exchange. In the haplotype network there were two “star” clusters. Haplotypes from populations east of the Luoxiao Mountains were represented within one cluster and haplotypes from populations west of the mountain range within the other, with haplotypes from populations south of the Nanling Mountains in between. Lineage sorting between mainland and island populations is incomplete. It remains unknown as to how much adaptive differentiation there is between population groups or within each group. We caution against long-distance transfers within any group, especially when environmental differences are apparent. PMID:25184236

  7. The phylogeographical pattern and conservation of the Chinese cobra (Naja atra) across its range based on mitochondrial control region sequences.

    Science.gov (United States)

    Lin, Long-Hui; Hua, Lei; Qu, Yan-Fu; Gao, Jian-Fang; Ji, Xiang

    2014-01-01

    The vulnerable Chinese cobra (Naja atra) ranges from southeastern China south of the Yangtze River to northern Vietnam and Laos. Large mountain ranges and water bodies may influence the pattern of genetic diversity of this species. We sequenced the mitochondrial DNA control region (1029 bp) using 285 individuals collected from 23 localities across the species' range and obtained 18 sequences unique to Taiwan from GenBank for phylogenetic and population analysis. Two distinct clades were identified, one including haplotypes from the two westernmost localities (Hekou and Miyi) and the other including haplotypes from all sampling sites except Miyi. A strong population structure was found (Φst = 0.76, P<0.0001) with high haplotype diversity (h = 1.00) and low nucleotide diversity (π = 0.0049). The Luoxiao and Nanling Mountains act as historical geographical barriers limiting gene exchange. In the haplotype network there were two "star" clusters. Haplotypes from populations east of the Luoxiao Mountains were represented within one cluster and haplotypes from populations west of the mountain range within the other, with haplotypes from populations south of the Nanling Mountains in between. Lineage sorting between mainland and island populations is incomplete. It remains unknown as to how much adaptive differentiation there is between population groups or within each group. We caution against long-distance transfers within any group, especially when environmental differences are apparent.

  8. Evolutionary process of a tetranucleotide microsatellite locus in Acipenseriformes.

    Science.gov (United States)

    Shao, Zhao Jun; Rivals, Eric; Zhao, Na; Lek, Sovan; Chang, Jianbo; Berrebi, Patrick

    2011-08-01

    The evolutionary dynamics of the tetra-nucleotide microsatellite locus Spl-106 were investigated at the repeat and flanking sequences in 137 individuals of 15 Acipenseriform species, giving 93 homologous sequences, which were detected in 11 out of 15 species. Twenty-three haplotypes of flanking sequences and three distinct types of repeats, type I, type II and type III, were found within these 93 sequences. The MS-Align hylogenetic method, newly applied to microsatellite sequences, permitted us to understand the repeat and flanking sequence evolution of Spl-106 locus. The flanking region of locus Spl-106 was highly conserved among the species of genera Acipenser, Huso and Scaphirhynchus, which diverged about 150 million years ago (Mya). The rate of flanking sequence divergence at the microsatellite locus Spl-106 in sturgeons is between 0.011% and 0.079% with an average at 0.028% per million years. Sequence alignment and phylogenetic trees produced by MS-Align showed that both the flanking and repeat regions can cluster the alleles of different species into Pacific and Atlantic lineages. Our results show a synchronous evolutionary pattern between the flanking and repeat regions. Moreover, the coexistence of different repeat types in the same species, even in the same individual, is probably due to two duplication events encompassing the locus Spl-106 that occurred during the divergence of Pacific lineage. The first occured before the diversification of Pacific species (121-96 Mya) and led to repeat types I and II. The second occurred more recently, just before the speciation of A. sinensis and A. dabryanus (69-10 Mya), and led to repeat type III. Sequences in the same species with different repeat types probably corresponds to paralogous loci. This study sheds a new light on the evolutionary mechanisms that shape the complex microsatellite loci involving different repeat types.

  9. Evolutionary molecular medicine.

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    Nesse, Randolph M; Ganten, Detlev; Gregory, T Ryan; Omenn, Gilbert S

    2012-05-01

    Evolution has long provided a foundation for population genetics, but some major advances in evolutionary biology from the twentieth century that provide foundations for evolutionary medicine are only now being applied in molecular medicine. They include the need for both proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, competition between alleles, co-evolution, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are transforming evolutionary biology in ways that create even more opportunities for progress at its interfaces with genetics, medicine, and public health. This article reviews 15 evolutionary principles and their applications in molecular medicine in hopes that readers will use them and related principles to speed the development of evolutionary molecular medicine.

  10. Conservation biology of Malagasy strepsirhines: a phylogenetic approach.

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    Lehman, Shawn M

    2006-06-01

    The phylogenetic diversity of extant lemurs represents one of the most important but least studied aspects of the conservation biology of primates. The phylogenetic diversity of a species is inversely proportional to the relative number and closeness of its phylogenetic relatives. Phylogenetic diversity can then be used to determine conservation priorities for specific biogeographic regions. Although Malagasy strepsirhines represent the highest phylogenetic diversity among primates at the global level, there are few phylogenetic data on species-specific and regional conservation plans for lemurs in Madagascar. Therefore, in this paper the following questions are addressed for extant lemurs: 1) how does the measure of taxonomic uniqueness used by Mittermeier et al. (1992 Lemurs of Madagascar; Gland, Switzerland: IUCN) equate with an index of phylogenetic diversity, 2) what are the regional conservation priorities based on analyses of phylogenetic diversity in extant lemurs, and 3) what conservation recommendations can be made based on analyses of phylogenetic diversity in lemurs? Taxonomic endemicity standardized weight (TESW) indices of phylogenetic diversity were used to determine the evolutionary component of biodiversity and to prioritize regions for conserving lemur taxa. TESW refers to the standardization of phylogenetic diversity indices for widespread taxa and endemicity of species. The phylogenetic data came from recent genetic studies of Malagasy strepsirhines at the species level. Lemur species were assigned as being either present or absent in six biogeographic regions. TESW indices were combined with data on lemur complementarity and protected areas to assign conservation priorities at the regional level. Although there were no overall differences between taxonomic ranks and phylogenetic rankings, there were significant differences for the top-ranked taxa. The phylogenetic component of lemur diversity is greatest for Daubentonia madagascariensis

  11. Sequence analysis of 96 genomic regions identifies distinct evolutionary lineages within CC156, the largest Streptococcus pneumoniae clonal complex in the MLST database.

