WorldWideScience

Sample records for methylation pattern diversity

  1. Adenine N6-methylation in diverse fungi

    NARCIS (Netherlands)

    Seidl, Michael F.

    2017-01-01

    A DNA modification - methylation of cytosines and adenines - has important roles in diverse processes such as regulation of gene expression and genome stability, yet until recently adenine methylation had been considered to be only a hallmark of prokaryotes. A new study identifies abundant

  2. Methylation patterns in marginal zone lymphoma.

    Science.gov (United States)

    Arribas, Alberto J; Bertoni, Francesco

    Promoter DNA methylation is a major regulator of gene expression and transcription. The identification of methylation changes is important for understanding disease pathogenesis, for identifying prognostic markers and can drive novel therapeutic approaches. In this review we summarize the current knowledge regarding DNA methylation in MALT lymphoma, splenic marginal zone lymphoma, nodal marginal zone lymphoma. Despite important differences in the study design for different publications and the existence of a sole large and genome-wide methylation study for splenic marginal zone lymphoma, it is clear that DNA methylation plays an important role in marginal zone lymphomas, in which it contributes to the inactivation of tumor suppressors but also to the expression of genes sustaining tumor cell survival and proliferation. Existing preclinical data provide the rationale to target the methylation machinery in these disorders. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. Dynamic instability of genomic methylation patterns in pluripotent stem cells

    Directory of Open Access Journals (Sweden)

    Ooi Steen KT

    2010-09-01

    Full Text Available Abstract Background Genomic methylation patterns are established during gametogenesis, and perpetuated in somatic cells by faithful maintenance methylation. There have been previous indications that genomic methylation patterns may be less stable in embryonic stem (ES cells than in differentiated somatic cells, but it is not known whether different mechanisms of de novo and maintenance methylation operate in pluripotent stem cells compared with differentiating somatic cells. Results In this paper, we show that ablation of the DNA methyltransferase regulator DNMT3L (DNA methyltransferase 3-like in mouse ES cells renders them essentially incapable of de novo methylation of newly integrated retroviral DNA. We also show that ES cells lacking DNMT3L lose DNA methylation over time in culture, suggesting that DNA methylation in ES cells is the result of dynamic loss and gain of DNA methylation. We found that wild-type female ES cells lose DNA methylation at a much faster rate than do male ES cells; this defect could not be attributed to sex-specific differences in expression of DNMT3L or of any DNA methyltransferase. We also found that human ES and induced pluripotent stem cell lines showed marked but variable loss of methylation that could not be attributed to sex chromosome constitution or time in culture. Conclusions These data indicate that DNA methylation in pluripotent stem cells is much more dynamic and error-prone than is maintenance methylation in differentiated cells. DNA methylation requires DNMT3L in stem cells, but DNMT3L is not expressed in differentiating somatic cells. Error-prone maintenance methylation will introduce unpredictable phenotypic variation into clonal populations of pluripotent stem cells, and this variation is likely to be much more pronounced in cultured female cells. This epigenetic variability has obvious negative implications for the clinical applications of stem cells.

  4. Differential DNA Methylation Patterns Are Related to Phellogen Origin and Quality of Quercus suber Cork.

    Science.gov (United States)

    Inácio, Vera; Barros, Pedro M; Costa, Augusta; Roussado, Cristóvão; Gonçalves, Elsa; Costa, Rita; Graça, José; Oliveira, M Margarida; Morais-Cecílio, Leonor

    2017-01-01

    DNA methylation is thought to influence Quercus suber cork quality, which is the main constraint for its economic valorisation. However, a deep knowledge of the cytosine methylation patterns disclosing the epigenetic variability of trees with different cork quality types is totally missing. This study investigates the hypothesis that variations in DNA methylation contribute to differences in cork cellular characteristics directly related to original or traumatic phellogen activity. We used MSAPs (Methylation Sensitive Amplified Polymorphism) to assess DNA methylation patterns of cork and leaf tissues of Q. suber adult trees growing in three cork oak stands. The relationship between the detected polymorphisms and the diversity of cork quality traits was explored by a marker-trait analysis focusing on the most relevant quality characteristics. Populations differed widely in cork quality, but only slightly in degree of epigenetic differentiation. Four MSAP markers (1.3% of the total) were significantly associated with the most noteworthy quality traits: wood inclusions (nails) and porosity. This evidence supports the potential role of cytosine methylation in the modulation of differential phellogen activity either involved in localized cell death or in pore production, resulting in different cork qualities. Although, the underlying basis of the methylation polymorphism of loci affecting cork quality traits remain unclear, the disclosure of markers statistically associated with cork quality strengthens the potential role of DNA methylation in the regulation of these traits, namely at the phellogen level.

  5. Spatial patterns of species diversity in Kenya

    NARCIS (Netherlands)

    Oindo, B.O.

    2001-01-01

    The most striking feature of Earth is the existence of life and the most striking feature of life is its diversity. Explaining patterns of species diversity is one of the most complex problems in ecology. This is because diversity is usually the outcome of many contributing factors whose relative

  6. Global variation in elevational diversity patterns

    Science.gov (United States)

    Qinfeng Guo; Douglas A. Kelt; Zhongyu Sun; Hongxiao Liu; Liangjun Hu; Hai Ren; Jun We

    2013-01-01

    While horizontal gradients of biodiversity have been examined extensively in the past, vertical diversity gradients (elevation, water depth) are attracting increasing attention. We compiled data from 443 elevational gradients involving diverse organisms worldwide to investigate how elevational diversity patterns may vary between the Northern and Southern hemispheres...

  7. Methylation pattern of IFNG in periapical granulomas and radicular cysts.

    Science.gov (United States)

    Campos, Kelma; Gomes, Carolina Cavaliéri; de Fátima Correia-Silva, Jeane; Farias, Lucyana Conceição; Fonseca-Silva, Thiago; Bernardes, Vanessa Fátima; Pereira, Cláudia Maria; Gomez, Ricardo Santiago

    2013-04-01

    Interferon-γ plays an important role in the pathogenesis of periapical lesions, and the methylation of IFNG has been associated with transcriptional inactivation. The purpose of the present study was to investigate IFNG promoter methylation in association with gene transcription and protein levels in periapical granulomas and radicular cysts. Methylation-specific polymerase chain reaction was used to assess the DNA methylation pattern of the IFNG gene in 16 periapical granulomas and 13 radicular cyst samples. The transcription levels of IFNG mRNA were verified by quantitative real-time polymerase chain reaction, and protein expression was evaluated by immunohistochemistry. All the periapical lesion samples exhibited partial or total methylation of the IFNG gene. In addition, an increased methylation profile was found in radicular cysts compared with periapical granulomas. Increased IFNG mRNA expression was observed in the partially methylated periapical lesion samples relative to the samples that were completely methylated. The present study provides the first evidence of the possible impact of IFNG methylation on IFNG transcription in periapical lesions. Copyright © 2013 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  8. Analysis of DNA Cytosine Methylation Patterns Using Methylation-Sensitive Amplification Polymorphism (MSAP).

    Science.gov (United States)

    Guevara, María Ángeles; de María, Nuria; Sáez-Laguna, Enrique; Vélez, María Dolores; Cervera, María Teresa; Cabezas, José Antonio

    2017-01-01

    Different molecular techniques have been developed to study either the global level of methylated cytosines or methylation at specific gene sequences. One of them is the methylation-sensitive amplified polymorphism technique (MSAP) which is a modification of amplified fragment length polymorphism (AFLP). It has been used to study methylation of anonymous CCGG sequences in different fungi, plants, and animal species. The main variation of this technique resides on the use of isoschizomers with different methylation sensitivity (such as HpaII and MspI) as a frequent-cutter restriction enzyme. For each sample, MSAP analysis is performed using both EcoRI/HpaII- and EcoRI/MspI-digested samples. A comparative analysis between EcoRI/HpaII and EcoRI/MspI fragment patterns allows the identification of two types of polymorphisms: (1) methylation-insensitive polymorphisms that show common EcoRI/HpaII and EcoRI/MspI patterns but are detected as polymorphic amplified fragments among samples and (2) methylation-sensitive polymorphisms which are associated with the amplified fragments that differ in their presence or absence or in their intensity between EcoRI/HpaII and EcoRI/MspI patterns. This chapter describes a detailed protocol of this technique and discusses the modifications that can be applied to adjust the technology to different species of interest.

  9. Genetic diversity analysis of Jatropha curcas L. (Euphorbiaceae) based on methylation-sensitive amplification polymorphism.

    Science.gov (United States)

    Kanchanaketu, T; Sangduen, N; Toojinda, T; Hongtrakul, V

    2012-04-13

    Genetic analysis of 56 samples of Jatropha curcas L. collected from Thailand and other countries was performed using the methylation-sensitive amplification polymorphism (MSAP) technique. Nine primer combinations were used to generate MSAP fingerprints. When the data were interpreted as amplified fragment length polymorphism (AFLP) markers, 471 markers were scored. All 56 samples were classified into three major groups: γ-irradiated, non-toxic and toxic accessions. Genetic similarity among the samples was extremely high, ranging from 0.95 to 1.00, which indicated very low genetic diversity in this species. The MSAP fingerprint was further analyzed for DNA methylation polymorphisms. The results revealed differences in the DNA methylation level among the samples. However, the samples collected from saline areas and some species hybrids showed specific DNA methylation patterns. AFLP data were used, together with methylation-sensitive AFLP (MS-AFLP) data, to construct a phylogenetic tree, resulting in higher efficiency to distinguish the samples. This combined analysis separated samples previously grouped in the AFLP analysis. This analysis also distinguished some hybrids. Principal component analysis was also performed; the results confirmed the separation in the phylogenetic tree. Some polymorphic bands, involving both nucleotide and DNA methylation polymorphism, that differed between toxic and non-toxic samples were identified, cloned and sequenced. BLAST analysis of these fragments revealed differences in DNA methylation in some known genes and nucleotide polymorphism in chloroplast DNA. We conclude that MSAP is a powerful technique for the study of genetic diversity for organisms that have a narrow genetic base.

  10. Global patterns of amphibian phylogenetic diversity

    DEFF Research Database (Denmark)

    Fritz, Susanne; Rahbek, Carsten

    2012-01-01

    Aim  Phylogenetic diversity can provide insight into how evolutionary processes may have shaped contemporary patterns of species richness. Here, we aim to test for the influence of phylogenetic history on global patterns of amphibian species richness, and to identify areas where macroevolutionary...... processes such as diversification and dispersal have left strong signatures on contemporary species richness. Location  Global; equal-area grid cells of approximately 10,000 km2. Methods  We generated an amphibian global supertree (6111 species) and repeated analyses with the largest available molecular...... phylogeny (2792 species). We combined each tree with global species distributions to map four indices of phylogenetic diversity. To investigate congruence between global spatial patterns of amphibian species richness and phylogenetic diversity, we selected Faith’s phylogenetic diversity (PD) index...

  11. Genome-wide methylation patterns in Salmonella enterica Subsp. enterica Serovars.

    Directory of Open Access Journals (Sweden)

    Cary Pirone-Davies

    Full Text Available The methylation of DNA bases plays an important role in numerous biological processes including development, gene expression, and DNA replication. Salmonella is an important foodborne pathogen, and methylation in Salmonella is implicated in virulence. Using single molecule real-time (SMRT DNA-sequencing, we sequenced and assembled the complete genomes of eleven Salmonella enterica isolates from nine different serovars, and analysed the whole-genome methylation patterns of each genome. We describe 16 distinct N6-methyladenine (m6A methylated motifs, one N4-methylcytosine (m4C motif, and one combined m6A-m4C motif. Eight of these motifs are novel, i.e., they have not been previously described. We also identified the methyltransferases (MTases associated with 13 of the motifs. Some motifs are conserved across all Salmonella serovars tested, while others were found only in a subset of serovars. Eight of the nine serovars contained a unique methylated motif that was not found in any other serovar (most of these motifs were part of Type I restriction modification systems, indicating the high diversity of methylation patterns present in Salmonella.

  12. Mapping global diversity patterns for migratory birds.

    Directory of Open Access Journals (Sweden)

    Marius Somveille

    Full Text Available Nearly one in five bird species has separate breeding and overwintering distributions, and the regular migrations of these species cause a substantial seasonal redistribution of avian diversity across the world. However, despite its ecological importance, bird migration has been largely ignored in studies of global avian biodiversity, with few studies having addressed it from a macroecological perspective. Here, we analyse a dataset on the global distribution of the world's birds in order to examine global spatial patterns in the diversity of migratory species, including: the seasonal variation in overall species diversity due to migration; the contribution of migratory birds to local bird diversity; and the distribution of narrow-range and threatened migratory birds. Our analyses reveal a striking asymmetry between the Northern and Southern hemispheres, evident in all of the patterns investigated. The highest migratory bird diversity was found in the Northern Hemisphere, with high inter-continental turnover in species composition between breeding and non-breeding seasons, and extensive regions (at high latitudes where migratory birds constitute the majority of the local avifauna. Threatened migratory birds are concentrated mainly in Central and Southern Asia, whereas narrow-range migratory species are mainly found in Central America, the Himalayas and Patagonia. Overall, global patterns in the diversity of migratory birds indicate that bird migration is mainly a Northern Hemisphere phenomenon. The asymmetry between the Northern and Southern hemispheres could not have easily been predicted from the combined results of regional scale studies, highlighting the importance of a global perspective.

  13. Divergent methylation pattern in adult stage between two forms of Tetranychus urticae (Acari: Tetranychidae).

    Science.gov (United States)

    Yang, Si-Xia; Guo, Chao; Zhao, Xiu-Ting; Sun, Jing-Tao; Hong, Xiao-Yue

    2017-02-19

    The two-spotted spider mite, Tetranychus urticae Koch has two forms: green form and red form. Understanding the molecular basis of how these two forms established without divergent genetic background is an intriguing area. As a well-known epigenetic process, DNA methylation has particularly important roles in gene regulation and developmental variation across diverse organisms that do not alter genetic background. Here, to investigate whether DNA methylation could be associated with different phenotypic consequences in the two forms of T. urticae, we surveyed the genome-wide cytosine methylation status and expression level of DNA methyltransferase 3 (Tudnmt3) throughout their entire life cycle. Methylation-sensitive amplification polymorphism (MSAP) analyses of 585 loci revealed variable methylation patterns in the different developmental stages. In particular, principal coordinates analysis (PCoA) indicates a significant epigenetic differentiation between female adults of the two forms. The gene expression of Tudnmt3 was detected in all examined developmental stages, which was significantly different in the adult stage of the two forms. Together, our results reveal the epigenetic distance between the two forms of T. urticae, suggesting that DNA methylation might be implicated in different developmental demands, and contribute to different phenotypes in the adult stage of these two forms. © 2017 Institute of Zoology, Chinese Academy of Sciences.

  14. DNA methylation and genetic diversity analysis of genus Cycas in ...

    African Journals Online (AJOL)

    10 Cycas species as well as one subspecies localized in Thailand were studied using the methylation sensitive amplification polymorphism (MSAP) technique. 11 MSAP primer combinations were used and 720 MSAP bands were generated. The percentages of DNA methylation estimated from MSAP fingerprints were in ...

  15. Comparative Genomics Reveals the Diversity of Restriction-Modification Systems and DNA Methylation Sites in Listeria monocytogenes.

    Science.gov (United States)

    Chen, Poyin; den Bakker, Henk C; Korlach, Jonas; Kong, Nguyet; Storey, Dylan B; Paxinos, Ellen E; Ashby, Meredith; Clark, Tyson; Luong, Khai; Wiedmann, Martin; Weimer, Bart C

    2017-02-01

    Listeria monocytogenes is a bacterial pathogen that is found in a wide variety of anthropogenic and natural environments. Genome sequencing technologies are rapidly becoming a powerful tool in facilitating our understanding of how genotype, classification phenotypes, and virulence phenotypes interact to predict the health risks of individual bacterial isolates. Currently, 57 closed L. monocytogenes genomes are publicly available, representing three of the four phylogenetic lineages, and they suggest that L. monocytogenes has high genomic synteny. This study contributes an additional 15 closed L. monocytogenes genomes that were used to determine the associations between the genome and methylome with host invasion magnitude. In contrast to previous findings, large chromosomal inversions and rearrangements were detected in five isolates at the chromosome terminus and within rRNA genes, including a previously undescribed inversion within rRNA-encoding regions. Each isolate's epigenome contained highly diverse methyltransferase recognition sites, even within the same serotype and methylation pattern. Eleven strains contained a single chromosomally encoded methyltransferase, one strain contained two methylation systems (one system on a plasmid), and three strains exhibited no methylation, despite the occurrence of methyltransferase genes. In three isolates a new, unknown DNA modification was observed in addition to diverse methylation patterns, accompanied by a novel methylation system. Neither chromosome rearrangement nor strain-specific patterns of epigenome modification observed within virulence genes were correlated with serotype designation, clonal complex, or in vitro infectivity. These data suggest that genome diversity is larger than previously considered in L. monocytogenes and that as more genomes are sequenced, additional structure and methylation novelty will be observed in this organism. Listeria monocytogenes is the causative agent of listeriosis, a disease

  16. ViralEpi v1.0: a high-throughput spectrum of viral epigenomic methylation profiles from diverse diseases.

    Science.gov (United States)

    Khan, Mohd Shoaib; Gupta, Amit Kumar; Kumar, Manoj

    2016-01-01

    To develop a computational resource for viral epigenomic methylation profiles from diverse diseases. Methylation patterns of Epstein-Barr virus and hepatitis B virus genomic regions are provided as web platform developed using open source Linux-Apache-MySQL-PHP (LAMP) bundle: programming and scripting languages, that is, HTML, JavaScript and PERL. A comprehensive and integrated web resource ViralEpi v1.0 is developed providing well-organized compendium of methylation events and statistical analysis associated with several diseases. Additionally, it also facilitates 'Viral EpiGenome Browser' for user-affable browsing experience using JavaScript-based JBrowse. This web resource would be helpful for research community engaged in studying epigenetic biomarkers for appropriate prognosis and diagnosis of diseases and its various stages.

  17. Investigation of differential HDAC4 methylation patterns in eating disorders.

    Science.gov (United States)

    Subramanian, Subha; Braun, Patricia R; Han, Shizhong; Potash, James B

    2018-02-01

    The objective of this study was to investigate the relationship between methylation patterns of the histone deacetylase 4 gene and eating disorders in a site previously associated with anorexia nervosa (AN). Women with AN (N=28) or bulimia nervosa (BN) (N=19) were age-matched and sex-matched to controls (N=45). We obtained saliva-derived DNA and use bisulfite pyrosequencing to examine region-specific methylation differences between cases and controls. The region assayed includes 15 CpGs. We found no significant association between the previously implicated CpG and either AN or BN. We found that three CpGs were nominally associated with AN (P=0.02-0.03); the largest difference was a 9% hypermethylation in AN. One CpG was nominally associated with BN (P=0.04), with 4% hypomethylation. None of these results remained significant after correction for multiple testing. We did not replicate previous findings, though through expanded coverage, we identified additional CpGs that were nominally associated with eating disorders.

  18. Detecting differential DNA methylation from sequencing of bisulfite converted DNA of diverse species.

    Science.gov (United States)

    Huh, Iksoo; Wu, Xin; Park, Taesung; Yi, Soojin V

    2017-07-21

    DNA methylation is one of the most extensively studied epigenetic modifications of genomic DNA. In recent years, sequencing of bisulfite-converted DNA, particularly via next-generation sequencing technologies, has become a widely popular method to study DNA methylation. This method can be readily applied to a variety of species, dramatically expanding the scope of DNA methylation studies beyond the traditionally studied human and mouse systems. In parallel to the increasing wealth of genomic methylation profiles, many statistical tools have been developed to detect differentially methylated loci (DMLs) or differentially methylated regions (DMRs) between biological conditions. We discuss and summarize several key properties of currently available tools to detect DMLs and DMRs from sequencing of bisulfite-converted DNA. However, the majority of the statistical tools developed for DML/DMR analyses have been validated using only mammalian data sets, and less priority has been placed on the analyses of invertebrate or plant DNA methylation data. We demonstrate that genomic methylation profiles of non-mammalian species are often highly distinct from those of mammalian species using examples of honey bees and humans. We then discuss how such differences in data properties may affect statistical analyses. Based on these differences, we provide three specific recommendations to improve the power and accuracy of DML and DMR analyses of invertebrate data when using currently available statistical tools. These considerations should facilitate systematic and robust analyses of DNA methylation from diverse species, thus advancing our understanding of DNA methylation. © The Author 2017. Published by Oxford University Press.

  19. The highly heterogeneous methylated genomes and diverse restriction-modification systems of bloom-forming Microcystis.

    Science.gov (United States)

    Zhao, Liang; Song, Yulong; Li, Lin; Gan, Nanqin; Brand, Jerry J; Song, Lirong

    2018-05-01

    The occurrence of harmful Microcystis blooms is increasing in frequency in a myriad of freshwater ecosystems. Despite considerable research pertaining to the cause and nature of these blooms, the molecular mechanisms behind the cosmopolitan distribution and phenotypic diversity in Microcystis are still unclear. We compared the patterns and extent of DNA methylation in three strains of Microcystis, PCC 7806SL, NIES-2549 and FACHB-1757, using Single Molecule Real-Time (SMRT) sequencing technology. Intact restriction-modification (R-M) systems were identified from the genomes of these strains, and from two previously sequenced strains of Microcystis, NIES-843 and TAIHU98. A large number of methylation motifs and R-M genes were identified in these strains, which differ substantially among different strains. Of the 35 motifs identified, eighteen had not previously been reported. Strain NIES-843 contains a larger number of total putative methyltransferase genes than have been reported previously from any bacterial genome. Genomic comparisons reveal that methyltransferases (some partial) may have been acquired from the environment through horizontal gene transfer. Copyright © 2018 Elsevier B.V. All rights reserved.

  20. Methyl vinyl glycolate as a diverse platform molecule

    DEFF Research Database (Denmark)

    Sølvhøj, Amanda Birgitte; Taarning, Esben; Madsen, Robert

    2016-01-01

    and various long-chain terminal olefins give unsaturated α-hydroxy fatty acid methyl esters in good yields. [3,3]-Sigmatropic rearrangements of MVG also proceed in good yields to give unsaturated adipic acid derivatives. Finally, rearrangement of the allylic acetate of MVG proceeds in acceptable yield...

  1. Patterns of DNMT1 Promoter Methylation in Patients with Acute Lymphoblastic Leukemia.

    Science.gov (United States)

    Rahmani, Tirdad; Azad, Mehdi; Chahardouli, Bahram; Nasiri, Hajar; Vatanmakanian, Mousa; Kaviani, Saeid

    2017-07-01

    Background: Acute lymphoblastic leukemia (ALL) is a clonal malignant disorder characterized by an uncontrolled proliferation of immature T or B lymphocytes. Extensive studies have shown that the epigenetic changes, especially modified DNA methylation patterns in the regulatory regions through the DNA methyltransferase (DNMTs), play an important role in the development of genetic disorders and abnormal growth and maturation capacity of leukemic stem cells (LSCs).The aim of this study was to evaluate the changes in DNMT1 promoter methylation and its expression pattern in patients with ALL. Materials and Methods: In this experimental study, methylation specific PCR (MSP) was used to assess the methylation status of DNMT1 promoter regions in samples collected from ALL patients (n=45) and healthy control subjects. According to this method, un-methylated cytosine nucleotides are converted to uracil by sodium bisulfite and the proliferation of methylated and un-methylated regions are performed using specific primers for target sequences. Results: None of the patients with B and T-ALL showed methylated promoter regions of the DNMT1 gene, while the methylation pattern of both pre-B ALL patients and the control group showed a relative promoter methylation. Conclusion: Analysis of promoter methylation patterns in various subgroups of ALL has revealed the importance of DNMT1 in the regulation of gene expression. Likewise, extensive data have also highlighted the methylation-based mechanisms exerted by DNAM1 as one of the main participants regulating gene expression in B-ALL and T-ALL patients. Investigation of the overall DNA methylation pattern offers significant improvements in the prediction of disease prognosis and treatment response.

  2. Shotgun Bisulfite Sequencing of the Betula platyphylla Genome Reveals the Tree’s DNA Methylation Patterning

    Directory of Open Access Journals (Sweden)

    Chang Su

    2014-12-01

    Full Text Available DNA methylation plays a critical role in the regulation of gene expression. Most studies of DNA methylation have been performed in herbaceous plants, and little is known about the methylation patterns in tree genomes. In the present study, we generated a map of methylated cytosines at single base pair resolution for Betula platyphylla (white birch by bisulfite sequencing combined with transcriptomics to analyze DNA methylation and its effects on gene expression. We obtained a detailed view of the function of DNA methylation sequence composition and distribution in the genome of B. platyphylla. There are 34,460 genes in the whole genome of birch, and 31,297 genes are methylated. Conservatively, we estimated that 14.29% of genomic cytosines are methylcytosines in birch. Among the methylation sites, the CHH context accounts for 48.86%, and is the largest proportion. Combined transcriptome and methylation analysis showed that the genes with moderate methylation levels had higher expression levels than genes with high and low methylation. In addition, methylated genes are highly enriched for the GO subcategories of binding activities, catalytic activities, cellular processes, response to stimulus and cell death, suggesting that methylation mediates these pathways in birch trees.

  3. DNA methylation patterns provide insight into epigenetic regulation in the Pacific oyster (Crassostrea gigas

    Directory of Open Access Journals (Sweden)

    Gavery Mackenzie R

    2010-08-01

    Full Text Available Abstract Background DNA methylation is an epigenetic mechanism with important regulatory functions in animals. While the mechanism itself is evolutionarily ancient, the distribution and function of DNA methylation is diverse both within and among phylogenetic groups. Although DNA methylation has been well studied in mammals, there are limited data on invertebrates, particularly molluscs. Here we characterize the distribution and investigate potential functions of DNA methylation in the Pacific oyster (Crassostrea gigas. Results Methylation sensitive PCR and bisulfite sequencing PCR approaches were used to identify CpG methylation in C. gigas genes and demonstrated that this species possesses intragenic methylation. In silico analysis of CpGo/e ratios in publicly available sequence data suggests that DNA methylation is a common feature of the C. gigas genome, and that specific functional categories of genes have significantly different levels of methylation. Conclusions The Pacific oyster genome displays intragenic DNA methylation and contains genes necessary for DNA methylation in animals. Results of this investigation suggest that DNA methylation has regulatory functions in Crassostrea gigas, particularly in gene families that have inducible expression, including those involved in stress and environmental responses.

  4. Early Developmental and Evolutionary Origins of Gene Body DNA Methylation Patterns in Mammalian Placentas.

    Directory of Open Access Journals (Sweden)

    Diane I Schroeder

    2015-08-01

    Full Text Available Over the last 20-80 million years the mammalian placenta has taken on a variety of morphologies through both divergent and convergent evolution. Recently we have shown that the human placenta genome has a unique epigenetic pattern of large partially methylated domains (PMDs and highly methylated domains (HMDs with gene body DNA methylation positively correlating with level of gene expression. In order to determine the evolutionary conservation of DNA methylation patterns and transcriptional regulatory programs in the placenta, we performed a genome-wide methylome (MethylC-seq analysis of human, rhesus macaque, squirrel monkey, mouse, dog, horse, and cow placentas as well as opossum extraembryonic membrane. We found that, similar to human placenta, mammalian placentas and opossum extraembryonic membrane have globally lower levels of methylation compared to somatic tissues. Higher relative gene body methylation was the conserved feature across all mammalian placentas, despite differences in PMD/HMDs and absolute methylation levels. Specifically, higher methylation over the bodies of genes involved in mitosis, vesicle-mediated transport, protein phosphorylation, and chromatin modification was observed compared with the rest of the genome. As in human placenta, higher methylation is associated with higher gene expression and is predictive of genic location across species. Analysis of DNA methylation in oocytes and preimplantation embryos shows a conserved pattern of gene body methylation similar to the placenta. Intriguingly, mouse and cow oocytes and mouse early embryos have PMD/HMDs but their placentas do not, suggesting that PMD/HMDs are a feature of early preimplantation methylation patterns that become lost during placental development in some species and following implantation of the embryo.

  5. DNA methylation and genetic diversity analysis of genus Cycas in ...

    African Journals Online (AJOL)

    mallory

    2012-01-12

    Jan 12, 2012 ... elucidate the role of epigenetics in the genetic diversity of these plants. MATERIALS AND METHODS. Plant materials and DNA extraction. 66 Cycas samples consisting of 10 species and one subspecies were collected from the Nong Nooch Tropical Garden, Chonburi province, Thailand. For each species ...

  6. Assessment of the genetic diversity and pattern of relationship of ...

    African Journals Online (AJOL)

    An understanding of the extent, distribution and patterns of genetic variation is useful for estimation of any possible loss of genetic diversity and assessment of genetic variability and its potential use in breeding programs, including establishment of heterotic groups. This study assessed patterns of genetic diversity and ...

  7. Climate change and amphibian diversity patterns in Mexico

    DEFF Research Database (Denmark)

    Ochoa-Ochoa, Leticia M.; Rodríguez, Pilar; Mora, Franz

    2012-01-01

    The aim of this article is to characterize at fine scale alpha and beta diversity patterns for Mexican amphibians and analyze how these patterns might change under a moderate climate-change scenario, highlighting the overall consequences for amphibian diversity at the country level. We used a geo...

  8. Biodiversity patterns along ecological gradients: unifying β-diversity indices.

    Science.gov (United States)

    Szava-Kovats, Robert C; Pärtel, Meelis

    2014-01-01

    Ecologists have developed an abundance of conceptions and mathematical expressions to define β-diversity, the link between local (α) and regional-scale (γ) richness, in order to characterize patterns of biodiversity along ecological (i.e., spatial and environmental) gradients. These patterns are often realized by regression of β-diversity indices against one or more ecological gradients. This practice, however, is subject to two shortcomings that can undermine the validity of the biodiversity patterns. First, many β-diversity indices are constrained to range between fixed lower and upper limits. As such, regression analysis of β-diversity indices against ecological gradients can result in regression curves that extend beyond these mathematical constraints, thus creating an interpretational dilemma. Second, despite being a function of the same measured α- and γ-diversity, the resultant biodiversity pattern depends on the choice of β-diversity index. We propose a simple logistic transformation that rids beta-diversity indices of their mathematical constraints, thus eliminating the possibility of an uninterpretable regression curve. Moreover, this transformation results in identical biodiversity patterns for three commonly used classical beta-diversity indices. As a result, this transformation eliminates the difficulties of both shortcomings, while allowing the researcher to use whichever beta-diversity index deemed most appropriate. We believe this method can help unify the study of biodiversity patterns along ecological gradients.

  9. Variation in DNA Methylation Patterns is More Common among Maize Inbreds than among Tissues

    Directory of Open Access Journals (Sweden)

    Steven R. Eichten

    2013-07-01

    Full Text Available Chromatin modifications, such as DNA methylation, can provide heritable, epigenetic regulation of gene expression in the absence of genetic changes. A role for DNA methylation in meiotically stable marking of repetitive elements and other sequences has been demonstrated in plants. Methylation of DNA is also proposed to play a role in development through providing a mitotic memory of gene expression states established during cellular differentiation. We sought to clarify the relative levels of DNA methylation variation among different genotypes and tissues in maize ( L.. We have assessed genomewide DNA methylation patterns in leaf, immature tassel, embryo, and endosperm tissues of two inbred maize lines: B73 and Mo17. There are hundreds of regions of differential methylation present between the two genotypes. In general, the same regions exhibit differential methylation between B73 and Mo17 in each of the tissues that were surveyed. In contrast, there are few examples of tissue-specific DNA methylation variation. Only a subset of regions with tissue-specific variation in DNA methylation show similar patterns in both genotypes of maize and even fewer are associated with altered gene expression levels among the tissues. Our data indicates a limited impact of DNA methylation on developmental gene regulation within maize.

  10. Epigenomic diversity of colorectal cancer indicated by LINE-1 methylation in a database of 869 tumors

    Directory of Open Access Journals (Sweden)

    Schernhammer Eva S

    2010-05-01

    Full Text Available Abstract Background Genome-wide DNA hypomethylation plays a role in genomic instability and carcinogenesis. LINE-1 (L1 retrotransposon constitutes a substantial portion of the human genome, and LINE-1 methylation correlates with global DNA methylation status. LINE-1 hypomethylation in colon cancer has been strongly associated with poor prognosis. However, whether LINE-1 hypomethylators constitute a distinct cancer subtype remains uncertain. Recent evidence for concordant LINE-1 hypomethylation within synchronous colorectal cancer pairs suggests the presence of a non-stochastic mechanism influencing tumor LINE-1 methylation level. Thus, it is of particular interest to examine whether its wide variation can be attributed to clinical, pathologic or molecular features. Design Utilizing a database of 869 colorectal cancers in two prospective cohort studies, we constructed multivariate linear and logistic regression models for LINE-1 methylation (quantified by Pyrosequencing. Variables included age, sex, body mass index, family history of colorectal cancer, smoking status, tumor location, stage, grade, mucinous component, signet ring cells, tumor infiltrating lymphocytes, CpG island methylator phenotype (CIMP, microsatellite instability, expression of TP53 (p53, CDKN1A (p21, CTNNB1 (β-catenin, PTGS2 (cyclooxygenase-2, and FASN, and mutations in KRAS, BRAF, and PIK3CA. Results Tumoral LINE-1 methylation ranged from 23.1 to 90.3 of 0-100 scale (mean 61.4; median 62.3; standard deviation 9.6, and distributed approximately normally except for extreme hypomethylators [LINE-1 methylation Conclusions LINE-1 extreme hypomethylators appear to constitute a previously-unrecognized, distinct subtype of colorectal cancers, which needs to be confirmed by additional studies. Our tumor LINE-1 methylation data indicate enormous epigenomic diversity of individual colorectal cancers.

  11. Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer.

    Science.gov (United States)

    Kim, Jung H; Dhanasekaran, Saravana M; Prensner, John R; Cao, Xuhong; Robinson, Daniel; Kalyana-Sundaram, Shanker; Huang, Christina; Shankar, Sunita; Jing, Xiaojun; Iyer, Matthew; Hu, Ming; Sam, Lee; Grasso, Catherine; Maher, Christopher A; Palanisamy, Nallasivam; Mehra, Rohit; Kominsky, Hal D; Siddiqui, Javed; Yu, Jindan; Qin, Zhaohui S; Chinnaiyan, Arul M

    2011-07-01

    Beginning with precursor lesions, aberrant DNA methylation marks the entire spectrum of prostate cancer progression. We mapped the global DNA methylation patterns in select prostate tissues and cell lines using MethylPlex-next-generation sequencing (M-NGS). Hidden Markov model-based next-generation sequence analysis identified ∼68,000 methylated regions per sample. While global CpG island (CGI) methylation was not differential between benign adjacent and cancer samples, overall promoter CGI methylation significantly increased from ~12.6% in benign samples to 19.3% and 21.8% in localized and metastatic cancer tissues, respectively (P-value prostate tissues, 2481 differentially methylated regions (DMRs) are cancer-specific, including numerous novel DMRs. A novel cancer-specific DMR in the WFDC2 promoter showed frequent methylation in cancer (17/22 tissues, 6/6 cell lines), but not in the benign tissues (0/10) and normal PrEC cells. Integration of LNCaP DNA methylation and H3K4me3 data suggested an epigenetic mechanism for alternate transcription start site utilization, and these modifications segregated into distinct regions when present on the same promoter. Finally, we observed differences in repeat element methylation, particularly LINE-1, between ERG gene fusion-positive and -negative cancers, and we confirmed this observation using pyrosequencing on a tissue panel. This comprehensive methylome map will further our understanding of epigenetic regulation in prostate cancer progression.

  12. Differential DNA methylation patterns define status epilepticus and epileptic tolerance.

    Science.gov (United States)

    Miller-Delaney, Suzanne F C; Das, Sudipto; Sano, Takanori; Jimenez-Mateos, Eva M; Bryan, Kenneth; Buckley, Patrick G; Stallings, Raymond L; Henshall, David C

    2012-02-01

    Prolonged seizures (status epilepticus) produce pathophysiological changes in the hippocampus that are associated with large-scale, wide-ranging changes in gene expression. Epileptic tolerance is an endogenous program of cell protection that can be activated in the brain by previous exposure to a non-harmful seizure episode before status epilepticus. A major transcriptional feature of tolerance is gene downregulation. Here, through methylation analysis of 34,143 discrete loci representing all annotated CpG islands and promoter regions in the mouse genome, we report the genome-wide DNA methylation changes in the hippocampus after status epilepticus and epileptic tolerance in adult mice. A total of 321 genes showed altered DNA methylation after status epilepticus alone or status epilepticus that followed seizure preconditioning, with >90% of the promoters of these genes undergoing hypomethylation. These profiles included genes not previously associated with epilepsy, such as the polycomb gene Phc2. Differential methylation events generally occurred throughout the genome without bias for a particular chromosomal region, with the exception of a small region of chromosome 4, which was significantly overrepresented with genes hypomethylated after status epilepticus. Surprisingly, only few genes displayed differential hypermethylation in epileptic tolerance. Nevertheless, gene ontology analysis emphasized the majority of differential methylation events between the groups occurred in genes associated with nuclear functions, such as DNA binding and transcriptional regulation. The present study reports select, genome-wide DNA methylation changes after status epilepticus and in epileptic tolerance, which may contribute to regulating the gene expression environment of the seizure-damaged hippocampus.

  13. Regional genetic diversity patterns in Antarctic hairgrass (Deschampsia antartica Desv.)

    NARCIS (Netherlands)

    van de Wouw, M.J.; Van Dijk, P.J.; Huiskes, A.H.L.

    2008-01-01

    Aim To determine patterns in diversity of a major Antarctic plant species, including relationships of Antarctic populations with those outside the Antarctic zone. Location Antarctic Peninsula, Maritime Antarctica, sub-Antarctic islands, Falkland Islands and South America. Methods Amplified fragment

  14. Does DNA methylation pattern mark generative development in winter rape?

    Czech Academy of Sciences Publication Activity Database

    Filek, M.; Janiak, A.; Szarejko, I.; Grabczynska, J.; Macháčková, Ivana; Krekule, Jan

    2006-01-01

    Roč. 61, 5-6 (2006), s. 387-396 ISSN 0939-5075 R&D Projects: GA AV ČR IAA600040612 Institutional research plan: CEZ:AV0Z50380511 Keywords : DNA methylation * rape * vernalization Subject RIV: EF - Botanics Impact factor: 0.720, year: 2006

  15. Aberrant methylation patterns affect the molecular pathogenesis of rheumatoid arthritis.

    Science.gov (United States)

    Lin, Yang; Luo, Zhengqiang

    2017-05-01

    This study aims to investigate DNA methylation signatures in fibroblast-like synoviocytes (FLS) from patients with rheumatoid arthritis (RA), and to explore the relationship with transcription factors (TFs) that help to distinguish RA from osteoarthritis (OA). Microarray dataset of GSE46346, including six FLS samples from patients with RA and five FLS samples from patients with OA, was downloaded from the Gene Expression Omnibus database. RA and OA samples were screened for differentially methylated loci (DMLs). The corresponding differentially methylated genes (DMGs) were identified, followed by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) enrichment analysis. A transcriptional regulatory network was built with TFs and their corresponding DMGs. Overall, 280 hypomethylated loci and 561 hypermethylated loci were screened. Genes containing hypermethylated loci were enriched in pathways in cancer, ECM-receptor interaction, focal adhesion and neurotrophin signaling pathways. Genes containing hypomethylated loci were enriched in the neurotrophin signaling pathway. Moreover, we found that CCCTC-binding factor (CTCF), Yin Yang 1 (YY1), v-myc avian myelocytomatosis viral oncogene homolog (c-MYC), and early growth response 1 (EGR1) were important TFs in the transcriptional regulatory network. Therefore, DMGs might participate in the neurotrophin signaling pathway, pathways in cancer, ECM-receptor interaction and focal adhesion pathways in RA. Furthermore, CTCF, c-MYC, YY1, and EGR1 may play important roles in RA through regulating DMGs. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Three dimensional analysis of histone methylation patterns in normal and tumor cell nuclei

    Directory of Open Access Journals (Sweden)

    M Cremer

    2009-06-01

    Full Text Available Histone modifications represent an important epigenetic mechanism for the organization of higher order chromatin structure and gene regulation. Methylation of position-specific lysine residues in the histone H3 and H4 amino termini has been linked with the formation of constitutive and facultative heterochromatin as well as with specifically repressed single gene loci. Using an antibody, directed against dimethylated lysine 9 of histone H3 and several other lysine methylation sites, we visualized the nuclear distribution pattern of chromatin flagged by these methylated lysines in 3D preserved nuclei of normal and malignant cell types. Optical confocal serial sections were used for a quantitative evaluation. We demonstrate distinct differences of these histone methylation patterns among nuclei of different cell types after exit of the cell cycle. Changes in the pattern formation were also observed during the cell cycle. Our data suggest an important role of methylated histones in the reestablishment of higher order chromatin arrangements during telophase/early G1. Cell type specific histone methylation patterns are possibly causally involved in the formation of cell type specific heterochromatin compartments, composed of (pericentromeric regions and chromosomal subregions from neighboring chromosome territories, which contain silent genes.

  17. Regulation of DNA Methylation Patterns by CK2-Mediated Phosphorylation of Dnmt3a

    Directory of Open Access Journals (Sweden)

    Rachel Deplus

    2014-08-01

    Full Text Available DNA methylation is a central epigenetic modification that is established by de novo DNA methyltransferases. The mechanisms underlying the generation of genomic methylation patterns are still poorly understood. Using mass spectrometry and a phosphospecific Dnmt3a antibody, we demonstrate that CK2 phosphorylates endogenous Dnmt3a at two key residues located near its PWWP domain, thereby downregulating the ability of Dnmt3a to methylate DNA. Genome-wide DNA methylation analysis shows that CK2 primarily modulates CpG methylation of several repeats, most notably of Alu SINEs. This modulation can be directly attributed to CK2-mediated phosphorylation of Dnmt3a. We also find that CK2-mediated phosphorylation is required for localization of Dnmt3a to heterochromatin. By revealing phosphorylation as a mode of regulation of de novo DNA methyltransferase function and by uncovering a mechanism for the regulation of methylation at repetitive elements, our results shed light on the origin of DNA methylation patterns.

  18. Epigenetic Patterns of PTSD: DNA Methylation In Serum of OIF/OEF Servicemembers

    Science.gov (United States)

    2011-01-01

    also have no data on other relevant exposures which are known to affect DNA methylation , such as dietary factors ( folate , vitamin B12 intake), (54, 55...ANSI Std. Z39.18 W81XWH-08-2-0053 31 MAR 2008 - 31 DEC 2010Final01-01-2011 Epigenetic Patterns of PTSD: DNA Methylation in Serum of OIF/OEF...distribution unlimited PTSD, epigenetics, DNA methylation , cytokines, serum, pre-deployment, post-deployment Abstract on next page. 38 jrusiecki@usuhs.mil

  19. Genome-wide DNA methylation patterns and transcription analysis in sheep muscle.

    Directory of Open Access Journals (Sweden)

    Christine Couldrey

    Full Text Available DNA methylation plays a central role in regulating many aspects of growth and development in mammals through regulating gene expression. The development of next generation sequencing technologies have paved the way for genome-wide, high resolution analysis of DNA methylation landscapes using methodology known as reduced representation bisulfite sequencing (RRBS. While RRBS has proven to be effective in understanding DNA methylation landscapes in humans, mice, and rats, to date, few studies have utilised this powerful method for investigating DNA methylation in agricultural animals. Here we describe the utilisation of RRBS to investigate DNA methylation in sheep Longissimus dorsi muscles. RRBS analysis of ∼1% of the genome from Longissimus dorsi muscles provided data of suitably high precision and accuracy for DNA methylation analysis, at all levels of resolution from genome-wide to individual nucleotides. Combining RRBS data with mRNAseq data allowed the sheep Longissimus dorsi muscle methylome to be compared with methylomes from other species. While some species differences were identified, many similarities were observed between DNA methylation patterns in sheep and other more commonly studied species. The RRBS data presented here highlights the complexity of epigenetic regulation of genes. However, the similarities observed across species are promising, in that knowledge gained from epigenetic studies in human and mice may be applied, with caution, to agricultural species. The ability to accurately measure DNA methylation in agricultural animals will contribute an additional layer of information to the genetic analyses currently being used to maximise production gains in these species.

  20. Patterns of cytosine methylation in an elite rice hybrid and its parental lines, detected by a methylation-sensitive amplification polymorphism technique.

    Science.gov (United States)

    Xiong, L Z; Xu, C G; Saghai Maroof, M A; Zhang, Q

    1999-04-01

    DNA methylation is known to play an important role in the regulation of gene expression in eukaryotes. In this study, we assessed the extent and pattern of cytosine methylation in the rice genome, using the technique of methylation-sensitive amplified polymorphism (MSAP), which is a modification of the amplified fragment length polymorphism (AFLP) method that makes use of the differential sensitivity of a pair of isoschizomers to cytosine methylation. The tissues assayed included seedlings and flag leaves of an elite rice hybrid, Shanyou 63, and the parental lines Zhenshan 97 and Minghui 63. In all, 1076 fragments, each representing a recognition site cleaved by either or both of the isoschizomers, were amplified using 16 pairs of selective primers. A total of 195 sites were found to be methylated at cytosines in one or both parents, and the two parents showed approximately the same overall degree of methylation (16.3%), as revealed by the incidence of differential digestion by the isoschizomers. Four classes of patterns were identified in a comparative assay of cytosine methylation in the parents and hybrid; increased methylation was detected in the hybrid compared to the parents at some of the recognition sites, while decreased methylation in the hybrid was detected at other sites. A small proportion of the sites was found to be differentially methylated in seedlings and flag leaves; DNA from young seedlings was methylated to a greater extent than that from flag leaves. Almost all of the methylation patterns detected by MSAP could be confirmed by Southern analysis using the isolated amplified fragments as probes. The results clearly demonstrate that the MSAP technique is highly efficient for large-scale detection of cytosine methylation in the rice genome. We believe that the technique can be adapted for use in other plant species.

  1. DNA methylation patterns in bladder cancer and washing cell sediments: a perspective for tumor recurrence detection

    Directory of Open Access Journals (Sweden)

    Goldberg José

    2008-08-01

    Full Text Available Abstract Background Epigenetic alterations are a hallmark of human cancer. In this study, we aimed to investigate whether aberrant DNA methylation of cancer-associated genes is related to urinary bladder cancer recurrence. Methods A set of 4 genes, including CDH1 (E-cadherin, SFN (stratifin, RARB (retinoic acid receptor, beta and RASSF1A (Ras association (RalGDS/AF-6 domain family 1, had their methylation patterns evaluated by MSP (Methylation-Specific Polymerase Chain Reaction analysis in 49 fresh urinary bladder carcinoma tissues (including 14 cases paired with adjacent normal bladder epithelium, 3 squamous cell carcinomas and 2 adenocarcinomas and 24 cell sediment samples from bladder washings of patients classified as cancer-free by cytological analysis (control group. A third set of samples included 39 archived tumor fragments and 23 matched washouts from 20 urinary bladder cancer patients in post-surgical monitoring. After genomic DNA isolation and sodium bisulfite modification, methylation patterns were determined and correlated with standard clinic-histopathological parameters. Results CDH1 and SFN genes were methylated at high frequencies in bladder cancer as well as in paired normal adjacent tissue and exfoliated cells from cancer-free patients. Although no statistically significant differences were found between RARB and RASSF1A methylation and the clinical and histopathological parameters in bladder cancer, a sensitivity of 95% and a specificity of 71% were observed for RARB methylation (Fisher's Exact test (p RASSF1A gene, respectively, in relation to the control group. Conclusion Indistinct DNA hypermethylation of CDH1 and SFN genes between tumoral and normal urinary bladder samples suggests that these epigenetic features are not suitable biomarkers for urinary bladder cancer. However, RARB and RASSF1A gene methylation appears to be an initial event in urinary bladder carcinogenesis and should be considered as defining a panel of

  2. Mutual Coupling Effects on Pattern Diversity Antennas for MIMO Femtocells

    Directory of Open Access Journals (Sweden)

    Yue Gao

    2010-01-01

    Full Text Available Diversity antennas play an important role in wireless communications. However, mutual coupling between multiple ports of a diversity antenna has significant effects on wireless radio links and channel capacity. In this paper, dual-port pattern diversity antennas for femtocell applications are proposed to cover GSM1800, UMTS, and WLAN frequency bands. The channel capacities of the proposed antennas and two ideal dipoles with different mutual coupling levels are investigated in an indoor environment. The relation between mutual coupling and channel capacity is observed through investigations of these antennas.

  3. Diversity Patterns of Benthic Macrofauna Caused by Marine Fish Farming

    Directory of Open Access Journals (Sweden)

    Arnaldo Marín

    2011-04-01

    Full Text Available This paper reviews the patterns observed in the diversity and structure of the macrofauna benthic community under the influence of fish farming. First, we explain the effects of organic enrichment on the sediment and the consequences for the inhabiting communities. We describe the diversity trends in spatial and temporal gradients affected by fish farming and compare them with those described by the Pearson and Rosenberg model. We found that in general terms, the trends of diversity and other community parameters followed the Pearson and Rosenberg model but they can vary to some extent due to sediment local characteristics or to secondary disturbances. We also show the different mechanisms by which wild fish can affect macrofauna diversity patterns under fish farming influence. In addition, we comment the importance of the macrofauna diversity in the ecosystem functions and propose some guidelines to measure functional diversity related to relevant processes at ecosystem level. We propose more research efforts in the main topics commented in this review to improve management strategies to guarantee a good status of the diversity and ecosystem functioning of sediments influenced by fish farming.

  4. Temporal Patterns in Diversity Change on Earth Over Time

    Science.gov (United States)

    Bambach, Richard

    2007-05-01

    Multi-celled animals and plants did not originate until about 600 million years ago. Since then the diversity of life has expanded greatly, but this has not been a monotonic increase. Diversity, as taxonomic variety or richness, is produced by the interaction of origination and extinction. Origination and extinction are almost equally balanced; it has taken 600 million years to accumulate 10 to 30 million living species. With most species life spans in the range of one to fifteen million years most species that have ever originated are extinct and global diversity has “turned over” many times. Paleontologists recognize about 18 short-term events of elevated extinction intensity and diversity loss of sufficient magnitude to warrant the term “mass extinction.” Interestingly, in only one instance, the end-Cretaceous extinction, is there a consensus for the triggering event, but the kill mechanism or mechanisms that caused the widespread death of lineages is not established. We know less about the cause-effect relationships for other events. Recently a 62 million-year periodicity in the fluctuation of diversity has been documented, expressed primarily in the variation of diversity of marine genera that survived 45 million years or less. Analysis of the pattern of diversity change at the finest temporal scale possible suggests that the short-term mass extinctions are superimposed on this regular pattern of diversity fluctuations, rather than causal of them. However, most mass extinctions (14 of 18) occurred during the intervals of general diversity loss. It remains to be seen how origination and extinction interact to produce the periodic fluctuation in diversity.

  5. The concerted impact of domestication and transposon insertions on methylation patterns between dogs and gray wolves

    Science.gov (United States)

    Koch, Ilana Janowitz; Clark, Michelle M.; Thompson, Michael J.; Deere-Machemer, Kerry A.; Wang, Jun; Duarte, Lionel; Gnanadesikan, Gitanjali E.; McCoy, Eskender L.; Rubbi, Liudmilla; Stahler, Daniel R.; Pellegrini, Matteo; Ostrander, Elaine A.; Wayne, Robert K.; Sinsheimer, Janet S.; vonHoldt, Bridgett M.

    2015-01-01

    The process of domestication can exert intense trait-targeted selection on genes and regulatory regions. Specifically, rapid shifts in the structure and sequence of genomic regulatory elements could provide an explanation for the extensive, and sometimes extreme, variation in phenotypic traits observed in domesticated species. Here, we explored methylation differences from >24,000 cytosines distributed across the genomes of the domesticated dog (Canis familiaris) and the gray wolf (C. lupus). PCA and model-based cluster analyses identified two primary groups, domestic versus wild canids. A scan for significantly differentially methylated sites (DMSs) revealed species-specific patterns at 68 sites after correcting for cell heterogeneity, with weak yet significant hyper-methylation typical of purebred dogs when compared to wolves (59% and 58%, p66%) of differentially methylated regions contained or were associated with repetitive elements, indicative of a genotype-mediated trend. However, DMSs were also often linked to functionally relevant genes (e.g. neurotransmitters). Finally, we utilized known genealogical relationships among Yellowstone wolves to survey transmission stability of methylation marks, from which we found a substantial fraction that demonstrated high heritability (both H2 and h2>0.99). These analyses provide a unique epigenetic insight into the molecular consequences of recent selection and radiation of our most ancient domesticated companion, the dog. These findings suggest selection has acted on methylation patterns, providing a new genomic perspective on phenotypic diversification in domesticated species. PMID:27112634

  6. Geographical patterns in the beta diversity of China's woody plants

    DEFF Research Database (Denmark)

    Wang, Zhiheng; Fang, Jingyun; Tang, Zhiyao

    2012-01-01

    Beta diversity (i.e. species turnover rate across space) is fundamental for understanding mechanisms controlling large-scale species richness patterns. However, the influences on beta diversity are still a matter of debate. In particular, the relative role of environmental and spatial processes (e.......g. environmental niche versus dispersal limitation of species) remains elusive, and the influence of species range size has been poorly tested. Here, using distribution maps of 11 405 woody species in China (ca 9.6 ¿ 106 km2), we investigated 1) the geographical and directional patterns of beta diversity for all...... with their environmental niches due to dispersal limitation induced by China’s topography and/or their low dispersal ability. The projected rapid climatic changes will likely endanger such species. Species dispersal processes should be taken into account in future conservation strategies in China....

  7. Large-scale diversity of slope fishes: pattern inconsistency between multiple diversity indices.

    Science.gov (United States)

    Gaertner, Jean-Claude; Maiorano, Porzia; Mérigot, Bastien; Colloca, Francesco; Politou, Chrissi-Yianna; Gil De Sola, Luis; Bertrand, Jacques A; Murenu, Matteo; Durbec, Jean-Pierre; Kallianiotis, Argyris; Mannini, Alessandro

    2013-01-01

    Large-scale studies focused on the diversity of continental slope ecosystems are still rare, usually restricted to a limited number of diversity indices and mainly based on the empirical comparison of heterogeneous local data sets. In contrast, we investigate large-scale fish diversity on the basis of multiple diversity indices and using 1454 standardized trawl hauls collected throughout the upper and middle slope of the whole northern Mediterranean Sea (36°3'- 45°7' N; 5°3'W - 28°E). We have analyzed (1) the empirical relationships between a set of 11 diversity indices in order to assess their degree of complementarity/redundancy and (2) the consistency of spatial patterns exhibited by each of the complementary groups of indices. Regarding species richness, our results contrasted both the traditional view based on the hump-shaped theory for bathymetric pattern and the commonly-admitted hypothesis of a large-scale decreasing trend correlated with a similar gradient of primary production in the Mediterranean Sea. More generally, we found that the components of slope fish diversity we analyzed did not always show a consistent pattern of distribution according either to depth or to spatial areas, suggesting that they are not driven by the same factors. These results, which stress the need to extend the number of indices traditionally considered in diversity monitoring networks, could provide a basis for rethinking not only the methodological approach used in monitoring systems, but also the definition of priority zones for protection. Finally, our results call into question the feasibility of properly investigating large-scale diversity patterns using a widespread approach in ecology, which is based on the compilation of pre-existing heterogeneous and disparate data sets, in particular when focusing on indices that are very sensitive to sampling design standardization, such as species richness.

  8. Differential DNA methylation patterns of polycystic ovarian syndrome in whole blood of Chinese women

    DEFF Research Database (Denmark)

    Li, Shuxia; Zhu, Dongyi; Duan, Hongmei

    2017-01-01

    As a universally common endocrinopathy in women of reproductive age, the polycystic ovarian syndrome is characterized by composite clinical phenotypes reflecting the contributions of reproductive impact of ovarian dysfunction and metabolic abnormalities with widely varying symptoms resulting from...... interference of the genome with the environment through integrative biological mechanisms including epigenetics. We have performed a genome-wide DNA methylation analysis on polycystic ovarian syndrome and identified a substantial number of genomic sites differentially methylated in the whole blood of PCOS...... in the DNA methylome from ovarian tissue under PCOS condition. Most importantly, our genome-wide profiling focusing on PCOS patients revealed a large number of DNA methylation sites and their enriched functional pathways significantly associated with diverse clinical features (levels of prolactin, estradiol...

  9. Differential DNA methylation patterns of polycystic ovarian syndrome in whole blood of Chinese women.

    Science.gov (United States)

    Li, Shuxia; Zhu, Dongyi; Duan, Hongmei; Ren, Anran; Glintborg, Dorte; Andersen, Marianne; Skov, Vibe; Thomassen, Mads; Kruse, Torben; Tan, Qihua

    2017-03-28

    As a universally common endocrinopathy in women of reproductive age, the polycystic ovarian syndrome is characterized by composite clinical phenotypes reflecting the contributions of reproductive impact of ovarian dysfunction and metabolic abnormalities with widely varying symptoms resulting from interference of the genome with the environment through integrative biological mechanisms including epigenetics. We have performed a genome-wide DNA methylation analysis on polycystic ovarian syndrome and identified a substantial number of genomic sites differentially methylated in the whole blood of PCOS patients and healthy controls (52 sites, false discovery rate ovarian tissue under PCOS condition. Most importantly, our genome-wide profiling focusing on PCOS patients revealed a large number of DNA methylation sites and their enriched functional pathways significantly associated with diverse clinical features (levels of prolactin, estradiol, progesterone and menstrual cycle) that could serve as novel molecular basis of the clinical heterogeneity observed in PCOS women.

  10. DNA Methylation Pattern in Overweight Women under an Energy-Restricted Diet Supplemented with Fish Oil

    Directory of Open Access Journals (Sweden)

    Cátia Lira do Amaral

    2014-01-01

    Full Text Available Dietary factors modulate gene expression and are able to alter epigenetic signatures in peripheral blood mononuclear cells (PBMC. However, there are limited studies about the effects of omega-3 polyunsaturated fatty acids (n-3 PUFA on the epigenetic mechanisms that regulate gene expression. This research investigates the effects of n-3-rich fish oil supplementation on DNA methylation profile of several genes whose expression has been reported to be downregulated by n-3 PUFA in PBMC: CD36, FFAR3, CD14, PDK4, and FADS1. Young overweight women were supplemented with fish oil or control in a randomized 8-week intervention trial following a balanced diet with 30% energy restriction. Fatty acid receptor CD36 decreased DNA methylation at CpG +477 due to energy restriction. Hypocaloric diet-induced weight loss also reduced the methylation percentages of CpG sites located in CD14, PDK4, and FADS1. The methylation patterns of these genes were only slightly affected by the fish oil supplementation, being the most relevant to the attenuation of the weight loss-induced decrease in CD36 methylation after adjusting by baseline body weight. These results suggest that the n-3 PUFA-induced changes in the expression of these genes in PBMC are not mediated by DNA methylation, although other epigenetic mechanisms cannot be discarded.

  11. The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves.

    Science.gov (United States)

    Janowitz Koch, Ilana; Clark, Michelle M; Thompson, Michael J; Deere-Machemer, Kerry A; Wang, Jun; Duarte, Lionel; Gnanadesikan, Gitanjali E; McCoy, Eskender L; Rubbi, Liudmilla; Stahler, Daniel R; Pellegrini, Matteo; Ostrander, Elaine A; Wayne, Robert K; Sinsheimer, Janet S; vonHoldt, Bridgett M

    2016-04-01

    The process of domestication can exert intense trait-targeted selection on genes and regulatory regions. Specifically, rapid shifts in the structure and sequence of genomic regulatory elements could provide an explanation for the extensive, and sometimes extreme, variation in phenotypic traits observed in domesticated species. Here, we explored methylation differences from >24 000 cytosines distributed across the genomes of the domesticated dog (Canis familiaris) and the grey wolf (Canis lupus). PCA and model-based cluster analyses identified two primary groups, domestic vs. wild canids. A scan for significantly differentially methylated sites (DMSs) revealed species-specific patterns at 68 sites after correcting for cell heterogeneity, with weak yet significant hypermethylation typical of purebred dogs when compared to wolves (59% and 58%, P 66%) of differentially methylated regions contained or were associated with repetitive elements, indicative of a genotype-mediated trend. However, DMSs were also often linked to functionally relevant genes (e.g. neurotransmitters). Finally, we utilized known genealogical relationships among Yellowstone wolves to survey transmission stability of methylation marks, from which we found a substantial fraction that demonstrated high heritability (both H(2) and h(2 ) > 0.99). These analyses provide a unique epigenetic insight into the molecular consequences of recent selection and radiation of our most ancient domesticated companion, the dog. These findings suggest selection has acted on methylation patterns, providing a new genomic perspective on phenotypic diversification in domesticated species. © 2015 John Wiley & Sons Ltd.

  12. The Effect of Metabolic and Bariatric Surgery on DNA Methylation Patterns.

    Science.gov (United States)

    Morcillo, Sonsoles; Macías-González, Manuel; Tinahones, Francisco J

    2017-08-30

    Metabolic and bariatric surgery (MBS) is considered to be the most effective treatment for obesity. Not only due to the significant weight reduction but also because of the many health benefits associated with it. In the last 5 years, several studies have suggested that epigenetic modifications could be involved in the mechanisms underlying the response to bariatric surgery. In this review, we will compile the different studies (2012-2017) concerning the effect of this surgical procedure on DNA methylation patterns (the most studied epigenetic marker) and its association with metabolic improvement. This is an emerging area, and currently, there are not many studies in the literature. The aim is to show what has been done so far and what the future direction in this emerging area might be. Recent findings have shown how metabolic and bariatric surgery modifies the DNA methylation profile of the specific genes associated with the pathophysiology of the disease. The studies were performed in morbidly obese subjects, mainly in women, with the aim of reducing weight and improving the obesity-associated comorbidities. DNA methylation has been measured both in specific tissue and in peripheral blood samples. In general, studies about site-specific DNA methylation have shown a change in the methylation profile after surgery, whereas the studies analyzing global DNA methylation are not so conclusive. Summing up, metabolic and bariatric surgery can modify the DNA methylation profile of different genes and contributes to the metabolic health benefits that are often seen after metabolic and bariatric surgery. Although there are still many issues to be resolved, the capacity to revert the DNA methylation profile of specific sites opens a window for searching for target markers to treat obesity-related comorbidities.

  13. Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences

    Directory of Open Access Journals (Sweden)

    De Marzo Angelo M

    2011-06-01

    Full Text Available Abstract Background DNA methylation has been linked to genome regulation and dysregulation in health and disease respectively, and methods for characterizing genomic DNA methylation patterns are rapidly emerging. We have developed/refined methods for enrichment of methylated genomic fragments using the methyl-binding domain of the human MBD2 protein (MBD2-MBD followed by analysis with high-density tiling microarrays. This MBD-chip approach was used to characterize DNA methylation patterns across all non-repetitive sequences of human chromosomes 21 and 22 at high-resolution in normal and malignant prostate cells. Results Examining this data using computational methods that were designed specifically for DNA methylation tiling array data revealed widespread methylation of both gene promoter and non-promoter regions in cancer and normal cells. In addition to identifying several novel cancer hypermethylated 5' gene upstream regions that mediated epigenetic gene silencing, we also found several hypermethylated 3' gene downstream, intragenic and intergenic regions. The hypermethylated intragenic regions were highly enriched for overlap with intron-exon boundaries, suggesting a possible role in regulation of alternative transcriptional start sites, exon usage and/or splicing. The hypermethylated intergenic regions showed significant enrichment for conservation across vertebrate species. A sampling of these newly identified promoter (ADAMTS1 and SCARF2 genes and non-promoter (downstream or within DSCR9, C21orf57 and HLCS genes hypermethylated regions were effective in distinguishing malignant from normal prostate tissues and/or cell lines. Conclusions Comparison of chromosome-wide DNA methylation patterns in normal and malignant prostate cells revealed significant methylation of gene-proximal and conserved intergenic sequences. Such analyses can be easily extended for genome-wide methylation analysis in health and disease.

  14. Methylation patterns in sentinel genes in peripheral blood cells of heavy smokers: Influence of cruciferous vegetables in an intervention study.

    Science.gov (United States)

    Scoccianti, Chiara; Ricceri, Fulvio; Ferrari, Pietro; Cuenin, Cyrille; Sacerdote, Carlotta; Polidoro, Silvia; Jenab, Mazda; Hainaut, Pierre; Vineis, Paolo; Herceg, Zdenko

    2011-09-01

    Changes in DNA methylation patterns are a hallmark of tobacco-induced carcinogenesis. We have conducted a randomized 4-week intervention trial to investigate the effects of three dietary regimens to modify DNA methylation patterns in peripheral white blood cells of heavy smokers. A group of 88 smokers were randomly assigned to and distributed among three diets, including (1) normal isocaloric diet (balanced in fruits and vegetables), according to international guidelines; (2) a diet enriched in flavonoids and isothiocyanates (particularly cruciferous vegetables); (3) a regimen consisting of diet 1 supplemented with flavonoids (green tea and soy products). Methylation patterns were analyzed by pyrosequencing in LINE1 (Long Interspersed DNA Elements), RASSF1A, ARF and CDKN2a (tumor suppressor genes), MLH1 (mismatch DNA repair) and MTHFR (folate metabolism). Three distinct patterns of methylation were observed. In LINE1, methylation showed a small but reproducible increase with all three regimens. MTHFR was constitutively methylated with no significant modulation by diets. The four other loci showed low basal levels of methylation with no substantial change after intervention. These data suggest that the isocaloric diet may stabilize global epigenetic (LINE1 DNA methylation) patterns in peripheral white blood cells but does not provide evidence for methylation changes in specific genes associated with this short-term dietary intervention.

  15. Effects of altered maternal folic acid, vitamin B12 and docosahexaenoic acid on placental global DNA methylation patterns in Wistar rats.

    Directory of Open Access Journals (Sweden)

    Asmita Kulkarni

    Full Text Available Potential adverse effects of excess maternal folic acid supplementation on a vegetarian population deficient in vitamin B(12 are poorly understood. We have previously shown in a rat model that maternal folic acid supplementation at marginal protein levels reduces brain omega-3 fatty acid levels in the adult offspring. We have also reported that reduced docosahexaenoic acid (DHA levels may result in diversion of methyl groups towards DNA in the one carbon metabolic pathway ultimately resulting in DNA methylation. This study was designed to examine the effect of normal and excess folic acid in the absence and presence of vitamin B(12 deficiency on global methylation patterns in the placenta. Further, the effect of maternal omega 3 fatty acid supplementation on the above vitamin B(12 deficient diets was also examined. Our results suggest maternal folic acid supplementation in the absence of vitamin B(12 lowers plasma and placental DHA levels (p<0.05 and reduces global DNA methylation levels (p<0.05. When this group was supplemented with omega 3 fatty acids there was an increase in placental DHA levels and subsequently DNA methylation levels revert back to the levels of the control group. Our results suggest for the first time that DHA plays an important role in one carbon metabolism thereby influencing global DNA methylation in the placenta.

  16. DNA methylation patterns in bladder cancer and washing cell sediments: a perspective for tumor recurrence detection

    International Nuclear Information System (INIS)

    Negraes, Priscilla D; Favaro, Francine P; Camargo, João Lauro V; Oliveira, Maria Luiza CS; Goldberg, José; Rainho, Cláudia A; Salvadori, Daisy MF

    2008-01-01

    Epigenetic alterations are a hallmark of human cancer. In this study, we aimed to investigate whether aberrant DNA methylation of cancer-associated genes is related to urinary bladder cancer recurrence. A set of 4 genes, including CDH1 (E-cadherin), SFN (stratifin), RARB (retinoic acid receptor, beta) and RASSF1A (Ras association (RalGDS/AF-6) domain family 1), had their methylation patterns evaluated by MSP (Methylation-Specific Polymerase Chain Reaction) analysis in 49 fresh urinary bladder carcinoma tissues (including 14 cases paired with adjacent normal bladder epithelium, 3 squamous cell carcinomas and 2 adenocarcinomas) and 24 cell sediment samples from bladder washings of patients classified as cancer-free by cytological analysis (control group). A third set of samples included 39 archived tumor fragments and 23 matched washouts from 20 urinary bladder cancer patients in post-surgical monitoring. After genomic DNA isolation and sodium bisulfite modification, methylation patterns were determined and correlated with standard clinic-histopathological parameters. CDH1 and SFN genes were methylated at high frequencies in bladder cancer as well as in paired normal adjacent tissue and exfoliated cells from cancer-free patients. Although no statistically significant differences were found between RARB and RASSF1A methylation and the clinical and histopathological parameters in bladder cancer, a sensitivity of 95% and a specificity of 71% were observed for RARB methylation (Fisher's Exact test (p < 0.0001; OR = 48.89) and, 58% and 17% (p < 0.05; OR = 0.29) for RASSF1A gene, respectively, in relation to the control group. Indistinct DNA hypermethylation of CDH1 and SFN genes between tumoral and normal urinary bladder samples suggests that these epigenetic features are not suitable biomarkers for urinary bladder cancer. However, RARB and RASSF1A gene methylation appears to be an initial event in urinary bladder carcinogenesis and should be considered as defining a

  17. Multifractal spatial patterns and diversity in an ecological succession.

    Directory of Open Access Journals (Sweden)

    Leonardo Ariel Saravia

    Full Text Available We analyzed the relationship between biodiversity and spatial biomass heterogeneity along an ecological succession developed in the laboratory. Periphyton (attached microalgae biomass spatial patterns at several successional stages were obtained using digital image analysis and at the same time we estimated the species composition and abundance. We show that the spatial pattern was self-similar and as the community developed in an homogeneous environment the pattern is self-organized. To characterize it we estimated the multifractal spectrum of generalized dimensions D(q. Using D(q we analyze the existence of cycles of heterogeneity during succession and the use of the information dimension D(1 as an index of successional stage. We did not find cycles but the values of D(1 showed an increasing trend as the succession developed and the biomass was higher. D(1 was also negatively correlated with Shannon's diversity. Several studies have found this relationship in different ecosystems but here we prove that the community self-organizes and generates its own spatial heterogeneity influencing diversity. If this is confirmed with more experimental and theoretical evidence D(1 could be used as an index, easily calculated from remote sensing data, to detect high or low diversity areas.

  18. DNA methylation patterns in cord blood DNA and body size in childhood.

    Directory of Open Access Journals (Sweden)

    Caroline L Relton

    Full Text Available Epigenetic markings acquired in early life may have phenotypic consequences later in development through their role in transcriptional regulation with relevance to the developmental origins of diseases including obesity. The goal of this study was to investigate whether DNA methylation levels at birth are associated with body size later in childhood.A study design involving two birth cohorts was used to conduct transcription profiling followed by DNA methylation analysis in peripheral blood. Gene expression analysis was undertaken in 24 individuals whose biological samples and clinical data were collected at a mean ± standard deviation (SD age of 12.35 (0.95 years, the upper and lower tertiles of body mass index (BMI were compared with a mean (SD BMI difference of 9.86 (2.37 kg/m(2. This generated a panel of differentially expressed genes for DNA methylation analysis which was then undertaken in cord blood DNA in 178 individuals with body composition data prospectively collected at a mean (SD age of 9.83 (0.23 years. Twenty-nine differentially expressed genes (>1.2-fold and p<10(-4 were analysed to determine DNA methylation levels at 1-3 sites per gene. Five genes were unmethylated and DNA methylation in the remaining 24 genes was analysed using linear regression with bootstrapping. Methylation in 9 of the 24 (37.5% genes studied was associated with at least one index of body composition (BMI, fat mass, lean mass, height at age 9 years, although only one of these associations remained after correction for multiple testing (ALPL with height, p(Corrected = 0.017.DNA methylation patterns in cord blood show some association with altered gene expression, body size and composition in childhood. The observed relationship is correlative and despite suggestion of a mechanistic epigenetic link between in utero life and later phenotype, further investigation is required to establish causality.

  19. Altered DNA Methylation Patterns Associated With Clinically Relevant Increases in PTSD Symptoms and PTSD Symptom Profiles in Military Personnel.

    Science.gov (United States)

    Martin, Christiana; Cho, Young-Eun; Kim, Hyungsuk; Yun, Sijung; Kanefsky, Rebekah; Lee, Hyunhwa; Mysliwiec, Vincent; Cashion, Ann; Gill, Jessica

    2018-05-01

    Military personnel experience posttraumatic stress disorder (PTSD), which is associated with differential DNA methylation across the whole genome. However, the relationship between these DNA methylation patterns and clinically relevant increases in PTSD severity is not yet clearly understood. The purpose of this study was to identify differences in DNA methylation associated with PTSD symptoms and investigate DNA methylation changes related to increases in the severity of PTSD in military personnel. In this pilot study, a cross-sectional comparison was made between military personnel with PTSD (n = 8) and combat-matched controls without PTSD (n = 6). Symptom measures were obtained, and genome-wide DNA methylation was measured using methylated DNA immunoprecipitation (MeDIP-seq) from whole blood samples at baseline and 3 months later. A longitudinal comparison measured DNA methylation changes in military personnel with clinically relevant increases in PTSD symptoms between time points (PTSD onset) and compared methylation patterns to controls with no clinical changes in PTSD. In military personnel with elevated PTSD symptoms 3 months following baseline, 119 genes exhibited reduced methylation and 8 genes exhibited increased methylation. Genes with reduced methylation in the PTSD-onset group relate to the canonical pathways of netrin signaling, Wnt/Ca + pathway, and axonal guidance signaling. These gene pathways relate to neurological disorders, and the current findings suggest that these epigenetic changes potentially relate to PTSD symptomology. This study provides some novel insights into the role of epigenetic changes in PTSD symptoms and the progression of PTSD symptoms in military personnel.

  20. Salinity induced differential methylation patterns in contrasting cultivars of foxtail millet (Setaria italica L.).

    Science.gov (United States)

    Pandey, Garima; Yadav, Chandra Bhan; Sahu, Pranav Pankaj; Muthamilarasan, Mehanathan; Prasad, Manoj

    2017-05-01

    Genome-wide methylation analysis of foxtail millet cultivars contrastingly differing in salinity tolerance revealed DNA demethylation events occurring in tolerant cultivar under salinity stress, eventually modulating the expression of stress-responsive genes. Reduced productivity and significant yield loss are the adverse effects of environmental conditions on physiological and biochemical pathways in crop plants. In this context, understanding the epigenetic machinery underlying the tolerance traits in a naturally stress tolerant crop is imperative. Foxtail millet (Setaria italica) is known for its better tolerance to abiotic stresses compared to other cereal crops. In the present study, methylation-sensitive amplified polymorphism (MSAP) technique was used to quantify the salt-induced methylation changes in two foxtail millet cultivars contrastingly differing in their tolerance levels to salt stress. The study highlighted that the DNA methylation level was significantly reduced in tolerant cultivar compared to sensitive cultivar. A total of 86 polymorphic MSAP fragments were identified, sequenced and functionally annotated. These fragments showed sequence similarity to several genes including ABC transporter, WRKY transcription factor, serine threonine-protein phosphatase, disease resistance, oxidoreductases, cell wall-related enzymes and retrotransposon and transposase like proteins, suggesting salt stress-induced methylation in these genes. Among these, four genes were chosen for expression profiling which showed differential expression pattern between both cultivars of foxtail millet. Altogether, the study infers that salinity stress induces genome-wide DNA demethylation, which in turn, modulates expression of corresponding genes.

  1. Patterns of Vertebrate Diversity and Protection in Brazil.

    Directory of Open Access Journals (Sweden)

    Clinton N Jenkins

    Full Text Available Most conservation decisions take place at national or finer spatial scales. Providing useful information at such decision-making scales is essential for guiding the practice of conservation. Brazil is one of the world's megadiverse countries, and consequently decisions about conservation in the country have a disproportionate impact on the survival of global biodiversity. For three groups of terrestrial vertebrates (birds, mammals, and amphibians, we examined geographic patterns of diversity and protection in Brazil, including that of endemic, small-ranged, and threatened species. To understand potential limitations of the data, we also explored how spatial bias in collection localities may influence the perceived patterns of diversity. The highest overall species richness is in the Amazon and Atlantic Forests, while the Atlantic Forest dominates in terms of country endemics and small-ranged species. Globally threatened species do not present a consistent pattern. Patterns for birds were similar to overall species richness, with higher concentrations of threatened species in the Atlantic Forest, while mammals show a more generalized pattern across the country and a high concentration in the Amazon. Few amphibians are listed as threatened, mostly in the Atlantic Forest. Data deficient mammals occur across the country, concentrating in the Amazon and southeast Atlantic Forest, and there are no data deficient birds in Brazil. In contrast, nearly a third of amphibians are data deficient, widespread across the country, but with a high concentration in the far southeast. Spatial biases in species locality data, however, possibly influence the perceived patterns of biodiversity. Regions with low sampling density need more biological studies, as do the many data deficient species. All biomes except the Amazon have less than 3% of their area under full protection. Reassuringly though, rates of protection do correlate with higher biodiversity, including

  2. Prenatal phthalate exposure and altered patterns of DNA methylation in cord blood.

    Science.gov (United States)

    Solomon, Olivia; Yousefi, Paul; Huen, Karen; Gunier, Robert B; Escudero-Fung, Maria; Barcellos, Lisa F; Eskenazi, Brenda; Holland, Nina

    2017-07-01

    Epigenetic changes such as DNA methylation may be a molecular mechanism through which environmental exposures affect health. Phthalates are known endocrine disruptors with ubiquitous exposures in the general population including pregnant women, and they have been linked with a number of adverse health outcomes. We examined the association between in utero phthalate exposure and altered patterns of cord blood DNA methylation in 336 Mexican-American newborns. Concentrations of 11 phthalate metabolites were analyzed in maternal urine samples collected at 13 and 26 weeks gestation as a measure of fetal exposure. DNA methylation was assessed using the Infinium HumanMethylation 450K BeadChip adjusting for cord blood cell composition. To identify differentially methylated regions (DMRs) that may be more informative than individual CpG sites, we used two different approaches, DMRcate and comb-p. Regional assessment by both methods identified 27 distinct DMRs, the majority of which were in relation to multiple phthalate metabolites. Most of the significant DMRs (67%) were observed for later pregnancy (26 weeks gestation). Further, 51% of the significant DMRs were associated with the di-(2-ethylhexyl) phthalate metabolites. Five individual CpG sites were associated with phthalate metabolite concentrations after multiple comparisons adjustment (FDR), all showing hypermethylation. Genes with DMRs were involved in inflammatory response (IRAK4 and ESM1), cancer (BRCA1 and LASP1), endocrine function (CNPY1), and male fertility (IFT140, TESC, and PRDM8). These results on differential DNA methylation in newborns with prenatal phthalate exposure provide new insights and targets to explore mechanism of adverse effects of phthalates on human health. Environ. Mol. Mutagen. 58:398-410, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  3. Changes in IL12A methylation pattern in livers from mice fed DDC.