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    Monica Moschioni

    Full Text Available Multi-Locus Sequence Typing (MLST of Streptococcus pneumoniae is based on the sequence of seven housekeeping gene fragments. The analysis of MLST allelic profiles by eBURST allows the grouping of genetically related strains into Clonal Complexes (CCs including those genotypes with a common descent from a predicted ancestor. However, the increasing use of MLST to characterize S. pneumoniae strains has led to the identification of a large number of new Sequence Types (STs causing the merger of formerly distinct lineages into larger CCs. An example of this is the CC156, displaying a high level of complexity and including strains with allelic profiles differing in all seven of the MLST loci, capsular type and the presence of the Pilus Islet-1 (PI-1. Detailed analysis of the CC156 indicates that the identification of new STs, such as ST4945, induced the merging of formerly distinct clonal complexes. In order to discriminate the strain diversity within CC156, a recently developed typing schema, 96-MLST, was used to analyse 66 strains representative of 41 different STs. Analysis of allelic profiles by hierarchical clustering and a minimum spanning tree identified ten genetically distinct evolutionary lineages. Similar results were obtained by phylogenetic analysis on the concatenated sequences with different methods. The identified lineages are homogenous in capsular type and PI-1 presence. ST4945 strains were unequivocally assigned to one of the lineages. In conclusion, the identification of new STs through an exhaustive analysis of pneumococcal strains from various laboratories has highlighted that potentially unrelated subgroups can be grouped into a single CC by eBURST. The analysis of additional loci, such as those included in the 96-MLST schema, will be necessary to accurately discriminate the clonal evolution of the pneumococcal population.

  12. The Participatory Construction of Agro-Ecological Knowledge As A Soil Conservation Strategy In The Mountain Region of Rio de Janeiro State (Brazil

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    de Assis Renato Linhares

    2018-01-01

    Full Text Available Agriculture in the mountain region of Rio de Janeiro State is characterized by intensive soil use and input. Such mountainous environments are vulnerable to climate events; thus, the current article presents a report on methods applied to exchange academic and traditional knowledge. The aim is to expand farmers’ perception about the need of implementing agro-ecological practices, mainly soil management practices, which are important for agricultural sustainability in mountainous environments. The study was conducted in a Nova Friburgo family production unit, in the mountain region of Rio de Janeiro State (Brazil. It consisted of implementing three observation and soil organic-matter management units. The idea was to reduce the incidence of clubroot of crucifers disease caused by Plasmidiophora brassicae. The soil fauna was discussed with local farmers, with emphasis on the association between ecological processes and soil management. The present study improved the discussion with farmers and the need of introducing other innovative conservation practices such as no-tillage system and participatory research based on agro-ecological propositions.

  13. The Central Conserved Region (CCR) of Respiratory Syncytial Virus (RSV) G Protein Modulates Host miRNA Expression and Alters the Cellular Response to Infection

    Science.gov (United States)

    Haynes, Lia M.; Anderson, Larry J.

    2017-01-01

    Respiratory Syncytial Virus (RSV) infects respiratory epithelial cells and deregulates host gene expression by many mechanisms including expression of RSV G protein (RSV G). RSV G protein encodes a central conserved region (CCR) containing a CX3C motif that functions as a fractalkine mimic. Disruption of the CX3C motif (a.a. 182–186) located in the CCR of the G protein has been shown to affect G protein function in vitro and the severity of RSV disease pathogenesis in vivo. We show that infection of polarized Calu3 respiratory cells with recombinant RSV having point mutations in Cys173 and 176 (C173/176S) (rA2-GC12), or Cys186 (C186S) (rA2-GC4) is associated with a decline in the integrity of polarized Calu-3 cultures and decreased virus production. This is accompanied with downregulation of miRNAs let-7f and miR-24 and upregulation of interferon lambda (IFNλ), a primary antiviral cytokine for RSV in rA2-GC12/rA2-GC4 infected cells. These results suggest that residues in the cysteine noose region of RSV G protein can modulate IFN λ expression accompanied by downregulation of miRNAs, and are important for RSV G protein function and targeting. PMID:28671606

  14. Long-term follow up of human T-cell responses to conserved HIV-1 regions elicited by DNA/simian adenovirus/MVA vaccine regimens.

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    Nathifa Moyo

    Full Text Available Durability of vaccine-elicited immune responses is one of the key determinants for vaccine success. Our aim is to develop a vaccination strategy against the human immunodeficiency virus type 1 (HIV-1, which induces protective and durable CD8+ T-cell responses. The central theorem of our approach is to focus T cells on highly conserved regions of the HIV-1 proteome and this is achieved through the use of the first-generation conserved vaccine immunogen HIVconsv. This immunogen vectored by plasmid DNA, simian adenovirus and poxvirus MVA was tested in healthy, HIV-1-negative adults in UK and induced high magnitudes of HIVconsv-specific plurifunctional CD8+ T cells capable of in vitro HIV-1 inhibition. Here, we assessed the durability of these responses.Vaccine recipients in trial HIV-CORE 002 were invited to provide a blood sample at 1 and 2 years after vaccination. Their PBMCs were tested in IFN-γ ELISPOT, 25-analyte Luminex, CFSE proliferation and intracellular cytokine staining assays, the last enhanced by HLA-peptide dextramer analysis.12/12 (1 year and 8/8 (2 years returning subjects had median (range of 990 (150-2495 and 763 (70-1745 IFN-γ SFU/106 PBMC specific for HIVconsv, respectively, and recognized 5 (1-6 out of 6 peptide pools at 2 years. Over one-half of the HIVconsv-specific cells expressed at least 3 functions IFN-γ, TNF-α and CD107a, and were capable of proliferation. Among dextramer-reactive cells, naïve, transitional, effector and terminally differentiated memory subsets were similarly represented.First generation HIVconsv vaccine induced human T cells, which were plurifunctional and persisted for at least 2 years.ClinicalTrials.gov NCT01151319.

  15. The highly conserved 5' untranslated region as an effective target towards the inhibition of Enterovirus 71 replication by unmodified and appropriate 2'-modified siRNAs

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    Deng Jun-Xia

    2012-08-01

    Full Text Available Abstract Background Enterovirus 71 (EV71 is a highly infectious agent that plays an etiological role in hand, foot, and mouth disease. It is associated with severe neurological complications and has caused significant mortalities in recent large-scale outbreaks. Currently, no effective vaccine or specific clinical therapy is available against EV71. Methods Unmodified 21 nucleotide small interfering RNAs (siRNAs and classic 2′-modified (2′-O-methylation or 2′-fluoro modification siRNAs were designed to target highly conserved 5′ untranslated region (UTR of the EV71 genome and employed as anti-EV71 agents. Real-time TaqMan RT-PCR, western blot analysis and plaque assays were carried out to evaluate specific viral inhibition by the siRNAs. Results Transfection of rhabdomyosarcoma (RD cells with siRNAs targeting the EV71 genomic 5′ UTR significantly delayed and alleviated the cytopathic effects of EV71 infection, increased cell viability in EV71-infected RD cells. The inhibitory effect on EV71 replication was sequence-specific and dosage-dependent, with significant corresponding decreases in viral RNA, VP1 protein and viral titer. Appropriate 2′-modified siRNAs exhibited similar RNA interference (RNAi activity with dramatically increased serum stability in comparison with unmodified counterparts. Conclusion Sequences were identified within the highly conserved 5′ UTR that can be targeted to effectively inhibit EV71 replication through RNAi strategies. Appropriate 2′-modified siRNAs provide a promising approach to optimizing siRNAs to overcome barriers on RNAi-based antiviral therapies for broader administration.

  16. The highly conserved 5' untranslated region as an effective target towards the inhibition of Enterovirus 71 replication by unmodified and appropriate 2'-modified siRNAs.

    Science.gov (United States)

    Deng, Jun-Xia; Nie, Xiao-Jing; Lei, Ying-Feng; Ma, Chao-Feng; Xu, Dong-Liang; Li, Biao; Xu, Zhi-Kai; Zhang, Guo-Cheng

    2012-08-13

    Enterovirus 71 (EV71) is a highly infectious agent that plays an etiological role in hand, foot, and mouth disease. It is associated with severe neurological complications and has caused significant mortalities in recent large-scale outbreaks. Currently, no effective vaccine or specific clinical therapy is available against EV71. Unmodified 21 nucleotide small interfering RNAs (siRNAs) and classic 2'-modified (2'-O-methylation or 2'-fluoro modification) siRNAs were designed to target highly conserved 5' untranslated region (UTR) of the EV71 genome and employed as anti-EV71 agents. Real-time TaqMan RT-PCR, western blot analysis and plaque assays were carried out to evaluate specific viral inhibition by the siRNAs. Transfection of rhabdomyosarcoma (RD) cells with siRNAs targeting the EV71 genomic 5' UTR significantly delayed and alleviated the cytopathic effects of EV71 infection, increased cell viability in EV71-infected RD cells. The inhibitory effect on EV71 replication was sequence-specific and dosage-dependent, with significant corresponding decreases in viral RNA, VP1 protein and viral titer. Appropriate 2'-modified siRNAs exhibited similar RNA interference (RNAi) activity with dramatically increased serum stability in comparison with unmodified counterparts. Sequences were identified within the highly conserved 5' UTR that can be targeted to effectively inhibit EV71 replication through RNAi strategies. Appropriate 2'-modified siRNAs provide a promising approach to optimizing siRNAs to overcome barriers on RNAi-based antiviral therapies for broader administration.

  17. Inability to induce consistent T-cell responses recognizing conserved regions within HIIV-1 antigens: a potential mechanism for lack of vaccine efficacy in the step study

    Energy Technology Data Exchange (ETDEWEB)

    Korber, Bette [Los Alamos National Laboratory; Szinger, James [Los Alamos National Laboratory

    2009-01-01

    T cell based vaccines are based upon the induction of CD8+ T cell memory responses that would be effective in inhibiting infection and subsequent replication of an infecting HIV-1 strain, a process that requires a high probability of matching the epitope induced by vaccination with the infecting viral strain. We compared the frequency and specificity of the CTL epitopes elicited by the replication defective AdS gag/pol/nef vaccine used in the STEP trial with the likelihood of encountering those epitopes among recently sequenced Clade B isolates of HIV-1. On average vaccination elicited only one epitope per gene. Importantly, the highly conserved epitopes in gag, pol, and nef (> 80% of strains in the current collection of the Los Alamos database [www.hiv.lanl.gov]) were rarely elicited by vaccination. Moreover there was a statistically significant skewing of the T cell response to relative variable epitopes of each gene; only 20% of persons possessed > 3 T cell responses to epitopes likely to be found in circulating strains in the CladeB populations in which the Step trial was conducted. This inability to elicit T cell responses likely to be found in circulating viral strains is a likely factor in the lack of efficacy of the vaccine utilized in the STEP trial. Modeling of the epitope specific responses elicited by vaccination, we project that a median of 8-10 CD8+ T cell epitopes are required to provide >80% likelihood of eliciting at least 3 CD8+ T cell epitopes that would be found on a circulating population of viruses. Development of vaccine regimens which elicit either a greater breadth of responses or elicit responses to conserved regions of the HIV-1 genome are needed to fully evaluate the concept of whether induction of T cell immunity can alter HIV-1 in vivo.

  18. Loco-regional morbidity after breast conservation and axillary lymph node dissection for early breast cancer with or without regional nodes radiotherapy, perspectives in modern breast cancer treatment: the Skagen Trial 1 is active.

    Science.gov (United States)

    Nielsen, Hanne Melgaard; Friis, Rasmus Blechingberg; Linnet, Søren; Offersen, Birgitte Vrou

    2017-05-01

    Axillary lymph node dissection (ALND) and adjuvant radiotherapy (RT) in early breast cancer are associated with a risk of morbidity, including lymphedema and impaired shoulder mobility. The aim of this study was to evaluate loco-regional morbidity after breast conserving surgery (BCS), ALND, taxane-based chemotherapy and whole breast irradiation (WBI) with or without regional nodes RT. Eligible patients had BCS and ALND from 2007 to 2012 followed by adjuvant taxane-based chemotherapy and if indicated, trastuzumab and endocrine treatment. The RT consisted of WBI and regional nodes RT in case of ≥ pN1 disease (group 1) and WBI only in case of pN0-1(mic) disease (group 2). The dose was 50 Gy in 25 fractions. The patients were invited to participate in a cross-sectional study evaluating morbidity. Of the 347 eligible patients, 277 patients (79%) accepted the invitation. Of these, 185 patients (67%) belonged to group 1 and 92 patients (33%) to group 2. The median time from RT to evaluation of morbidity was 3.3 years (group 1) and 4.3 years (group 2). In group 1, 34 patients (18%) and in group 2, 15 patients (16%) had ≥2 cm enlargement in circumference of ipsilateral upper or lower arm (p = .67). The frequence of impairment of ipsilateral shoulder abduction to ≤120° was 3% in both groups and of shoulder flexion to ≤120° was 1% and 2% (group 1 versus 2). No difference in patient reported outcome measure (PROM) data regarding heaviness or enlargement of ipsilateral upper and lower arm or mobility and sensory disturbances. The risk of lymphedema was low in patients after ALND and not related to use of regional nodes RT. Impairment of shoulder function was rare, and no differences in PROM were detected regarding use or not of regional nodes RT.