    Science.gov (United States)

    Oliva, J; French, S W

    2012-04-01

    Mallory-Denk body (MDB) formation is a component of alcoholic and non alcoholic hepatitis. Proteins of the TLR pathway were shown to be involved in the formation of MDBs, in mice fed DDC. TLR genes are upregulated and SAMe supplementation prevents this up regulation and prevented the formation of MDBs. DNA of livers from control mice, from mice fed DDC 10weeks, refed 1week with DDC and with DDC+SAMe were extracted and used to study the methylation pattern of genes involves in the TLR pathway. A PCR array was used to analyze it. Using PCR arrays for the mouse TLR pathway,24 genes were found whose expression of IL12A was regulated by the methylation of its gene. DDC fed for 10weeks reduced the methylation of the IL12A gene expression. This expression was also reduced when DDC was refed. However, when SAMe was fed, the intermediate level methylation of IL12A was up regulated to the intermediate level and the methylation of the promoter decreased compared to DDC refeeding or DDC 10weeks. IL12A is known to induce the production of IFNg by NK and L(T). We showed in a previous publication that IFNg is one of the major cytokines involved in the induction of MDB formation. The low expression of IL12A associated with the intermediate methylation of its promoter could explain one step in the mechanism which leads to the formation of MDBs. Copyright © 2012 Elsevier Inc. All rights reserved.

  4. Altered placental DNA methylation patterns associated with maternal smoking: current perspectives

    Directory of Open Access Journals (Sweden)

    Maccani JZ

    2015-05-01

    Full Text Available Jennifer ZJ Maccani, Matthew A Maccani Penn State Tobacco Center of Regulatory Science, College of Medicine, Department of Public Health Sciences, Hershey, PA, USA Abstract: The developmental origins of health and disease hypothesis states that adverse early life exposures can have lasting, detrimental effects on lifelong health. Exposure to maternal cigarette smoking during pregnancy is associated with morbidity and mortality in offspring, including increased risks for miscarriage, stillbirth, low birth weight, preterm birth, asthma, obesity, altered neurobehavior, and other conditions. Maternal cigarette smoking during pregnancy interferes with placental growth and functioning, and it has been proposed that this may occur through the disruption of normal and necessary placental epigenetic patterns. Epigenome-wide association studies have identified a number of differentially methylated placental genes that are associated with maternal smoking during pregnancy, including RUNX3, PURA, GTF2H2, GCA, GPR135, and HKR1. The placental methylation status of RUNX3 and NR3C1 has also been linked to adverse infant outcomes, including preterm birth and low birth weight, respectively. Candidate gene analyses have also found maternal smoking-associated placental methylation differences in the NR3C1, CYP1A1, HTR2A, and HSD11B2 genes, as well as in the repetitive elements LINE-1 and AluYb8. The differential methylation patterns of several genes have been confirmed to also exhibit altered gene expression patterns, including CYP1A1, CYP19A1, NR3C1, and HTR2A. Placental methylation patterns associated with maternal smoking during pregnancy may be largely gene-specific and tissue-specific and, to a lesser degree, involve global changes. It is important for future research to investigate the mechanistic roles that these differentially methylated genes may play in mediating the association between maternal smoking during pregnancy and disease in later life, as well

  5. A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues.

    Directory of Open Access Journals (Sweden)

    Athma A Pai

    2011-02-01

    Full Text Available The modification of DNA by methylation is an important epigenetic mechanism that affects the spatial and temporal regulation of gene expression. Methylation patterns have been described in many contexts within and across a range of species. However, the extent to which changes in methylation might underlie inter-species differences in gene regulation, in particular between humans and other primates, has not yet been studied. To this end, we studied DNA methylation patterns in livers, hearts, and kidneys from multiple humans and chimpanzees, using tissue samples for which genome-wide gene expression data were also available. Using the multi-species gene expression and methylation data for 7,723 genes, we were able to study the role of promoter DNA methylation in the evolution of gene regulation across tissues and species. We found that inter-tissue methylation patterns are often conserved between humans and chimpanzees. However, we also found a large number of gene expression differences between species that might be explained, at least in part, by corresponding differences in methylation levels. In particular, we estimate that, in the tissues we studied, inter-species differences in promoter methylation might underlie as much as 12%-18% of differences in gene expression levels between humans and chimpanzees.

  6. Characterizing genes with distinct methylation patterns in the context of protein-protein interaction network: application to human brain tissues.

    Science.gov (United States)

    Li, Yongsheng; Xu, Juan; Chen, Hong; Zhao, Zheng; Li, Shengli; Bai, Jing; Wu, Aiwei; Jiang, Chunjie; Wang, Yuan; Su, Bin; Li, Xia

    2013-01-01

    DNA methylation is an essential epigenetic mechanism involved in transcriptional control. However, how genes with different methylation patterns are assembled in the protein-protein interaction network (PPIN) remains a mystery. In the present study, we systematically dissected the characterization of genes with different methylation patterns in the PPIN. A negative association was detected between the methylation levels in the brain tissues and topological centralities. By focusing on two classes of genes with considerably different methylation levels in the brain tissues, namely the low methylated genes (LMGs) and high methylated genes (HMGs), we found that their organizing principles in the PPIN are distinct. The LMGs tend to be the center of the PPIN, and attacking them causes a more deleterious effect on the network integrity. Furthermore, the LMGs express their functions in a modular pattern and substantial differences in functions are observed between the two types of genes. The LMGs are enriched in the basic biological functions, such as binding activity and regulation of transcription. More importantly, cancer genes, especially recessive cancer genes, essential genes, and aging-related genes were all found more often in the LMGs. Additionally, our analysis presented that the intra-classes communications are enhanced, but inter-classes communications are repressed. Finally, a functional complementation was revealed between methylation and miRNA regulation in the human genome. We have elucidated the assembling principles of genes with different methylation levels in the context of the PPIN, providing key insights into the complex epigenetic regulation mechanisms.

  7. Acceleration of Age-Associated Methylation Patterns in HIV-1-Infected Adults

    Science.gov (United States)

    Sehl, Mary; Sinsheimer, Janet S.; Hultin, Patricia M.; Hultin, Lance E.; Quach, Austin; Martínez-Maza, Otoniel; Horvath, Steve; Vilain, Eric; Jamieson, Beth D.

    2015-01-01

    Patients with treated HIV-1-infection experience earlier occurrence of aging-associated diseases, raising speculation that HIV-1-infection, or antiretroviral treatment, may accelerate aging. We recently described an age-related co-methylation module comprised of hundreds of CpGs; however, it is unknown whether aging and HIV-1-infection exert negative health effects through similar, or disparate, mechanisms. We investigated whether HIV-1-infection would induce age-associated methylation changes. We evaluated DNA methylation levels at >450,000 CpG sites in peripheral blood mononuclear cells (PBMC) of young (20-35) and older (36-56) adults in two separate groups of participants. Each age group for each data set consisted of 12 HIV-1-infected and 12 age-matched HIV-1-uninfected samples for a total of 96 samples. The effects of age and HIV-1 infection on methylation at each CpG revealed a strong correlation of 0.49, pmodules; module 3 (ME3) was significantly correlated with age (cor=0.70) and HIV-1 status (cor=0.31). Older HIV-1+ individuals had a greater number of hypermethylated CpGs across ME3 (p=0.015). In a multivariate model, ME3 was significantly associated with age and HIV status (Data set 1: βage= 0.007088, p=2.08 x 10-9; βHIV= 0.099574, p=0.0011; Data set 2: βage= 0.008762, p=1.27x 10-5; βHIV= 0.128649, p= 0.0001). Using this model, we estimate that HIV-1 infection accelerates age-related methylation by approximately 13.7 years in data set 1 and 14.7 years in data set 2. The genes related to CpGs in ME3 are enriched for polycomb group target genes known to be involved in cell renewal and aging. The overlap between ME3 and an aging methylation module found in solid tissues is also highly significant (Fisher-exact p=5.6 x 10-6, odds ratio=1.91). These data demonstrate that HIV-1 infection is associated with methylation patterns that are similar to age-associated patterns and suggest that general aging and HIV-1 related aging work through some common cellular

  8. Depleted uranium induces sex- and tissue-specific methylation patterns in adult zebrafish

    International Nuclear Information System (INIS)

    Gombeau, Kewin; Pereira, Sandrine; Ravanat, Jean-Luc; Camilleri, Virginie; Cavalie, Isabelle; Bourdineaud, Jean-Paul; Adam-Guillermin, Christelle

    2016-01-01

    We examined the effects of chronic exposure to different concentrations (2 and 20 μg L"−"1) of environmentally relevant waterborne depleted uranium (DU) on the DNA methylation patterns both at HpaII restriction sites (5′-CCGG-3′) and across the whole genome in the zebrafish brain, gonads, and eyes. We first identified sex-dependent differences in the methylation level of HpaII sites after exposure. In males, these effects were present as early as 7 days after exposure to 20 μg L"−"1 DU, and were even more pronounced in the brain, gonads, and eyes after 24 days. However, in females, hypomethylation was only observed in the gonads after exposure to 20 μg L"−"1 DU for 24 days. Sex-specific effects of DU were also apparent at the whole-genome level, because in males, exposure to 20 μg L"−"1 DU for 24 days resulted in cytosine hypermethylation in the brain and eyes and hypomethylation in the gonads. In contrast, in females, hypermethylation was observed in the brain after exposure to both concentrations of DU for 7 days. Based on our current knowledge of uranium toxicity, several hypotheses are proposed to explain these findings, including the involvement of oxidative stress, alteration of demethylation enzymes and the calcium signaling pathway. This study reports, for the first time, the sex- and tissue-specific epigenetic changes that occur in a nonhuman organism after exposure to environmentally relevant concentrations of uranium, which could induce transgenerational epigenetic effects. - Highlights: • This study demonstrates a sex-related effect of DU exposure on DNA methylation patterns. • Impacts on DNA methylation patterns revealed a tissue-specific effect of DU exposure. • The MS–AFLP and HPLC–MS/MS sensitively and complementarily demonstrated the responses to environmental concentrations of DU.

  9. Who intermarries in Britain? Explaining ethnic diversity in intermarriage patterns.

    Science.gov (United States)

    Muttarak, Raya; Heath, Anthony

    2010-06-01

    This paper investigates trends, patterns and determinants of intermarriage (and partnership) comparing patterns among men and women and among different ethnic groups in Britain. We distinguish between endogamous (co-ethnic), majority/minority and minority/minority marriages. Hypotheses are derived from the theoretical literatures on assimilation, segmented assimilation and opportunity structures. The empirical analysis is based on the 1988-2006 General Household Surveys (N = 115,494). Consistent with assimilation theory we find that, for all ethnic minority groups, the propensity to intermarry is higher in the second generation than in the first. Consistent with ideas drawn from segmented assimilation theory, we also find that substantial differences in propensity to form majority/minority marriages persist after controls for individual characteristics such as age, educational level, generation and length of residence in Britain, with men and women of Indian, Pakistani or Bangladeshi background having higher propensities to form endogamous partnerships. However, we also find that opportunity structures affect intermarriage propensities for all groups alike, with individuals in more diverse residential areas (as measured by the ratio of majority to minority residents in the area) having higher likelihood to form majority/minority partnerships. We conclude then that, beginning from very different starting points, all groups, both minority and the majority groups exhibit common patterns of generational change and response to opportunity structures. Even the groups that are believed to have the strongest community structures and the strongest norms supporting endogamy appear to be experiencing increasing exogamy in the second generation and in more diverse residential settings. This suggests that a weak rather than a strong version of segmented assimilation provides the best account of British patterns.

  10. Modulation of the degree and pattern of methyl-esterification of pectic homogalacturonan in plant cell walls. Implications for pectin methyl esterase action, matrix properties, and cell adhesion.

    Science.gov (United States)

    Willats, W G; Orfila, C; Limberg, G; Buchholt, H C; van Alebeek, G J; Voragen, A G; Marcus, S E; Christensen, T M; Mikkelsen, J D; Murray, B S; Knox, J P

    2001-06-01

    Homogalacturonan (HG) is a multifunctional pectic polysaccharide of the primary cell wall matrix of all land plants. HG is thought to be deposited in cell walls in a highly methyl-esterified form but can be subsequently de-esterified by wall-based pectin methyl esterases (PMEs) that have the capacity to remove methyl ester groups from HG. Plant PMEs typically occur in multigene families/isoforms, but the precise details of the functions of PMEs are far from clear. Most are thought to act in a processive or blockwise fashion resulting in domains of contiguous de-esterified galacturonic acid residues. Such de-esterified blocks of HG can be cross-linked by calcium resulting in gel formation and can contribute to intercellular adhesion. We demonstrate that, in addition to blockwise de-esterification, HG with a non-blockwise distribution of methyl esters is also an abundant feature of HG in primary plant cell walls. A partially methyl-esterified epitope of HG that is generated in greatest abundance by non-blockwise de-esterification is spatially regulated within the cell wall matrix and occurs at points of cell separation at intercellular spaces in parenchymatous tissues of pea and other angiosperms. Analysis of the properties of calcium-mediated gels formed from pectins containing HG domains with differing degrees and patterns of methyl-esterification indicated that HG with a non-blockwise pattern of methyl ester group distribution is likely to contribute distinct mechanical and porosity properties to the cell wall matrix. These findings have important implications for our understanding of both the action of pectin methyl esterases on matrix properties and mechanisms of intercellular adhesion and its loss in plants.

  11. Disentangling diversity patterns in sandy beaches along environmental gradients.

    Science.gov (United States)

    Barboza, Francisco R; Gómez, Julio; Lercari, Diego; Defeo, Omar

    2012-01-01

    importance that salinity and morphodynamic gradients have on macroscale diversity patterns in sandy beaches.

  12. Environmental Drivers of Patterns of Plant Diversity Along a Wide Environmental Gradient in Korean Temperate Forests

    Directory of Open Access Journals (Sweden)

    Chang-Bae Lee

    2016-01-01

    Full Text Available Understanding patterns of biodiversity and their drivers along environmental gradients is one of the central topics in ecology. However, whether diversity patterns along environmental gradients differ among diversity components as well as life forms and what kind of variables control or interact to shape the diversity patterns are poorly known. This study scrutinized the distribution patterns of three plant groups with four diversity indices and evaluated the effects of regional area, topography, topographic heterogeneity, climate, primary productivity, vegetation structure diversity and vegetation type diversity along an extensive elevational gradient on the Baekdudaegan Mountains in South Korea. Different elevational patterns, including hump-shaped, reversed hump-shaped, increasing, multimodal and no relationship, were observed among both the diversity indices and the plant groups. Regional area, habitat heterogeneity and climate were included to explain most of the elevational diversity patterns. In particular, habitat heterogeneity was the most important variable for explaining the patterns of diversity. The results suggest that patterns of elevational diversity may differ not only among plant groups but also among diversity indices and that such patterns are primarily caused by habitat heterogeneity in the Baekdudaegan Mountains because more heterogeneous and diverse habitats can support more coexisting species.

  13. Acceleration of age-associated methylation patterns in HIV-1-infected adults.

    Directory of Open Access Journals (Sweden)

    Tammy M Rickabaugh

    Full Text Available Patients with treated HIV-1-infection experience earlier occurrence of aging-associated diseases, raising speculation that HIV-1-infection, or antiretroviral treatment, may accelerate aging. We recently described an age-related co-methylation module comprised of hundreds of CpGs; however, it is unknown whether aging and HIV-1-infection exert negative health effects through similar, or disparate, mechanisms. We investigated whether HIV-1-infection would induce age-associated methylation changes. We evaluated DNA methylation levels at >450,000 CpG sites in peripheral blood mononuclear cells (PBMC of young (20-35 and older (36-56 adults in two separate groups of participants. Each age group for each data set consisted of 12 HIV-1-infected and 12 age-matched HIV-1-uninfected samples for a total of 96 samples. The effects of age and HIV-1 infection on methylation at each CpG revealed a strong correlation of 0.49, p<1 x 10(-200 and 0.47, p<1 x 10(-200. Weighted gene correlation network analysis (WGCNA identified 17 co-methylation modules; module 3 (ME3 was significantly correlated with age (cor=0.70 and HIV-1 status (cor=0.31. Older HIV-1+ individuals had a greater number of hypermethylated CpGs across ME3 (p=0.015. In a multivariate model, ME3 was significantly associated with age and HIV status (Data set 1: βage=0.007088, p=2.08 x 10(-9; βHIV=0.099574, p=0.0011; Data set 2: βage=0.008762, p=1.27 x 10(-5; βHIV=0.128649, p=0.0001. Using this model, we estimate that HIV-1 infection accelerates age-related methylation by approximately 13.7 years in data set 1 and 14.7 years in data set 2. The genes related to CpGs in ME3 are enriched for polycomb group target genes known to be involved in cell renewal and aging. The overlap between ME3 and an aging methylation module found in solid tissues is also highly significant (Fisher-exact p=5.6 x 10(-6, odds ratio=1.91. These data demonstrate that HIV-1 infection is associated with methylation patterns that

  14. Domestication rewired gene expression and nucleotide diversity patterns in tomato.

    Science.gov (United States)

    Sauvage, Christopher; Rau, Andrea; Aichholz, Charlotte; Chadoeuf, Joël; Sarah, Gautier; Ruiz, Manuel; Santoni, Sylvain; Causse, Mathilde; David, Jacques; Glémin, Sylvain

    2017-08-01

    Plant domestication has led to considerable phenotypic modifications from wild species to modern varieties. However, although changes in key traits have been well documented, less is known about the underlying molecular mechanisms, such as the reduction of molecular diversity or global gene co-expression patterns. In this study, we used a combination of gene expression and population genetics in wild and crop tomato to decipher the footprints of domestication. We found a set of 1729 differentially expressed genes (DEG) between the two genetic groups, belonging to 17 clusters of co-expressed DEG, suggesting that domestication affected not only individual genes but also regulatory networks. Five co-expression clusters were enriched in functional terms involving carbohydrate metabolism or epigenetic regulation of gene expression. We detected differences in nucleotide diversity between the crop and wild groups specific to DEG. Our study provides an extensive profiling of the rewiring of gene co-expression induced by the domestication syndrome in one of the main crop species. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

  15. Epigenetic Diversity of Clonal White Poplar (Populus alba L. Populations: Could Methylation Support the Success of Vegetative Reproduction Strategy?

    Directory of Open Access Journals (Sweden)

    Francesco Guarino

    Full Text Available The widespread poplar populations of Sardinia are vegetatively propagated and live in different natural environments forming large monoclonal stands. The main goals of the present study were: i to investigate/measure the epigenetic diversity of the poplar populations by determining their DNA methylation status; ii to assess if and how methylation status influences population clustering; iii to shed light on the changes that occur in the epigenome of ramets of the same poplar clone. To these purposes, 83 white poplar trees were sampled at different locations on the island of Sardinia. Methylation sensitive amplified polymorphism analysis was carried out on the genomic DNA extracted from leaves at the same juvenile stage. The study showed that the genetic biodiversity of poplars is quite limited but it is counterbalanced by epigenetic inter-population molecular variability. The comparison between MspI and HpaII DNA fragmentation profiles revealed that environmental conditions strongly influence hemi-methylation of the inner cytosine. The variable epigenetic status of Sardinian white poplars revealed a decreased number of population clusters. Landscape genetics analyses clearly demonstrated that ramets of the same clone were differentially methylated in relation to their geographic position. Therefore, our data support the notion that studies on plant biodiversity should no longer be restricted to genetic aspects, especially in the case of vegetatively propagated plant species.

  16. ∆DNMT3B4-del Contributes to Aberrant DNA Methylation Patterns in Lung Tumorigenesis

    Directory of Open Access Journals (Sweden)

    Mark Z. Ma

    2015-10-01

    Full Text Available Aberrant DNA methylation is a hallmark of cancer but mechanisms contributing to the abnormality remain elusive. We have previously shown that ∆DNMT3B is the predominantly expressed form of DNMT3B. In this study, we found that most of the lung cancer cell lines tested predominantly expressed DNMT3B isoforms without exons 21, 22 or both 21 and 22 (a region corresponding to the enzymatic domain of DNMT3B termed DNMT3B/∆DNMT3B-del. In normal bronchial epithelial cells, DNMT3B/ΔDNMT3B and DNMT3B/∆DNMT3B-del displayed equal levels of expression. In contrast, in patients with non-small cell lung cancer NSCLC, 111 (93% of the 119 tumors predominantly expressed DNMT3B/ΔDNMT3B-del, including 47 (39% tumors with no detectable DNMT3B/∆DNMT3B. Using a transgenic mouse model, we further demonstrated the biological impact of ∆DNMT3B4-del, the ∆DNMT3B-del isoform most abundantly expressed in NSCLC, in global DNA methylation patterns and lung tumorigenesis. Expression of ∆DNMT3B4-del in the mouse lungs resulted in an increased global DNA hypomethylation, focal DNA hypermethylation, epithelial hyperplastia and tumor formation when challenged with a tobacco carcinogen. Our results demonstrate ∆DNMT3B4-del as a critical factor in developing aberrant DNA methylation patterns during lung tumorigenesis and suggest that ∆DNMT3B4-del may be a target for lung cancer prevention.

  17. Marine diversity: the paradigms in patterns of species richness examined

    Directory of Open Access Journals (Sweden)

    John S. Gray

    2001-12-01

    Full Text Available The two central paradigms of marine diversity are that there is a latitudinal cline of increasing species richness from poles to tropics and that species richness increases with depth to a maximum around 2,000 m and thereafter decreases. However, these paradigms were based on data collected in the late 1950´s and early 1960´s. Here I show that the 1960´s data, are not representative and thus the paradigms need re-examination. New data from coastal areas in the northern hemisphere record species richness as high as the highest recorded in the deep-sea. Whilst this suggests that the cline of increasing diversity from shallow to deep-sea does not exist, however, the database for the deep sea is not sufficient to draw such a conclusion. The basic problem with the data from the 1960s is that samples were taken on ecological scales and yet they are used to answer evolutionary questions. The questions that such data were to answer were why do the tropics have higher species richness than polar regions or why do deep-sea sediments have more species than coastal sediments? Evolutionary questions need data from much larger spatial areas. Recently, data representative of large scales have been collected from coastal areas in the northern hemisphere and show that there is a cline of increasing species richness from the Arctic to the tropics, but there does not yet seem to be a similar cline in the southern hemisphere. A number of hypotheses have been proposed for the observed patterns in biodiversity. In terrestrial ecology the energy-productivity hypothesis has gained wide acceptance as an explanation for the latitudinal gradient. Here I examine this and other hypotheses critically. Finally an analysis of research priorities is made. Assessment is urgently needed of the spatial scales and dynamics of species richness from point samples to assemblages, habitats and landscapes, especially in coastal areas and in the tropics, where the threats to

  18. Patterns of cis regulatory variation in diverse human populations.

    Directory of Open Access Journals (Sweden)

    Barbara E Stranger

    Full Text Available The genetic basis of gene expression variation has long been studied with the aim to understand the landscape of regulatory variants, but also more recently to assist in the interpretation and elucidation of disease signals. To date, many studies have looked in specific tissues and population-based samples, but there has been limited assessment of the degree of inter-population variability in regulatory variation. We analyzed genome-wide gene expression in lymphoblastoid cell lines from a total of 726 individuals from 8 global populations from the HapMap3 project and correlated gene expression levels with HapMap3 SNPs located in cis to the genes. We describe the influence of ancestry on gene expression levels within and between these diverse human populations and uncover a non-negligible impact on global patterns of gene expression. We further dissect the specific functional pathways differentiated between populations. We also identify 5,691 expression quantitative trait loci (eQTLs after controlling for both non-genetic factors and population admixture and observe that half of the cis-eQTLs are replicated in one or more of the populations. We highlight patterns of eQTL-sharing between populations, which are partially determined by population genetic relatedness, and discover significant sharing of eQTL effects between Asians, European-admixed, and African subpopulations. Specifically, we observe that both the effect size and the direction of effect for eQTLs are highly conserved across populations. We observe an increasing proximity of eQTLs toward the transcription start site as sharing of eQTLs among populations increases, highlighting that variants close to TSS have stronger effects and therefore are more likely to be detected across a wider panel of populations. Together these results offer a unique picture and resource of the degree of differentiation among human populations in functional regulatory variation and provide an estimate for

  19. Diverse patterns of neuroendocrine activity in maltreated children.

    Science.gov (United States)

    Cicchetti, D; Rogosch, F A

    2001-01-01

    Cortisol regulation was investigated in a sample of school-aged maltreated (n = 175) and demographically comparable low-income nonmaltreated (n = 209) children in the context of a day camp research program. Overall group differences between maltreated and nonmaltreated children were not found for average morning or average afternoon cortisol levels. However, significant variations were found that were based on the subtypes of maltreatment that the children had experienced. Maltreated children who had been both physically and sexually abused (as well as neglected or emotionally maltreated) exhibited substantial elevations in morning cortisol levels; children who had high (>1 SD) cortisol levels in both the morning and afternoon were also overrepresented in the multiple abuse group. Developmental timing of maltreatment did not account for these group differences, whereas the severity of sexual abuse was implicated. In contrast to the multiple abuse group, a subgroup of physically abused children showed evidence of a trend toward lower morning cortisol relative to nonmaltreated children with a significantly smaller decrease in cortisol levels from morning to afternoon. The findings are discussed in terms of the diversity of atypical cortisol regulation patterns that are exhibited among maltreated children.

  20. Patterns of Macroinvertebrate and Fish Diversity in Freshwater Sulphide Springs

    Directory of Open Access Journals (Sweden)

    Ryan Greenway

    2014-09-01

    Full Text Available Extreme environments are characterised by the presence of physicochemical stressors and provide unique study systems to address problems in evolutionary ecology research. Sulphide springs provide an example of extreme freshwater environments; because hydrogen sulphide’s adverse physiological effects induce mortality in metazoans even at micromolar concentrations. Sulphide springs occur worldwide, but while microbial communities in sulphide springs have received broad attention, little is known about macroinvertebrates and fish inhabiting these toxic environments. We reviewed qualitative occurrence records of sulphide spring faunas on a global scale and present a quantitative case study comparing diversity patterns in sulphidic and adjacent non-sulphidic habitats across replicated river drainages in Southern Mexico. While detailed studies in most regions of the world remain scarce, available data suggests that sulphide spring faunas are characterised by low species richness. Dipterans (among macroinvertebrates and cyprinodontiforms (among fishes appear to dominate the communities in these habitats. At least in fish, there is evidence for the presence of highly endemic species and populations exclusively inhabiting sulphide springs. We provide a detailed discussion of traits that might predispose certain taxonomic groups to colonize sulphide springs, how colonizers subsequently adapt to cope with sulphide toxicity, and how adaptation may be linked to speciation processes.

  1. Transgenerational inheritance of modified DNA methylation patterns and enhanced tolerance induced by heavy metal stress in rice (Oryza sativa L.).

    Science.gov (United States)

    Ou, Xiufang; Zhang, Yunhong; Xu, Chunming; Lin, Xiuyun; Zang, Qi; Zhuang, Tingting; Jiang, Lili; von Wettstein, Diter; Liu, Bao

    2012-01-01

    DNA methylation is sensitive and responsive to stressful environmental conditions. Nonetheless, the extent to which condition-induced somatic methylation modifications can impose transgenerational effects remains to be fully understood. Even less is known about the biological relevance of the induced epigenetic changes for potentially altered well-being of the organismal progenies regarding adaptation to the specific condition their progenitors experienced. We analyzed DNA methylation pattern by gel-blotting at genomic loci representing transposable elements and protein-coding genes in leaf-tissue of heavy metal-treated rice (Oryza sativa) plants (S0), and its three successive organismal generations. We assessed expression of putative genes involved in establishing and/or maintaining DNA methylation patterns by reverse transcription (RT)-PCR. We measured growth of the stressed plants and their unstressed progenies vs. the control plants. We found (1) relative to control, DNA methylation patterns were modified in leaf-tissue of the immediately treated plants, and the modifications were exclusively confined to CHG hypomethylation; (2) the CHG-demethylated states were heritable via both maternal and paternal germline, albeit often accompanying further hypomethylation; (3) altered expression of genes encoding for DNA methyltransferases, DNA glycosylase and SWI/SNF chromatin remodeling factor (DDM1) were induced by the stress; (4) progenies of the stressed plants exhibited enhanced tolerance to the same stress their progenitor experienced, and this transgenerational inheritance of the effect of condition accompanying heritability of modified methylation patterns. Our findings suggest that stressful environmental condition can produce transgenerational epigenetic modifications. Progenies of stressed plants may develop enhanced adaptability to the condition, and this acquired trait is inheritable and accord with transmission of the epigenetic modifications. We suggest

  2. DNA methylation patterns of genes related to immune response in the different clinical forms of oral lichen planus.

    Science.gov (United States)

    Cruz, Aline Fernanda; de Resende, Renata Gonçalves; de Lacerda, Júlio César Tanos; Pereira, Núbia Braga; Melo, Leonardo Augusto; Diniz, Marina Gonçalves; Gomes, Carolina Cavalieri; Gomez, Ricardo Santiago

    2018-01-01

    The oral lichen planus is a chronic inflammatory disease. Although its aetiology is not well understood, the role of T lymphocytes in its inflammatory events is recognised. Identifying the epigenetic mechanisms involved in the pathogenesis of this immune-mediated condition is fundamental for understanding the inflammatory reaction that occurs in the disease. The purpose of this work was to evaluate the methylation pattern of 21 immune response-related genes in the different clinical forms of oral lichen planus. A cross-sectional study was performed to analyse the DNA methylation patterns in three distinct groups of oral lichen planus: (i) reticular/plaque lesions; (ii) erosive lesions; (iii) normal oral mucosa (control group). After DNA extraction from biopsies, the samples were submitted to digestions by methylation-sensitive and methylation-dependent enzymes and double digestion. The relative percentage of methylated DNA for each gene was provided using real-time polymerase chain reaction arrays. Hypermethylation of the STAT5A gene was observed only in the control group (59.0%). A higher hypermethylation of the ELANE gene was found in reticular/plaque lesions (72.1%) compared to the erosive lesions (50.0%). Our results show variations in the methylation profile of immune response-related genes, according to the clinical type of oral lichen planus after comparing with the normal oral mucosa. Further studies are necessary to validate these findings using gene expression analysis. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  3. Mean annual precipitation explains spatiotemporal patterns of Cenozoic mammal beta diversity and latitudinal diversity gradients in North America.

    Directory of Open Access Journals (Sweden)

    Danielle Fraser

    Full Text Available Spatial diversity patterns are thought to be driven by climate-mediated processes. However, temporal patterns of community composition remain poorly studied. We provide two complementary analyses of North American mammal diversity, using (i a paleontological dataset (2077 localities with 2493 taxon occurrences spanning 21 discrete subdivisions of the Cenozoic based on North American Land Mammal Ages (36 Ma--present, and (ii climate space model predictions for 744 extant mammals under eight scenarios of future climate change. Spatial variation in fossil mammal community structure (β diversity is highest at intermediate values of continental mean annual precipitation (MAP estimated from paleosols (∼ 450 mm/year and declines under both wetter and drier conditions, reflecting diversity patterns of modern mammals. Latitudinal gradients in community change (latitudinal turnover gradients, aka LTGs increase in strength through the Cenozoic, but also show a cyclical pattern that is significantly explained by MAP. In general, LTGs are weakest when continental MAP is highest, similar to modern tropical ecosystems in which latitudinal diversity gradients are weak or undetectable. Projections under modeled climate change show no substantial change in β diversity or LTG strength for North American mammals. Our results suggest that similar climate-mediated mechanisms might drive spatial and temporal patterns of community composition in both fossil and extant mammals. We also provide empirical evidence that the ecological processes on which climate space models are based are insufficient for accurately forecasting long-term mammalian response to anthropogenic climate change and inclusion of historical parameters may be essential.

  4. A Mimicking-of-DNA-Methylation-Patterns Pipeline for Overcoming the Restriction Barrier of Bacteria

    Science.gov (United States)

    Zhang, Guoqiang; Wang, Wenzhao; Deng, Aihua; Sun, Zhaopeng; Zhang, Yun; Liang, Yong; Che, Yongsheng; Wen, Tingyi

    2012-01-01

    Genetic transformation of bacteria harboring multiple Restriction-Modification (R-M) systems is often difficult using conventional methods. Here, we describe a mimicking-of-DNA-methylation-patterns (MoDMP) pipeline to address this problem in three difficult-to-transform bacterial strains. Twenty-four putative DNA methyltransferases (MTases) from these difficult-to-transform strains were cloned and expressed in an Escherichia coli strain lacking all of the known R-M systems and orphan MTases. Thirteen of these MTases exhibited DNA modification activity in Southwestern dot blot or Liquid Chromatography–Mass Spectrometry (LC–MS) assays. The active MTase genes were assembled into three operons using the Saccharomyces cerevisiae DNA assembler and were co-expressed in the E. coli strain lacking known R-M systems and orphan MTases. Thereafter, results from the dot blot and restriction enzyme digestion assays indicated that the DNA methylation patterns of the difficult-to-transform strains are mimicked in these E. coli hosts. The transformation of the Gram-positive Bacillus amyloliquefaciens TA208 and B. cereus ATCC 10987 strains with the shuttle plasmids prepared from MoDMP hosts showed increased efficiencies (up to four orders of magnitude) compared to those using the plasmids prepared from the E. coli strain lacking known R-M systems and orphan MTases or its parental strain. Additionally, the gene coding for uracil phosphoribosyltransferase (upp) was directly inactivated using non-replicative plasmids prepared from the MoDMP host in B. amyloliquefaciens TA208. Moreover, the Gram-negative chemoautotrophic Nitrobacter hamburgensis strain X14 was transformed and expressed Green Fluorescent Protein (GFP). Finally, the sequence specificities of active MTases were identified by restriction enzyme digestion, making the MoDMP system potentially useful for other strains. The effectiveness of the MoDMP pipeline in different bacterial groups suggests a universal potential

  5. Analysis of mutation/rearrangement frequencies and methylation patterns at a given DNA locus using restriction fragment length polymorphism.

    Science.gov (United States)

    Boyko, Alex; Kovalchuk, Igor

    2010-01-01

    Restriction fragment length polymorphism (RFLP) is a difference in DNA sequences of organisms belonging to the same species. RFLPs are typically detected as DNA fragments of different lengths after digestion with various restriction endonucleases. The comparison of RFLPs allows investigators to analyze the frequency of occurrence of mutations, such as point mutations, deletions, insertions, and gross chromosomal rearrangements, in the progeny of stressed plants. The assay involves restriction enzyme digestion of DNA followed by hybridization of digested DNA using a radioactively or enzymatically labeled probe. Since DNA can be digested with methylation sensitive enzymes, the assay can also be used to analyze a methylation pattern of a particular locus. Here, we describe RFLP analysis using methylation-insensitive and methylation-sensitive enzymes.

  6. Patterns of DNA methylation in the normal colon vary by anatomical location, gender, and age

    Science.gov (United States)

    Kaz, Andrew M; Wong, Chao-Jen; Dzieciatkowski, Slavomir; Luo, Yanxin; Schoen, Robert E; Grady, William M

    2014-01-01

    Alterations in DNA methylation have been proposed to create a field cancerization state in the colon, where molecular alterations that predispose cells to transformation occur in histologically normal tissue. However, our understanding of the role of DNA methylation in field cancerization is limited by an incomplete characterization of the methylation state of the normal colon. In order to determine the colon’s normal methylation state, we extracted DNA from normal colon biopsies from the rectum, sigmoid, transverse, and ascending colon and assessed the methylation status of the DNA by pyrosequencing candidate loci as well as with HumanMethylation450 arrays. We found that methylation levels of repetitive elements LINE-1 and SAT-α showed minimal variability throughout the colon in contrast to other loci. Promoter methylation of EVL was highest in the rectum and progressively lower in the proximal segments, whereas ESR1 methylation was higher in older individuals. Genome-wide methylation analysis of normal DNA revealed 8388, 82, and 93 differentially methylated loci that distinguished right from left colon, males from females, and older vs. younger individuals, respectively. Although variability in methylation between biopsies and among different colon segments was minimal for repetitive elements, analyses of specific cancer-related genes as well as a genome-wide methylation analysis demonstrated differential methylation based on colon location, individual age, and gender. These studies advance our knowledge regarding the variation of DNA methylation in the normal colon, a prerequisite for future studies aimed at understanding methylation differences indicative of a colon field effect. PMID:24413027

  7. Adolescent binge-pattern alcohol exposure alters genome-wide DNA methylation patterns in the hypothalamus of alcohol-naïve male offspring.

    Science.gov (United States)

    Asimes, AnnaDorothea; Torcaso, Audrey; Pinceti, Elena; Kim, Chun K; Zeleznik-Le, Nancy J; Pak, Toni R

    2017-05-01

    Teenage binge drinking is a major health concern in the United States, with 21% of teenagers reporting binge-pattern drinking behavior in the previous 30 days. Recently, our lab showed that alcohol-naïve offspring of rats exposed to alcohol during adolescence exhibited altered gene expression profiles in the hypothalamus, a brain region involved in stress regulation. We employed Enhanced Reduced Representation Bisulfite Sequencing as an unbiased approach to test the hypothesis that parental exposure to binge-pattern alcohol during adolescence alters DNA methylation profiles in their alcohol-naïve offspring. Wistar rats were administered a repeated binge-ethanol exposure paradigm during early (postnatal day (PND) 37-44) and late (PND 67-74) adolescent development. Animals were mated 24 h after the last ethanol dose and subsequent offspring were produced. Analysis of male PND7 offspring revealed that offspring of alcohol-exposed parents exhibited differential DNA methylation patterns in the hypothalamus. The differentially methylated cytosines (DMCs) were distinct between offspring depending on which parent was exposed to ethanol. Moreover, novel DMCs were observed when both parents were exposed to ethanol and many DMCs from single parent ethanol exposure were not recapitulated with dual parent exposure. We also measured mRNA expression of several differentially methylated genes and some, but not all, showed correlative changes in expression. Importantly, methylation was not a direct predictor of expression levels, underscoring the complexity of transcriptional regulation. Overall, we demonstrate that adolescent binge ethanol exposure causes altered genome-wide DNA methylation patterns in the hypothalamus of alcohol-naïve offspring. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. Variation in the DNA methylation pattern of expressed and nonexpressed genes in chicken.