  19. Substitutions in conserved regions preceding and within the linker affect activity and flexibility of tRNase ZL, the long form of tRNase Z.

    Directory of Open Access Journals (Sweden)

    Makenzie Saoura

    Full Text Available The enzyme tRNase Z, a member of the metallo-β-lactamase family, endonucleolytically removes 3' trailers from precursor tRNAs, preparing them for CCA addition and aminoacylation. The short form of tRNase Z, tRNase ZS, functions as a homodimer and is found in all prokaryotes and some eukaryotes. The long form, tRNase ZL, related to tRNase ZS through tandem duplication and found only in eukaryotes, possesses ~2,000-fold greater catalytic efficiency than tRNase ZS. tRNase ZL consists of related but diverged amino and carboxy domains connected by a flexible linker (also referred to as a flexible tether and functions as a monomer. The amino domain retains the flexible arm responsible for substrate recognition and binding while the carboxy domain retains the active site. The linker region was explored by Ala-scanning through two conserved regions of D. melanogaster tRNase Z: NdomTprox, located at the carboxy end of the amino domain proximal to the linker, and Tflex, a flexible site in the linker. Periodic substitutions in a hydrophobic patch (F329 and L332 at the carboxy end of NdomTprox show 2,700 and 670-fold impairment relative to wild type, respectively, accompanied by reduced linker flexibility at N-T inside the Ndom- linker boundary. The Ala substitution for N378 in the Tflex region has 10-fold higher catalytic efficiency than wild type and locally decreased flexibility, while the Ala substitution at R382 reduces catalytic efficiency ~50-fold. These changes in pre-tRNA processing kinetics and protein flexibility are interpreted in light of a recent crystal structure for S. cerevisiae tRNase Z, suggesting transmission of local changes in hydrophobicity into the skeleton of the amino domain.

  20. Euryhalinity in an evolutionary context

    Science.gov (United States)

    Schultz, Eric T.; McCormick, Stephen D.; McCormick, Stephen D.; Farrell, Anthony Peter; Brauner, Colin J.

    2013-01-01

    This chapter focuses on the evolutionary importance and taxonomic distribution of euryhalinity. Euryhalinity refers to broad halotolerance and broad halohabitat distribution. Salinity exposure experiments have demonstrated that species vary tenfold in their range of tolerable salinity levels, primarily because of differences in upper limits. Halotolerance breadth varies with the species’ evolutionary history, as represented by its ordinal classification, and with the species’ halohabitat. Freshwater and seawater species tolerate brackish water; their empirically-determined fundamental haloniche is broader than their realized haloniche, as revealed by the halohabitats they occupy. With respect to halohabitat distribution, a minority of species (<10%) are euryhaline. Habitat-euryhalinity is prevalent among basal actinopterygian fishes, is largely absent from orders arising from intermediate nodes, and reappears in the most derived taxa. There is pronounced family-level variability in the tendency to be halohabitat-euryhaline, which may have arisen during a burst of diversification following the Cretaceous-Palaeogene extinction. Low prevalence notwithstanding, euryhaline species are potent sources of evolutionary diversity. Euryhalinity is regarded as a key innovation trait whose evolution enables exploitation of new adaptive zone, triggering cladogenesis. We review phylogenetically-informed studies that demonstrate freshwater species diversifying from euryhaline ancestors through processes such as landlocking. These studies indicate that some euryhaline taxa are particularly susceptible to changes in halohabitat and subsequent diversification, and some geographic regions have been hotspots for transitions to freshwater. Comparative studies on mechanisms among multiple taxa and at multiple levels of biological integration are needed to clarify evolutionary pathways to, and from, euryhalinity.

  1. Fossil and modern sponge fauna of southern Australia and adjacent regions compared: interpretation, evolutionary and biogeographic significance of the late Eocene ‘soft’ sponges

    NARCIS (Netherlands)

    Łukowiak, M.

    2016-01-01

    The late Eocene ‘soft’ sponge fauna of southern Australia is reconstructed based on disassociated spicules and is used to interpret the paleoecology and environmental context of shallow marine communities in this region. The reconstructed sponge association was compared with coeval sponge

  2. Optimization procedures for establishing reserve networks for biodiversity conservation taking into account population genetic structure

    Directory of Open Access Journals (Sweden)

    José Alexandre Felizola Diniz Filho

    2006-01-01

    Full Text Available Conservation genetics has been focused on the ecological and evolutionary persistence of targets (species or other intraspecific units, especially when dealing with narrow-ranged species, and no generalized solution regarding the problem of where to concentrate conservation efforts for multiple genetic targets has yet been achieved. Broadly distributed and abundant species allow the identification of evolutionary significant units, management units, phylogeographical units or other spatial patterns in genetic variability, including those generated by effects of habitat fragmentation caused by human activities. However, these genetic units are rarely considered as priority conservation targets in regional conservation planning procedures. In this paper, we discuss a theoretical framework in which target persistence and genetic representation of targets defined using multiple genetic criteria can be explicitly incorporated into the broad-scale reserve network models used to optimize biodiversity conservation based on multiple species data. When genetic variation can be considered discrete in geographical space, the solution is straightforward, and each spatial unit must be considered as a distinct target. But methods for dealing with continuous genetic variation in space are not trivial and optimization procedures must still be developed. We present a simple heuristic and sequential algorithm to deal with this problem by combining multiple networks of local populations of multiple species in which minimum separation distance between conserved populations is a function of spatial autocorrelation patterns of genetic variability within each species.

  3. Positive evolutionary selection of an HD motif on Alzheimer precursor protein orthologues suggests a functional role.

    Directory of Open Access Journals (Sweden)

    István Miklós

    2012-02-01

    Full Text Available HD amino acid duplex has been found in the active center of many different enzymes. The dyad plays remarkably different roles in their catalytic processes that usually involve metal coordination. An HD motif is positioned directly on the amyloid beta fragment (Aβ and on the carboxy-terminal region of the extracellular domain (CAED of the human amyloid precursor protein (APP and a taxonomically well defined group of APP orthologues (APPOs. In human Aβ HD is part of a presumed, RGD-like integrin-binding motif RHD; however, neither RHD nor RXD demonstrates reasonable conservation in APPOs. The sequences of CAEDs and the position of the HD are not particularly conserved either, yet we show with a novel statistical method using evolutionary modeling that the presence of HD on CAEDs cannot be the result of neutral evolutionary forces (p<0.0001. The motif is positively selected along the evolutionary process in the majority of APPOs, despite the fact that HD motif is underrepresented in the proteomes of all species of the animal kingdom. Position migration can be explained by high probability occurrence of multiple copies of HD on intermediate sequences, from which only one is kept by selective evolutionary forces, in a similar way as in the case of the "transcription binding site turnover." CAED of all APP orthologues and homologues are predicted to bind metal ions including Amyloid-like protein 1 (APLP1 and Amyloid-like protein 2 (APLP2. Our results suggest that HDs on the CAEDs are most probably key components of metal-binding domains, which facilitate and/or regulate inter- or intra-molecular interactions in a metal ion-dependent or metal ion concentration-dependent manner. The involvement of naturally occurring mutations of HD (Tottori (D7N and English (H6R mutations in early onset Alzheimer's disease gives additional support to our finding that HD has an evolutionary preserved function on APPOs.