    Science.gov (United States)

    Cooper, D N; Errington, L H; Clayton, R M

    1983-01-01

    Using methyl-sensitive and -insensitive restriction enzymes, Hpa II and Msp I, the methylation status of various chicken genes was examined in different tissues and developmental stages. Tissue-specific differences in methylation were found for the delta-crystallin, beta-tubulin, G3PDH, rDNA, and actin genes but not for the histone genes. Developmental decreases in methylation were noted for the delta-crystallin and actin genes in chicken kidney between embryo and adult. Since most of the sequences examined were housekeeping genes, transcriptional differences are apparently not a necessary accompaniment to changes in DNA methylation at the CpG sites examined. The only exception is sperm DNA where the delta-crystallin, beta-tubulin, and actin genes are highly methylated and almost certainly not transcribed. However the G3PDH genes are no more highly methylated in sperm than in other somatic tissues. Many sequences homologous to the rDNA and histone probes used are unmethylated in all tissues examined including sperm, but a methylated rDNA subfraction is more heavily methylated in sperm than in other tissues. We speculate as to the significance of these differences in sperm DNA methylation in the light of possible requirements for early gene activation and the probable deleterious mutagenic effects of heavy methylation within coding sequences.

  9. Assessment of the genetic diversity and pattern of relationship of ...

    African Journals Online (AJOL)

    SAM

    2014-04-02

    Apr 2, 2014 ... Cluster and principal coordinate analysis of the 30 ... The FST value (0.63) indicated a very high genetic differentiation as expected for ..... diversity) using Markov chain method showed that the ..... WL, Lee M, Porter K (2000).

  10. Diversity patterns in the terrestrial avifauna of the Salton sea

    Science.gov (United States)

    Mark B. Mendelsohn; William I. Boarman; Robert N. Fisher

    2005-01-01

    We performed bird point counts monthly March-June 2001 and bi-monthly August 2001-February 2002 across a sampling grid of 35 points along the west edge of Salton Sea. We found that landbird species diversity (both in numbers of species, and numbers per species) was dependent on proximity to the sea. Diversity was at a maximum nearest the shore, and was significantly...

  11. Polymorphism and methylation patterns in Agave tequilana Weber var. 'Azul' plants propagated asexually by three different methods.

    Science.gov (United States)

    Díaz-Martínez, Miriam; Nava-Cedillo, Alejandro; Guzmán-López, José Alfredo; Escobar-Guzmán, Rocío; Simpson, June

    2012-04-01

    Genetic variation in three forms of asexually propagated Agave tequilana Weber var. 'Azul' plants namely offsets, bulbils and in vitro cultured individuals was studied by AFLP analysis. Low levels of variation were observed between mother plants and offsets and a higher level between mother plant and bulbils. Families obtained from commercial plantations showed lower levels of variation in comparison to families grown as ornamentals. No variation was observed between the original explant and four generations of in vitro cultured plants. Epigenetic variation was also studied by analyzing changes in methylation patterns between mother plants and offspring in each form of asexual reproduction. Offsets and bulbils showed an overall decrease in methylation whereas in vitro cultured plants showed patterns specific to each generation: Generations 1 and 4 showed overall demethylation whereas Generations 2 and 3 showed increased methylation. Analysis of ESTs associated with transposable elements revealed higher proportions of ESTs from Ty1-copia-like, Gypsy and CACTA transposable elements in cDNA libraries obtained from pluripotent tissue suggesting a possible correlation between methylation patterns, expression of transposable element associated genes and somaclonal variation. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  12. Large-Scale Spatio-Temporal Patterns of Mediterranean Cephalopod Diversity.

    Directory of Open Access Journals (Sweden)

    Stefanie Keller

    Full Text Available Species diversity is widely recognized as an important trait of ecosystems' functioning and resilience. Understanding the causes of diversity patterns and their interaction with the environmental conditions is essential in order to effectively assess and preserve existing diversity. While diversity patterns of most recurrent groups such as fish are commonly studied, other important taxa such as cephalopods have received less attention. In this work we present spatio-temporal trends of cephalopod diversity across the entire Mediterranean Sea during the last 19 years, analysing data from the annual bottom trawl survey MEDITS conducted by 5 different Mediterranean countries using standardized gears and sampling protocols. The influence of local and regional environmental variability in different Mediterranean regions is analysed applying generalized additive models, using species richness and the Shannon Wiener index as diversity descriptors. While the western basin showed a high diversity, our analyses do not support a steady eastward decrease of diversity as proposed in some previous studies. Instead, high Shannon diversity was also found in the Adriatic and Aegean Seas, and high species richness in the eastern Ionian Sea. Overall diversity did not show any consistent trend over the last two decades. Except in the Adriatic Sea, diversity showed a hump-shaped trend with depth in all regions, being highest between 200-400 m depth. Our results indicate that high Chlorophyll a concentrations and warmer temperatures seem to enhance species diversity, and the influence of these parameters is stronger for richness than for Shannon diversity.

  13. Promoter DNA methylation pattern identifies prognostic subgroups in childhood T-cell acute lymphoblastic leukemia.

    Directory of Open Access Journals (Sweden)

    Magnus Borssén

    Full Text Available BACKGROUND: Treatment of pediatric T-cell acute lymphoblastic leukemia (T-ALL has improved, but there is a considerable fraction of patients experiencing a poor outcome. There is a need for better prognostic markers and aberrant DNA methylation is a candidate in other malignancies, but its potential prognostic significance in T-ALL is hitherto undecided. DESIGN AND METHODS: Genome wide promoter DNA methylation analysis was performed in pediatric T-ALL samples (n = 43 using arrays covering >27000 CpG sites. Clinical outcome was evaluated in relation to methylation status and compared with a contemporary T-ALL group not tested for methylation (n = 32. RESULTS: Based on CpG island methylator phenotype (CIMP, T-ALL samples were subgrouped as CIMP+ (high methylation and CIMP- (low methylation. CIMP- T-ALL patients had significantly worse overall and event free survival (p = 0.02 and p = 0.001, respectively compared to CIMP+ cases. CIMP status was an independent factor for survival in multivariate analysis including age, gender and white blood cell count. Analysis of differently methylated genes in the CIMP subgroups showed an overrepresentation of transcription factors, ligands and polycomb target genes. CONCLUSIONS: We identified global promoter methylation profiling as being of relevance for subgrouping and prognostication of pediatric T-ALL.

  14. Global patterns of guild composition and functional diversity of spiders.

    Directory of Open Access Journals (Sweden)

    Pedro Cardoso

    Full Text Available The objectives of this work are: (1 to define spider guilds for all extant families worldwide; (2 test if guilds defined at family level are good surrogates of species guilds; (3 compare the taxonomic and guild composition of spider assemblages from different parts of the world; (4 compare the taxonomic and functional diversity of spider assemblages and; (5 relate functional diversity with habitat structure. Data on foraging strategy, prey range, vertical stratification and circadian activity was collected for 108 families. Spider guilds were defined by hierarchical clustering. We searched for inconsistencies between family guild placement and the known guild of each species. Richness and abundance per guild before and after correcting guild placement were compared, as were the proportions of each guild and family between all possible pairs of sites. Functional diversity per site was calculated based on hierarchical clustering. Eight guilds were discriminated: (1 sensing, (2 sheet, (3 space, and (4 orb web weavers; (5 specialists; (6 ambush, (7 ground, and (8 other hunters. Sixteen percent of the species richness corresponding to 11% of all captured individuals was incorrectly attributed to a guild by family surrogacy; however, the correlation of uncorrected vs. corrected guilds was invariably high. The correlation of guild richness or abundances was generally higher than the correlation of family richness or abundances. Functional diversity was not always higher in the tropics than in temperate regions. Families may potentially serve as ecological surrogates for species. Different families may present similar roles in the ecosystems, with replacement of some taxa by other within the same guild. Spiders in tropical regions seem to have higher redundancy of functional roles and/or finer resource partitioning than in temperate regions. Although species and family diversity were higher in the tropics, functional diversity seems to be also

  15. Patterning and predicting aquatic macroinvertebrate diversities using artificial neural network

    NARCIS (Netherlands)

    Park, Y.S.; Verdonschot, P.F.M.; Chon, T.S.; Lek, S.

    2003-01-01

    A counterpropagation neural network (CPN) was applied to predict species richness (SR) and Shannon diversity index (SH) of benthic macroinvertebrate communities using 34 environmental variables. The data were collected at 664 sites at 23 different water types such as springs, streams, rivers,

  16. Trajectories of Neighborhood Change : Spatial Patterns of Increasing Ethnic Diversity

    NARCIS (Netherlands)

    Zwiers, M.D.; van Ham, M.; Manley, D.J.

    Western cities are increasingly ethnically diverse and in most cities the share of ethnic minorities is growing. Studies analyzing changing ethnic geographies often limit their analysis to changes in ethnic concentrations in neighborhoods between two points in time. Such a static approach limits our

  17. Genetic diversity of gliadin pattern, morphological traits and baking ...

    African Journals Online (AJOL)

    USER

    2010-02-15

    Feb 15, 2010 ... diversity of 102 double haploids of wheat (sent from. CIMMYT) through studying gliadin protein ... biomass, yield per plant, harvest index, number of grains per spike, spike density, spike length, plant ... per spike, also 6 baking quality traits, protein content, gluten index,. SDS sedimentation, sedimentation ...

  18. Genome-wide DNA methylation patterns in wild samples of two morphotypes of threespine stickleback (Gasterosteus aculeatus).

    Science.gov (United States)

    Smith, Gilbert; Smith, Carl; Kenny, John G; Chaudhuri, Roy R; Ritchie, Michael G

    2015-04-01

    Epigenetic marks such as DNA methylation play important biological roles in gene expression regulation and cellular differentiation during development. To examine whether DNA methylation patterns are potentially associated with naturally occurring phenotypic differences, we examined genome-wide DNA methylation within Gasterosteus aculeatus, using reduced representation bisulfite sequencing. First, we identified highly methylated regions of the stickleback genome, finding such regions to be located predominantly within genes, and associated with genes functioning in metabolism and biosynthetic processes, cell adhesion, signaling pathways, and blood vessel development. Next, we identified putative differentially methylated regions (DMRs) of the genome between complete and low lateral plate morphs of G. aculeatus. We detected 77 DMRs that were mainly located in intergenic regions. Annotations of genes associated with these DMRs revealed potential functions in a number of known divergent adaptive phenotypes between G. aculeatus ecotypes, including cardiovascular development, growth, and neuromuscular development. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  19. Patterns of diversity in soft-bodied meiofauna

    DEFF Research Database (Denmark)

    Curini-Galletti, Marco; Artois, Tom; Delogu, Valentina

    2012-01-01

    Biogeographical and macroecological principles are derived from patterns of distribution in large organisms, whereas microscopic ones have often been considered uninteresting, because of their supposed wide distribution. Here, after reporting the results of an intensive faunistic survey of marine...

  20. Cord blood hematopoietic cells from preterm infants display altered DNA methylation patterns.

    Science.gov (United States)

    de Goede, Olivia M; Lavoie, Pascal M; Robinson, Wendy P

    2017-01-01

    Premature infants are highly vulnerable to infection. This is partly attributable to the preterm immune system, which differs from that of the term neonate in cell composition and function. Multiple studies have found differential DNA methylation (DNAm) between preterm and term infants' cord blood; however, interpretation of these studies is limited by the confounding factor of blood cell composition. This study evaluates the epigenetic impact of preterm birth in isolated hematopoietic cell populations, reducing the concern of cell composition differences. Genome-wide DNAm was measured using the Illumina 450K array in T cells, monocytes, granulocytes, and nucleated red blood cells (nRBCs) isolated from cord blood of 5 term and 5 preterm (blood cells (nRBCs) showed the most extensive changes in DNAm, with 9258 differentially methylated (DM) sites (FDR  0.10) discovered between preterm and term infants compared to the blood cell populations. The direction of DNAm change with gestational age at these prematurity-DM sites followed known patterns of hematopoietic differentiation, suggesting that term hematopoietic cell populations are more epigenetically mature than their preterm counterparts. Consistent shifts in DNAm between preterm and term cells were observed at 25 CpG sites, with many of these sites located in genes involved in growth and proliferation, hematopoietic lineage commitment, and the cytoskeleton. DNAm in preterm and term hematopoietic cells conformed to previously identified DNAm signatures of fetal liver and bone marrow, respectively. This study presents the first genome-wide mapping of epigenetic differences in hematopoietic cells across the late gestational period. DNAm differences in hematopoietic cells between term and <31 weeks were consistent with the hematopoietic origin of these cells during ontogeny, reflecting an important role of DNAm in their regulation. Due to the limited sample size and the high coincidence of prematurity and

  1. Changes in genomic methylation patterns during the formation of triploid asexual dandelion lineages

    NARCIS (Netherlands)

    Verhoeven, K.J.F.; Van Dijk, P.J.; Biere, A.

    2010-01-01

    DNA methylation is an epigenetic mechanism that has the potential to affect plant phenotypes and that is responsive to environmental and genomic stresses such as hybridization and polyploidization. We explored de novo methylation variation that arises during the formation of triploid asexual

  2. Variation of DNA methylation patterns associated with gene expression in rice (Oryza sativa) exposed to cadmium.

    Science.gov (United States)

    Feng, Sheng Jun; Liu, Xue Song; Tao, Hua; Tan, Shang Kun; Chu, Shan Shan; Oono, Youko; Zhang, Xian Duo; Chen, Jian; Yang, Zhi Min

    2016-12-01

    We report genome-wide single-base resolution maps of methylated cytosines and transcriptome change in Cd-exposed rice. Widespread differences were identified in CG and non-CG methylation marks between Cd-exposed and Cd-free rice genomes. There are 2320 non-redundant differentially methylated regions detected in the genome. RNA sequencing revealed 2092 DNA methylation-modified genes differentially expressed under Cd exposure. More genes were found hypermethylated than those hypomethylated in CG, CHH and CHG (where H is A, C or T) contexts in upstream, gene body and downstream regions. Many of the genes were involved in stress response, metal transport and transcription factors. Most of the DNA methylation-modified genes were transcriptionally altered under Cd stress. A subset of loss of function mutants defective in DNA methylation and histone modification activities was used to identify transcript abundance of selected genes. Compared with wide type, mutation of MET1 and DRM2 resulted in general lower transcript levels of the genes under Cd stress. Transcripts of OsIRO2, OsPR1b and Os09g02214 in drm2 were significantly reduced. A commonly used DNA methylation inhibitor 5-azacytidine was employed to investigate whether DNA demethylation affected physiological consequences. 5-azacytidine provision decreased general DNA methylation levels of selected genes, but promoted growth of rice seedlings and Cd accumulation in rice plant. © 2016 John Wiley & Sons Ltd.

  3. Evaluation of methylation pattern in promoter region of E-cadherin ...

    African Journals Online (AJOL)

    user

    2011-03-07

    Mar 7, 2011 ... promoter methylation in CDH1 gene inactivation in breast cancer, the CpG methylation status of E- ..... 5'CpG island of CDH1 in prostate, lung, liver, bladder, .... and estrogen receptor alpha from Sp1 sites to induce cell cycle.

  4. Resource diversity and provenance underpin spatial patterns in functional diversity across native and exotic species.

    Science.gov (United States)

    Méndez, Verónica; Wood, Jamie R; Butler, Simon J

    2018-05-01

    Functional diversity metrics are increasingly used to augment or replace taxonomic diversity metrics to deliver more mechanistic insights into community structure and function. Metrics used to describe landscape structure and characteristics share many of the same limitations as taxonomy-based metrics, particularly their reliance on anthropogenically defined typologies with little consideration of structure, management, or function. However, the development of alternative metrics to describe landscape characteristics has been limited. Here, we extend the functional diversity framework to characterize landscapes based on the diversity of resources available across habitats present. We then examine the influence of resource diversity and provenance on the functional diversities of native and exotic avian communities in New Zealand. Invasive species are increasingly prevalent and considered a global threat to ecosystem function, but the characteristics of and interactions between sympatric native and exotic communities remain unresolved. Understanding their comparative responses to environmental change and the mechanisms underpinning them is of growing importance in predicting community dynamics and changing ecosystem function. We use (i) matrices of resource use (species) and resource availability (habitats) and (ii) occurrence data for 62 native and 25 exotic species and 19 native and 13 exotic habitats in 2015 10 × 10 km quadrats to examine the relationship between native and exotic avian and landscape functional diversity. The numbers of species in, and functional diversities of, native and exotic communities were positively related. Each community displayed evidence of environmental filtering, but it was significantly stronger for exotic species. Less environmental filtering occurred in landscapes providing a more diverse combination of resources, with resource provenance also an influential factor. Landscape functional diversity explained a greater

  5. Female human pluripotent stem cells rapidly lose X chromosome inactivation marks and progress to a skewed methylation pattern during culture.

    Science.gov (United States)

    Geens, M; Seriola, A; Barbé, L; Santalo, J; Veiga, A; Dée, K; Van Haute, L; Sermon, K; Spits, C

    2016-04-01

    Does a preferential X chromosome inactivation (XCI) pattern exist in female human pluripotent stem cells (hPSCs) and does the pattern change during long-term culture or upon differentiation? We identified two independent phenomena that lead to aberrant XCI patterns in female hPSC: a rapid loss of histone H3 lysine 27 trimethylation (H3K27me3) and long non-coding X-inactive specific transcript (XIST) expression during culture, often accompanied by erosion of XCI-specific methylation, and a frequent loss of random XCI in the cultures. Variable XCI patterns have been reported in female hPSC, not only between different hPSC lines, but also between sub-passages of the same cell line, however the reasons for this variability remain unknown. Moreover, while non-random XCI-linked DNA methylation patterns have been previously reported, their origin and extent have not been investigated. We investigated the XCI patterns in 23 human pluripotent stem cell (hPSC) lines, during long-term culture and after differentiation, by gene expression analysis, histone modification assessment and study of DNA methylation. The presence and location of H3K27me3 was studied by immunofluorescence, XIST expression by real-time PCR, and mono- or bi-allelic expression of X-linked genes was studied by sequencing of cDNA. XCI-specific DNA methylation was analysed using methylation-sensitive restriction and PCR, and more in depth by massive parallel bisulphite sequencing. All hPSC lines showed XCI, but we found a rapid loss of XCI marks during the early stages of in vitro culture. While this loss of XCI marks was accompanied in several cases by an extensive erosion of XCI-specific methylation, it did not result in X chromosome reactivation. Moreover, lines without strong erosion of methylation frequently displayed non-random DNA methylation, which occurred independently from the loss of XCI marks. This bias in X chromosome DNA methylation did not appear as a passenger event driven by clonal culture

  6. Staphylococcus pseudintermedius colonization patterns and strain diversity in healthy dogs

    DEFF Research Database (Denmark)

    Paul, Narayan Chandra; Bärgman, Sofia Cathrine; Moodley, Arshnee

    2012-01-01

    This is the first large-scale study of Staphylococcus pseudintermedius colonization and diversity in healthy dogs where samples were collected over a long time and strains were identified by PCR according to the current taxonomy of the S. intermedius group and typed by a highly discriminatory...... method such as pulsed field gel electrophoresis (PFGE). A cross-sectional study of nasal, oral, perineal and inguinal carriage in 119 healthy dogs was followed by a longitudinal study where oral and perineal carriage was examined in 16 dogs for 10 times over a period of 1 year. Altogether we collected...... 762 samples and 285 S. pseudintermedius isolates, 182 of which were typed by PFGE to determine spatial and temporal strain diversity within individual carriers. In the cross-sectional study, S. pseudintermedius was isolated from at least one body site in 82 (69%) of the 119 dogs. The most frequent...

  7. Host diversity and latitude drive the trematode diversity patterns in the European freshwater fauna

    DEFF Research Database (Denmark)

    Thieltges, David W.; Hof, Christian; Dehling, D. Matthias

    2011-01-01

    biogeographical regions in Europe from the Limnofauna Europaea and used multiple regression analyses to test for correlations between the diversity of definitive (vertebrates) or first intermediate (gastropods) hosts and that of trematodes, and for latitudinal gradients in trematode diversity. In particular, we...... faunas. Results Latitude or first intermediate host richness had no effect on trematode richness, but definitive host richness was a strong predictor of trematode richness, among both allogenic and autogenic parasites. We found that beta diversity of trematode faunas within latitudinal bands decreased...... to the north, with similar values for allogenic and autogenic trematodes. Finally, we observed an increasing proportion of autogenic species toward the north of Europe. Main conclusions The richness of definitive hosts appears to be the driver of trematode diversity at a continental scale. The latitudinal...

  8. Evolution of DNA Methylation across Insects.

    Science.gov (United States)

    Bewick, Adam J; Vogel, Kevin J; Moore, Allen J; Schmitz, Robert J

    2017-03-01

    DNA methylation contributes to gene and transcriptional regulation in eukaryotes, and therefore has been hypothesized to facilitate the evolution of plastic traits such as sociality in insects. However, DNA methylation is sparsely studied in insects. Therefore, we documented patterns of DNA methylation across a wide diversity of insects. We predicted that underlying enzymatic machinery is concordant with patterns of DNA methylation. Finally, given the suggestion that DNA methylation facilitated social evolution in Hymenoptera, we tested the hypothesis that the DNA methylation system will be associated with presence/absence of sociality among other insect orders. We found DNA methylation to be widespread, detected in all orders examined except Diptera (flies). Whole genome bisulfite sequencing showed that orders differed in levels of DNA methylation. Hymenopteran (ants, bees, wasps and sawflies) had some of the lowest levels, including several potential losses. Blattodea (cockroaches and termites) show all possible patterns, including a potential loss of DNA methylation in a eusocial species whereas solitary species had the highest levels. Species with DNA methylation do not always possess the typical enzymatic machinery. We identified a gene duplication event in the maintenance DNA methyltransferase 1 (DNMT1) that is shared by some Hymenoptera, and paralogs have experienced divergent, nonneutral evolution. This diversity and nonneutral evolution of underlying machinery suggests alternative DNA methylation pathways may exist. Phylogenetically corrected comparisons revealed no evidence that supports evolutionary association between sociality and DNA methylation. Future functional studies will be required to advance our understanding of DNA methylation in insects. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  9. Spatial pattern of tree diversity and evenness across forest types in Majella National Park, Italy

    Directory of Open Access Journals (Sweden)

    Mohammad Redowan

    2015-09-01

    Full Text Available Background Estimation of tree diversity at broader scale is important for conservation planning. Tree diversity should be measured and understood in terms of diversity and evenness, two integral components to describe the structure of a biological community. Variation of the tree diversity and evenness with elevation, topographic relief, aspect, terrain shape, slope, soil nutrient, solar radiation etc. are well documented. Methods Present study explores the variation of tree diversity (measured as Shannon diversity and evenness indices of Majella National Park, Italy with five available forest types namely evergreen oak woods, deciduous oak woods, black/aleppo pine stands, hop-hornbeam forest and beech forest, using satellite, environmental and field data. Results Hop-hornbeam forest was found to be most diverse and even while evergreen Oak woods was the lowest diverse and even. Diversity and evenness of forest types were concurrent to each other i.e. forest type which was more diverse was also more even. As a broad pattern, majority portion of the study area belonged to medium diversity and high evenness class. Conclusions Satellite images and other GIS data proved useful tools in monitoring variation of tree diversity and evenness across various forest types. Present study findings may have implications in prioritizing conservation zones of high tree diversity at Majella.

  10. Genomic patterns in Acropora cervicornis show extensive population structure and variable genetic diversity.

    Science.gov (United States)

    Drury, Crawford; Schopmeyer, Stephanie; Goergen, Elizabeth; Bartels, Erich; Nedimyer, Ken; Johnson, Meaghan; Maxwell, Kerry; Galvan, Victor; Manfrino, Carrie; Lirman, Diego

    2017-08-01

    Threatened Caribbean coral communities can benefit from high-resolution genetic data used to inform management and conservation action. We use Genotyping by Sequencing (GBS) to investigate genetic patterns in the threatened coral, Acropora cervicornis , across the Florida Reef Tract (FRT) and the western Caribbean. Results show extensive population structure at regional scales and resolve previously unknown structure within the FRT. Different regions also exhibit up to threefold differences in genetic diversity (He), suggesting targeted management based on the goals and resources of each population is needed. Patterns of genetic diversity have a strong spatial component, and our results show Broward and the Lower Keys are among the most diverse populations in Florida. The genetic diversity of Caribbean staghorn coral is concentrated within populations and within individual reefs (AMOVA), highlighting the complex mosaic of population structure. This variance structure is similar over regional and local scales, which suggests that in situ nurseries are adequately capturing natural patterns of diversity, representing a resource that can replicate the average diversity of wild assemblages, serving to increase intraspecific diversity and potentially leading to improved biodiversity and ecosystem function. Results presented here can be translated into specific goals for the recovery of A. cervicornis , including active focus on low diversity areas, protection of high diversity and connectivity, and practical thresholds for responsible restoration.

  11. Endothelial heterogeneity in the umbilico-placental unit: DNA methylation as an innuendo of epigenetic diversity

    Science.gov (United States)

    Casanello, Paola; Schneider, Daniela; Herrera, Emilio A.; Uauy, Ricardo; Krause, Bernardo J.

    2014-01-01

    The endothelium is a multifunctional heterogeneous tissue playing a key role in the physiology of every organ. To accomplish this role the endothelium presents a phenotypic diversity that is early prompted during vascular development, allowing it to cope with specific requirements in a time- and site-specific manner. During the last decade several reports show that endothelial diversity is also present in the umbilico-placental vasculature, with differences between macro- and microvascular vessels as well as arterial and venous endothelium. This diversity is evidenced in vitro as a higher angiogenic capacity in the microcirculation; or disparity in the levels of several molecules that control endothelial function (i.e., receptor for growth factors, vasoactive mediators, and adhesion molecules) which frequently are differentially expressed between arterial and venous endothelium. Emerging evidence suggests that endothelial diversity would be prominently driven by epigenetic mechanisms which also control the basal expression of endothelial-specific genes. This review outlines evidence for endothelial diversity since early stages of vascular development and how this heterogeneity is expressed in the umbilico-placental vasculature. Furthermore a brief picture of epigenetic mechanisms and their role on endothelial physiology emphasizing new data on umbilical and placental endothelial cells is presented. Unraveling the role of epigenetic mechanisms on long term endothelial physiology and its functional diversity would contribute to develop more accurate therapeutic interventions. Altogether these data show that micro- versus macro-vascular, or artery versus vein comparisons are an oversimplification of the complexity occurring in the endothelium at different levels, and the necessity for the future research to establish the precise source of cells which are under study. PMID:24723887

  12. Endothelial heterogeneity in the umbilico-placental unit: DNA methylation as an innuendo of epigenetic diversity

    Directory of Open Access Journals (Sweden)

    Paola eCasanello

    2014-03-01

    Full Text Available The endothelium is a multifunctional heterogeneous tissue playing a key role in the physiology of every organ. To accomplish this role the endothelium presents a phenotypic diversity that is early prompted during vascular development, allowing it to cope with specific requirements in a time- and site-specific manner. During the last decade several reports show that endothelial diversity is also present in the umbilico-placental vasculature, with differences between macro- and microvascular vessels as well as arterial and venous endothelium. This diversity is evidenced in vitro as a higher angiogenic capacity in the microcirculation; or disparity in the levels of several molecules that control endothelial function (i.e. receptor for growth factors, vasoactive mediators and adhesion molecules which frequently are differentially expressed between arterial and venous endothelium. Emerging evidence suggests that endothelial diversity would be prominently driven by epigenetic mechanisms which also control the basal expression of endothelial-specific genes. This review outlines evidence for endothelial diversity since early stages of vascular development and how this heterogeneity is expressed in the umbilico-placental vasculature. Furthermore a brief picture of epigenetic mechanisms and their role on endothelial physiology emphasising new data on umbilical and placental endothelial cells is presented. Unravelling the role of epigenetic mechanisms on long-term endothelial physiology and its functional diversity would contribute to develop more accurate therapeutic interventions. Altogether these data show that micro- versus macro-vascular, or artery versus vein comparisons are an oversimplification of the complexity occurring in the endothelium at different levels, and the necessity for the future research to establish the precise source of cells which are under study.

  13. Statistical Image Recovery From Laser Speckle Patterns With Polarization Diversity

    Science.gov (United States)

    2010-09-01

    several techniques for speckle suppression in optical imaging [19]. However, averaging nonimaged laser speckle patterns does not yield the same result...Comparison”. Applied Optics , 21(15):2758–2769, August 1982. 13. Fienup, James R. “Image Formation from Nonimaged Laser Speckle Patterns”. S. R. Robinson...6 ν Optical Frequency . . . . . . . . . . . . . . . . . . . . . . 6 t Time . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 ϕ

  14. Patterns of Tree Species Diversity in Relation to Climatic Factors on the Sierra Madre Occidental, Mexico

    Science.gov (United States)

    Silva-Flores, Ramón; Pérez-Verdín, Gustavo; Wehenkel, Christian

    2014-01-01

    Biological diversity can be defined as variability among living organisms from all sources, including terrestrial organisms, marine and other aquatic ecosystems, and the ecological complexes which they are part of. This includes diversity within species, between species, and of ecosystems. Numerous diversity indices combine richness and evenness in a single expression, and several climate-based explanations have been proposed to explain broad-scale diversity patterns. However, climate-based water-energy dynamics appears to be an essential factor that determines patterns of diversity. The Mexican Sierra Madre Occidental occupies an area of about 29 million hectares and is located between the Neotropical and Holarctic ecozones. It shelters a high diversity of flora, including 24 different species of Pinus (ca. 22% on the whole), 54 species of Quercus (ca. 9–14%), 7 species of Arbutus (ca. 50%) and many other trees species. The objectives of this study were to model how tree species diversity is related to climatic and geographic factors and stand density and to test the Metabolic Theory, Productivity-Diversity Hypothesis, Physiological Tolerance Hypothesis, Mid-Domain Effect, and the Water-Energy Dynamic Theory on the Sierra Madre Occidental, Durango. The results supported the Productivity-Diversity Hypothesis, Physiological Tolerance Hypothesis and Water-Energy Dynamic Theory, but not the Mid-Domain Effect or Metabolic Theory. The annual aridity index was the variable most closely related to the diversity indices analyzed. Contemporary climate was found to have moderate to strong effects on the minimum, median and maximum tree species diversity. Because water-energy dynamics provided a satisfactory explanation for the patterns of minimum, median and maximum diversity, an understanding of this factor is critical to future biodiversity research. Quantile regression of the data showed that the three diversity parameters of tree species are generally higher in cold

  15. Patterns of tree species diversity in relation to climatic factors on the Sierra Madre Occidental, Mexico.

    Science.gov (United States)

    Silva-Flores, Ramón; Pérez-Verdín, Gustavo; Wehenkel, Christian

    2014-01-01

    Biological diversity can be defined as variability among living organisms from all sources, including terrestrial organisms, marine and other aquatic ecosystems, and the ecological complexes which they are part of. This includes diversity within species, between species, and of ecosystems. Numerous diversity indices combine richness and evenness in a single expression, and several climate-based explanations have been proposed to explain broad-scale diversity patterns. However, climate-based water-energy dynamics appears to be an essential factor that determines patterns of diversity. The Mexican Sierra Madre Occidental occupies an area of about 29 million hectares and is located between the Neotropical and Holarctic ecozones. It shelters a high diversity of flora, including 24 different species of Pinus (ca. 22% on the whole), 54 species of Quercus (ca. 9-14%), 7 species of Arbutus (ca. 50%) and many other trees species. The objectives of this study were to model how tree species diversity is related to climatic and geographic factors and stand density and to test the Metabolic Theory, Productivity-Diversity Hypothesis, Physiological Tolerance Hypothesis, Mid-Domain Effect, and the Water-Energy Dynamic Theory on the Sierra Madre Occidental, Durango. The results supported the Productivity-Diversity Hypothesis, Physiological Tolerance Hypothesis and Water-Energy Dynamic Theory, but not the Mid-Domain Effect or Metabolic Theory. The annual aridity index was the variable most closely related to the diversity indices analyzed. Contemporary climate was found to have moderate to strong effects on the minimum, median and maximum tree species diversity. Because water-energy dynamics provided a satisfactory explanation for the patterns of minimum, median and maximum diversity, an understanding of this factor is critical to future biodiversity research. Quantile regression of the data showed that the three diversity parameters of tree species are generally higher in cold

  16. Methylation patterns of repetitive DNA sequences in germ cells of Mus musculus.

    Science.gov (United States)

    Sanford, J; Forrester, L; Chapman, V; Chandley, A; Hastie, N

    1984-03-26

    The major and the minor satellite sequences of Mus musculus were undermethylated in both sperm and oocyte DNAs relative to the amount of undermethylation observed in adult somatic tissue DNA. This hypomethylation was specific for satellite sequences in sperm DNA. Dispersed repetitive and low copy sequences show a high degree of methylation in sperm DNA; however, a dispersed repetitive sequence was undermethylated in oocyte DNA. This finding suggests a difference in the amount of total genomic DNA methylation between sperm and oocyte DNA. The methylation levels of the minor satellite sequences did not change during spermiogenesis, and were not associated with the onset of meiosis or a specific stage in sperm development.

  17. Biogeographical Interpretation of Elevational Patterns of Genus Diversity of Seed Plants in Nepal.

    Science.gov (United States)

    Li, Miao; Feng, Jianmeng

    2015-01-01

    This study tests if the biogeographical affinities of genera are relevant for explaining elevational plant diversity patterns in Nepal. We used simultaneous autoregressive (SAR) models to investigate the explanatory power of several predictors in explaining the diversity-elevation relationships shown in genera with different biogeographical affinities. Delta akaike information criterion (ΔAIC) was used for multi-model inferences and selections. Our results showed that both the total and tropical genus diversity peaked below the mid-point of the elevational gradient, whereas that of temperate genera had a nearly symmetrical, unimodal relationship with elevation. The proportion of temperate genera increased markedly with elevation, while that of tropical genera declined. Compared to tropical genera, temperate genera had wider elevational ranges and were observed at higher elevations. Water-related variables, rather than mid-domain effects (MDE), were the most significant predictors of elevational patterns of tropical genus diversity. The temperate genus diversity was influenced by energy availability, but only in quadratic terms of the models. Though climatic factors and mid-domain effects jointly explained most of the variation in the diversity of temperate genera with elevation, the former played stronger roles. Total genus diversity was most strongly influenced by climate and the floristic overlap of tropical and temperate floras, while the influences of mid-domain effects were relatively weak. The influences of water-related and energy-related variables may vary with biogeographical affinities. The elevational patterns may be most closely related to climatic factors, while MDE may somewhat modify the patterns. Caution is needed when investigating the causal factors underlying diversity patterns for large taxonomic groups composed of taxa of different biogeographical affinities. Right-skewed diversity-elevation patterns may be produced by the differential

  18. Patterns of copepod diversity in the Chilean coastal upwelling system

    Science.gov (United States)

    Hidalgo, Pamela; Escribano, Ruben; Vergara, Odette; Jorquera, Erika; Donoso, Katty; Mendoza, Paula

    2010-12-01

    The copepod community structure from the Northern and Central/southern upwelling regions off Chile was studied and compared. The derived community descriptors were species abundance (N), species richness (R) and the Shannon-Wiener diversity index (H'). These descriptors were related to distinct habitats and conditions, sea surface temperature (SST) and depth of the upper boundary of the oxygen minimum zone (OMZ). From 159 samples, obtained between 2002 and 2008, a total number of 118 species were found of which the calanoids Paracalanus indicus, Acartia tonsa and Eucalanus inermis, along with the cyclopoid Oithona similis, and the poecilostomatoids Triconia conifera and Oncaea media were the dominant species. H' was higher in the northern region, but no differences in N and R were detected between regions. N was higher in the epipelagic vs the deep habitat, but R and H' did not differ. N, R and H' correlated positively to SST and negatively to OMZ depth. The ascent of the OMZ to the upper layer forced by upwelling was proposed as a mechanism that aggregates and increases copepod diversity in the food-rich photic zone. All these findings suggest a fundamental role of upwelling variation for modulating copepod dynamics and community structure in this highly productive but strongly variable marine ecosystem.

  19. Patterns of bryophyte diversity in arable fields of Lithuania

    Directory of Open Access Journals (Sweden)

    Danguolė Andriušaitytė

    2013-03-01

    Full Text Available The paper presents research data on bryophyte diversity in arable land throughout the territory of Lithuania. The bryoflora was analyzed regarding systematic structure and morphological forms, life-history strategies, mode of reproduction and frequency of species. Bryophyte diversity in arable fields of Lithuania was compared with that of Slovakia and the British Isles, which are positioned in different geographical regions of Europe. A total of 97 species of bryophytes of 25 families and 48 genera were ascertained. Dominance of acrocarpous mosses and thalloid liverworts, high representation of Pottiaceae, Bryaceae, Mielichhoferiaceae and Ricciaceae families as well as Bryum, Dicranella, Pohlia and Riccia genera, wide distribution of annual shuttles and ephemeral colonists, high reproduction effort of the species (frequent sporophytes and asexual propagules were specific features of the bryophytes of the studied habitats as a result of adaptations to regular disturbances. The distribution of species into six frequency groups seemed to be uneven. The most abundant group of species with the lowest frequency (1–3 records covered 53.6% of all species. The group contained about 90% of all many-year potential life span species recorded in the habitat. Species with short life span were distributed quite evenly throughout frequency groups. No regionally-specific species were ascertained in the studied habitat. Most of arable-land-specific species recorded in Lithuania is distributed throughout different regions of Europe.

  20. Diversity and distribution patterns in high southern latitude sponges.

    Directory of Open Access Journals (Sweden)

    Rachel V Downey

    Full Text Available Sponges play a key role in Antarctic marine benthic community structure and dynamics and are often a dominant component of many Southern Ocean benthic communities. Understanding the drivers of sponge distribution in Antarctica enables us to understand many of general benthic biodiversity patterns in the region. The sponges of the Antarctic and neighbouring oceanographic regions were assessed for species richness and biogeographic patterns using over 8,800 distribution records. Species-rich regions include the Antarctic Peninsula, South Shetland Islands, South Georgia, Eastern Weddell Sea, Kerguelen Plateau, Falkland Islands and north New Zealand. Sampling intensity varied greatly within the study area, with sampling hotspots found at the Antarctic Peninsula, South Georgia, north New Zealand and Tierra del Fuego, with limited sampling in the Bellingshausen and Amundsen seas in the Southern Ocean. In contrast to previous studies we found that eurybathy and circumpolar distributions are important but not dominant characteristics in Antarctic sponges. Overall Antarctic sponge species endemism is ∼43%, with a higher level for the class Hexactinellida (68%. Endemism levels are lower than previous estimates, but still indicate the importance of the Polar Front in isolating the Southern Ocean fauna. Nineteen distinct sponge distribution patterns were found, ranging from regional endemics to cosmopolitan species. A single, distinct Antarctic demosponge fauna is found to encompass all areas within the Polar Front, and the sub-Antarctic regions of the Kerguelen Plateau and Macquarie Island. Biogeographical analyses indicate stronger faunal links between Antarctica and South America, with little evidence of links between Antarctica and South Africa, Southern Australia or New Zealand. We conclude that the biogeographic and species distribution patterns observed are largely driven by the Antarctic Circumpolar Current and the timing of past continent

  1. Analysis of methylated patterns and quality-related genes in tobacco (Nicotiana tabacum) cultivars.

    Science.gov (United States)

    Jiao, Junna; Jia, Yanlong; Lv, Zhuangwei; Sun, Chuanfei; Gao, Lijie; Yan, Xiaoxiao; Cui, Liusu; Tang, Zongxiang; Yan, Benju

    2014-08-01

    Methylation-sensitive amplified polymorphism was used in this study to investigate epigenetic information of four tobacco cultivars: Yunyan 85, NC89, K326, and Yunyan 87. The DNA fragments with methylated information were cloned by reamplified PCR and sequenced. The results of Blast alignments showed that the genes with methylation information included chitinase, nitrate reductase, chloroplast DNA, mitochondrial DNA, ornithine decarboxylase, ribulose carboxylase, and promoter sequences. Homologous comparison in three cloned gene sequences (nitrate reductase, ornithine decarboxylase, and ribulose decarboxylase) indicated that geographic factors had significant influence on the whole genome methylation. Introns also contained different information in different tobacco cultivars. These findings suggest that synthetic mechanisms for tobacco aromatic components could be affected by different environmental factors leading to variation of noncoding regions in the genome, which finally results in different fragrance and taste in different tobacco cultivars.

  2. Pubertal development in healthy children is mirrored by DNA methylation patterns in peripheral blood

    DEFF Research Database (Denmark)

    Almstrup, Kristian; Johansen, Marie Lindhardt; Busch, Alexander S.

    2016-01-01

    Puberty marks numerous physiological processes which are initiated by central activation of the hypothalamic–pituitary–gonadal axis, followed by development of secondary sexual characteristics. To a large extent, pubertal timing is heritable, but current knowledge of genetic polymorphismsonly...... explains few months in the large inter-individual variation in the timing of puberty. We have analysed longitudinal genome-wide changes in DNA methylation in peripheral blood samples (n = 102) obtained from 51 healthy children before and after pubertal onset. We show that changes in single methylation...... sites are tightly associated with physiological pubertal transition and altered reproductive hormone levels. These methylation sites cluster in and around genes enriched for biological functions related to pubertal development. Importantly, we identified that methylation of the genomic region containing...

  3. Diversity patterns and freshwater molluscs similarities in small water reservoirs

    Directory of Open Access Journals (Sweden)

    Tomáš Čejka

    2011-02-01

    Full Text Available The survey presents the molluscan fauna from six impoundment systems of two sides (NW and SE of the Small Carpathians. Altogether 25 species (15 gastropod and 10 bivalve species were identified in reservoirs and their subsystems (inflows and outlets. The number of species per site ranged from 2 to 12, the mean number of species per site was 7. The mean number of individuals per site ranged from 15 to 905 (mean 174 ind/m2. Radix auricularia, R. ovata, Gyraulus albus, Gyraulus parvus/laevis, Hippeutis complanatus and Pisidium casertanum were present in more than 50% of reservoirs. The most abundant and frequent species in the entire area and all subsystems were Pisidium casertanum, Pisidium subtruncatum and Gyraulus parvus/laevis. Faunistic similarity indices indicate moderate degree of beta diversity i.e., differentiation among the sites; good separation of sites by cluster analysis indicates a different composition among inflows/outlets and littoral molluscan faunas of reservoirs.

  4. Ecological patterns of seed microbiome diversity, transmission, and assembly.

    Science.gov (United States)

    Shade, Ashley; Jacques, Marie-Agnès; Barret, Matthieu

    2017-06-01

    Seeds are involved in the transmission of microorganisms from one plant generation to another and consequently act as the initial inoculum for the plant microbiota. The purpose of this mini-review is to provide an overview of current knowledge on the diversity, structure and role of the seed microbiota. The relative importance of the mode of transmission (vertical vs horizontal) of the microbial entities composing the seed microbiota as well as the potential connections existing between seed and other plant habitats such as the anthosphere and the spermosphere is discussed. Finally the governing processes (niche vs neutral) involved in the assembly and the dynamics of the seed microbiota are examined. Copyright © 2017. Published by Elsevier Ltd.

  5. Identification of exotic genetic components and DNA methylation pattern analysis of three cotton introgression lines from Gossypium bickii.

    Science.gov (United States)

    He, Shou-Pu; Sun, Jun-Ling; Zhang, Chao; Du, Xiong-Ming

    2011-01-01

    The impact of alien DNA fragments on plant genome has been studied in many species. However, little is known about the introgression lines of Gossypium. To study the consequences of introgression in Gossypium, we investigated 2000 genomic and 800 epigenetic sites in three typical cotton introgression lines, as well as their cultivar (Gossypium hirsutum) and wild parents (Gossypium bickii), by amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP). The results demonstrate that an average of 0.5% of exotic DNA segments from wild cotton is transmitted into the genome of each introgression line, with the addition of other forms of genetic variation. In total, an average of 0.7% of genetic variation sites is identified in introgression lines. Simultaneously, the overall cytosine methylation level in each introgression line is very close to that of the upland cotton parent (an average of 22.6%). Further dividing patterns reveal that both hypomethylation and hypermethylation occurred in introgression lines in comparison with the upland cotton parent. Sequencing of nine methylation polymorphism fragments showed that most (7 of 9) of the methylation alternations occurred in the noncoding sequences. The molecular evidence of introgression from wild cotton into introgression lines in our study is identified by AFLP. Moreover, the causes of petal variation in introgression lines are discussed.

  6. Changes in DNA Methylation Pattern at Two Seedling Stages in Water Saving and Drought-Resistant Rice Variety after Drought Stress Domestication

    Directory of Open Access Journals (Sweden)

    Xiao-guo ZHENG

    2014-09-01

    Full Text Available Recent studies revealed that DNA methylation plays an important role in plant growth and development. In this study, a water-saving and drought-resistant rice variety Huhan 3 was subjected to drought stress from tillering to grain-filling stages in six successive growth cycles. The variations in DNA methylation pattern between the original generation (G0 and the sixth generation (G6 were analyzed by using methylation sensitive amplification polymorphism method. The results revealed that the methylated loci accounted for 34.3% to 34.8% of the total loci. Among these methylated loci, 83.1% to 84.8% were full- and hyper-methylated and 15.2% to 16.9% were hemi-methylated. The DNA methylation level decreased from the three-leaf to four-leaf stages in Huhan 3. Differentially methylated loci (DML between generations or/and between different developmental stages accounted for 4.0% of the total loci, most of which were only related to plant development (57.9%. Compared to G0, the DNA methylation pattern of G6 changed after drought domestication, at the three-leaf stage, de-methylation accounting for 59.1%, while at the four-leaf stage, re-methylation for 47.9%. Genome-wide alternations of DNA methylation were observed between the two seedling stages, and DML mainly occurred on the gene's promoter and exon region. The genes related to DML involved in a wide range of functional biology and participated in many important biological processes.

  7. High-technology exports of EEC countries: Persistence and diversity of specialization patterns

    International Nuclear Information System (INIS)

    Papagni, E.

    1992-01-01

    This analysis of the persistence and diversity of specialization patterns in EEC high technology exports is based on a package of products selected from the Eurostat database, COMEXT. High technology goods are considered as an innovative output indicator. A test of hypotheses of hysteresis and diversity of trade patterns at a national level is performed to verify some claims made by the 'evolutionary' theory of innovation and trade. The three-mode principal component analysis carried out confirms the persistence of specialization patterns of each EEC country in high technology exports, and highlights their sharp differences

  8. Patterns of genome size diversity in bats (order Chiroptera).

    Science.gov (United States)

    Smith, Jillian D L; Bickham, John W; Gregory, T Ryan

    2013-08-01

    Despite being a group of particular interest in considering relationships between genome size and metabolic parameters, bats have not been well studied from this perspective. This study presents new estimates for 121 "microbat" species from 12 families and complements a previous study on members of the family Pteropodidae ("megabats"). The results confirm that diversity in genome size in bats is very limited even compared with other mammals, varying approximately 2-fold from 1.63 pg in Lophostoma carrikeri to 3.17 pg in Rhinopoma hardwickii and averaging only 2.35 pg ± 0.02 SE (versus 3.5 pg overall for mammals). However, contrary to some other vertebrate groups, and perhaps owing to the narrow range observed, genome size correlations were not apparent with any chromosomal, physiological, flight-related, developmental, or ecological characteristics within the order Chiroptera. Genome size is positively correlated with measures of body size in bats, though the strength of the relationships differs between pteropodids ("megabats") and nonpteropodids ("microbats").

  9. DNA methylation patterns of candidate genes regulated by thymine DNA glycosylase in patients with TP53 germline mutations

    Energy Technology Data Exchange (ETDEWEB)

    Fortes, F.P. [CIPE, Laboratrio de Oncogentica Molecular, A.C. Camargo Cancer Center, São Paulo, SP (Brazil); Kuasne, H. [CIPE, Laboratrio NeoGene, A.C. Camargo Cancer Center, São Paulo, SP (Brazil); Departamento de Urologia, Faculdade de Medicina, Universidade Estadual Paulista, Botucatu, SP (Brazil); Marchi, F.A. [CIPE, Laboratrio NeoGene, A.C. Camargo Cancer Center, São Paulo, SP (Brazil); Programa Inter-Institucional em Bioinformtica, Instituto de Matemtica e Estatstica, Universidade So Paulo, So Paulo, SP (Brazil); Miranda, P.M. [CIPE, Laboratrio NeoGene, A.C. Camargo Cancer Center, São Paulo, SP (Brazil); Rogatto, S.R. [CIPE, Laboratrio NeoGene, A.C. Camargo Cancer Center, São Paulo, SP (Brazil); Departamento de Urologia, Faculdade de Medicina, Universidade Estadual Paulista, Botucatu, SP (Brazil); Achatz, M.I. [CIPE, Laboratrio de Oncogentica Molecular, A.C. Camargo Cancer Center, São Paulo, SP (Brazil); Departamento de Oncogentica, A.C. Camargo Cancer Center, So Paulo, SP (Brazil)

    2015-04-28

    Li-Fraumeni syndrome (LFS) is a rare, autosomal dominant, hereditary cancer predisposition disorder. In Brazil, the p.R337H TP53 founder mutation causes the variant form of LFS, Li-Fraumeni-like syndrome. The occurrence of cancer and age of disease onset are known to vary, even in patients carrying the same mutation, and several mechanisms such as genetic and epigenetic alterations may be involved in this variability. However, the extent of involvement of such events has not been clarified. It is well established that p53 regulates several pathways, including the thymine DNA glycosylase (TDG) pathway, which regulates the DNA methylation of several genes. This study aimed to identify the DNA methylation pattern of genes potentially related to the TDG pathway (CDKN2A, FOXA1, HOXD8, OCT4, SOX2, and SOX17) in 30 patients with germline TP53mutations, 10 patients with wild-type TP53, and 10 healthy individuals. We also evaluated TDG expression in patients with adrenocortical tumors (ADR) with and without the p.R337H TP53 mutation. Gene methylation patterns of peripheral blood DNA samples assessed by pyrosequencing revealed no significant differences between the three groups. However, increased TDG expression was observed by quantitative reverse transcription PCR in p.R337H carriers with ADR. Considering the rarity of this phenotype and the relevance of these findings, further studies using a larger sample set are necessary to confirm our results.

  10. Different DNA methylation patterns detected by the Amplified Methylation Polymorphism Polymerase Chain Reaction (AMP PCR) technique among various cell types of bulls

    OpenAIRE

    Phutikanit, Nawapen; Suwimonteerabutr, Junpen; Harrison, Dion; D'Occhio, Michael; Carroll, Bernie; Techakumphu, Mongkol

    2010-01-01

    Abstract Background The purpose of this study was to apply an arbitrarily primed methylation sensitive polymerase chain reaction (PCR) assay called Amplified Methylation Polymorphism Polymerase Chain Reaction (AMP PCR) to investigate the methylation profiles of somatic and germ cells obtained from Holstein bulls. Methods Genomic DNA was extracted from sperm, leukocytes and fibroblasts obtained from three bulls and digested with a methylation sensitive endonuclease (HpaII). The native genomic ...

  11. Global patterns of diversity and selection in human tyrosinase gene.

    Science.gov (United States)

    Hudjashov, Georgi; Villems, Richard; Kivisild, Toomas

    2013-01-01

    Global variation in skin pigmentation is one of the most striking examples of environmental adaptation in humans. More than two hundred loci have been identified as candidate genes in model organisms and a few tens of these have been found to be significantly associated with human skin pigmentation in genome-wide association studies. However, the evolutionary history of different pigmentation genes is rather complex: some loci have been subjected to strong positive selection, while others evolved under the relaxation of functional constraints in low UV environment. Here we report the results of a global study of the human tyrosinase gene, which is one of the key enzymes in melanin production, to assess the role of its variation in the evolution of skin pigmentation differences among human populations. We observe a higher rate of non-synonymous polymorphisms in the European sample consistent with the relaxation of selective constraints. A similar pattern was previously observed in the MC1R gene and concurs with UV radiation-driven model of skin color evolution by which mutations leading to lower melanin levels and decreased photoprotection are subject to purifying selection at low latitudes while being tolerated or even favored at higher latitudes because they facilitate UV-dependent vitamin D production. Our coalescent date estimates suggest that the non-synonymous variants, which are frequent in Europe and North Africa, are recent and have emerged after the separation of East and West Eurasian populations.

  12. Diversity patterns of microbial eukaryotes mirror those of bacteria in Antarctic cryoconite holes.

    Science.gov (United States)

    Sommers, Pacifica; Darcy, John L; Gendron, Eli M S; Stanish, Lee F; Bagshaw, Elizabeth A; Porazinska, Dorota L; Schmidt, Steven K

    2018-01-01

    Ice-lidded cryoconite holes on glaciers in the Taylor Valley, Antarctica, provide a unique system of natural mesocosms for studying community structure and assembly. We used high-throughput DNA sequencing to characterize both microbial eukaryotic communities and bacterial communities within cryoconite holes across three glaciers to study similarities in their spatial patterns. We expected that the alpha (phylogenetic diversity) and beta (pairwise community dissimilarity) diversity patterns of eukaryotes in cryoconite holes would be related to those of bacteria, and that they would be related to the biogeochemical gradient within the Taylor Valley. We found that eukaryotic alpha and beta diversity were strongly related to those of bacteria across scales ranging from 140 m to 41 km apart. Alpha diversity of both was significantly related to position in the valley and surface area of the cryoconite hole, with pH also significantly correlated with the eukaryotic diversity. Beta diversity for both bacteria and eukaryotes was significantly related to position in the valley, with bacterial beta diversity also related to nitrate. These results are consistent with transport of sediments onto glaciers occurring primarily at local scales relative to the size of the valley, thus creating feedbacks in local chemistry and diversity. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  13. Different Planctomycetes diversity patterns in latitudinal surface seawater of the open sea and in sediment.

    Science.gov (United States)

    Shu, Qinglong; Jiao, Nianzhi

    2008-04-01

    The 16S rRNA gene approach was applied to investigate the diversity of Planctomycetes in latitudinal surface seawater of the Western Pacific Ocean. The results revealed that the Pirellula-Rhodopirellula-Blastopirellula clade dominated the Planctomycetes community at all surface seawater sites while the minority genera Gemmata and Planctomyces were only found at sites H5 and H2 respectively. Although the clone frequency of the PRB clade seemed stable (between 83.3% and 94.1%) for all surface seawater sites, the retrieved Pirellula-Rhodopirellula-Blastopirellula clade presented unexpected diversity. Interestingly, low latitude seawater appeared to have higher diversity than mid-latitudes. integral-LIBSHUFF software analysis revealed significantly different diversity patterns between in latitudinal surface seawater and in the sediment of South China Sea station M2896. Our data suggested that different hydrological and geographic features contributed to the shift of Planctomycetes diversity in marine environments. This is, to our knowledge, the first systematic assessment of Planctomycetes in latitudinal surface seawater of the open sea and the first comparison of diversity pattern between surface seawater and sediments and has broadened our understanding of Planctomycetes diversity in marine environments.

  14. Genome organization and DNA methylation patterns of B chromosomes in the red fox and Chinese raccoon dogs.

    Science.gov (United States)

    Bugno-Poniewierska, Monika; Solek, Przemysław; Wronski, Mariusz; Potocki, Leszek; Jezewska-Witkowska, Grażyna; Wnuk, Maciej

    2014-12-01

    The molecular structure of B chromosomes (Bs) is relatively well studied. Previous research demonstrates that Bs of various species usually contain two types of repetitive DNA sequences, satellite DNA and ribosomal DNA, but Bs also contain genes encoding histone proteins and many others. However, many questions remain regarding the origin and function of these chromosomes. Here, we focused on the comparative cytogenetic characteristics of the red fox and Chinese raccoon dog B chromosomes with particular attention to the distribution of repetitive DNA sequences and their methylation status. We confirmed that the small Bs of the red fox show a typical fluorescent telomeric distal signal, whereas medium-sized Bs of the Chinese raccoon dog were characterized by clusters of telomeric sequences along their length. We also found different DNA methylation patterns for the B chromosomes of both species. Therefore, we concluded that DNA methylation may maintain the transcriptional inactivation of DNA sequences localized to B chromosomes and may prevent genetic unbalancing and several negative phenotypic effects. © 2014 The Authors.

  15. DNA Methylation Patterns in Cord Blood of Neonates Across Gestational Age: Association With Cell-Type Proportions.

    Science.gov (United States)

    Braid, Susan M; Okrah, Kwame; Shetty, Amol; Corrada Bravo, Hector

    A statistical methodology is available to estimate the proportion of cell types (cellular heterogeneity) in adult whole blood specimens used in epigenome-wide association studies (EWAS). However, there is no methodology to estimate the proportion of cell types in umbilical cord blood (also a heterogeneous tissue) used in EWAS. The objectives of this study were to determine whether differences in DNA methylation (DNAm) patterns in umbilical cord blood are the result of blood cell type proportion changes that typically occur across gestational age and to demonstrate the effect of cell type proportion confounding by comparing preterm infants exposed and not exposed to antenatal steroids. We obtained DNAm profiles of cord blood using the Illumina HumanMethylation27k BeadChip array for 385 neonates from the Boston Birth Cohort. We estimated cell type proportions for six cell types using the deconvolution method developed by . The cell type proportion estimates segregated into two groups that were significantly different by gestational age, indicating that gestational age was associated with cell type proportion. Among infants exposed to antenatal steroids, the number of differentially methylated CpGs dropped from 127 to 1 after controlling for cell type proportion. EWAS utilizing cord blood are confounded by cell type proportion. Careful study design including correction for cell type proportion and interpretation of results of EWAS using cord blood are critical.

  16. Promoter methylation patterns in Richter syndrome affect stem-cell maintenance and cell cycle regulation and differ from de novo diffuse large B-cell lymphoma.

    Science.gov (United States)

    Rinaldi, Andrea; Mensah, Afua Adjeiwaa; Kwee, Ivo; Forconi, Francesco; Orlandi, Ester M; Lucioni, Marco; Gattei, Valter; Marasca, Roberto; Berger, Françoise; Cogliatti, Sergio; Cavalli, Franco; Zucca, Emanuele; Gaidano, Gianluca; Rossi, Davide; Bertoni, Francesco

    2013-10-01

    In a fraction of patients, chronic lymphocytic leukaemia (CLL) can transform to Richter syndrome (RS), usually a diffuse large B-cell lymphoma (DLBCL). We studied genome-wide promoter DNA methylation in RS and clonally related CLL-phases of transformed patients, alongside de novo DLBCL (of non-germinal centre B type), untransformed-CLL and normal B-cells. The greatest differences in global DNA methylation levels were observed between RS and DLBCL, indicating that these two diseases, although histologically similar, are epigenetically distinct. RS was more highly methylated for genes involved in cell cycle regulation. When RS was compared to the preceding CLL-phase and with untransformed-CLL, RS presented a higher degree of methylation for genes possessing the H3K27me3 mark and PRC2 targets, as well as for gene targets of TP53 and RB1. Comparison of the methylation levels of individual genes revealed that OSM, a stem cell regulatory gene, exhibited significantly higher methylation levels in RS compared to CLL-phases. Its transcriptional repression by DNA methylation was confirmed by 5-aza-2'deoxycytidine treatment of DLBCL cells, determining an increased OSM expression. Our results showed that methylation patterns in RS are largely different from de novo DLBCL. Stem cell-related genes and cell cycle regulation genes are targets of DNA methylation in RS. © 2013 John Wiley & Sons Ltd.

  17. Cross-Cultural Dietary Patterns: A College Course on Ethnically Diverse Eating Patterns.

    Science.gov (United States)

    Head, Mary K.; Stuhldreher, Wendy L.

    1998-01-01

    A course on cross-cultural dietary patterns provides family and consumer sciences students with information about influences on ethnic diets while introducing food preparation and computer nutrient evaluation techniques. (SK)

  18. Behavioural, ecological, and evolutionary aspects of diversity in frog colour patterns

    OpenAIRE

    Rojas Zuluaga, Bibiana

    2017-01-01

    The role of colours and colour patterns in behavioural ecology has been extensively studied in a variety of contexts and taxa, while almost overlooked in many others. For decades anurans have been the focus of research on acoustic signalling due to the prominence of vocalisations in their communication. Much less attention has been paid to the enormous diversity of colours, colour patterns, and other types of putative visual signals exhibited by frogs. With the exception of some anecdotal obs...

  19. Methylation patterns of repetitive DNA sequences in germ cells of Mus musculus.

    OpenAIRE

    Sanford, J; Forrester, L; Chapman, V; Chandley, A; Hastie, N

    1984-01-01

    The major and the minor satellite sequences of Mus musculus were undermethylated in both sperm and oocyte DNAs relative to the amount of undermethylation observed in adult somatic tissue DNA. This hypomethylation was specific for satellite sequences in sperm DNA. Dispersed repetitive and low copy sequences show a high degree of methylation in sperm DNA; however, a dispersed repetitive sequence was undermethylated in oocyte DNA. This finding suggests a difference in the amount of total genomic...

  20. Distinct patterns of histone methylation and acetylation in human interphase nuclei

    Czech Academy of Sciences Publication Activity Database

    Skalníková, M.; Bártová, Eva; Ulman, V.; Matula, P.; Svoboda, D.; Harničarová, Andrea; Kozubek, Michal; Kozubek, Stanislav

    2007-01-01

    Roč. 56, č. 6 (2007), s. 797-806 ISSN 0862-8408 R&D Projects: GA ČR(CZ) GA204/06/0978; GA MŠk(CZ) LC535 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : histone methylation * acetylation * X chromosome Subject RIV: BO - Biophysics Impact factor: 1.505, year: 2007

  1. Dual DNA methylation patterns in the CNS reveal developmentally poised chromatin and monoallelic expression of critical genes.

    Directory of Open Access Journals (Sweden)

    Jinhui Wang

    Full Text Available As a first step towards discovery of genes expressed from only one allele in the CNS, we used a tiling array assay for DNA sequences that are both methylated and unmethylated (the MAUD assay. We analyzed regulatory regions of the entire mouse brain transcriptome, and found that approximately 10% of the genes assayed showed dual DNA methylation patterns. They include a large subset of genes that display marks of both active and silent, i.e., poised, chromatin during development, consistent with a link between differential DNA methylation and lineage-specific differentiation within the CNS. Sixty-five of the MAUD hits and 57 other genes whose function is of relevance to CNS development and/or disorders were tested for allele-specific expression in F(1 hybrid clonal neural stem cell (NSC lines. Eight MAUD hits and one additional gene showed such expression. They include Lgi1, which causes a subtype of inherited epilepsy that displays autosomal dominance with incomplete penetrance; Gfra2, a receptor for glial cell line-derived neurotrophic factor GDNF that has been linked to kindling epilepsy; Unc5a, a netrin-1 receptor important in neurodevelopment; and Cspg4, a membrane chondroitin sulfate proteoglycan associated with malignant melanoma and astrocytoma in human. Three of the genes, Camk2a, Kcnc4, and Unc5a, show preferential expression of the same allele in all clonal NSC lines tested. The other six genes show a stochastic pattern of monoallelic expression in some NSC lines and bi-allelic expression in others. These results support the estimate that 1-2% of genes expressed in the CNS may be subject to allelic exclusion, and demonstrate that the group includes genes implicated in major disorders of the CNS as well as neurodevelopment.

  2. Diversity of dietary patterns observed in the European Prospective Investigation into Cancer and Nutrition (EPIC) project

    NARCIS (Netherlands)

    Slimani, N.; Fahey, M.; Welch, A.A.; Wirfalt, E.; Stripp, C.; Bergstrom, E.; Linseisen, J.; Schulze, M.B.; Bamia, C.; Chloptsios, Y.; Veglia, F.; Panico, S.; Bueno de Mesquita, B.; Ocké, M.C.; Brustadt, M.; Lund, E.; Gonzalez, C.A.; Barcos, A.; Berglund, G.; Winkvist, A.; Mulligan, A.; Appleby, P.; Overvad, K.; Tjonneland, A.; Clavel-Chapelon, F.; Kesse, E.; Ferrari, P.; Staveren, van W.A.; Riboli, E.

    2002-01-01

    Objective: To describe the diversity in dietary patterns existing across centres/regions participating in the European Prospective Investigation into Cancer and Nutrition (EPIC). Design and setting: Single 24-hour dietary recall measurements were obtained by means of standardised face-to-face

  3. Realization of diverse displays for multiple color patterns on metal surfaces

    International Nuclear Information System (INIS)

    Li, Guoqiang; Li, Jiawen; Hu, Yanlei; Zhang, Chenchu; Li, Xiaohong; Chu, Jiaru; Huang, Wenhao

    2014-01-01

    Highlights: • We have demonstrated that the combined influence of incident white light angle and the ripples orientation on the diversity of structural colors. • Our investigation revealed that multi-patterns constituted by ripples with different orientations could be precisely designed on metal surfaces. • The diverse display for the desired ones can be realized by exquisitely varying the incident light angle and rotating sample angle. - Abstract: Enhanced colors can be formed when white light is irradiated on the surface ripples induced by femtosecond laser. In this paper, we have demonstrated the ability to display the diverse colors by simultaneously adjusting the incident white light angle and the ripples orientation. Furthermore, our investigation revealed that multi-patterns constituted by ripples with different orientations could be designed on metal surfaces. The diverse display for the desired ones can be realized by exquisitely varying the incident light angle and rotating sample angle. More interestingly, it is found that, although the same patterns could be displayed under different conditions, the colors might be different. These findings can provide a novel method to carry and identify high quantity of information, which may find potential applications in the fields of information storage, identifying codes and anti-counterfeiting patterns

  4. Tree species diversity and distribution patterns in tropical forests of Garo Hills.

    Science.gov (United States)

    A. Kumar; B.G. Marcot; A. Saxena

    2006-01-01

    We analyzed phytosociological characteristics and diversity patterns of tree species of tropical forests of Garo Hills, western Meghalaya, northeast India. The main vegetation of the region included primary forests, secondary forests, and sal (Shorea robusta) plantations, with 162, 132, and 87 tree species, respectively. The Shannon-Wiener...

  5. Large-scale diversity patterns in spore communities of Arbuscular mycorrhizal fungi [Chapter 2

    Science.gov (United States)

    Javier Alvarez-Sanchez; Nancy C. Johnson; Anita Antoninka; V. Bala Chaudhary; Matthew K. Lau; Suzanne M. Owen; Patricia Gauadarrama; Silvia. Castillo

    2010-01-01

    Surprising little is known about the factors controlling Arbuscular Mycorrhizal (AM) fungal diversity and distribution patterns. A better understanding of these factors is necessary before mycorrhizas can be effectively managed for their benefits in ecosystem restoration and agriculture. The goal of this chapter is to examine the relationships between AM fungal...

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

    Science.gov (United States)

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

    2005-01-01

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

  7. Diversity of genetic events associated with MLH1 promoter methylation in Lynch syndrome families with heritable constitutional epimutation.

    Science.gov (United States)

    Leclerc, Julie; Flament, Cathy; Lovecchio, Tonio; Delattre, Lucie; Ait Yahya, Emilie; Baert-Desurmont, Stéphanie; Burnichon, Nelly; Bronner, Myriam; Cabaret, Odile; Lejeune, Sophie; Guimbaud, Rosine; Morin, Gilles; Mauillon, Jacques; Jonveaux, Philippe; Laurent-Puig, Pierre; Frébourg, Thierry; Porchet, Nicole; Buisine, Marie-Pierre

    2018-04-12

    PurposeConstitutional epimutations are an alternative to genetic mutations in the etiology of genetic diseases. Some of these epimutations, termed secondary, correspond to the epigenetic effects of cis-acting genetic defects transmitted to the offspring following a Mendelian inheritance pattern. In Lynch syndrome, a few families with such apparently heritable MLH1 epimutations have been reported so far.MethodsWe designed a long-range polymerase chain reaction next-generation sequencing strategy to screen MLH1 entire gene and applied it to 4 French families with heritable epimutations and 10 additional patients with no proven transmission of their epimutations.ResultsThis strategy successfully detected the insertion of an Alu element in MLH1 coding sequence in one family. Two previously unreported MLH1 variants were also identified in other epimutation carriers: a nucleotide substitution within intron 1 and a single-nucleotide deletion in the 5'-UTR. Detection of a partial MLH1 duplication in another family required multiplex ligation-dependent probe amplification technology. We demonstrated the segregation of these variants with MLH1 methylation and studied the functional consequences of these defects on transcription.ConclusionThis is the largest cohort of patients with MLH1 secondary epimutations associated with a broad spectrum of genetic defects. This study provides further insight into the complexity of molecular mechanisms leading to secondary epimutations.GENETICS in MEDICINE advance online publication, 12 April 2018; doi:10.1038/gim.2018.47.

  8. Genome-Wide DNA Methylation Patterns of Bovine Blastocysts Developed In Vivo from Embryos Completed Different Stages of Development In Vitro.

    Directory of Open Access Journals (Sweden)

    Dessie Salilew-Wondim

    Full Text Available Early embryonic loss and altered gene expression in in vitro produced blastocysts are believed to be partly caused by aberrant DNA methylation. However, specific embryonic stage which is sensitive to in vitro culture conditions to alter the DNA methylation profile of the resulting blastocysts remained unclear. Therefore, the aim of this study was to investigate the stage specific effect of in vitro culture environment on the DNA methylation response of the resulting blastocysts. For this, embryos cultured in vitro until zygote (ZY, 4-cell (4C or 16-cell (16C were transferred to recipients and the blastocysts were recovery at day 7 of the estrous cycle. Another embryo group was cultured in vitro until blastocyst stage (IVP. Genome-wide DNA methylation profiles of ZY, 4C, 16C and IVP blastocyst groups were then determined with reference to blastocysts developed completely under in vivo condition (VO using EmbryoGENE DNA Methylation Array. To assess the contribution of methylation changes on gene expression patterns, the DNA methylation data was superimposed to the transcriptome profile data. The degree of DNA methylation dysregulation in the promoter and/or gene body regions of the resulting blastocysts was correlated with successive stages of development the embryos advanced under in vitro culture before transfer to the in vivo condition. Genomic enrichment analysis revealed that in 4C and 16C blastocyst groups, hypermethylated loci were outpacing the hypomethylated ones in intronic, exonic, promoter and proximal promoter regions, whereas the reverse was observed in ZY blastocyst group. However, in the IVP group, as much hypermethylated as hypomethylated probes were detected in gene body and promoter regions. In addition, gene ontology analysis indicated that differentially methylated regions were found to affected several biological functions including ATP binding in the ZY group, programmed cell death in the 4C, glycolysis in 16C and genetic

  9. Continental scale patterns and predictors of fern richness and phylogenetic diversity

    Directory of Open Access Journals (Sweden)

    Nathalie eNagalingum

    2015-04-01

    Full Text Available Because ferns have a wide range of habitat preferences and are widely distributed, they are an ideal group for understanding how diversity is distributed. Here we examine fern diversity on a broad-scale using standard and corrected richness measures as well as phylogenetic indices; in addition we determine the environmental predictors of each diversity metric. Using the combined records of Australian herbaria, a dataset of over 60,000 records was obtained for 89 genera to infer richness. A phylogenetic tree of all the genera was constructed and combined with the herbarium records to obtain phylogenetic diversity patterns. A hotspot of both taxic and phylogenetic diversity occurs in the Wet Tropics of northeastern Australia. Although considerable diversity is distributed along the eastern coast, some important regions of diversity are identified only after sample-standardization of richness and through the phylogenetic metric. Of all of the metrics, annual precipitation was identified as the most explanatory variable, in part, in agreement with global and regional fern studies. Precipitation was combined with a different variable for each different metric. For corrected richness, precipitation is combined with temperature seasonality, while correlation of phylogenetic diversity to precipitation plus radiation indicates support for the species-energy hypothesis. Significantly high and significantly low phylogenetic diversity were found in geographically separate areas. These areas are correlated with different climatic conditions such as seasonality in precipitation. The use of phylogenetic metrics identifies additional areas of significant diversity, some of which have not been revealed using traditional taxonomic analyses, suggesting that different ecological and evolutionary processes have operated over the continent. Our study demonstrates that it is possible and vital to incorporate evolutionary metrics when inferring biodiversity hotspots

  10. Subgenomic Diversity Patterns Caused by Directional Selection in Bread Wheat Gene Pools

    Directory of Open Access Journals (Sweden)

    Kai Voss-Fels

    2015-07-01

    Full Text Available Genetic diversity represents the fundamental key to breeding success, providing the basis for breeders to select varieties with constantly improving yield performance. On the other hand, strong selection during domestication and breeding have eliminated considerable genetic diversity in the breeding pools of major crops, causing erosion of genetic potential for adaptation to emerging challenges like climate change. High-throughput genomic technologies can address this dilemma by providing detailed knowledge to characterize and replenish genetic diversity in breeding programs. In hexaploid bread wheat ( L., the staple food for 35% of the world’s population, bottlenecks during allopolyploidisation followed by strong artificial selection have considerably narrowed diversity to the extent that yields in many regions appear to be unexpectedly stagnating. In this study, we used a 90,000 single nucleotide polymorphism (SNP wheat genotyping array to assay high-frequency, polymorphic SNP markers in 460 accessions representing different phenological diversity groups from Asian, Australian, European, and North American bread wheat breeding materials. Detailed analysis of subgroup diversity at the chromosome and subgenome scale revealed highly distinct patterns of conserved linkage disequilibrium between different gene pools. The data enable identification of genome regions in most need of rejuvenation with novel diversity and provide a high-resolution molecular basis for genomic-assisted introgression of new variation into chromosome segments surrounding directionally selected metaloci conferring important adaptation and quality traits.

  11. Contrasting diversity patterns of crenarchaeal, bacterial and fungal soil communities in an alpine landscape.

    Directory of Open Access Journals (Sweden)

    Lucie Zinger

    2011-05-01

    Full Text Available The advent of molecular techniques in microbial ecology has aroused interest in gaining an understanding about the spatial distribution of regional pools of soil microbes and the main drivers responsible of these spatial patterns. Here, we assessed the distribution of crenarcheal, bacterial and fungal communities in an alpine landscape displaying high turnover in plant species over short distances. Our aim is to determine the relative contribution of plant species composition, environmental conditions, and geographic isolation on microbial community distribution.Eleven types of habitats that best represent the landscape heterogeneity were investigated. Crenarchaeal, bacterial and fungal communities were described by means of Single Strand Conformation Polymorphism. Relationships between microbial beta diversity patterns were examined by using Bray-Curtis dissimilarities and Principal Coordinate Analyses. Distance-based redundancy analyses and variation partitioning were used to estimate the relative contributions of different drivers on microbial beta diversity. Microbial communities tended to be habitat-specific and did not display significant spatial autocorrelation. Microbial beta diversity correlated with soil pH. Fungal beta-diversity was mainly related to soil organic matter. Though the effect of plant species composition was significant for all microbial groups, it was much stronger for Fungi. In contrast, geographic distances did not have any effect on microbial beta diversity.Microbial communities exhibit non-random spatial patterns of diversity in alpine landscapes. Crenarcheal, bacterial and fungal community turnover is high and associated with plant species composition through different set of soil variables, but is not caused by geographical isolation.

  12. Patterns of genetic diversity in three plant lineages endemic to the Cape Verde Islands.

    Science.gov (United States)

    Romeiras, Maria M; Monteiro, Filipa; Duarte, M Cristina; Schaefer, Hanno; Carine, Mark

    2015-05-15

    Conservation of plant diversity on islands relies on a good knowledge of the taxonomy, distribution and genetic diversity of species. In recent decades, a combination of morphology- and DNA-based approaches has become the standard for investigating island plant lineages and this has led, in some cases, to the discovery of previously overlooked diversity, including 'cryptic species'. The flora of the Cape Verde archipelago in the North Atlantic is currently thought to comprise ∼740 vascular plant species, 92 of them endemics. Despite the fact that it is considered relatively well known, there has been a 12 % increase in the number of endemics in the last two decades. Relatively few of the Cape Verde plant lineages have been included in genetic studies so far and little is known about the patterns of diversification in the archipelago. Here we present an updated list for the endemic Cape Verde flora and analyse diversity patterns for three endemic plant lineages (Cynanchum, Globularia and Umbilicus) based on one nuclear (ITS) and four plastid DNA regions. In all three lineages, we find genetic variation. In Cynanchum, we find two distinct haplotypes with no clear geographical pattern, possibly reflecting different ploidy levels. In Globularia and Umbilicus, differentiation is evident between populations from northern and southern islands. Isolation and drift resulting from the small and fragmented distributions, coupled with the significant distances separating the northern and southern islands, could explain this pattern. Overall, our study suggests that the diversity in the endemic vascular flora of Cape Verde is higher than previously thought and further work is necessary to characterize the flora. Published by Oxford University Press on behalf of the Annals of Botany Company.

  13. Contrasting elevational diversity patterns for soil bacteria between two ecosystems divided by the treeline.

    Science.gov (United States)

    Li, Guixiang; Xu, Guorui; Shen, Congcong; Tang, Yong; Zhang, Yuxin; Ma, Keming

    2016-11-01

    Above- and below-ground organisms are closely linked, but how elevational distribution pattern of soil microbes shifting across the treeline still remains unknown. Sampling of 140 plots with transect, we herein investigated soil bacterial distribution pattern from a temperate forest up to a subalpine meadow along an elevational gradient using Illumina sequencing. Our results revealed distinct elevational patterns of bacterial diversity above and below the treeline in responding to changes in soil conditions: a hollow elevational pattern in the forest (correlated with soil temperature, pH, and C:N ratio) and a significantly decreasing pattern in the meadow (correlated with soil pH, and available phosphorus). The bacterial community structure was also distinct between the forest and meadow, relating to soil pH in the forest and soil temperature in the meadow. Soil bacteria did not follow the distribution pattern of herb diversity, but bacterial community structure could be predicted by herb community composition. These results suggest that plant communities have an important influence on soil characteristics, and thus change the elevational distribution of soil bacteria. Our findings are useful for future assessments of climate change impacts on microbial community.

  14. Cord blood PRF1 methylation patterns and risk of lower respiratory tract infections in infants: findings from the Ulm Birth Cohort.