  4. Wetting of nonconserved residue-backbones: A feature indicative of aggregation associated regions of proteins.

    Science.gov (United States)

    Pradhan, Mohan R; Pal, Arumay; Hu, Zhongqiao; Kannan, Srinivasaraghavan; Chee Keong, Kwoh; Lane, David P; Verma, Chandra S

    2016-02-01

    Aggregation is an irreversible form of protein complexation and often toxic to cells. The process entails partial or major unfolding that is largely driven by hydration. We model the role of hydration in aggregation using "Dehydrons." "Dehydrons" are unsatisfied backbone hydrogen bonds in proteins that seek shielding from water molecules by associating with ligands or proteins. We find that the residues at aggregation interfaces have hydrated backbones, and in contrast to other forms of protein-protein interactions, are under less evolutionary pressure to be conserved. Combining evolutionary conservation of residues and extent of backbone hydration allows us to distinguish regions on proteins associated with aggregation (non-conserved dehydron-residues) from other interaction interfaces (conserved dehydron-residues). This novel feature can complement the existing strategies used to investigate protein aggregation/complexation. © 2015 Wiley Periodicals, Inc.

  5. Conservation and genetic characterisation of common bean landraces from Cilento region (southern Italy): high differentiation in spite of low genetic diversity.

    Science.gov (United States)

    De Luca, Daniele; Cennamo, Paola; Del Guacchio, Emanuele; Di Novella, Riccardo; Caputo, Paolo

    2018-02-01

    Since its introduction from Central-South America to Italy almost 500 years ago, the common bean (Phaseolus vulgaris L.) was largely cultivated across the peninsula in hundreds of different landraces. However, globalisation and technological modernisation of agricultural practices in the last decades promoted the cultivation of few varieties at the expense of traditional and local agro-ecotypes, which have been confined to local markets or have completely disappeared. The aim of this study was to evaluate the genetic diversity and differentiation in 12 common bean landraces once largely cultivated in the Cilento region (Campania region, southern Italy), and now the object of a recovery program to save them from extinction. The analysis conducted using 13 nuclear microsatellite loci in 140 individuals revealed a high degree of homozygosity within each landrace and a strong genetic differentiation that was reflected in the success in assigning individuals to the source landrace. On the contrary, internal transcribed spacers 1 and 2, analysed in one individual per landrace, were highly similar among common bean landraces but allowed the identification of a cowpea variety (Vigna unguiculata Walp.), a crop largely cultivated in the Old World before the arrival of common bean from Americas. In conclusion, our study highlighted that conservation of landraces is important not only for the cultural and socio-economic value that they have for local communities, but also because the time and conditions in which they have been selected have led to that genetic distinctiveness that is at the basis of many potential agronomical applications and dietary benefits.

  6. Structure of the mitochondrial control region of the Eurasian otter (Lutra lutra; Carnivora, Mustelidae): patterns of genetic heterogeneity and implications for conservation of the species in Italy.

    Science.gov (United States)

    Ketmaier, V; Bernardini, C

    2005-01-01

    In this study we determined the complete sequence of the mitochondrial DNA (mtDNA) control region of the Eurasian otter (Lutra lutra). We then compared these new sequences with orthologues of nine carnivores belonging to six families (Mustelidae, Mephitidae, Canidae, Hyaenidae, Ursidae, and Felidae). The comparative analyses identified all the conserved regions previously found in mammals. The Eurasian otter and seven other species have a single location with tandem repeats in the right domain, while the spotted hyena (Hyaenidae) and the tiger (Felidae) have repeated sequences in both the right and left domains. To assess the degree of genetic heterogeneity of the Eurasian otter in Italy we sequenced two fragments of the gene and analyzed length polymorphisms of repeated sequences and heteroplasmy in 32 specimens. The study includes 23 museum specimens collected in northern, central, and southern Italy; most of these specimens are from extinct populations, while the southern Italian samples belong to the sole extant Italian population of the Eurasian otter. The study also includes all the captive-reared animals living in the colony "Centro Lontra, Caramanico Terme" (Pescara, central Italy). The colony is maintained for reintroduction of the species. We found a low level of genetic polymorphism; a single haplotype is dominant, but our data indicate the presence in central and southern Italy of two slightly divergent haplotypes. One haplotype belongs to an extinct population, the other is present in the single extant Italian population. Analyses of length polymorphisms and heteroplasmy indicate that the autochthonous Italian samples are characterized by a distinct array of repeated sequences from captive-reared animals.

  7. Immune complexes in chronic Chagas disease patients are formed by exovesicles from Trypanosoma cruzi carrying the conserved MASP N-terminal region

    Science.gov (United States)

    Díaz Lozano, Isabel María; de Pablos, Luis Miguel; Longhi, Silvia Andrea; Zago, María Paola; Schijman, Alejandro Gabriel; Osuna, Antonio

    2017-03-01

    The exovesicles (EVs) are involved in pathologic host-parasite immune associations and have been recently used as biomarkers for diagnosis of infectious diseases. The release of EVs by Trypanosoma cruzi, the causative agent of Chagas disease, has recently been described, with different protein cargoes including the MASP multigene family of proteins MASPs are specific to this parasite and characterized by a conserved C-terminal (C-term) region and an N-terminal codifying for a signal peptide (SP). In this investigation, we identified immature MASP proteins containing the MASP SP in EVs secreted by the infective forms of the parasite. Those EVs are responsible for the formation of immune complexes (ICs) containing anti-MASP SP IgGs in patients with different (cardiac, digestive and asymptomatic) chronic Chagas disease manifestations. Moreover, purified EVs as well as the MASP SP inhibit the action of the complement system and also show a significant association with the humoral response in patients with digestive pathologies. These findings reveal a new route for the secretion of MASP proteins in T. cruzi, which uses EVs as vehicles for immature and misfolded proteins, forming circulating immune complexes. Such complexes could be used in the prognosis of digestive pathologies of clinical forms of Chagas disease.