    Science.gov (United States)

    Elgizouli, Magdeldin; Logan, Chad; Nieters, Alexandra; Brenner, Hermann; Rothenbacher, Dietrich

    2015-01-01

    Lower respiratory tract infections (LRTIs) are a major cause of morbidity in children. DNA methylation provides a mechanism for transmitting environmental effects on the genome, but its potential role in LRTIs is not well studied. We investigated the methylation pattern of an enhancer region of the immune effector gene perforin-1 (PRF1), which encodes a cytolytic molecule of cytotoxic T lymphocytes (CTLs) and natural killer cells (NK), in cord blood DNA of children recruited in a German birth cohort in association with LRTIs in the first year of life.Pyrosequencing was used to determine the methylation levels of target cytosine-phosphate-guanines (CpGs) in a 2-stage case-control design. Cases were identified as children who developed ≥2 episodes of physician-recorded LRTIs during the first year of life and controls as children who had none. Discovery (n = 87) and replication (n = 90) sets were arranged in trios of 1 case and 2 controls matched for sex and season of birth.Logistic regression analysis revealed higher levels of methylation at a CpG that corresponds to a signal transducer and activator of transcription 5 (STAT5) responsive enhancer in the discovery (odds ratio [OR] per 1% methylation difference 1.24, 95% confidence interval [CI] 1.03-1.50) and replication (OR per 1% methylation difference 1.25, 95% CI 1.04-1.50) sets. Adjustment for having siblings blood PRF1 enhancer methylation patterns and subsequent risk of LRTIs in infants. Methylation levels at specific CpGs of the PRF1 enhancer varied according to maternal and family environmental factors suggesting a role for DNA methylation in mediating environmental influences on gene function.

  15. Methylation pattern of the intergenic spacer of rRNA genes in excised cotyledons of Cucurbita pepo L. (Zucchini) after hormone treatment

    International Nuclear Information System (INIS)

    Ananiev, E.; Abdulova, G.; Grozdanov, P.; Karagyozov, L.

    2003-01-01

    High molecular mass genomic DNA was isolated from excised marrow cotyledons (Cucurbita pepo L. zucchini) treated with 6-benzyladenine (BA) of methyl ester of jasmonic acid (MeJA) for 24 h in darkness. DNA purified from contaminating polysaccharides with Celite column was completely digested with the restriction enzyme Eco RI and the changes in the methylation pattern of the intergenic spacer (IGS) of r RNA genes were studied after subsequent digestion with the couple of restriction enzymes-isoschizomers MSP I and Hpa II by the method of 'indirect end labelling'. As rDNA units probe a cloned 32 P-labelled Eco RI 2.1 kb fragment spanning in the most part of 18S r RNA gene from flax rDNA was used. Results showed heavy methylation of the rRNA genes. As judged from the almost total lack of digestion with HPA II, there were no methylation free regions in repeated rDNA units or little if any were observed. A hypo methylated Hps II site was detected near the promoter region in some of the repeats. Digestion with Msp I affected nearly 50% of the repeating units. The Msp digestion fragments of the 6.2 kb Eco RI fragment of r DNA were few in number and large in size (0.5 - 2.5 kb). This suggested that in addition with -CpG- sequences, methylation in -CpNpG- might not be random. Methylation pattern in IGS was not changed upon treatment of the cotyledons in vivo with BA and MeJA. Thus, previously observed hormone-mediated effects on the eactivity of rRNA gene expression were not accompanied by any significant changes of the methylation pattern in IGS. (authors)

  16. Biogeographic distribution patterns and their correlates in the diverse frog fauna of the Atlantic Forest hotspot.

    Science.gov (United States)

    Vasconcelos, Tiago S; Prado, Vitor H M; da Silva, Fernando R; Haddad, Célio F B

    2014-01-01

    Anurans are a highly diverse group in the Atlantic Forest hotspot (AF), yet distribution patterns and species richness gradients are not randomly distributed throughout the biome. Thus, we explore how anuran species are distributed in this complex and biodiverse hotspot, and hypothesize that this group can be distinguished by different cohesive regions. We used range maps of 497 species to obtain a presence/absence data grid, resolved to 50×50 km grain size, which was submitted to k-means clustering with v-fold cross-validation to determine the biogeographic regions. We also explored the extent to which current environmental variables, topography, and floristic structure of the AF are expected to identify the cluster patterns recognized by the k-means clustering. The biogeographic patterns found for amphibians are broadly congruent with ecoregions identified in the AF, but their edges, and sometimes the whole extent of some clusters, present much less resolved pattern compared to previous classification. We also identified that climate, topography, and vegetation structure of the AF explained a high percentage of variance of the cluster patterns identified, but the magnitude of the regression coefficients shifted regarding their importance in explaining the variance for each cluster. Specifically, we propose that the anuran fauna of the AF can be split into four biogeographic regions: a) less diverse and widely-ranged species that predominantly occur in the inland semideciduous forests; b) northern small-ranged species that presumably evolved within the Pleistocene forest refugia; c) highly diverse and small-ranged species from the southeastern Brazilian mountain chain and its adjacent semideciduous forest; and d) southern species from the Araucaria forest. Finally, the high congruence among the cluster patterns and previous eco-regions identified for the AF suggests that preserving the underlying habitat structure helps to preserve the historical and ecological

  17. Different DNA methylation patterns detected by the Amplified Methylation Polymorphism Polymerase Chain Reaction (AMP PCR technique among various cell types of bulls

    Directory of Open Access Journals (Sweden)

    Carroll Bernie

    2010-03-01

    Full Text Available Abstract Background The purpose of this study was to apply an arbitrarily primed methylation sensitive polymerase chain reaction (PCR assay called Amplified Methylation Polymorphism Polymerase Chain Reaction (AMP PCR to investigate the methylation profiles of somatic and germ cells obtained from Holstein bulls. Methods Genomic DNA was extracted from sperm, leukocytes and fibroblasts obtained from three bulls and digested with a methylation sensitive endonuclease (HpaII. The native genomic and enzyme treated DNA samples were used as templates in an arbitrarily primed-PCR assay with 30 sets of single short oligonucleotide primer. The PCR products were separated on silver stained denaturing polyacrylamide gels. Three types of PCR markers; digestion resistant-, digestion sensitive-, and digestion dependent markers, were analyzed based on the presence/absence polymorphism of the markers between the two templates. Results Approximately 1,000 PCR markers per sample were produced from 27 sets of primer and most of them (>90% were digestion resistant markers. The highest percentage of digestion resistant markers was found in leukocytic DNA (94.8% and the lowest in fibroblastic DNA (92.3%, P ≤ 0.05. Spermatozoa contained a higher number of digestion sensitive markers when compared with the others (3.6% vs. 2.2% and 2.6% in leukocytes and fibroblasts respectively, P ≤ 0.05. Conclusions The powerfulness of the AMP PCR assay was the generation of methylation-associated markers without any prior knowledge of the genomic sequence. The data obtained from different primers provided an overview of genome wide DNA methylation content in different cell types. By using this technique, we found that DNA methylation profile is tissue-specific. Male germ cells were hypomethylated at the HpaII locations when compared with somatic cells, while the chromatin of the well-characterized somatic cells was heavily methylated when compared with that of the versatile somatic

  18. Maintaining mimicry diversity: optimal warning colour patterns differ among microhabitats in Amazonian clearwing butterflies.

    Science.gov (United States)

    Willmott, Keith R; Robinson Willmott, Julia C; Elias, Marianne; Jiggins, Chris D

    2017-05-31

    Mimicry is one of the best-studied examples of adaptation, and recent studies have provided new insights into the role of mimicry in speciation and diversification. Classical Müllerian mimicry theory predicts convergence in warning signal among protected species, yet tropical butterflies are exuberantly diverse in warning colour patterns, even within communities. We tested the hypothesis that microhabitat partitioning in aposematic butterflies and insectivorous birds can lead to selection for different colour patterns in different microhabitats and thus help maintain mimicry diversity. We measured distribution across flight height and topography for 64 species of clearwing butterflies (Ithomiini) and their co-mimics, and 127 species of insectivorous birds, in an Amazon rainforest community. For the majority of bird species, estimated encounter rates were non-random for the two most abundant mimicry rings. Furthermore, most butterfly species in these two mimicry rings displayed the warning colour pattern predicted to be optimal for anti-predator defence in their preferred microhabitats. These conclusions were supported by a field trial using butterfly specimens, which showed significantly different predation rates on colour patterns in two microhabitats. We therefore provide the first direct evidence to support the hypothesis that different mimicry patterns can represent stable, community-level adaptations to differing biotic environments. © 2017 The Author(s).

  19. Evolving cellular automata for diversity generation and pattern recognition: deterministic versus random strategy

    International Nuclear Information System (INIS)

    De Menezes, Marcio Argollo; Brigatti, Edgardo; Schwämmle, Veit

    2013-01-01

    Microbiological systems evolve to fulfil their tasks with maximal efficiency. The immune system is a remarkable example, where the distinction between self and non-self is made by means of molecular interaction between self-proteins and antigens, triggering affinity-dependent systemic actions. Specificity of this binding and the infinitude of potential antigenic patterns call for novel mechanisms to generate antibody diversity. Inspired by this problem, we develop a genetic algorithm where agents evolve their strings in the presence of random antigenic strings and reproduce with affinity-dependent rates. We ask what is the best strategy to generate diversity if agents can rearrange their strings a finite number of times. We find that endowing each agent with an inheritable cellular automaton rule for performing rearrangements makes the system more efficient in pattern-matching than if transformations are totally random. In the former implementation, the population evolves to a stationary state where agents with different automata rules coexist. (paper)

  20. Relative role of contemporary environment versus history in shaping diversity patterns of China's woody plants

    DEFF Research Database (Denmark)

    Wang, Zhiheng; Fang, Jingyun; Tang, Zhiyao

    2012-01-01

    What determines large-scale patterns of species diversity is a central and controversial topic in biogeography and ecology. In this study, we compared the effects of contemporary environment and historical contingencies on species richness patterns of woody plants in China, using fine-resolution ......-plant species richness across China, while historical contingencies generate regional deviations from this trend. Our findings imply that both species diversity and regional evolutionary and ecological histories should be taken into account for future nature conservation......., and the Tibetan Plateau, perhaps reflecting their special geological features and history. Nevertheless, partial regression indicated that historical effects were less important relative to contemporary environment. In conclusion, contemporary environment (notably climate) determines the general trend in woody...

  1. Influence of ethnolinguistic diversity on the sorghum genetic patterns in subsistence farming systems in eastern Kenya.

    Directory of Open Access Journals (Sweden)

    Vanesse Labeyrie

    Full Text Available Understanding the effects of actions undertaken by human societies on crop evolution processes is a major challenge for the conservation of genetic resources. This study investigated the mechanisms whereby social boundaries associated with patterns of ethnolinguistic diversity have influenced the on-farm distribution of sorghum diversity. Social boundaries limit the diffusion of planting material, practices and knowledge, thus shaping crop diversity in situ. To assess the effect of social boundaries, this study was conducted in the contact zone between the Chuka, Mbeere and Tharaka ethnolinguistic groups in eastern Kenya. Sorghum varieties were inventoried and samples collected in 130 households. In all, 297 individual plants derived from seeds collected under sixteen variety names were characterized using a set of 18 SSR molecular markers and 15 morphological descriptors. The genetic structure was investigated using both a Bayesian assignment method and distance-based clustering. Principal Coordinates Analysis was used to describe the structure of the morphological diversity of the panicles. The distribution of the varieties and the main genetic clusters across ethnolinguistic groups was described using a non-parametric MANOVA and pairwise Fisher tests. The spatial distribution of landrace names and the overall genetic spatial patterns were significantly correlated with ethnolinguistic partition. However, the genetic structure inferred from molecular makers did not discriminate the short-cycle landraces despite their morphological distinctness. The cases of two improved varieties highlighted possible fates of improved materials. The most recent one was often given the name of local landraces. The second one, that was introduced a dozen years ago, displays traces of admixture with local landraces with differential intensity among ethnic groups. The patterns of congruence or discordance between the nomenclature of farmers' varieties and the

  2. Emergent Patterns of Diversity and Dynamics in Natural Populations of Planktonic Vibrio Bacteria

    Science.gov (United States)

    2005-06-01

    1973. Ecology of Vibrio parahemolyticus in mixed-template amplifications: formation, consequences and elimination by Chesapeake Bay. J. Bacteriol. 113...Science 1930 and Engineering DOCTORAL DISSERTATION Emergent Patterns of Diversity and Dynamics in Natural Populations of Planktonic Vibrio Bacteria by...DYNAMICS IN NATURAL POPULATIONS OF PLANKTONIC VIBRIO BACTERIA by Janelle Ren6e Thompson B.S. Biological Sciences, Stanford University 1998 M.S

  3. Patterns of bird functional diversity on land-bridge island fragments.

    Science.gov (United States)

    Ding, Zhifeng; Feeley, Kenneth J; Wang, Yanping; Pakeman, Robin J; Ding, Ping

    2013-07-01

    The loss of species diversity due to habitat fragmentation has been extensively studied. In contrast, the impacts of habitat fragmentation on functional diversity remains relatively poorly understood. We conducted bird functional diversity studies on a set of 41 recently isolated land-bridge islands in the Thousand Island Lake, China. We analysed differences in bird species richness and a recently developed suite of complementary functional diversity indices (FRic, volume of functional space occupied; FEve, evenness of abundance distribution in the functional trait space; FDiv, divergence in the distribution of abundance in the trait volume) across different gradients (island area and isolation). We found no correlations between FRic and FEve or FEve and FDiv, but negative correlations between FRic and FDiv. As predicted, island area accounted for most of the variation in bird species richness, whereas isolation explained most of the variation in species evenness (decreasing species evenness with increasing isolation). Functional diversity appears to be more strongly influenced by habitat filtering as opposed to limiting similarity. More specifically, across all islands, both FRic and FEve were significantly lower than expected for randomly assembled communities, but FDiv showed no clear patterns. FRic increased with island area, FEve decreased with island area and FDiv showed no clear patterns. Our finding that FEve decreases with island area at TIL may indicate low functional stability on such islands, and as such large islands and habitat patches may deserve extra attention and/or protection. These results help to demonstrate the importance of considering the effects of fragmentation on functional diversity in habitat management and reserve design plans. © 2013 The Authors. Journal of Animal Ecology © 2013 British Ecological Society.

  4. Patterns of plant species diversity during succession under different disturbance regimes.

    Science.gov (United States)

    Denslow, Julie Sloan

    1980-07-01

    I suggest that between-community variations in diversity patterns during succession in plant communities are due to the effects of selection on life history strategies under different disturbance regimes. Natural disturbances to plant communities are simultaneously a source of mortality for some individuals and a source of establishment sites for others. The plant community consists of a mosaic of disturbance patches (gaps) of different environmental conditions. The composition of the mosaic is described by the size-frequency distribution of the gaps and is dependent on the rates and scales of disturbance. The life-history strategies of plant species dependent on some form of disturbance for establishment of propagules should reflect this size-frequency distribution of disturbance patches. An extension of island biogeographic theory to encompass relative habitat area predicts that a community should be most rich in species adapted to growth and establishment in the spatially most common patch types. Changes in species diversity during succession following large scale disturbance reflect the prevalent life history patterns under historically common disturbance regimes. Communities in which the greatest patch area is in large-scale clearings (e.g. following fire) are most diverse in species establishing seedlings in xeric, high light conditions. Species diversity decreases during succession. Communities in which such large patches are rare are characterized by a large number of species that reach the canopy through small gaps and realtively few which regenerate in the large clearings. Diversity increases during succession following a large scale disturbance.Evidence from communities characterized by different disturbance regimes is summarized from the literature. This hypothesis provides an evolutionary mechanism with which to examine the changes in plant community structure during succession. Diversity peaks occurring at "intermediate levels" of disturbance as

  5. DNA methylation patterns in tissues from mid-gestation bovine foetuses produced by somatic cell nuclear transfer show subtle abnormalities in nuclear reprogramming

    Directory of Open Access Journals (Sweden)

    Lee Rita SF

    2010-03-01

    Full Text Available Abstract Background Cloning of cattle by somatic cell nuclear transfer (SCNT is associated with a high incidence of pregnancy failure characterized by abnormal placental and foetal development. These abnormalities are thought to be due, in part, to incomplete re-setting of the epigenetic state of DNA in the donor somatic cell nucleus to a state that is capable of driving embryonic and foetal development to completion. Here, we tested the hypothesis that DNA methylation patterns were not appropriately established during nuclear reprogramming following SCNT. A panel of imprinted, non-imprinted genes and satellite repeat sequences was examined in tissues collected from viable and failing mid-gestation SCNT foetuses and compared with similar tissues from gestation-matched normal foetuses generated by artificial insemination (AI. Results Most of the genomic regions examined in tissues from viable and failing SCNT foetuses had DNA methylation patterns similar to those in comparable tissues from AI controls. However, statistically significant differences were found between SCNT and AI at specific CpG sites in some regions of the genome, particularly those associated with SNRPN and KCNQ1OT1, which tended to be hypomethylated in SCNT tissues. There was a high degree of variation between individuals in methylation levels at almost every CpG site in these two regions, even in AI controls. In other genomic regions, methylation levels at specific CpG sites were tightly controlled with little variation between individuals. Only one site (HAND1 showed a tissue-specific pattern of DNA methylation. Overall, DNA methylation patterns in tissues of failing foetuses were similar to apparently viable SCNT foetuses, although there were individuals showing extreme deviant patterns. Conclusion These results show that SCNT foetuses that had developed to mid-gestation had largely undergone nuclear reprogramming and that the epigenetic signature at this stage was not a

  6. Diversity

    Science.gov (United States)

    Portraits In Courage Vol. VIII Portraits In Courage Vol. IX Portraits In Courage Vol. X AF Sites Social -Wide Initiative to Promote Diversity and Inclusion in the Federal Workforce Executive Order 13548 : Virtual Diversity Conference Air Force Diversity & Inclusion Air Force Diversity Graphic There is no

  7. A metric for quantifying El Niño pattern diversity with implications for ENSO-mean state interaction

    Science.gov (United States)

    Lemmon, Danielle E.; Karnauskas, Kristopher B.

    2018-04-01

    Recent research on the El Niño-Southern Oscillation (ENSO) phenomenon increasingly reveals the highly complex and diverse nature of ENSO variability. A method of quantifying ENSO spatial pattern uniqueness and diversity is presented, which enables (1) formally distinguishing between unique and "canonical" El Niño events, (2) testing whether historical model simulations aptly capture ENSO diversity by comparing with instrumental observations, (3) projecting future ENSO diversity using future model simulations, (4) understanding the dynamics that give rise to ENSO diversity, and (5) analyzing the associated diversity of ENSO-related atmospheric teleconnection patterns. Here we develop a framework for measuring El Niño spatial SST pattern uniqueness and diversity for a given set of El Niño events using two indices, the El Niño Pattern Uniqueness (EPU) index and El Niño Pattern Diversity (EPD) index, respectively. By applying this framework to instrumental records, we independently confirm a recent regime shift in El Niño pattern diversity with an increase in unique El Niño event sea surface temperature patterns. However, the same regime shift is not observed in historical CMIP5 model simulations; moreover, a comparison between historical and future CMIP5 model scenarios shows no robust change in future ENSO diversity. Finally, we support recent work that asserts a link between the background cooling of the eastern tropical Pacific and changes in ENSO diversity. This robust link between an eastern Pacific cooling mode and ENSO diversity is observed not only in instrumental reconstructions and reanalysis, but also in historical and future CMIP5 model simulations.

  8. Altitudinal patterns of plant diversity on the Jade Dragon Snow Mountain, southwestern China.

    Science.gov (United States)

    Xu, Xiang; Zhang, Huayong; Tian, Wang; Zeng, Xiaoqiang; Huang, Hai

    2016-01-01

    Understanding altitudinal patterns of biological diversity and their underlying mechanisms is critically important for biodiversity conservation in mountainous regions. The contribution of area to plant diversity patterns is widely acknowledged and may mask the effects of other determinant factors. In this context, it is important to examine altitudinal patterns of corrected taxon richness by eliminating the area effect. Here we adopt two methods to correct observed taxon richness: a power-law relationship between richness and area, hereafter "method 1"; and richness counted in equal-area altitudinal bands, hereafter "method 2". We compare these two methods on the Jade Dragon Snow Mountain, which is the nearest large-scale altitudinal gradient to the Equator in the Northern Hemisphere. We find that seed plant species richness, genus richness, family richness, and species richness of trees, shrubs, herbs and Groups I-III (species with elevational range size 500 m, respectively) display distinct hump-shaped patterns along the equal-elevation altitudinal gradient. The corrected taxon richness based on method 2 (TRcor2) also shows hump-shaped patterns for all plant groups, while the one based on method 1 (TRcor1) does not. As for the abiotic factors influencing the patterns, mean annual temperature, mean annual precipitation, and mid-domain effect explain a larger part of the variation in TRcor2 than in TRcor1. In conclusion, for biodiversity patterns on the Jade Dragon Snow Mountain, method 2 preserves the significant influences of abiotic factors to the greatest degree while eliminating the area effect. Our results thus reveal that although the classical method 1 has earned more attention and approval in previous research, method 2 can perform better under certain circumstances. We not only confirm the essential contribution of method 1 in community ecology, but also highlight the significant role of method 2 in eliminating the area effect, and call for more

  9. Large herbivores maintain termite-caused differences in herbaceous species diversity patterns.

    Science.gov (United States)

    Okullo, Paul; Moe, Stein R

    2012-09-01

    Termites and large herbivores affect African savanna plant communities. Both functional groups are also important for nutrient redistribution across the landscape. We conducted an experiment to study how termites and large herbivores, alone and in combination, affect herbaceous species diversity patterns in an African savanna. Herbaceous vegetation on large vegetated Macrotermes mounds (with and without large herbivores) and on adjacent savanna areas (with and without large herbivores) was monitored over three years in Lake Mburo National Park, Uganda. We found substantial differences in species richness, alpha diversity, evenness, and stability between termite mound herbaceous vegetation and adjacent savanna vegetation. Within months of fencing, levels of species richness, evenness, and stability were no longer significantly different between savanna and mounds. However, fencing reduced the cumulative number of species, particularly for forbs, of which 48% of the species were lost. Fencing increased the beta diversity (dissimilarity among plots) on the resource-poor (in terms of both nutrients and soil moisture) savanna areas, while it did not significantly affect beta diversity on the resource-rich termite mounds. While termites cause substantial heterogeneity in savanna vegetation, large herbivores further amplify these differences by reducing beta diversity on the savanna areas. Large herbivores are, however, responsible for the maintenance of a large number of forbs at the landscape level. These findings suggest that the mechanisms underlying the effects of termites and large herbivores on savanna plant communities scale up to shape community structure and dynamics at a landscape level.

  10. Genetic diversity patterns of arbuscular mycorrhizal fungi associated with the mycoheterotroph Arachnitis uniflora Phil. (Corsiaceae).

    Science.gov (United States)

    Renny, Mauricio; Acosta, M Cristina; Cofré, Noelia; Domínguez, Laura S; Bidartondo, Martin I; Sérsic, Alicia N

    2017-06-01

    Arachnitis uniflora is a mycoheterotrophic plant that exploits arbuscular mycorrhizal fungi of neighbouring plants. We tested A. uniflora 's specificity towards fungi across its large latitudinal range, as well as the role of historical events and current environmental, geographical and altitudinal variables on fungal genetic diversity. Arachnitis uniflora mycorrhizas were sampled at 25 sites. Fungal phylogenetic relationships were reconstructed, genetic diversity was calculated and the main divergent lineages were dated. Phylogeographical analysis was performed with the main fungal clade. Fungal diversity correlations with environmental factors were investigated. Glomeraceae fungi dominated, with a main clade that likely originated in the Upper Cretaceous and diversified in the Miocene. Two other arbuscular mycorrhizal fungal families not previously known to be targeted by A. uniflora were detected rarely and appear to be facultative associations. High genetic diversity, found in Bolivia and both northern and southern Patagonia, was correlated with temperature, rainfall and soil features. Fungal genetic diversity and its distribution can be explained by the ancient evolutionary history of the target fungi and by micro-scale environmental conditions with a geographical mosaic pattern. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  11. Bird diversity and dissimilarity show contrasting patterns along heavy metal pollution gradients in the Urals, Russia.

    Science.gov (United States)

    Belskii, Eugen A; Mikryukov, Vladimir S

    2018-05-07

    The effects of industrial pollution on bird diversity have been widely studied using traditional diversity measures, which assume all species to be equivalent. We compared species richness and Shannon index with distance-based measures of taxonomic, functional, and phylogenetic diversity (the abundance-weighted mean nearest taxon distances), which describe within-community dissimilarity at terminal branches. Analysis of dissimilarity can shed light on the processes underlying community assembly, i.e., environmental filtering decreases dissimilarity whereas competitive exclusion increases it. In the 2-year study near Karabash and Revda copper smelters in Russia, point counts of nesting birds and habitat descriptions were taken at 10 sites (40 plots) along each pollution gradient. The abundance and diversity of birds showed good repeatability in both regions. The total density of birds, number of species per plot, and Shannon diversity decreased at high toxic load in both regions. The taxonomic, functional, and phylogenetic nearest taxon distances showed the same pattern within regions. Species dissimilarity within communities increased with pollution in Karabash (due to loss of functionally similar species), but did not change in Revda (due to mass replacement of forest species by species of open habitats). Pollution-induced changes in bird communities near Karabash were greater due to the stronger deterioration of the forest ecosystems and less favorable natural conditions (more arid climate, lower diversity and vitality of the tree stand and understorey) compared to Revda. This study emphasizes the need for a multi-level approach to the analysis of bird communities using traditional indices of diversity, functional, taxonomic, or phylogenetic distances between species and environmental variables.

  12. Species diversity and distribution patterns of the ants of Amazonian Ecuador.

    Directory of Open Access Journals (Sweden)

    Kari T Ryder Wilkie

    2010-10-01

    Full Text Available Ants are among the most diverse, abundant and ecologically significant organisms on earth. Although their species richness appears to be greatest in the New World tropics, global patterns of ant diversity and distribution are not well understood. We comprehensively surveyed ant diversity in a lowland primary rainforest in Western Amazonia, Ecuador using canopy fogging, pitfall traps, baits, hand collecting, mini-Winkler devices and subterranean probes to sample ants. A total of 489 ant species comprising 64 genera in nine subfamilies were identified from samples collected in only 0.16 square kilometers. The most species-rich genera were Camponotus, Pheidole, Pseudomyrmex, Pachycondyla, Brachymyrmex, and Crematogaster. Camponotus and Pseudomyrmex were most diverse in the canopy, while Pheidole was most diverse on the ground. The three most abundant ground-dwelling ant genera were Pheidole, Solenopsis and Pyramica. Crematogaster carinata was the most abundant ant species in the canopy; Wasmannia auropunctata was most abundant on the ground, and the army ant Labidus coecus was the most abundant subterranean species. Ant species composition among strata was significantly different: 80% of species were found in only one stratum, 17% in two strata, and 3% in all three strata. Elevation and the number of logs and twigs available as nest sites were significant predictors of ground-dwelling ant species richness. Canopy species richness was not correlated with any ecological variable measured. Subterranean species richness was negatively correlated with depth in the soil. When ant species were categorized using a functional group matrix based on diet, nest-site preference and foraging ecology, the greatest diversity was found in Omnivorous Canopy Nesters. Our study indicates ant species richness is exceptionally high at Tiputini. We project 647-736 ant species in this global hotspot of biodiversity. Considering the relatively small area surveyed, this

  13. Disturbance, neutral theory, and patterns of beta diversity in soil communities.

    Science.gov (United States)

    Maaß, Stefanie; Migliorini, Massimo; Rillig, Matthias C; Caruso, Tancredi

    2014-12-01

    Beta diversity describes how local communities within an area or region differ in species composition/abundance. There have been attempts to use changes in beta diversity as a biotic indicator of disturbance, but lack of theory and methodological caveats have hampered progress. We here propose that the neutral theory of biodiversity plus the definition of beta diversity as the total variance of a community matrix provide a suitable, novel, starting point for ecological applications. Observed levels of beta diversity (BD) can be compared to neutral predictions with three possible outcomes: Observed BD equals neutral prediction or is larger (divergence) or smaller (convergence) than the neutral prediction. Disturbance might lead to either divergence or convergence, depending on type and strength. We here apply these ideas to datasets collected on oribatid mites (a key, very diverse soil taxon) under several regimes of disturbances. When disturbance is expected to increase the heterogeneity of soil spatial properties or the sampling strategy encompassed a range of diverging environmental conditions, we observed diverging assemblages. On the contrary, we observed patterns consistent with neutrality when disturbance could determine homogenization of soil properties in space or the sampling strategy encompassed fairly homogeneous areas. With our method, spatial and temporal changes in beta diversity can be directly and easily monitored to detect significant changes in community dynamics, although the method itself cannot inform on underlying mechanisms. However, human-driven disturbances and the spatial scales at which they operate are usually known. In this case, our approach allows the formulation of testable predictions in terms of expected changes in beta diversity, thereby offering a promising monitoring tool.

  14. Patterns of Symbiodinium (Dinophyceae) diversity and assemblages among diverse hosts and the coral reef environment of Lizard Island, Australia

    KAUST Repository

    Ziegler, Maren

    2018-04-26

    Large-scale environmental disturbances may impact both partners in coral host-Symbiodinium systems. Elucidation of the assembly patterns in such complex and interdependent communities may enable better prediction of environmental impacts across coral reef ecosystems. In this study, we investigated how the community composition and diversity of dinoflagellate symbionts in the genus Symbiodinium were distributed among 12 host species from six taxonomic orders (Actinaria, Alcyonacea, Miliolida, Porifera, Rhizostoma, Scleractinia) and in the reef water and sediments at Lizard Island, Great Barrier Reef before the 3rd Global Coral Bleaching Event. 454 pyrosequencing of the ITS2 region of Symbiodinium yielded 83 Operational Taxonomic Units (OTUs) at a 97% similarity cut-off. Approximately half of the Symbiodinium OTUs from reef water or sediments were also present in symbio. OTUs belonged to six clades (A-D, F-G), but community structure was uneven. The two most abundant OTUs (100% matches to types C1 and A3) comprised 91% of reads and OTU C1 was shared by all species. However, sequence-based analysis of these dominant OTUs revealed host species-specificity, suggesting that genetic similarity cut-offs of Symbiodinium ITS2 data sets need careful evaluation. Of the less abundant OTUs, roughly half occurred at only one site or in one species and the background Symbiodinium communities were distinct between individual samples. We conclude that sampling multiple host taxa with differing life history traits will be critical to fully understand the symbiont diversity of a given system and to predict coral ecosystem responses to environmental change and disturbance considering the differential stress response of the taxa within. This article is protected by copyright. All rights reserved.

  15. Effect of Cutting Pattern and Fertilization Level on Species Diversity and Evaluation of Grassland Quality

    Directory of Open Access Journals (Sweden)

    Josef Raus

    2014-01-01

    Full Text Available The effects of fertilization level and cutting pattern on the species diversity and quality of a meadow stand were assessed in 2004–2012 in the small plot trial established in 2003 in Vatín, Vysočina Region, Czech Republic. Four levels of fertilization (none; N0 + P30 + K60 kg∙ha−1; N90 + P30 + K60 kg∙ha−1; N180 + P30 + K60 kg∙ha−1 were combined with four treatments of exploitation intensity (4 cuts per year, first cut on 15th May, every next after 45 days; 3 cuts per year, first cut on 30th May, every next after 60 days; 2 cuts per year, first cut on 15th June, next after 90 days; 2 cuts per year, first cut on 30th June, next after 90 days. Numbers of species, Simpson’s diversity index and evaluation of grassland quality according to Novák (2004 were evaluated. Numbers of species and Simpson’s diversity index were significantly affected by both fertilization level and cutting pattern. Species richness decreased along with increasing fertilization rates from 29.4 (no fertilization to 27.8 (N180PK. When comparing cutting pattern treatments the highest species richness was found in four-cut swards (29.6 in average of fertilization levels and it declines towards late double-cut regime (27.2. The Simpson’s index generally increased from two-cut swards to four-cut and from fertilized treatments to control. Grassland quality was significantly affected by cutting pattern. Values increased from four-cut swards (38.1 to two-cut ones (43.8 and 44.0 in early and late harvest respectively.

  16. Multiscale patterns in the diversity and organization of benthic intertidal fauna among French Atlantic estuaries

    Science.gov (United States)

    Blanchet, Hugues; Gouillieux, Benoît; Alizier, Sandrine; Amouroux, Jean-Michel; Bachelet, Guy; Barillé, Anne-Laure; Dauvin, Jean-Claude; de Montaudouin, Xavier; Derolez, Valérie; Desroy, Nicolas; Grall, Jacques; Grémare, Antoine; Hacquebart, Pascal; Jourde, Jérôme; Labrune, Céline; Lavesque, Nicolas; Meirland, Alain; Nebout, Thiebaut; Olivier, Frédéric; Pelaprat, Corine; Ruellet, Thierry; Sauriau, Pierre-Guy; Thorin, Sébastien

    2014-07-01

    Based on a parallel sampling conducted during autumn 2008, a comparative study of the intertidal benthic macrofauna among 10 estuarine systems located along the Channel and Atlantic coasts of France was performed in order to assess the level of fauna similarity among these sites and to identify possible environmental factors involved in the observed pattern at both large (among sites) and smaller (benthic assemblages) scales. More precisely this study focused on unraveling the observed pattern of intertidal benthic fauna composition and diversity observed at among-site scale by exploring both biotic and abiotic factors acting at the among- and within-site scales. Results showed a limited level of similarity at the among-site level in terms of intertidal benthic fauna composition and diversity. The observed pattern did not fit with existing transitional water classification methods based on fish or benthic assemblages developed in the frame of the European Water Framework Directive (WFD). More particularly, the coastal plain estuaries displayed higher among-site similarity compared to ria systems. These coastal plain estuaries were characterized by higher influence of river discharge, lower communication with the ocean and high suspended particulate matter levels. On the other hand, the ria-type systems were more dissimilar and different from the coastal plain estuaries. The level of similarity among estuaries was mainly linked to the relative extent of the intertidal "Scrobicularia plana-Cerastoderma edule" and "Tellina tenuis" or "Venus" communities as a possible consequence of salinity regime, suspended matter concentrations and fine particles supply with consequences on the trophic functioning, structure and organization of benthic fauna. Despite biogeographical patterns, the results also suggest that, in the context of the WFD, these estuaries should only be compared on the basis of the most common intertidal habitat occurring throughout all estuarine systems

  17. Visualizing Patterns of Marine Eukaryotic Diversity from Metabarcoding Data Using QIIME.

    Science.gov (United States)

    Leray, Matthieu; Knowlton, Nancy

    2016-01-01

    PCR amplification followed by deep sequencing of homologous gene regions is increasingly used to characterize the diversity and taxonomic composition of marine eukaryotic communities. This approach may generate millions of sequences for hundreds of samples simultaneously. Therefore, tools that researchers can use to visualize complex patterns of diversity for these massive datasets are essential. Efforts by microbiologists to understand the Earth and human microbiomes using high-throughput sequencing of the 16S rRNA gene has led to the development of several user-friendly, open-source software packages that can be similarly used to analyze eukaryotic datasets. Quantitative Insights Into Microbial Ecology (QIIME) offers some of the most helpful data visualization tools. Here, we describe functionalities to import OTU tables generated with any molecular marker (e.g., 18S, COI, ITS) and associated metadata into QIIME. We then present a range of analytical tools implemented within QIIME that can be used to obtain insights about patterns of alpha and beta diversity for marine eukaryotes.

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

    Science.gov (United States)

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

    2016-01-01

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

  19. Evolutionary Pattern and Regulation Analysis to Support Why Diversity Functions Existed within PPAR Gene Family Members

    Directory of Open Access Journals (Sweden)

    Tianyu Zhou

    2015-01-01

    Full Text Available Peroxisome proliferators-activated receptor (PPAR gene family members exhibit distinct patterns of distribution in tissues and differ in functions. The purpose of this study is to investigate the evolutionary impacts on diversity functions of PPAR members and the regulatory differences on gene expression patterns. 63 homology sequences of PPAR genes from 31 species were collected and analyzed. The results showed that three isolated types of PPAR gene family may emerge from twice times of gene duplication events. The conserved domains of HOLI (ligand binding domain of hormone receptors domain and ZnF_C4 (C4 zinc finger in nuclear in hormone receptors are essential for keeping basic roles of PPAR gene family, and the variant domains of LCRs may be responsible for their divergence in functions. The positive selection sites in HOLI domain are benefit for PPARs to evolve towards diversity functions. The evolutionary variants in the promoter regions and 3′ UTR regions of PPARs result into differential transcription factors and miRNAs involved in regulating PPAR members, which may eventually affect their expressions and tissues distributions. These results indicate that gene duplication event, selection pressure on HOLI domain, and the variants on promoter and 3′ UTR are essential for PPARs evolution and diversity functions acquired.

  20. Evolutionary Pattern and Regulation Analysis to Support Why Diversity Functions Existed within PPAR Gene Family Members.

    Science.gov (United States)

    Zhou, Tianyu; Yan, Xiping; Wang, Guosong; Liu, Hehe; Gan, Xiang; Zhang, Tao; Wang, Jiwen; Li, Liang

    2015-01-01

    Peroxisome proliferators-activated receptor (PPAR) gene family members exhibit distinct patterns of distribution in tissues and differ in functions. The purpose of this study is to investigate the evolutionary impacts on diversity functions of PPAR members and the regulatory differences on gene expression patterns. 63 homology sequences of PPAR genes from 31 species were collected and analyzed. The results showed that three isolated types of PPAR gene family may emerge from twice times of gene duplication events. The conserved domains of HOLI (ligand binding domain of hormone receptors) domain and ZnF_C4 (C4 zinc finger in nuclear in hormone receptors) are essential for keeping basic roles of PPAR gene family, and the variant domains of LCRs may be responsible for their divergence in functions. The positive selection sites in HOLI domain are benefit for PPARs to evolve towards diversity functions. The evolutionary variants in the promoter regions and 3' UTR regions of PPARs result into differential transcription factors and miRNAs involved in regulating PPAR members, which may eventually affect their expressions and tissues distributions. These results indicate that gene duplication event, selection pressure on HOLI domain, and the variants on promoter and 3' UTR are essential for PPARs evolution and diversity functions acquired.

  1. Development of spatially diverse and complex dune-field patterns: Gran Desierto Dune Field, Sonora, Mexico

    Science.gov (United States)

    Beveridge, C.; Kocurek, G.; Ewing, R.C.; Lancaster, N.; Morthekai, P.; Singhvi, A.K.; Mahan, S.A.

    2006-01-01

    The pattern of dunes within the Gran Desierto of Sonora, Mexico, is both spatially diverse and complex. Identification of the pattern components from remote-sensing images, combined with statistical analysis of their measured parameters demonstrate that the composite pattern consists of separate populations of simple dune patterns. Age-bracketing by optically stimulated luminescence (OSL) indicates that the simple patterns represent relatively short-lived aeolian constructional events since ???25 ka. The simple dune patterns consist of: (i) late Pleistocene relict linear dunes; (ii) degraded crescentic dunes formed at ???12 ka; (iii) early Holocene western crescentic dunes; (iv) eastern crescentic dunes emplaced at ???7 ka; and (v) star dunes formed during the last 3 ka. Recognition of the simple patterns and their ages allows for the geomorphic backstripping of the composite pattern. Palaeowind reconstructions, based upon the rule of gross bedform-normal transport, are largely in agreement with regional proxy data. The sediment state over time for the Gran Desierto is one in which the sediment supply for aeolian constructional events is derived from previously stored sediment (Ancestral Colorado River sediment), and contemporaneous influx from the lower Colorado River valley and coastal influx from the Bahia del Adair inlet. Aeolian constructional events are triggered by climatic shifts to greater aridity, changes in the wind regime, and the development of a sediment supply. The rate of geomorphic change within the Gran Desierto is significantly greater than the rate of subsidence and burial of the accumulation surface upon which it rests. ?? 2006 The Authors. Journal compilation 2006 International Association of Sedimentologists.

  2. Spatial pattern affects diversity-productivity relationships in experimental meadow communities

    Science.gov (United States)

    Lamošová, Tereza; Doležal, Jiří; Lanta, Vojtěch; Lepš, Jan

    2010-05-01

    Plant species create aggregations of conspecifics as a consequence of limited seed dispersal, clonal growth and heterogeneous environment. Such intraspecific aggregation increases the importance of intraspecific competition relative to interspecific competition which may slow down competitive exclusion and promote species coexistence. To examine how spatial aggregation impacts the functioning of experimental assemblages of varying species richness, eight perennial grassland species of different growth form were grown in random and aggregated patterns in monocultures, two-, four-, and eight-species mixtures. In mixtures with an aggregated pattern, monospecific clumps were interspecifically segregated. Mixed model ANOVA was used to test (i) how the total productivity and productivity of individual species is affected by the number of species in a mixture, and (ii) how these relationships are affected by spatial pattern of sown plants. The main patterns of productivity response to species richness conform to other studies: non-transgressive overyielding is omnipresent (the productivity of mixtures is higher than the average of its constituent species so that the net diversity, selection and complementarity effects are positive), whereas transgressive overyielding is found only in a minority of cases (average of log(overyielding) being close to zero or negative). The theoretical prediction that plants in a random pattern should produce more than in an aggregated pattern (the distances to neighbours are smaller and consequently the competition among neighbours stronger) was confirmed in monocultures of all the eight species. The situation is more complicated in mixtures, probably as a consequence of complicated interplay between interspecific and intraspecific competition. The most productive species ( Achillea, Holcus, Plantago) were competitively superior and increased their relative productivity with mixture richness. The intraspecific competition of these species is

  3. DNA methylation map in circulating leukocytes mirrors subcutaneous adipose tissue methylation pattern: a genome-wide analysis from non-obese and obese patients

    Science.gov (United States)

    Crujeiras, A. B.; Diaz-Lagares, A.; Sandoval, J.; Milagro, F. I.; Navas-Carretero, S.; Carreira, M. C.; Gomez, A.; Hervas, D.; Monteiro, M. P.; Casanueva, F. F.; Esteller, M.; Martinez, J. A.

    2017-01-01

    The characterization of the epigenetic changes within the obesity-related adipose tissue will provide new insights to understand this metabolic disorder, but adipose tissue is not easy to sample in population-based studies. We aimed to evaluate the capacity of circulating leukocytes to reflect the adipose tissue-specific DNA methylation status of obesity susceptibility. DNA samples isolated from subcutaneous adipose tissue and circulating leukocytes were hybridized in the Infinium HumanMethylation 450 BeadChip. Data were compared between samples from obese (n = 45) and non-obese (n = 8–10) patients by Wilcoxon-rank test, unadjusted for cell type distributions. A global hypomethylation of the differentially methylated CpG sites (DMCpGs) was observed in the obese subcutaneous adipose tissue and leukocytes. The overlap analysis yielded a number of genes mapped by the common DMCpGs that were identified to reflect the obesity state in the leukocytes. Specifically, the methylation levels of FGFRL1, NCAPH2, PNKD and SMAD3 exhibited excellent and statistically significant efficiencies in the discrimination of obesity from non-obesity status (AUC > 0.80; p obesity-related adipose tissue pathogenesis through peripheral blood analysis, an easily accessible and minimally invasive biological material instead of adipose tissue. PMID:28211912

  4. Fumonisin FB1 treatment acts synergistically with methyl donor deficiency during rat pregnancy to produce alterations of H3- and H4-histone methylation patterns in fetuses.

    Science.gov (United States)

    Pellanda, Hélène; Forges, Thierry; Bressenot, Aude; Chango, Abalo; Bronowicki, Jean-Pierre; Guéant, Jean-Louis; Namour, Fares

    2012-06-01

    Prenatal folate and methyl donor malnutrition lead to epigenetic alterations that could enhance susceptibility to disease. Methyl-deficient diet (MDD) and fumonisin FB1 are risk factors for neural tube defects and cancers. Evidence indicates that FB1 impairs folate metabolism. Folate receptors and four heterochromatin markers were investigated in rat fetuses liver derived from dams exposed to MDD and/or FB1 administered at a dose twice higher than the provisional maximum tolerable daily intake (PMTDI = 2 μg/kg/day). Even though folate receptors transcription seemed up-regulated by methyl depletion regardless of FB1 treatment, combined MDD/FB1 exposure might reverse this up-regulation since folate receptors transcripts were lower in the MDD/FB1 versus MDD group. Methyl depletion decreased H4K20me3. Combined MDD/FB1 decreased H4K20me3 even more and increased H3K9me3. The elevated H3K9me3 can be viewed as a defense mechanism inciting the cell to resist heterochromatin disorganization. H3R2me2 and H4K16Ac varied according to this mechanism even though statistical significance was not consistent. Considering that humans are exposed to FB1 levels above the PMTDI, this study is relevant because it suggests that low doses of FB1 interact with MDD thus contributing to disrupt the epigenetic landscape. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Evaluation of Diversity Antenna Designs Using Ray Tracing, Measured Radiation Patterns, and MIMO Channel Measurements

    Directory of Open Access Journals (Sweden)

    Arindam Pal

    2007-01-01

    Full Text Available This paper presents an evaluation of the MIMO performance of three candidate antenna array designs, each embedded within a PDA footprint, using indoor wideband channel measurements at 5.2 GHz alongside channel simulations. A channel model which employs the plane-wave approximation was used to combine the embedded antenna radiation patterns of the candidate devices obtained from far-field pattern measurements and multipath component parameters from an indoor ray-tracer. The 4-element candidate arrays were each constructed using a different type of antenna element, and despite the diverse element directivities, pattern characteristics, and polarization purities, all three devices were constructed to fully exploit diversity in polarization, space, and angle. Thus, low correlation and high information theoretic capacity was observed in each case. A good match between the model and the measurements is also demonstrated, especially for 2×2 MIMO subsets of identically or orthogonally polarized linear slot antennas. The interdependencies between the channel XPD, directional spread and pathloss, and the respective impact on channel capacity are also discussed in this paper.

  6. Evaluation of Diversity Antenna Designs Using Ray Tracing, Measured Radiation Patterns, and MIMO Channel Measurements

    Directory of Open Access Journals (Sweden)

    Pal Arindam

    2007-01-01

    Full Text Available This paper presents an evaluation of the MIMO performance of three candidate antenna array designs, each embedded within a PDA footprint, using indoor wideband channel measurements at 5.2 GHz alongside channel simulations. A channel model which employs the plane-wave approximation was used to combine the embedded antenna radiation patterns of the candidate devices obtained from far-field pattern measurements and multipath component parameters from an indoor ray-tracer. The 4-element candidate arrays were each constructed using a different type of antenna element, and despite the diverse element directivities, pattern characteristics, and polarization purities, all three devices were constructed to fully exploit diversity in polarization, space, and angle. Thus, low correlation and high information theoretic capacity was observed in each case. A good match between the model and the measurements is also demonstrated, especially for MIMO subsets of identically or orthogonally polarized linear slot antennas. The interdependencies between the channel XPD, directional spread and pathloss, and the respective impact on channel capacity are also discussed in this paper.

  7. Contrasting patterns in lichen diversity in the continental and maritime Antarctic

    Science.gov (United States)

    Singh, Shiv Mohan; Olech, Maria; Cannone, Nicoletta; Convey, Peter

    2015-09-01

    Systematic surveys of the lichen floras of Schirmacher Oasis (Queen Maud Land, continental Antarctic), Victoria Land (Ross Sector, continental Antarctic) and Admiralty Bay (South Shetland Islands, maritime Antarctic) were compared to help infer the major factors influencing patterns of diversity and biogeography in the three areas. Biogeographic patterns were determined using a variety of multivariate statistical tools. A total of 54 lichen species were documented from Schirmacher Oasis (SO), 48 from Victoria Land (VL) and 244 from Admiralty Bay (AB). Of these, 21 species were common to all areas. Most lichens from the SO and VL areas were microlichens, the dominant genus being Buellia. In AB, in contrast, many macrolichens were also present and the dominant genus was Caloplaca. In SO and VL large areas lacked any visible lichen cover, even where the ground was snow-free in summer. Small-scale diversity patterns were present in AB, where the number of species and genera was greater close to the coast. Most species recorded were rare in the study areas in which they were present and endemic to Antarctica.

  8. Polarized Uniform Linear Array System: Beam Radiation Pattern, Beamforming Diversity Order, and Channel Capacity

    Directory of Open Access Journals (Sweden)

    Xin Su

    2015-01-01

    Full Text Available There have been many studies regarding antenna polarization; however, there have been few publications on the analysis of the channel capacity for polarized antenna systems using the beamforming technique. According to Chung et al., the channel capacity is determined by the density of scatterers and the transmission power, which is obtained based on the assumption that scatterers are uniformly distributed on a 3D spherical scattering model. However, it contradicts the practical scenario, where scatterers may not be uniformly distributed under outdoor environment, and lacks the consideration of fading channel gain. In this study, we derive the channel capacity of polarized uniform linear array (PULA systems using the beamforming technique in a practical scattering environment. The results show that, for PULA systems, the channel capacity, which is boosted by beamforming diversity, can be determined using the channel gain, beam radiation pattern, and beamforming diversity order (BDO, where the BDO is dependent on the antenna characteristics and array configurations.

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

    Directory of Open Access Journals (Sweden)

    Fleishman, E.

    2005-01-01

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

  10. Modelling patterns of pollinator species richness and diversity using satellite image texture.

    Directory of Open Access Journals (Sweden)

    Sylvia Hofmann

    Full Text Available Assessing species richness and diversity on the basis of standardised field sampling effort represents a cost- and time-consuming method. Satellite remote sensing (RS can help overcome these limitations because it facilitates the collection of larger amounts of spatial data using cost-effective techniques. RS information is hence increasingly analysed to model biodiversity across space and time. Here, we focus on image texture measures as a proxy for spatial habitat heterogeneity, which has been recognized as an important determinant of species distributions and diversity. Using bee monitoring data of four years (2010-2013 from six 4 × 4 km field sites across Central Germany and a multimodel inference approach we test the ability of texture features derived from Landsat-TM imagery to model local pollinator biodiversity. Textures were shown to reflect patterns of bee diversity and species richness to some extent, with the first-order entropy texture and terrain roughness being the most relevant indicators. However, the texture measurements accounted for only 3-5% of up to 60% of the variability that was explained by our final models, although the results are largely consistent across different species groups (bumble bees, solitary bees. While our findings provide indications in support of the applicability of satellite imagery textures for modeling patterns of bee biodiversity, they are inconsistent with the high predictive power of texture metrics reported in previous studies for avian biodiversity. We assume that our texture data captured mainly heterogeneity resulting from landscape configuration, which might be functionally less important for wild bees than compositional diversity of plant communities. Our study also highlights the substantial variability among taxa in the applicability of texture metrics for modelling biodiversity.

  11. Modelling patterns of pollinator species richness and diversity using satellite image texture.

    Science.gov (United States)

    Hofmann, Sylvia; Everaars, Jeroen; Schweiger, Oliver; Frenzel, Mark; Bannehr, Lutz; Cord, Anna F

    2017-01-01

    Assessing species richness and diversity on the basis of standardised field sampling effort represents a cost- and time-consuming method. Satellite remote sensing (RS) can help overcome these limitations because it facilitates the collection of larger amounts of spatial data using cost-effective techniques. RS information is hence increasingly analysed to model biodiversity across space and time. Here, we focus on image texture measures as a proxy for spatial habitat heterogeneity, which has been recognized as an important determinant of species distributions and diversity. Using bee monitoring data of four years (2010-2013) from six 4 × 4 km field sites across Central Germany and a multimodel inference approach we test the ability of texture features derived from Landsat-TM imagery to model local pollinator biodiversity. Textures were shown to reflect patterns of bee diversity and species richness to some extent, with the first-order entropy texture and terrain roughness being the most relevant indicators. However, the texture measurements accounted for only 3-5% of up to 60% of the variability that was explained by our final models, although the results are largely consistent across different species groups (bumble bees, solitary bees). While our findings provide indications in support of the applicability of satellite imagery textures for modeling patterns of bee biodiversity, they are inconsistent with the high predictive power of texture metrics reported in previous studies for avian biodiversity. We assume that our texture data captured mainly heterogeneity resulting from landscape configuration, which might be functionally less important for wild bees than compositional diversity of plant communities. Our study also highlights the substantial variability among taxa in the applicability of texture metrics for modelling biodiversity.

  12. Patterns of DNA methylation in development, division of labor and hybridization in an ant with genetic caste determination.

    Directory of Open Access Journals (Sweden)

    Chris R Smith

    Full Text Available BACKGROUND: DNA methylation is a common regulator of gene expression, including acting as a regulator of developmental events and behavioral changes in adults. Using the unique system of genetic caste determination in Pogonomyrmex barbatus, we were able to document changes in DNA methylation during development, and also across both ancient and contemporary hybridization events. METHODOLOGY/PRINCIPAL FINDINGS: Sodium bisulfite sequencing demonstrated in vivo methylation of symmetric CG dinucleotides in P. barbatus. We also found methylation of non-CpG sequences. This validated two bioinformatics methods for predicting gene methylation, the bias in observed to expected ratio of CpG dinucleotides and the density of CpG/TpG single nucleotide polymorphisms (SNP. Frequencies of genomic DNA methylation were determined for different developmental stages and castes using ms-AFLP assays. The genetic caste determination system (GCD is probably the product of an ancestral hybridization event between P. barbatus and P. rugosus. Two lineages obligately co-occur within a GCD population, and queens are derived from intra-lineage matings whereas workers are produced from inter-lineage matings. Relative DNA methylation levels of queens and workers from GCD lineages (contemporary hybrids were not significantly different until adulthood. Virgin queens had significantly higher relative levels of DNA methylation compared to workers. Worker DNA methylation did not vary among developmental stages within each lineage, but was significantly different between the currently hybridizing lineages. Finally, workers of the two genetic caste determination lineages had half as many methylated cytosines as workers from the putative parental species, which have environmental caste determination. CONCLUSIONS/SIGNIFICANCE: These results suggest that DNA methylation may be a conserved regulatory mechanism moderating division of labor in both bees and ants. Current and historic

  13. Frequency-Tunable and Pattern Diversity Antennas for Cognitive Radio Applications

    Directory of Open Access Journals (Sweden)

    A. H. Ramadan

    2014-01-01

    Full Text Available Frequency-tunable microstrip antennas, for cognitive radio applications, are proposed herein. The approach is based on tuning the operating frequency of a bandpass filter that is incorporated into a wideband antenna. The integration of an open loop resonator- (OLR- based adjustable bandpass filter into a wideband antenna to transform it into a tunable filter-antenna is presented. The same technique is employed to design a cognitive radio pattern diversity tunable filter-antenna. A good agreement between the simulated and measured results for the fabricated prototypes is obtained. The radiation characteristics of each designed tunable filter-antenna are included herein.

  14. Spatial Patterns in Biofilm Diversity across Hierarchical Levels of River-Floodplain Landscapes.

    Directory of Open Access Journals (Sweden)

    Marc Peipoch

    Full Text Available River-floodplain systems are among the most diverse and productive ecosystems, but the effects of biophysical complexity at multiple scales on microbial biodiversity have not been studied. Here, we investigated how the hierarchical organization of river systems (i.e., region, floodplain, zone, habitats, and microhabitats influences epilithic biofilm community assemblage patterns by characterizing microbial communities using 16S rRNA gene sequence data and analyzing bacterial species distribution across local and regional scales. Results indicate that regional and local environmental filters concurrently sort bacterial species, suggesting that spatial configuration of epilithic biofilms resembles patterns of larger organisms in floodplain ecosystems. Along the hierarchical organization of fluvial systems, floodplains constitute a vector of maximum environmental heterogeneity and consequently act as a major landscape filter for biofilm species. Thus, river basins and associated floodplains may simply reflect very large scale 'patches' within which environmental conditions select for community composition of epilithic biofilms.

  15. Diversity patterns, environmental drivers and changes in vegetation composition in dry inter-Andean valleys

    DEFF Research Database (Denmark)

    Quintana, Catalina; Girardello, Marco; Barfod, Anders

    2016-01-01

    Aims We studied diversity, patterns of endemism and turnover of vegetation composition in dry inter-Andean valleys (DIAVs) where little is known about the influence of the abiotic drivers controlling plant species composition and occurrences, and the life forms that contribute most to α- and β...... species with low abundance (e.g. 30 individuals ha−1), including four endemic species. Most of the endemic species were locally rare, and most of them were restricted to southern valleys...... results further highlight the influence of disturbance, water availability and low temperature on plant species composition and occurrence. We also found significant, contrasting patterns in responses to environmental drivers, when analyzing our data separately by life form. Our results show...

  16. Towards global patterns in the diversity and community structure of ectomycorrhizal fungi

    DEFF Research Database (Denmark)

    Tedersoo, Leho; Bahram, Mohammad; Toots, Märt

    2012-01-01

    Global species richness patterns of soil micro-organisms remain poorly understood compared to macro-organisms. We use a global analysis to disentangle the global determinants of diversity and community composition for ectomycorrhizal (EcM) fungi—microbial symbionts that play key roles in plant...... nutrition in most temperate and many tropical forest ecosystems. Host plant family has the strongest effect on the phylogenetic community composition of fungi, whereas temperature and precipitation mostly affect EcM fungal richness that peaks in the temperate and boreal forest biomes, contrasting...... with latitudinal patterns of macro-organisms. Tropical ecosystems experience rapid turnover of organic material and have weak soil stratification, suggesting that poor habitat conditions may contribute to the relatively low richness of EcM fungi, and perhaps other soil biota, in most tropical ecosystems. For EcM...

  17. Regulation and function of DNA methylation in plants and animals

    KAUST Repository

    He, Xinjian

    2011-02-15

    DNA methylation is an important epigenetic mark involved in diverse biological processes. In plants, DNA methylation can be established through the RNA-directed DNA methylation pathway, an RNA interference pathway for transcriptional gene silencing (TGS), which requires 24-nt small interfering RNAs. In mammals, de novo DNA methylation occurs primarily at two developmental stages: during early embryogenesis and during gametogenesis. While it is not clear whether establishment of DNA methylation patterns in mammals involves RNA interference in general, de novo DNA methylation and suppression of transposons in germ cells require 24-32-nt piwi-interacting small RNAs. DNA methylation status is dynamically regulated by DNA methylation and demethylation reactions. In plants, active DNA demethylation relies on the repressor of silencing 1 family of bifunctional DNA glycosylases, which remove the 5-methylcytosine base and then cleave the DNA backbone at the abasic site, initiating a base excision repair (BER) pathway. In animals, multiple mechanisms of active DNA demethylation have been proposed, including a deaminase- and DNA glycosylase-initiated BER pathway. New information concerning the effects of various histone modifications on the establishment and maintenance of DNA methylation has broadened our understanding of the regulation of DNA methylation. The function of DNA methylation in plants and animals is also discussed in this review. © 2011 IBCB, SIBS, CAS All rights reserved.

  18. Patterns of DNA Methylation in Development, Division of Labor and Hybridization in an Ant with Genetic Caste Determination

    OpenAIRE

    Smith, Chris R.; Mutti, Navdeep S.; Jasper, W. Cameron; Naidu, Agni; Smith, Christopher D.; Gadau, Jürgen

    2012-01-01

    BACKGROUND: DNA methylation is a common regulator of gene expression, including acting as a regulator of developmental events and behavioral changes in adults. Using the unique system of genetic caste determination in Pogonomyrmex barbatus, we were able to document changes in DNA methylation during development, and also across both ancient and contemporary hybridization events. METHODOLOGY/PRINCIPAL FINDINGS: Sodium bisulfite sequencing demonstrated in vivo methylation of symmetric CG dinucle...

  19. Size matters at deep-sea hydrothermal vents: different diversity and habitat fidelity patterns of meio- and macrofauna

    NARCIS (Netherlands)

    Gollner, S.; Govenar, B.; Fisher, C.R.; Bright, M.

    2015-01-01

    Species with markedly different sizes interact when sharing the same habitat. Unravelling mechanisms that control diversity thus requires consideration of a range of size classes. We compared patterns of diversity and community structure for meio- and macrofaunal communities sampled along a gradient

  20. Harmonization of Food-Frequency Questionnaires and Dietary Pattern Analysis in 4 Ethnically Diverse Birth Cohorts.

    Science.gov (United States)

    de Souza, Russell J; Zulyniak, Michael A; Desai, Dipika; Shaikh, Mateen R; Campbell, Natalie C; Lefebvre, Diana L; Gupta, Milan; Wilson, Julie; Wahi, Gita; Atkinson, Stephanie A; Teo, Koon K; Subbarao, Padmaja; Becker, Allan B; Mandhane, Piushkumar J; Turvey, Stuart E; Sears, Malcolm R; Anand, Sonia S

    2016-11-01

    Canada is an ethnically diverse nation, which introduces challenges for health care providers tasked with providing evidence-based dietary advice. We aimed to harmonize food-frequency questionnaires (FFQs) across 4 birth cohorts of ethnically diverse pregnant women to derive robust dietary patterns to investigate maternal and newborn outcomes. The NutriGen Alliance comprises 4 prospective birth cohorts and includes 4880 Canadian mother-infant pairs of predominantly white European [CHILD (Canadian Healthy Infant Longitudinal Development) and FAMILY (Family Atherosclerosis Monitoring In earLY life)], South Asian [START (SouTh Asian birth cohoRT)-Canada], or Aboriginal [ABC (Aboriginal Birth Cohort)] origins. CHILD used a multiethnic FFQ based on a previously validated instrument designed by the Fred Hutchinson Cancer Research Center, whereas FAMILY, START, and ABC used questionnaires specifically designed for use in white European, South Asian, and Aboriginal people, respectively. The serving sizes and consumption frequencies of individual food items within the 4 FFQs were harmonized and aggregated into 36 common food groups. Principal components analysis was used to identify dietary patterns that were internally validated against self-reported vegetarian status and externally validated against a modified Alternative Healthy Eating Index (mAHEI). Three maternal dietary patterns were identified-"plant-based," "Western," and "health-conscious"-which collectively explained 29% of the total variability in eating habits observed in the NutriGen Alliance. These patterns were strongly associated with self-reported vegetarian status (OR: 3.85; 95% CI: 3.47, 4.29; r 2 = 0.30, P < 0.001; for a plant-based diet), and average adherence to the plant-based diet was higher in participants in the fourth quartile of the mAHEI than in the first quartile (mean difference: 46.1%; r 2 = 0.81, P < 0.001). Dietary data collected by using FFQs from ethnically diverse pregnant women can be

  1. Diversion of drugs within health care facilities, a multiple-victim crime: patterns of diversion, scope, consequences, detection, and prevention.

    Science.gov (United States)

    Berge, Keith H; Dillon, Kevin R; Sikkink, Karen M; Taylor, Timothy K; Lanier, William L

    2012-07-01

    Mayo Clinic has been involved in an ongoing effort to prevent the diversion of controlled substances from the workplace and to rapidly identify and respond when such diversion is detected. These efforts have found that diversion of controlled substances is not uncommon and can result in substantial risk not only to the individual who is diverting the drugs but also to patients, co-workers, and employers. We believe that all health care facilities should have systems in place to deter controlled substance diversion and to promptly identify diversion and intervene when it is occurring. Such systems are multifaceted and require close cooperation between multiple stakeholders including, but not limited to, departments of pharmacy, safety and security, anesthesiology, nursing, legal counsel, and human resources. Ideally, there should be a broad-based appreciation of the dangers that diversion creates not only for patients but also for all employees of health care facilities, because diversion can occur at any point along a long supply chain. All health care workers must be vigilant for signs of possible diversion and must be aware of how to engage a preexisting group with expertise in investigating possible diversions. In addition, clear policies and procedures should be in place for dealing with such investigations and for managing the many possible outcomes of a confirmed diversion. This article provides an overview of the multiple types of risk that result from drug diversion from health care facilities. Further, we describe a system developed at Mayo Clinic for evaluating episodes of potential drug diversion and for taking action once diversion is confirmed. Copyright © 2012 Mayo Foundation for Medical Education and Research. Published by Elsevier Inc. All rights reserved.

  2. DNA methylation

    DEFF Research Database (Denmark)

    Williams, Kristine; Christensen, Jesper; Helin, Kristian

    2012-01-01

    DNA methylation is involved in key cellular processes, including X-chromosome inactivation, imprinting and transcriptional silencing of specific genes and repetitive elements. DNA methylation patterns are frequently perturbed in human diseases such as imprinting disorders and cancer. The recent...... discovery that the three members of the TET protein family can convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) has provided a potential mechanism leading to DNA demethylation. Moreover, the demonstration that TET2 is frequently mutated in haematopoietic tumours suggests that the TET...... proteins are important regulators of cellular identity. Here, we review the current knowledge regarding the function of the TET proteins, and discuss various mechanisms by which they contribute to transcriptional control. We propose that the TET proteins have an important role in regulating DNA methylation...

  3. Infraspecific DNA methylation polymorphism in cotton (Gossypium hirsutum L.).

    Science.gov (United States)

    Keyte, Anna L; Percifield, Ryan; Liu, Bao; Wendel, Jonathan F

    2006-01-01

    Cytosine methylation is important in the epigenetic regulation of gene expression and development in plants and has been implicated in silencing duplicate genes after polyploid formation in several plant groups. Relatively little information exists, however, on levels and patterns of methylation polymorphism (MP) at homologous loci within species. Here we explored the levels and patterns of methylation-polymorphism diversity at CCGG sites within allotetraploid cotton, Gossypium hirsutum, using a methylation-sensitive amplified fragment length polymorphism screen and a selected set of 20 G. hirsutum accessions for which we have information on genetic polymorphism levels and relationships. Methylation and MP exist at high levels within G. hirsutum: of 150 HpaII/MspI sites surveyed, 48 were methylated at the inner cytosine (32%) and 32 of these were polymorphic (67%). Both these values are higher than comparable measures of genetic diversity using restriction fragment length polymorphisms. The high percentage of methylation-polymorphic sites and potential relationship to gene expression underscore the potential significance of MP within and among populations. We speculate that biased correlation of methylation-polymorphic sites and genes in cotton may be a consequence of polyploidy and the attendant doubling of all genes.

  4. Patterns of species richness and the center of diversity in modern Indo-Pacific larger foraminifera.

    Science.gov (United States)

    Förderer, Meena; Rödder, Dennis; Langer, Martin R

    2018-05-29

    Symbiont-bearing Larger Benthic Foraminifera (LBF) are ubiquitous components of shallow tropical and subtropical environments and contribute substantially to carbonaceous reef and shelf sediments. Climate change is dramatically affecting carbonate producing organisms and threatens the diversity and structural integrity of coral reef ecosystems. Recent invertebrate and vertebrate surveys have identified the Coral Triangle as the planet's richest center of marine life delineating the region as a top priority for conservation. We compiled and analyzed extensive occurrence records for 68 validly recognized species of LBF from the Indian and Pacific Ocean, established individual range maps and applied Minimum Convex Polygon (MCP) and Species Distribution Model (SDM) methodologies to create the first ocean-wide species richness maps. SDM output was further used for visualizing latitudinal and longitudinal diversity gradients. Our findings provide strong support for assigning the tropical Central Indo-Pacific as the world's species-richest marine region with the Central Philippines emerging as the bullseye of LBF diversity. Sea surface temperature and nutrient content were identified as the most influential environmental constraints exerting control over the distribution of LBF. Our findings contribute to the completion of worldwide research on tropical marine biodiversity patterns and the identification of targeting centers for conservation efforts.

  5. Diversity and Distribution Patterns of Cetaceans in the Subtropical Southwestern Atlantic Outer Continental Shelf and Slope

    Science.gov (United States)

    Di Tullio, Juliana Couto; Gandra, Tiago B. R.; Zerbini, Alexandre N.; Secchi, Eduardo R.

    2016-01-01

    Temporal and spatial patterns of cetacean diversity and distribution were investigated through eight ship-based surveys carried out during spring and autumn between 2009 and 2014 on the outer continental shelf (~150m) and slope (1500m) off southeastern and southern Brazil (~23°S to ~34°S). The survey area was divided into southeast and south areas according to their oceanographic characteristics. Twenty-one species were observed in 503 sightings. The overall number of species was similar between the two areas, though it was higher in the spring in the south area. Five species were dominant and diversity varied more seasonally than spatially. ANOVA and kernel analyses showed that overall cetacean densities were higher in spring compared to autumn. Physeter macrocephalus, the most frequent species, concentrated throughout the south area at depths over 1000m in both seasons. Despite the overlapped occurrence at a broader scale, small delphinids presented latitudinal and in-offshore gradients as well as seasonal variation in distribution patterns, which could indicate habitat partitioning between some species. Delphinus delphis was only recorded in the south and its density decreased in areas where the presence of Stenella frontalis increased, mainly beyond the 250m isobath. Densities of S. longirostris and S. attenuata increased in lower latitudes and beyond the shelf break. The large delphinids Tursiops truncatus and Globicephala melas formed mixed groups in many occasions and were observed along the study area around depths of 500m. Grampus griseus was twice as frequent in the south area and densities increased in waters deeper than 600m. As expected, densities of both small and large migratory whales were higher during spring, over the continental slope, in the southeast area. The results presented here provided strong evidence on the importance of the outer continental shelf and slope to a diverse community of cetaceans occurring in the subtropical Southwestern

  6. Estimating planktonic diversity through spatial dominance patterns in a model ocean.

    Science.gov (United States)

    Soccodato, Alice; d'Ovidio, Francesco; Lévy, Marina; Jahn, Oliver; Follows, Michael J; De Monte, Silvia

    2016-10-01

    In the open ocean, the observation and quantification of biodiversity patterns is challenging. Marine ecosystems are indeed largely composed by microbial planktonic communities whose niches are affected by highly dynamical physico-chemical conditions, and whose observation requires advanced methods for morphological and molecular classification. Optical remote sensing offers an appealing complement to these in-situ techniques. Global-scale coverage at high spatiotemporal resolution is however achieved at the cost of restrained information on the local assemblage. Here, we use a coupled physical and ecological model ocean simulation to explore one possible metrics for comparing measures performed on such different scales. We show that a large part of the local diversity of the virtual plankton ecosystem - corresponding to what accessible by genomic methods - can be inferred from crude, but spatially extended, information - as conveyed by remote sensing. Shannon diversity of the local community is indeed highly correlated to a 'seascape' index, which quantifies the surrounding spatial heterogeneity of the most abundant functional group. The error implied in drastically reducing the resolution of the plankton community is shown to be smaller in frontal regions as well as in regions of intermediate turbulent energy. On the spatial scale of hundreds of kms, patterns of virtual plankton diversity are thus largely sustained by mixing communities that occupy adjacent niches. We provide a proof of principle that in the open ocean information on spatial variability of communities can compensate for limited local knowledge, suggesting the possibility of integrating in-situ and satellite observations to monitor biodiversity distribution at the global scale. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. Assessment of Quantitative and Allelic MGMT Methylation Patterns as a Prognostic Marker in Glioblastoma

    DEFF Research Database (Denmark)

    Kristensen, Lasse S; Michaelsen, Signe R; Dyrbye, Henrik

    2016-01-01

    Methylation of the O(6)-methylguanine-DNA methyltransferase (MGMT) gene is a predictive and prognostic marker in newly diagnosed glioblastoma patients treated with temozolomide but how MGMT methylation should be assessed to ensure optimal detection accuracy is debated. We developed a novel quanti...

  8. Multiple oxygen tension environments reveal diverse patterns of transcriptional regulation in primary astrocytes.

    Directory of Open Access Journals (Sweden)

    Wayne Chadwick

    Full Text Available The central nervous system normally functions at O(2 levels which would be regarded as hypoxic by most other tissues. However, most in vitro studies of neurons and astrocytes are conducted under hyperoxic conditions without consideration of O(2-dependent cellular adaptation. We analyzed the reactivity of astrocytes to 1, 4 and 9% O(2 tensions compared to the cell culture standard of 20% O(2, to investigate their ability to sense and translate this O(2 information to transcriptional activity. Variance of ambient O(2 tension for rat astrocytes resulted in profound changes in ribosomal activity, cytoskeletal and energy-regulatory mechanisms and cytokine-related signaling. Clustering of transcriptional regulation patterns revealed four distinct response pattern groups that directionally pivoted around the 4% O(2 tension, or demonstrated coherent ascending/decreasing gene expression patterns in response to diverse oxygen tensions. Immune response and cell cycle/cancer-related signaling pathway transcriptomic subsets were significantly activated with increasing hypoxia, whilst hemostatic and cardiovascular signaling mechanisms were attenuated with increasing hypoxia. Our data indicate that variant O(2 tensions induce specific and physiologically-focused transcript regulation patterns that may underpin important physiological mechanisms that connect higher neurological activity to astrocytic function and ambient oxygen environments. These strongly defined patterns demonstrate a strong bias for physiological transcript programs to pivot around the 4% O(2 tension, while uni-modal programs that do not, appear more related to pathological actions. The functional interaction of these transcriptional 'programs' may serve to regulate the dynamic vascular responsivity of the central nervous system during periods of stress or heightened activity.

  9. Contrasting patterns of Andean diversification among three diverse clades of Neotropical clearwing butterflies.

    Science.gov (United States)

    Chazot, Nicolas; De-Silva, Donna Lisa; Willmott, Keith R; Freitas, André V L; Lamas, Gerardo; Mallet, James; Giraldo, Carlos E; Uribe, Sandra; Elias, Marianne

    2018-04-01

    The Neotropical region is the most biodiverse on Earth, in a large part due to the highly diverse tropical Andean biota. The Andes are a potentially important driver of diversification within the mountains and for neighboring regions. We compared the role of the Andes in diversification among three subtribes of Ithomiini butterflies endemic to the Neotropics, Dircennina, Oleriina, and Godyridina. The diversification patterns of Godyridina have been studied previously. Here, we generate the first time-calibrated phylogeny for the largest ithomiine subtribe, Dircennina, and we reanalyze a published phylogeny of Oleriina to test different biogeographic scenarios involving the Andes within an identical framework. We found common diversification patterns across the three subtribes, as well as major differences. In Dircennina and Oleriina, our results reveal a congruent pattern of diversification related to the Andes with an Andean origin, which contrasts with the Amazonian origin and multiple Andean colonizations of Godyridina. In each of the three subtribes, a clade diversified in the Northern Andes at a faster rate. Diversification within Amazonia occurred in Oleriina and Godyridina, while virtually no speciation occurred in Dircennina in this region. Dircennina was therefore characterized by higher diversification rates within the Andes compared to non-Andean regions, while in Oleriina and Godyridina, we found no difference between these regions. Our results and discussion highlight the importance of comparative approaches in biogeographic studies.

  10. A dual-band reconfigurable Yagi-Uda antenna with diverse radiation patterns

    Science.gov (United States)

    Saurav, Kushmanda; Sarkar, Debdeep; Srivastava, Kumar Vaibhav

    2017-07-01

    In this paper, a dual-band pattern reconfigurable antenna is proposed. The antenna comprises of a dual-band complementary split ring resonators (CSRRs) loaded dipole as the driven element and two copper strips with varying lengths as parasitic segments on both sides of the driven dipole. PIN diodes are used with the parasitic elements to control their electrical length. The CSRRs loading provide a lower order mode in addition to the reference dipole mode, while the parasitic elements along with the PIN diodes are capable of switching the omni-directional radiation of the dual-band driven element to nine different configurations of radiation patterns which include bi-directional end-fire, broadside, and uni-directional end-fire in both the operating bands. A prototype of the designed antenna together with the PIN diodes and DC bias lines is fabricated to validate the concept of dual-band radiation pattern diversity. The simulation and measurement results are in good agreement. The proposed antenna can be used in wireless access points for PCS and WLAN applications.

  11. DNA methylation patterns of imprinting centers for H19, SNRPN, and KCNQ1OT1 in single-cell clones of human amniotic fluid mesenchymal stem cell

    Directory of Open Access Journals (Sweden)

    Hsiu-Huei Peng

    2012-09-01

    Conclusion: In conclusion, human amniotic fluid mesenchymal stem cells contain a unique epigenetic signature during in vitro cell culture. H19 and KCNQ1OT1 possessed a substantial degree of hypermethylation status, and variable DNA methylation patterns of SNRPN was observed during in vitro cell culture of human amniotic fluid mesenchymal stem cells. Our results urge further understanding of epigenetic status of human amniotic fluid mesenchymal stem cells before it is applied in cell replacement therapy.

  12. DNA methylation patterns in tissues from mid-gestation bovine foetuses produced by somatic cell nuclear transfer show subtle abnormalities in nuclear reprogramming

    OpenAIRE

    Lee Rita SF; Couldrey Christine

    2010-01-01

    Abstract Background Cloning of cattle by somatic cell nuclear transfer (SCNT) is associated with a high incidence of pregnancy failure characterized by abnormal placental and foetal development. These abnormalities are thought to be due, in part, to incomplete re-setting of the epigenetic state of DNA in the donor somatic cell nucleus to a state that is capable of driving embryonic and foetal development to completion. Here, we tested the hypothesis that DNA methylation patterns were not appr...

  13. Diversity and activity pattern of wildlife inhabiting catchment of Hulu Terengganu Hydroelectric Dam, Terengganu, Peninsular Malaysia

    Science.gov (United States)

    Adyla, M. N. Nurul; Ikhwan, Z.; Zuhairi, M.; Ngah, Shukor, M. N.

    2016-11-01

    A series of camera trapping surveys were conducted to study the diversity and distribution of wildlife within the catchment of Hulu Terengganu Hydroelectric Dam. A total of 124 camera traps were deployed at nine study sites, continuously from June 2014 until December 2015. The total effort of camera trap surveys from all the study sites during the 18-month sampling period was 29,128 night traps, from which a total of 32 species of wildlife representing nine Orders were recorded. The most common species were Eurasian Wild Pig (Sus scrofa), Barking Deer (Munticus muntjak), and Malayan Tapir (Tapirus indicus). Camera trap data on activity patterns show that Gallus gallus, Muntiacus muntjak and Sus scrofa are diurnal animals, whereas Tapirus indicus, Elephas maximus and Helarctos malayanus are nocturnal animals.