  8. The activity of a yeast Family 16 methyltransferase, Efm2, is affected by a conserved tryptophan and its N-terminal region.

    Science.gov (United States)

    Hamey, Joshua J; Hart-Smith, Gene; Erce, Melissa A; Wilkins, Marc R

    2016-12-01

    The Family 16 methyltransferases are a group of eukaryotic nonhistone protein methyltransferases. Sixteen of these have recently been described in yeast and human, but little is known about their sequence and structural features. Here we investigate one of these methyltransferases, Saccharomyces cerevisiae elongation factor methyltransferase 2 (Efm2), by site-directed mutagenesis and truncation. We show that an active site-associated tryptophan, invariant in Family 16 methyltransferases and at position 222 in Efm2, is important for methyltransferase activity. A second highly conserved tryptophan, at position 318 in Efm2, is likely involved in S-adenosyl methionine binding but is of lesser consequence for catalysis. By truncation analysis, we show that the N-terminal 50-200 amino acids of Efm2 are critical for its methyltransferase activity. As N-terminal regions are variable among Family 16 methyltransferases, this suggests a possible role in determining substrate specificity. This is consistent with recently solved structures that show the core of Family 16 methyltransferases to be near-identical but the N termini to be structurally quite different. Finally, we show that Efm2 can exist as an oligomer but that its N terminus is not necessary for oligomerisation to occur.

  9. Inhibition of hepatitis B virus by the CRISPR/Cas9 system via targeting the conserved regions of the viral genome.

    Science.gov (United States)

    Liu, Xing; Hao, Ruidong; Chen, Shuliang; Guo, Deyin; Chen, Yu

    2015-08-01

    Hepatitis B virus (HBV) remains a global health threat as chronic HBV infection may lead to liver cirrhosis or cancer. Current antiviral therapies with nucleoside analogues can inhibit the replication of HBV, but do not disrupt the already existing HBV covalently closed circular DNA. The newly developed CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated 9) system is a powerful tool to target cellular genome DNA for gene editing. In order to investigate the possibility of using the CRISPR/Cas9 system to disrupt the HBV DNA templates, we designed eight guide RNAs (gRNAs) that targeted the conserved regions of different HBV genotypes, which could significantly inhibit HBV replication both in vitro and in vivo. Moreover, the HBV-specific gRNA/Cas9 system could inhibit the replication of HBV of different genotypes in cells, and the viral DNA was significantly reduced by a single gRNA/Cas9 system and cleared by a combination of different gRNA/Cas9 systems.

  10. based conservation

    African Journals Online (AJOL)

    http://dx.doi.org/10.4314/mcd.v10i2.1. Increasing women's par- ticipation in community- based conservation: key to success? Ensuring that both men and women benefit equitably from conservation and development programs is likely to increase the long-term success of both conservation and development goals. However ...

  11. Landscape change and conservation priorities: Mexican herpetofaunal perspectives at local and regional scales Cambios en el paisaje y prioridades de conservación: una perspectiva herpetofaunística mexicana a escalas local y regional

    Directory of Open Access Journals (Sweden)

    J. Jesús Sigala-Rodríguez

    2009-04-01

    Full Text Available Few studies have demonstrated historical human impact on biodiversity at local and regional scales, largely due to lack of baseline information and long term monitoring for most taxa. In 1958 and 1959 researchers from the Museum of Vertebrate Zoology (MVZ visited the Mexican state of Aguascalientes and increased its documented amphibian and reptile fauna from 21 to 30 species. Using MVZ collections, field notes, and landscape photographs taken during that expedition, we resurveyed those same localities in 2004 to document herpetofaunal changes coincident with greatly increased human activities. Despite its small area, Aguascalientes encompasses several biogeographic regions and the threat of local extinction at species' distributional limits has broader implications for regional biotas. New discoveries raise to 71 the number of species known for that state, but our comparisons suggest a gloomy future for amphibians and reptiles in Aguascalientes. Paradoxically, human impact is managed primarily at state and municipal levels, often devoid of locally relevant context. Our findings illustrate the conservation value of intensive small-scale studies, focused on the natural history of particular species and localities, as complements to large-scale biodiversity assessments on country wide and continental scales.Pocos estudios han demostrado el impacto humano histórico en la biodiversidad a escalas local y regional debido a la carencia de monitoreo para la mayoría de los grupos taxonómicos. En 1958 y 1959 investigadores del Museum of Vertebrate Zoology (MVZ visitaron Aguascalientes, México y elevaron de 21 hasta 30 el número de especies de anfibios y reptiles para el estado. Usando la colección, notas de campo y fotografías de paisaje tomadas durante esas expediciones, visitamos esas localidades en 2004 para documentar cambios en la herpetofauna asociados con el incremento en actividades humanas. En Aguascalientes se encuentran varias regiones

  12. A systematic enhancer screen using lentivector transgenesis identifies conserved and non-conserved functional elements at the Olig1 and Olig2 locus.

    Directory of Open Access Journals (Sweden)

    Marc Friedli

    Full Text Available Finding sequences that control expression of genes is central to understanding genome function. Previous studies have used evolutionary conservation as an indicator of regulatory potential. Here, we present a method for the unbiased in vivo screen of putative enhancers in large DNA regions, using the mouse as a model. We cloned a library of 142 overlapping fragments from a 200 kb-long murine BAC in a lentiviral vector expressing LacZ from a minimal promoter, and used the resulting vectors to infect fertilized murine oocytes. LacZ staining of E11 embryos obtained by first using the vectors in pools and then testing individual candidates led to the identification of 3 enhancers, only one of which shows significant evolutionary conservation. In situ hybridization and 3C/4C experiments suggest that this enhancer, which is active in the neural tube and posterior diencephalon, influences the expression of the Olig1 and/or Olig2 genes. This work provides a new approach for the large-scale in vivo screening of transcriptional regulatory sequences, and further demonstrates that evolutionary conservation alone seems too limiting a criterion for the identification of enhancers.

  13. Towards an evolutionary model of transcription networks.

    Directory of Open Access Journals (Sweden)

    Dan Xie

    2011-06-01

    Full Text Available DNA evolution models made invaluable contributions to comparative genomics, although it seemed formidable to include non-genomic features into these models. In order to build an evolutionary model of transcription networks (TNs, we had to forfeit the substitution model used in DNA evolution and to start from modeling the evolution of the regulatory relationships. We present a quantitative evolutionary model of TNs, subjecting the phylogenetic distance and the evolutionary changes of cis-regulatory sequence, gene expression and network structure to one probabilistic framework. Using the genome sequences and gene expression data from multiple species, this model can predict regulatory relationships between a transcription factor (TF and its target genes in all species, and thus identify TN re-wiring events. Applying this model to analyze the pre-implantation development of three mammalian species, we identified the conserved and re-wired components of the TNs downstream to a set of TFs including Oct4, Gata3/4/6, cMyc and nMyc. Evolutionary events on the DNA sequence that led to turnover of TF binding sites were identified, including a birth of an Oct4 binding site by a 2nt deletion. In contrast to recent reports of large interspecies differences of TF binding sites and gene expression patterns, the interspecies difference in TF-target relationship is much smaller. The data showed increasing conservation levels from genomic sequences to TF-DNA interaction, gene expression, TN, and finally to morphology, suggesting that evolutionary changes are larger at molecular levels and smaller at functional levels. The data also showed that evolutionarily older TFs are more likely to have conserved target genes, whereas younger TFs tend to have larger re-wiring rates.

  14. Prognosis after treatment for loco-regional recurrence after mastectomy or breast conserving therapy in two randomised trials (EORTC 10801 and DBCG-82TM). EORTC Breast Cancer Cooperative Group and the Danish Breast Cancer Cooperative Group

    NARCIS (Netherlands)

    van Tienhoven, G.; Voogd, A. C.; Peterse, J. L.; Nielsen, M.; Andersen, K. W.; Mignolet, F.; Sylvester, R.; Fentiman, I. S.; van der Schueren, E.; van Zijl, K.; Blichert-Toft, M.; Bartelink, H.; van Dongen, J. A.

    1999-01-01

    The aim of this study was to investigate and compare the prognosis after treatment for loco-regional recurrences (LR) after (modified) radical mastectomy (MRM) or breast conserving therapy (BCT), in terms of overall survival and time to subsequent LR, in patients originally treated in two European

  15. Domain architecture conservation in orthologs.

    Science.gov (United States)

    Forslund, Kristoffer; Pekkari, Isabella; Sonnhammer, Erik L L

    2011-08-05

    As orthologous proteins are expected to retain function more often than other homologs, they are often used for functional annotation transfer between species. However, ortholog identification methods do not take into account changes in domain architecture, which are likely to modify a protein's function. By domain architecture we refer to the sequential arrangement of domains along a protein sequence.To assess the level of domain architecture conservation among orthologs, we carried out a large-scale study of such events between human and 40 other species spanning the entire evolutionary range. We designed a score to measure domain architecture similarity and used it to analyze differences in domain architecture conservation between orthologs and paralogs relative to the conservation of primary sequence. We also statistically characterized the extents of different types of domain swapping events across pairs of orthologs and paralogs. The analysis shows that orthologs exhibit greater domain architecture conservation than paralogous homologs, even when differences in average sequence divergence are compensated for, for homologs that have diverged beyond a certain threshold. We interpret this as an indication of a stronger selective pressure on orthologs than paralogs to retain the domain architecture required for the proteins to perform a specific function. In general, orthologs as well as the closest paralogous homologs have very similar domain architectures, even at large evolutionary separation.The most common domain architecture changes observed in both ortholog and paralog pairs involved insertion/deletion of new domains, while domain shuffling and segment duplication/deletion were very infrequent. On the whole, our results support the hypothesis that function conservation between orthologs demands higher domain architecture conservation than other types of homologs, relative to primary sequence conservation. This supports the notion that orthologs are

  16. Domain architecture conservation in orthologs

    Science.gov (United States)

    2011-01-01

    Background As orthologous proteins are expected to retain function more often than other homologs, they are often used for functional annotation transfer between species. However, ortholog identification methods do not take into account changes in domain architecture, which are likely to modify a protein's function. By domain architecture we refer to the sequential arrangement of domains along a protein sequence. To assess the level of domain architecture conservation among orthologs, we carried out a large-scale study of such events between human and 40 other species spanning the entire evolutionary range. We designed a score to measure domain architecture similarity and used it to analyze differences in domain architecture conservation between orthologs and paralogs relative to the conservation of primary sequence. We also statistically characterized the extents of different types of domain swapping events across pairs of orthologs and paralogs. Results The analysis shows that orthologs exhibit greater domain architecture conservation than paralogous homologs, even when differences in average sequence divergence are compensated for, for homologs that have diverged beyond a certain threshold. We interpret this as an indication of a stronger selective pressure on orthologs than paralogs to retain the domain architecture required for the proteins to perform a specific function. In general, orthologs as well as the closest paralogous homologs have very similar domain architectures, even at large evolutionary separation. The most common domain architecture changes observed in both ortholog and paralog pairs involved insertion/deletion of new domains, while domain shuffling and segment duplication/deletion were very infrequent. Conclusions On the whole, our results support the hypothesis that function conservation between orthologs demands higher domain architecture conservation than other types of homologs, relative to primary sequence conservation. This supports the

  17. Methodologies for conservation assessments of the genetic biodiversity of aquatic macro-organisms

    Directory of Open Access Journals (Sweden)

    BERT T. M.

    2002-01-01

    Full Text Available International organizations and biodiversity scientists recognize three levels of biodiversity: genetic, species, and ecosystem. However, most studies with the goal of assessing biodiversity collect data at only a single level -- that of the species. Even when multiple levels of biodiversity are considered, usually only ecosystem diversity is also evaluated. Genetic diversity is virtually never considered. Yet, genetic diversity is essential for the maintenance of populations and species over ecological and evolutionary time periods. Moreover, because components of genetic diversity are independent of either species or ecosystem diversity, genetic diversity can provide a unique measure by which to assess the value of regions for conservation. Regions can be valuable for conservation of their genetic resources regardless of their levels of species or ecosystem uniqueness or diversity. In general, the same methods and statistical programs that are used to answer questions about population genetics and phylogenetics are applicable to conservation genetics. Thus, numerous genetic techniques, laboratory methods, and statistical programs are available for assessing regional levels of genetic diversity for conservation considerations. Here, we provide the rationale, techniques available, field and laboratory protocols, and statistical programs that can be used to estimate the magnitude and type of genetic diversity in regions. We also provide information on how to obtain commonly utilized statistical programs and the type of analyses that they include. The guide that we present here can be used to conduct investigations of the genetic diversity of regions under consideration for conservation of their natural resources.

  18. Evolutionary Biology Today

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 7; Issue 11. Evolutionary Biology Today - The Domain of Evolutionary Biology. Amitabh Joshi. Series Article Volume 7 Issue 11 November 2002 pp 8-17. Fulltext. Click here to view fulltext PDF. Permanent link:

  19. Part E: Evolutionary Computation

    DEFF Research Database (Denmark)

    2015-01-01

    evolutionary algorithms, such as memetic algorithms, which have emerged as a very promising tool for solving many real-world problems in a multitude of areas of science and technology. Moreover, parallel evolutionary combinatorial optimization has been presented. Search operators, which are crucial in all...

  20. Evolutionary Biology Today

    Indian Academy of Sciences (India)

    Amitabh Joshi studies and teaches evolutionary ' genetics and population ecology at the Jawaharlal. Nehru Centre for Advanced. Scientific Research,. Bangalore. His current research interests are in life- history, evolution, the evolutionary genetics of biological clocks, the evolution of ecological specialization dynamics. He.

  1. Evolutionary humanoid robotics

    CERN Document Server

    Eaton, Malachy

    2015-01-01

    This book examines how two distinct strands of research on autonomous robots, evolutionary robotics and humanoid robot research, are converging. The book will be valuable for researchers and postgraduate students working in the areas of evolutionary robotics and bio-inspired computing.

  2. Evolutionary Biology Today

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 8; Issue 2. Evolutionary Biology Today - What do Evolutionary Biologists do? Amitabh Joshi. Series Article Volume 8 Issue 2 February 2003 pp 6-18. Fulltext. Click here to view fulltext PDF. Permanent link:

  3. Applying evolutionary anthropology

    OpenAIRE

    Gibson, Mhairi A; Lawson, David W

    2015-01-01

    Evolutionary anthropology provides a powerful theoretical framework for understanding how both current environments and legacies of past selection shape human behavioral diversity. This integrative and pluralistic field, combining ethnographic, demographic, and sociological methods, has provided new insights into the ultimate forces and proximate pathways that guide human adaptation and variation. Here, we present the argument that evolutionary anthropological studies of human behavior also h...

  4. Investigating Evolutionary Dynamics of RHA1 Operons.

    Science.gov (United States)

    Chen, Yong; Geng, Dandan; Ehrhardt, Kristina; Zhang, Shaoqiang

    2016-01-01

    Grouping genes as operons is an important genomic feature of prokaryotic organisms. The comprehensive understanding of the operon organizations would be helpful to decipher transcriptional mechanisms, cellular pathways, and the evolutionary landscape of prokaryotic genomes. Although thousands of prokaryotes have been sequenced, genome-wide investigation of the evolutionary dynamics (division and recombination) of operons among these genomes remains unexplored. Here, we systematically analyzed the operon dynamics of Rhodococcus jostii RHA1 (RHA1), an oleaginous bacterium with high potential applications in biofuel, by comparing 340 prokaryotic genomes that were carefully selected from different genera. Interestingly, 99% of RHA1 operons were observed to exhibit evolutionary events of division and recombination among the 340 compared genomes. An operon that encodes all enzymes related to histidine biosynthesis in RHA1 (His-operon) was found to be segmented into smaller gene groups (sub-operons) in diverse genomes. These sub-operons were further reorganized with different functional genes as novel operons that are related to different biochemical processes. Comparatively, the operons involved in the functional categories of lipid transport and metabolism are relatively conserved among the 340 compared genomes. At the pathway level, RHA1 operons found to be significantly conserved were involved in ribosome synthesis, oxidative phosphorylation, and fatty acid synthesis. These analyses provide evolutionary insights of operon organization and the dynamic associations of various biochemical pathways in different prokaryotes.

  5. Identification of expressed and conserved human noncoding RNAs

    DEFF Research Database (Denmark)

    Nielsen, Morten Muhlig; Tehler, Disa; Vang, Søren

    2014-01-01

    The past decade has shown mammalian genomes to be pervasively transcribed and identified thousands of noncoding (nc) transcripts. It is currently unclear to what extent these transcripts are of functional importance, as experimental functional evidence exists for only a small fraction. Here, we...... characterize the expression and evolutionary conservation properties of 12,115 known and novel nc transcripts, including structural RNAs, long nc RNAs (lncRNAs), antisense RNAs, EvoFold predictions, ultraconserved elements, and expressed nc regions. Expression levels are evaluated across 12 human tissues using...... a custom-designed microarray, supplemented with RNAseq. Conservation levels are evaluated at both the base level and at the syntenic level. We combine these measures with epigenetic mark annotations to identify subsets of novel nc transcripts that show characteristics similar to known functional ncRNAs...

  6. SubClonal Hierarchy Inference from Somatic Mutations: Automatic Reconstruction of Cancer Evolutionary Trees from Multi-region Next Generation Sequencing.

    Directory of Open Access Journals (Sweden)

    Noushin Niknafs

    2015-10-01

    Full Text Available Recent improvements in next-generation sequencing of tumor samples and the ability to identify somatic mutations at low allelic fractions have opened the way for new approaches to model the evolution of individual cancers. The power and utility of these models is increased when tumor samples from multiple sites are sequenced. Temporal ordering of the samples may provide insight into the etiology of both primary and metastatic lesions and rationalizations for tumor recurrence and therapeutic failures. Additional insights may be provided by temporal ordering of evolving subclones--cellular subpopulations with unique mutational profiles. Current methods for subclone hierarchy inference tightly couple the problem of temporal ordering with that of estimating the fraction of cancer cells harboring each mutation. We present a new framework that includes a rigorous statistical hypothesis test and a collection of tools that make it possible to decouple these problems, which we believe will enable substantial progress in the field of subclone hierarchy inference. The methods presented here can be flexibly combined with methods developed by others addressing either of these problems. We provide tools to interpret hypothesis test results, which inform phylogenetic tree construction, and we introduce the first genetic algorithm designed for this purpose. The utility of our framework is systematically demonstrated in simulations. For most tested combinations of tumor purity, sequencing coverage, and tree complexity, good power (≥ 0.8 can be achieved and Type 1 error is well controlled when at least three tumor samples are available from a patient. Using data from three published multi-region tumor sequencing studies of (murine small cell lung cancer, acute myeloid leukemia, and chronic lymphocytic leukemia, in which the authors reconstructed subclonal phylogenetic trees by manual expert curation, we show how different configurations of our tools can

  7. Atmospheric loss from the dayside open polar region and its dependence on geomagnetic activity: implications for atmospheric escape on evolutionary timescales

    Directory of Open Access Journals (Sweden)

    R. Slapak

    2017-06-01

    Full Text Available We have investigated the total O+ escape rate from the dayside open polar region and its dependence on geomagnetic activity, specifically Kp. Two different escape routes of magnetospheric plasma into the solar wind, the plasma mantle, and the high-latitude dayside magnetosheath have been investigated separately. The flux of O+ in the plasma mantle is s