  14. Patterns and drivers of bacterial α- and β-diversity across vertical profiles from surface to subsurface sediments.

    Science.gov (United States)

    Luna, Gian Marco; Corinaldesi, Cinzia; Rastelli, Eugenio; Danovaro, Roberto

    2013-10-01

    We investigated the patterns and drivers of bacterial α- and β-diversity, along with viral and prokaryotic abundance and the carbon production rates, in marine surface and subsurface sediments (down to 1 m depth) in two habitats: vegetated sediments (seagrass meadow) and non-vegetated sediments. Prokaryotic abundance and production decreased with depth in the sediment, but cell-specific production rates and the virus-to-prokaryote ratio increased, highlighting unexpectedly high activity in the subsurface. The highest diversity was observed in vegetated sediments. Bacterial β-diversity between sediment horizons was high, and only a minor number of taxa was shared between surface and subsurface layers. Viruses significantly contributed to explain α- and β-diversity patterns. Despite potential limitations due to the only use of fingerprinting techniques, this study indicates that the coastal subsurface host highly active and diversified bacterial assemblages, that subsurface cells are more active than expected and that viruses promote β-diversity and stimulate bacterial metabolism in subsurface layers. The limited number of taxa shared between habitats, and between surface and subsurface sediment horizons, suggests that future investigations of the shallow subsurface will provide insights into the census of bacterial diversity, and the comprehension of the patterns and drivers of prokaryotic diversity in marine ecosystems. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

  15. Transmission of epi-alleles with MET1-dependent dense methylation in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Michael Watson

    Full Text Available DNA methylation in plants targets cytosines in three sequence contexts, CG, CHG and CHH (H representing A, C or T. Each of these patterns has traditionally been associated with distinct DNA methylation pathways with CHH methylation being controlled by the RNA dependent DNA methylation (RdDM pathway employing small RNAs as a guide for the de novo DOMAINS REARRANGED METHYLTRANSFERASE (DRM2, and maintenance DNA METHYLTRANSFERASE1 (MET1 being responsible for faithful propagation of CG methylation. Here we report an unusual 'dense methylation' pattern under the control of MET1, with methylation in all three sequence contexts. We identified epi-alleles of dense methylation at a non coding RNA locus (At4g15242 in Arabidopsis ecotypes, with distinct dense methylation and expression characteristics, which are stably maintained and transmitted in genetic crosses and which can be heritably altered by depletion of MET1. This suggests that, in addition to its classical CG maintenance function, at certain loci MET1 plays a role in creating transcriptional diversity based on the generation of independent epi-alleles. Database inspection identified several other loci with MET1-dependent dense methylation patterns. Arabidopsis ecotypes contain distinct epi-alleles of these loci with expression patterns that inversely correlate with methylation density, predominantly within the transcribed region. In Arabidopsis, dense methylation appears to be an exception as it is only found at a small number of loci. Its presence does, however, highlight the potential for MET1 as a contributor to epigenetic diversity, and it will be interesting to investigate the representation of dense methylation in other plant species.

  16. Differing patterns of selection and geospatial genetic diversity within two leading Plasmodium vivax candidate vaccine antigens.

    Directory of Open Access Journals (Sweden)

    Christian M Parobek

    2014-04-01

    Full Text Available Although Plasmodium vivax is a leading cause of malaria around the world, only a handful of vivax antigens are being studied for vaccine development. Here, we investigated genetic signatures of selection and geospatial genetic diversity of two leading vivax vaccine antigens--Plasmodium vivax merozoite surface protein 1 (pvmsp-1 and Plasmodium vivax circumsporozoite protein (pvcsp. Using scalable next-generation sequencing, we deep-sequenced amplicons of the 42 kDa region of pvmsp-1 (n = 44 and the complete gene of pvcsp (n = 47 from Cambodian isolates. These sequences were then compared with global parasite populations obtained from GenBank. Using a combination of statistical and phylogenetic methods to assess for selection and population structure, we found strong evidence of balancing selection in the 42 kDa region of pvmsp-1, which varied significantly over the length of the gene, consistent with immune-mediated selection. In pvcsp, the highly variable central repeat region also showed patterns consistent with immune selection, which were lacking outside the repeat. The patterns of selection seen in both genes differed from their P. falciparum orthologs. In addition, we found that, similar to merozoite antigens from P. falciparum malaria, genetic diversity of pvmsp-1 sequences showed no geographic clustering, while the non-merozoite antigen, pvcsp, showed strong geographic clustering. These findings suggest that while immune selection may act on both vivax vaccine candidate antigens, the geographic distribution of genetic variability differs greatly between these two genes. The selective forces driving this diversification could lead to antigen escape and vaccine failure. Better understanding the geographic distribution of genetic variability in vaccine candidate antigens will be key to designing and implementing efficacious vaccines.

  17. Pervasive adaptive protein evolution apparent in diversity patterns around amino acid substitutions in Drosophila simulans.

    Directory of Open Access Journals (Sweden)

    Shmuel Sattath

    2011-02-01

    Full Text Available In Drosophila, multiple lines of evidence converge in suggesting that beneficial substitutions to the genome may be common. All suffer from confounding factors, however, such that the interpretation of the evidence-in particular, conclusions about the rate and strength of beneficial substitutions-remains tentative. Here, we use genome-wide polymorphism data in D. simulans and sequenced genomes of its close relatives to construct a readily interpretable characterization of the effects of positive selection: the shape of average neutral diversity around amino acid substitutions. As expected under recurrent selective sweeps, we find a trough in diversity levels around amino acid but not around synonymous substitutions, a distinctive pattern that is not expected under alternative models. This characterization is richer than previous approaches, which relied on limited summaries of the data (e.g., the slope of a scatter plot, and relates to underlying selection parameters in a straightforward way, allowing us to make more reliable inferences about the prevalence and strength of adaptation. Specifically, we develop a coalescent-based model for the shape of the entire curve and use it to infer adaptive parameters by maximum likelihood. Our inference suggests that ∼13% of amino acid substitutions cause selective sweeps. Interestingly, it reveals two classes of beneficial fixations: a minority (approximately 3% that appears to have had large selective effects and accounts for most of the reduction in diversity, and the remaining 10%, which seem to have had very weak selective effects. These estimates therefore help to reconcile the apparent conflict among previously published estimates of the strength of selection. More generally, our findings provide unequivocal evidence for strongly beneficial substitutions in Drosophila and illustrate how the rapidly accumulating genome-wide data can be leveraged to address enduring questions about the genetic basis

  18. Pervasive adaptive protein evolution apparent in diversity patterns around amino acid substitutions in Drosophila simulans.

    Science.gov (United States)

    Sattath, Shmuel; Elyashiv, Eyal; Kolodny, Oren; Rinott, Yosef; Sella, Guy

    2011-02-10

    In Drosophila, multiple lines of evidence converge in suggesting that beneficial substitutions to the genome may be common. All suffer from confounding factors, however, such that the interpretation of the evidence-in particular, conclusions about the rate and strength of beneficial substitutions-remains tentative. Here, we use genome-wide polymorphism data in D. simulans and sequenced genomes of its close relatives to construct a readily interpretable characterization of the effects of positive selection: the shape of average neutral diversity around amino acid substitutions. As expected under recurrent selective sweeps, we find a trough in diversity levels around amino acid but not around synonymous substitutions, a distinctive pattern that is not expected under alternative models. This characterization is richer than previous approaches, which relied on limited summaries of the data (e.g., the slope of a scatter plot), and relates to underlying selection parameters in a straightforward way, allowing us to make more reliable inferences about the prevalence and strength of adaptation. Specifically, we develop a coalescent-based model for the shape of the entire curve and use it to infer adaptive parameters by maximum likelihood. Our inference suggests that ∼13% of amino acid substitutions cause selective sweeps. Interestingly, it reveals two classes of beneficial fixations: a minority (approximately 3%) that appears to have had large selective effects and accounts for most of the reduction in diversity, and the remaining 10%, which seem to have had very weak selective effects. These estimates therefore help to reconcile the apparent conflict among previously published estimates of the strength of selection. More generally, our findings provide unequivocal evidence for strongly beneficial substitutions in Drosophila and illustrate how the rapidly accumulating genome-wide data can be leveraged to address enduring questions about the genetic basis of adaptation.

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

    Directory of Open Access Journals (Sweden)

    Assunção–Albuquerque, M. J. T.

    2012-06-01

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

  20. Floristic diversity and distribution pattern of plant communities along altitudinal gradient in Sangla Valley, Northwest Himalaya.

    Science.gov (United States)

    Sharma, Pankaj; Rana, J C; Devi, Usha; Randhawa, S S; Kumar, Rajesh

    2014-01-01

    Himalayas are globally important biodiversity hotspots and are facing rapid loss in floristic diversity and changing pattern of vegetation due to various biotic and abiotic factors. This has necessitated the qualitative and quantitative assessment of vegetation here. The present study was conducted in Sangla Valley of northwest Himalaya aiming to assess the structure of vegetation and its trend in the valley along the altitudinal gradient. In the forest and alpine zones of the valley, 15 communities were recorded. Study revealed 320 species belonging to 199 genera and 75 families. Asteraceae, Rosaceae, Apiaceae, and Ranunculaceae were dominant. Among genera, Artemisia followed by Polygonum, Saussurea, Berberis, and Thalictrum were dominant. Tree and shrub's density ranged from 205 to 600 and from 105 to 1030 individual per hectare, respectively, whereas herbs ranged from 22.08 to 78.95 individual/m(2). Nearly 182 species were native to the Himalaya. Maximum altitudinal distribution of few selected climate sensitive species was found to be highest in northeast and north aspects. This study gives an insight into the floristic diversity and community structure of the fragile Sangla Valley which was hitherto not available.

  1. Impact of age, BMI and HbA1c levels on the genome-wide DNA methylation and mRNA expression patterns in human adipose tissue and identification of epigenetic biomarkers in blood

    DEFF Research Database (Denmark)

    Rönn, Tina; Volkov, Petr; Gillberg, Linn

    2015-01-01

    Increased age, BMI and HbA1c levels are risk factors for several non-communicable diseases. However, the impact of these factors on the genome-wide DNA methylation pattern in human adipose tissue remains unknown. We analyzed the DNA methylation of ∼480 000 sites in human adipose tissue from 96 ma...

  2. Epigenetic factors in cancer risk: effect of chemical carcinogens on global DNA methylation pattern in human TK6 cells.

    Directory of Open Access Journals (Sweden)

    Ali M Tabish

    Full Text Available In the current study, we assessed the global DNA methylation changes in human lymphoblastoid (TK6 cells in vitro in response to 5 direct and 10 indirect-acting genotoxic agents. TK6 cells were exposed to the selected agents for 24 h in the presence and/or absence of S9 metabolic mix. Liquid chromatography-mass spectrometry was used for quantitative profiling of 5-methyl-2'-deoxycytidine. The effect of exposure on 5-methyl-2'-deoxycytidine between control and exposed cultures was assessed by applying the marginal model with correlated residuals on % global DNA methylation data. We reported the induction of global DNA hypomethylation in TK6 cells in response to S9 metabolic mix, under the current experimental settings. Benzene, hydroquinone, styrene, carbon tetrachloride and trichloroethylene induced global DNA hypomethylation in TK6 cells. Furthermore, we showed that dose did not have an effect on global DNA methylation in TK6 cells. In conclusion we report changes in global DNA methylation as an early event in response to agents traditionally considered as genotoxic.

  3. Climate vs. topography – spatial patterns of plant species diversity and endemism on a high-elevation island

    DEFF Research Database (Denmark)

    Irl, Severin David Howard; Harter, David E. V.; Steinbauer, Manuel

    2015-01-01

    the independent contribution of climatic and topographic variables to spatial diversity patterns. We constructed a presence/absence matrix of perennial endemic and native vascular plant species (including subspecies) in 890 plots on the environmentally very heterogeneous island of La Palma, Canary Islands......Climate and topography are among the most fundamental drivers of plant diversity. Here, we assessed the importance of climate and topography in explaining diversity patterns of species richness, endemic richness and endemicity on the landscape scale of an oceanic island and evaluated...... to ecological speciation and specialization to local conditions. We highlight the importance of incorporating climatic variability into future studies of plant species diversity and endemism. The spatial incongruence in hot spots of species richness, endemic richness and endemicity emphasizes the need...

  4. Patterns of alpha, beta and gamma diversity of the herpetofauna in Mexico’s Pacific lowlands and adjacent interior valleys

    Directory of Open Access Journals (Sweden)

    García, A.

    2007-12-01

    Full Text Available The latitudinal distribution patterns of alpha, beta and gamma diversity of reptiles, amphibians and herpetofauna were analyzed using individual binary models of potential distribution for 301 species predicted by ecological modelling for a grid of 9,932 quadrants of ~25 km2 each. We arranged quadrants in 312 latitudinal bands in which alpha, beta and gamma values were determined. Latitudinal trends of all scales of diversity were similar in all groups. Alpha and gamma responded inversely to latitude whereas beta showed a high latitudinal fluctuation due to the high number of endemic species. Alpha and gamma showed a strong correlation in all groups. Beta diversity is an important component of the herpetofauna distribution patterns as a continuous source of species diversity throughout the region.

  5. Identification of regioisomers of methylated kaempferol and quercetin by ultra high performance liquid chromatography quadrupole time-of-flight (UHPLC–QTOF) tandem mass spectrometry combined with diagnostic fragmentation pattern analysis

    International Nuclear Information System (INIS)

    Ma, Chengying; Lv, Haipeng; Zhang, Xinzhong; Chen, Zongmao; Shi, Jiang; Lu, Meiling; Lin, Zhi

    2013-01-01

    Highlights: •Found methane elimination is position-specific for methylated flavonols. •Found retro Diels–Alder fragments retained methoxy at original ring of flavonols. •Proposed a diagnostic pattern for discriminating regioisomers of flavonols. •Identified the specificity of three novel flavonol O-methyltransferases. •Identified six biologically active compounds and four new compounds. -- Abstract: The O-methylation of active flavonoids can enhance their antiallergic, anticancerous, and cardioprotective effects depending on the methylation position. Thus, it is biologically and pharmacologically important to differentiate methylated flavonoid regioisomers. In this study, we examined the regioisomers of methylated kaempferol and quercetin using ultra high performance liquid chromatography quadrupole time-of-flight tandem mass spectrometry. The methyl groups on the flavonoids can generally be cleaved as methyl radicals in a position-independent manner. We found that methyl groups can be cleaved as methane. If there are protons adjacent the methoxy on the flavonol rings, intra-molecule proton transfer can occur via collision-induced dissociation, and one molecule of methane can then be eliminated. The remaining charged fragment ([M+H−CH 4 ] + ) reflects the adjacent structure and is specific to the methoxy position. Furthermore, the retro Diels–Alder (RDA) fragmentation of methylated flavonols can generate fragments with the methoxy at the original methylated ring. Combining the position-specific [M+H−CH 4 ] + fragment with the RDA fragments provides a diagnostic pattern for rapidly identifying methylated regioisomeric flavonols. Along with their retention behaviour, we have successfully identified ten regioisomers of methylated kaempferol and quercetin, which include six compounds previously reported in plants and shown to be biologically active. The developed approach is sensitive, rapid, reliable, and requires few standard compounds. It is highly

  6. Diversity and distribution Patterns of the infralittoral green macroalgae from Potiguar basin, Rio Grande do Norte, Northeastern Brazil

    OpenAIRE

    Cocentino,Adilma de Lourdes Montenegro; Fujii,Mutue Toyota; Reis,Thiago Nogueira de Vasconcelos; Guimarães-Barros,Nathalia Cristina; Rocha,Marcia de França; Neumann-Leitão,Sigrid

    2010-01-01

    Diversity and distribution pattern of the infralittoral green macroalgae at Potiguar basin, Rio Grande do Norte, Northeastern Brazil were analyzed from material collected at depths varying from 2 to 100 m. Collections were carried out with two types of dredges during four campaigns: July 2002, May and November 2003 and May 2004 at 43 stations. Chlorophyta is represented by 54 species, five varieties and three forms. The most representative family is Caulerpaceae, and the most diverse genus is...

  7. Diversity of palatal rugae patterns and their reliability in sex discrimination in a South Indian population

    Directory of Open Access Journals (Sweden)

    Sai Madhavi Nallamilli

    2015-01-01

    Full Text Available Introduction and Aims: Array of palatal rugae in the realm of forensic odontology has been constantly explored owing to their individual uniqueness and resistance to postmortem procedures, while their scope in sex determination and racial profiling remains understated. In this context, the present study aimed to record the diversity of palatal rugae patterns in a South Indian population. Materials and Methods: A descriptive cross-sectional study was conducted among people who reported to the outpatient department of a dental institution. Sample comprised a total of 200 subjects divided into two groups of 100 each, based upon gender. Impressions of anterior maxilla were made of all the study subjects and casts obtained subsequently. Outline of palatal rugae pattern was traced on these models and the data computed. Z test and unpaired t-test were used for statistical analysis and the probability value calculated. In addition, logistic regression analysis was performed to estimate the accuracy of sex allocation. Results: The shape of rugae exhibited highly significant sex difference in the curved type, which was found to be higher in males, and in the wavy type which was higher in females, enabling sex differentiation using palatal rugae patterns. Logistic regression analysis predicted high power of sex allocation for males rather than females in the study population. Conclusion: This study highlighted the uniqueness and greater sex discrimination potential of curved shape of palatal rugae in categorizing males of South Indian population, substantiating their use in the identification of deceased, by relating the antemortem and postmortem dental records.

  8. Diversity of chasmophytes in the vascular flora of Greece: floristic analysis and phytogeographical patterns

    Directory of Open Access Journals (Sweden)

    Panitsa Maria

    2017-10-01

    Full Text Available Cliffs are among the environments with the most adverse conditions for living organisms because of the limited availability of soil, moisture, and nutrients, and owing to the harsh conditions of exposure. They constitute shelters for rare, endemic, and range-restricted plant taxa. A main database has been prepared which includes vascular plant taxa that are obligate or facultative chasmophytes and also contains information about their life form, chorology, protection status, occurrence in more than 135 places such as cliffs, gorges, or open rocky habitats, and their geographical distribution in the 13 phytogeographical regions of Greece based on available floristic, vegetation, and phytosociological literature and on the authors' own collections and observations. The paper presents an analysis of the total diversity of cliff plant species, as well as the diversity of obligate chasmophytic plant species, endemics, and range-restricted taxa, in addition to the results of studying the distribution patterns of different subsets of plant taxa in the different phytogeographical regions of Greece. Hemicryptophytes and chamaephytes are the dominant life forms of the chasmophytic taxa. Among 935 species and subspecies registered, 476 are obligate chasmophytes, of which the majority are Greek endemics. Hierarchical cluster analysis of different subsets of plant taxa revealed affinities of the cliff flora of different phytogeographical regions. Additionally, 15 chasmophytic taxa mentioned in Annexes II, IV, and V of EEC Directive 92/43 belong to the cliff flora, of which 10 are obligate chasmophytes and nine have a priority for protection. Eighteen taxa are included in the IUCN Red List of Threatened Species, of which four are critically endangered (CR, seven are vulnerable (VU, and three are endangered (EN. The distinct correlation between endemism and chasmophytic ecology is emphasized, since a detailed understanding of the local distribution and

  9. Diversity of Histologic Patterns and Expression of Cytoskeletal Proteins in Canine Skeletal Osteosarcoma.

    Science.gov (United States)

    Nagamine, E; Hirayama, K; Matsuda, K; Okamoto, M; Ohmachi, T; Kadosawa, T; Taniyama, H

    2015-09-01

    Osteosarcoma (OS), the most common bone tumor, includes OS of the head (OSH) and appendicular OS (OSA). In dogs, it is classified into 6 histologic subtypes: osteoblastic, chondroblastic, fibroblastic, telangiectatic, giant cell, and poorly differentiated. This study investigated the significance of the histologic classification relevant to clinical outcome and the histologic and immunohistochemical relationships between pleomorphism and expression of cytoskeletal proteins in 60 cases each of OSH and OSA. Most neoplasms exhibited histologic diversity, and 64% of OS contained multiple subtypes. In addition to the above 6 subtypes, myxoid, round cell, and epithelioid subtypes were observed. Although the epithelioid subtypes were observed in only OSH, no significant difference in the frequency of other subtypes was observed. Also, no significant relevance was observed between the clinical outcome and histologic subtypes. Cytokeratin (CK) was expressed in both epithelioid and sarcomatoid tumor cells in various subtypes, and all CK-positive tumor cells also expressed vimentin. Vimentin and α-smooth muscle actin (SMA) were expressed in all subtypes. A few SMA-positive spindle-shaped tumor cells exhibited desmin expression. Glial fibrillary acidic protein-positive tumor cells were observed in many subtypes, and some of these cells showed neurofilament expression. Although OSH exhibited significantly stronger immunoreactivity for SMA than OSA, no significant difference in other cytoskeletal proteins was observed. Some tumor cells had cytoskeletal protein expression compatible with the corresponding histologic subtypes, such as CK in the epithelioid subtype and SMA in the fibroblastic subtype. Thus, canine skeletal OS is composed of pleomorphic and heterogenous tumor cells as is reflected in the diversity of histologic patterns and expression of cytoskeletal proteins. © The Author(s) 2015.

  10. Long-Distance Dispersal Shaped Patterns of Human Genetic Diversity in Eurasia.

    Science.gov (United States)

    Alves, Isabel; Arenas, Miguel; Currat, Mathias; Sramkova Hanulova, Anna; Sousa, Vitor C; Ray, Nicolas; Excoffier, Laurent

    2016-04-01

    Most previous attempts at reconstructing the past history of human populations did not explicitly take geography into account or considered very simple scenarios of migration and ignored environmental information. However, it is likely that the last glacial maximum (LGM) affected the demography and the range of many species, including our own. Moreover, long-distance dispersal (LDD) may have been an important component of human migrations, allowing fast colonization of new territories and preserving high levels of genetic diversity. Here, we use a high-quality microsatellite data set genotyped in 22 populations to estimate the posterior probabilities of several scenarios for the settlement of the Old World by modern humans. We considered models ranging from a simple spatial expansion to others including LDD and a LGM-induced range contraction, as well as Neolithic demographic expansions. We find that scenarios with LDD are much better supported by data than models without LDD. Nevertheless, we show evidence that LDD events to empty habitats were strongly prevented during the settlement of Eurasia. This unexpected absence of LDD ahead of the colonization wave front could have been caused by an Allee effect, either due to intrinsic causes such as an inbreeding depression built during the expansion or due to extrinsic causes such as direct competition with archaic humans. Overall, our results suggest only a relatively limited effect of the LGM contraction on current patterns of human diversity. This is in clear contrast with the major role of LDD migrations, which have potentially contributed to the intermingled genetic structure of Eurasian populations. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  11. Patterns of plant diversity loss and species turnover resulting from land abandonment and intensification in semi-natural grasslands.

    Science.gov (United States)

    Uchida, Kei; Koyanagi, Tomoyo F; Matsumura, Toshikazu; Koyama, Asuka

    2018-07-15

    Land-use changes cause biodiversity loss in semi-natural ecosystems worldwide. Biotic homogenization has led to biodiversity loss, mainly through declines in species composition turnover. Elucidating patterns of turnover in species composition could enhance our understanding of how anthropogenic activities affect community assembly. Here, we focused on whether the decreasing patterns in plant diversity and turnover of species composition resulting from land-use change vary in two regions. We estimated the species diversity and composition of semi-natural grasslands surrounding paddy fields in satoyama landscapes. We examined the differences in species diversity and composition across three land-use types (abandoned, traditional, and intensified) in two regions (Hyogo and Niigata Prefectures, Japan), which were characterized by different climatic conditions. We then assessed alpha-, beta-, and gamma-diversity to compare the patterns of diversity losses in the two regions as a result of land-use changes. In each region, gamma-diversity was consistently higher in the traditional sites compared to abandoned or intensified sites. The analyses revealed that most of the beta-diversity in traditional sites differed significantly from those of abandoned and intensified sites in both regions. However, the beta-diversity of total and perennial species did not differ between traditional and abandoned sites in the Hyogo region. We noted that the beta-diversity of total and perennial species in intensified sites was much lower than that in the traditional sites of the Niigata region. Overall, the patterns of alpha- and gamma-diversity loss were similar in both study regions. Although the biotic homogenization was caused by intensified land-use in the Niigata region, this hypothesis did not completely explain the loss of biodiversity in the abandoned sites in the Hyogo region. The present study contributes to the growing body of work investigating changes in biodiversity as a

  12. Transgenerational effects of the endocrine disruptor vinclozolin on the methylation pattern of imprinted genes in the mouse sperm.

    Science.gov (United States)

    Stouder, Christelle; Paoloni-Giacobino, Ariane

    2010-02-01

    Endocrine-disrupting chemicals (EDCs), among which is the antiandrogen vinclozolin (VCZ), have been reported to affect the male reproductive system. In this study, VCZ was administered to pregnant mice at the time of embryo sex determination, and its possible effects on the differentially methylated domains (DMDs) of two paternally (H19 and Gtl2) and three maternally (Peg1, Snrpn, and Peg3) imprinted genes were tested in the male offspring. The CpGs methylation status within the five gene DMDs was analyzed in the sperm, tail, liver, and skeletal muscle DNAs by pyrosequencing. In the sperm of controls, the percentages of methylated CpGs were close to the theoretical values of 100 and 0% in paternally or maternally imprinted genes respectively. VCZ decreased the percentages of methylated CpGs of H19 and Gtl2 (respective values 83.1 and 91.5%) and increased those of Peg1, Snrpn, and Peg3 (respective values 11.3, 18.3, and 11.2%). The effects of VCZ were transgenerational, but they disappeared gradually from F1 to F3. The mean sperm concentration of the VCZ-administered female offspring was only 56% of that of the controls in the F1 offspring, and it was back to normal values in the F2 and F3 offspring. In the somatic cells of controls, the percentages of methylated CpGs were close to the theoretical value of 50% and, surprisingly, VCZ altered the methylation of Peg3. We propose that the deleterious effects of VCZ on the male reproductive system are mediated by imprinting defects in the sperm. The reported effects of EDCs on human male spermatogenesis might be mediated by analogous imprinting alterations.

  13. Nearly a decade-long repeatable seasonal diversity patterns of bacterioplankton communities in the eutrophic Lake Donghu (Wuhan, China)

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Qingyun [Environmental Microbiome Research Center and the School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou China; Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan China; Stegen, James C. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA USA; Yu, Yuhe [Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan China; Deng, Ye [CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing China; Li, Xinghao [Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan China; Wu, Shu [Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan China; Dai, Lili [Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan China; Zhang, Xiang [Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan China; Li, Jinjin [Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan China; Wang, Chun [Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan China; Ni, Jiajia [Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan China; Li, Xuemei [Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan China; Hu, Hongjuan [Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan China; Xiao, Fanshu [Environmental Microbiome Research Center and the School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou China; Feng, Weisong [Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan China; Ning, Daliang [Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman OK USA; He, Zhili [Environmental Microbiome Research Center and the School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou China; Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman OK USA; Van Nostrand, Joy D. [Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman OK USA; Wu, Liyou [Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman OK USA; Zhou, Jizhong [Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman OK USA; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing China; Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley CA USA

    2017-05-21

    Uncovering which environmental factors have the greatest influence on community diversity patterns and how ecological processes govern community turnover are key questions related to understanding community assembly mechanisms. Although we have good understanding of plant and animal community assembly, the mechanisms regulating diversity patterns of aquatic bacterial communities in lake ecosystems remains poorly understood. Here we present nearly a decade-long time-series study of bacterioplankton communities from the eutrophic Lake Donghu (Wuhan, China) using 16S rRNA gene amplicon sequencing. We found strong repeatable seasonal patterns for the overall community, common (detected in more than 50% samples) and dominant bacterial taxa (relative abundance > 1%). Moreover, community composition tracked the seasonal temperature gradient, indicating that temperature is an important environmental factor controlling observed diversity patterns. Total phosphorus also contributed significantly to the seasonal shifts in bacterioplankton composition. However, any spatial pattern across the main lake areas was overwhelmed by temporal variability in this eutrophic lake system. Phylogenetic analysis further indicated that 75%-82% of community turnover was governed by homogeneous selection, suggesting that the bacterioplankton communities are mainly controlled by niche-based processes. However, dominant niches available within seasons might be occupied by similar combinations of bacterial taxa with modest dispersal rates throughout this lake system. This study gives us important insights into community assembly and seasonal turnover of lake bacterioplankton, it may be also useful to predict temporal patterns of other planktonic communities.

  14. Diversity of developmental patterns in achelate lobsters-today and in the Mesozoic.

    Science.gov (United States)

    Haug, Joachim T; Audo, Denis; Charbonnier, Sylvain; Haug, Carolin

    2013-11-01

    Modern achelate lobsters, slipper and spiny lobsters, have a specific post-embryonic developmental pattern with the following phases: phyllosoma, nisto (slipper lobsters) or puerulus (spiny lobsters), juvenile and adult. The phyllosoma is a peculiar larva, which transforms through a metamorphic moult into another larval form, the nisto or puerulus which largely resembles the juvenile. Unlike the nisto and puerulus, the phyllosoma is characterised by numerous morphological differences to the adult, e.g. a thin head shield, elongate appendages, exopods on these appendages and a special claw. Our reinvestigation of the 85 million years old fossil "Eryoneicus sahelalmae" demonstrates that it represents an unusual type of achelatan lobster larva, characterised by a mixture of phyllosoma and post-phyllosoma characters. We ascribe it to its own genus: Polzicaris nov. gen. We study its significance by comparisons with other cases of Mesozoic fossil larvae also characterised by a mixture of characters. Accordingly, all these larvae are interpreted as ontogenetic intermediates between phyllosoma and post-phyllosoma morphology. Remarkably, most of the larvae show a unique mixture of retained larval and already developed post-larval features. Considering the different-and incompatible-mixture of characters of each of these larvae and their wide geographical and temporal distribution, we interpret all these larvae as belonging to distinct species. The particular character combinations in the different larvae make it currently difficult to reconstruct an evolutionary scenario with a stepwise character acquisition. Yet, it can be concluded that a larger diversity of larval forms and developmental patterns occurred in Mesozoic than in modern faunas.

  15. Patterns of diversity in soft-bodied meiofauna: dispersal ability and body size matter.

    Science.gov (United States)

    Curini-Galletti, Marco; Artois, Tom; Delogu, Valentina; De Smet, Willem H; Fontaneto, Diego; Jondelius, Ulf; Leasi, Francesca; Martínez, Alejandro; Meyer-Wachsmuth, Inga; Nilsson, Karin Sara; Tongiorgi, Paolo; Worsaae, Katrine; Todaro, M Antonio

    2012-01-01

    Biogeographical and macroecological principles are derived from patterns of distribution in large organisms, whereas microscopic ones have often been considered uninteresting, because of their supposed wide distribution. Here, after reporting the results of an intensive faunistic survey of marine microscopic animals (meiofauna) in Northern Sardinia, we test for the effect of body size, dispersal ability, and habitat features on the patterns of distribution of several groups. As a dataset we use the results of a workshop held at La Maddalena (Sardinia, Italy) in September 2010, aimed at studying selected taxa of soft-bodied meiofauna (Acoela, Annelida, Gastrotricha, Nemertodermatida, Platyhelminthes and Rotifera), in conjunction with data on the same taxa obtained during a previous workshop hosted at Tjärnö (Western Sweden) in September 2007. Using linear mixed effects models and model averaging while accounting for sampling bias and potential pseudoreplication, we found evidence that: (1) meiofaunal groups with more restricted distribution are the ones with low dispersal potential; (2) meiofaunal groups with higher probability of finding new species for science are the ones with low dispersal potential; (3) the proportion of the global species pool of each meiofaunal group present in each area at the regional scale is negatively related to body size, and positively related to their occurrence in the endobenthic habitat. Our macroecological analysis of meiofauna, in the framework of the ubiquity hypothesis for microscopic organisms, indicates that not only body size but mostly dispersal ability and also occurrence in the endobenthic habitat are important correlates of diversity for these understudied animals, with different importance at different spatial scales. Furthermore, since the Western Mediterranean is one of the best-studied areas in the world, the large number of undescribed species (37%) highlights that the census of marine meiofauna is still very far

  16. Beyond the average: Diverse individual migration patterns in a population of mesopelagic jellyfish

    KAUST Repository

    Kaartvedt, Stein; Titelman, Josefin; Rø stad, Anders; Klevjer, Thor A.

    2011-01-01

    We examined the diel behavior among the jellyfish Periphylla periphylla in Lurefjorden, Norway in a sampling campaign and by a > 3-month continuous acoustic study. Jellyfish distribution and behavior were recorded by an upward-facing, bottom-mounted echo sounder at 280-m depth. The population was typically divided into four groups, each with different behavior. Individuals of behavioral Mode 1 undertook synchronous diel vertical migrations (DVM) within the upper 100 m. Individuals of behavioral Mode 2, stayed at ~ 160-200-m depth during the day, and also exhibited synchronized DVM, ascending at dusk and descending at dawn. The smaller individuals of behavioral Mode 3 swam continuously up and down throughout both day and night, yet occurred below Mode 2 individuals in daytime (~ 200 m-bottom), while their vertical range encompassed the entire water column during night. Mode 4 behavior was displayed by large jellyfish located between ~ 130 m and the bottom. These animals shifted between remaining motionless and relocating in rapid steps during both day and night. These four main behavioral patterns persisted throughout the registration period, although the synchronously migrating Mode 2 behavior became weaker in spring. This acoustic study has unveiled more diverse migration behaviors than previously derived from net sampling and remote-operated vehicles methods and emphasizes the importance of studying individuals. DVM is complex because individuals in a plankton population may simultaneously engage in a range of various contrasting behaviors.

  17. Connectivity to the surface determines diversity patterns in subsurface aquifers of the Fennoscandian shield.

    Science.gov (United States)

    Hubalek, Valerie; Wu, Xiaofen; Eiler, Alexander; Buck, Moritz; Heim, Christine; Dopson, Mark; Bertilsson, Stefan; Ionescu, Danny

    2016-10-01

    Little research has been conducted on microbial diversity deep under the Earth's surface. In this study, the microbial communities of three deep terrestrial subsurface aquifers were investigated. Temporal community data over 6 years revealed that the phylogenetic structure and community dynamics were highly dependent on the degree of isolation from the earth surface biomes. The microbial community at the shallow site was the most dynamic and was dominated by the sulfur-oxidizing genera Sulfurovum or Sulfurimonas at all-time points. The microbial community in the meteoric water filled intermediate aquifer (water turnover approximately every 5 years) was less variable and was dominated by candidate phylum OD1. Metagenomic analysis of this water demonstrated the occurrence of key genes for nitrogen and carbon fixation, sulfate reduction, sulfide oxidation and fermentation. The deepest water mass (5000 year old waters) had the lowest taxon richness and surprisingly contained Cyanobacteria. The high relative abundance of phylogenetic groups associated with nitrogen and sulfur cycling, as well as fermentation implied that these processes were important in these systems. We conclude that the microbial community patterns appear to be shaped by the availability of energy and nutrient sources via connectivity to the surface or from deep geological processes.

  18. Patterns of genetic diversity of local pig populations in the State of Pernambuco, Brazil

    Directory of Open Access Journals (Sweden)

    Elizabete Cristina da Silva

    2011-08-01

    Full Text Available This study estimated the genetic diversity and structure of 12 genetic groups (GG of locally adapted and specialized pigs in the state of Pernambuco using 22 microsatellite markers. Nine locally adapted breeds (Baé, Caruncho, Canastra, Canastrão, Mamelado, Moura, Nilo, Piau and UDB (Undefined Breed and 3 specialized breeds (Duroc, Landrace and Large White, totaling 190 animals, were analyzed. The Analysis of Molecular Variance (AMOVA showed that 3.2% of the total variation was due to differences between genetic groups, and 3.6% to differences between local and commercial pigs. One hundred and ninety eight alleles were identified and apart from the Large White breed, all GG presented Hardy-Weinberg Equilibrium deviations for some loci. The total and effective allele means were lower for Duroc (3.65 and 3.01 and higher for UDB (8.89 and 4.53 and Canastra (8.61 and 4.58. Using Nei's standard genetic distance and the UPGMA method, it was possible to observe that the Landrace breed was grouped with the local genetic groups Canastra, Moura, Canastrão, Baé and Caruncho. Due to the complex admixture pattern, the genetic variability of the 12 genetic groups can be analyzed by distributing the individuals into two populations as demonstrated by a Bayesian analysis, corroborating the results from AMOVA, which revealed a low level of genetic differentiation between the inferred populations.

  19. Beyond the average: Diverse individual migration patterns in a population of mesopelagic jellyfish

    KAUST Repository

    Kaartvedt, Stein

    2011-11-01

    We examined the diel behavior among the jellyfish Periphylla periphylla in Lurefjorden, Norway in a sampling campaign and by a > 3-month continuous acoustic study. Jellyfish distribution and behavior were recorded by an upward-facing, bottom-mounted echo sounder at 280-m depth. The population was typically divided into four groups, each with different behavior. Individuals of behavioral Mode 1 undertook synchronous diel vertical migrations (DVM) within the upper 100 m. Individuals of behavioral Mode 2, stayed at ~ 160-200-m depth during the day, and also exhibited synchronized DVM, ascending at dusk and descending at dawn. The smaller individuals of behavioral Mode 3 swam continuously up and down throughout both day and night, yet occurred below Mode 2 individuals in daytime (~ 200 m-bottom), while their vertical range encompassed the entire water column during night. Mode 4 behavior was displayed by large jellyfish located between ~ 130 m and the bottom. These animals shifted between remaining motionless and relocating in rapid steps during both day and night. These four main behavioral patterns persisted throughout the registration period, although the synchronously migrating Mode 2 behavior became weaker in spring. This acoustic study has unveiled more diverse migration behaviors than previously derived from net sampling and remote-operated vehicles methods and emphasizes the importance of studying individuals. DVM is complex because individuals in a plankton population may simultaneously engage in a range of various contrasting behaviors.

  20. Identification and characterization of locus specific methylation patterns within novel loci undergoing hypermethylation during breast cancer pathogenesis

    DEFF Research Database (Denmark)

    Wojdacz, Tomasz K; Windeløv, Johanne Agerlin; Thestrup, Britta B

    2014-01-01

    (DMRs) was validated using Methylation Sensitive High Resolution Melting (MS-HRM) in a case control study on a panel of breast carcinomas (N = 275) and non-malignant controls (N = 74). RESULTS: Based on microarray results we selected 19 DMRs for large-scale screening of cases and controls. Analysis...

  1. Dietary patterns and diet quality among diverse older adults: The University of Alabama at Birmingham study of aging

    Science.gov (United States)

    Objectives: To characterize dietary patterns among a diverse sample of older adults (= 65 years). Design: Cross-sectional. Setting: Five counties in west central Alabama. Participants: Community-dwelling Medicare beneficiaries (N=416; 76.8 ± 5.2 years, 56% female, 39% African American) in the Univer...

  2. Diversity patterns in the flora of the Campo-Ma'an rain forest, Cameroon: do tree species tell it all?

    NARCIS (Netherlands)

    Tchouto, M.G.P.; Boer, de W.F.; Wilde, de J.J.F.E.; Maesen, van der L.J.G.

    2006-01-01

    This study describes diversity patterns in the flora of the Campo-Ma¿an rain forest, in south Cameroon. In this area, the structure and composition of the forests change progressively from the coastal forest on sandy shorelines through the lowland evergreen forest rich in Caesalpinioideae with

  3. Spatial patterns of littoral zooplankton assemblages along a salinity gradient in a brackish sea: A functional diversity perspective

    Science.gov (United States)

    Helenius, Laura K.; Leskinen, Elina; Lehtonen, Hannu; Nurminen, Leena

    2017-11-01

    The distribution patterns and diversity of littoral zooplankton are both key baseline information for understanding the functioning of coastal ecosystems, and for identifying the mechanisms by which the impacts of recently increased eutrophication are transferred through littoral food webs. In this study, zooplankton community structure and diversity along a shallow coastal area of the northern Baltic Sea were determined in terms of horizontal environmental gradients. Spatial heterogeneity of the zooplankton community was examined along the gradient. Altogether 31 sites in shallow sandy bays on the coast of southwest Finland were sampled in the summer periods of 2009 and 2010 for zooplankton and environmental variables (surface water temperature, salinity, turbidity, wave exposure, macrophyte coverage, chlorophyll a and nutrients). Zooplankton diversity was measured as both taxonomic as well as functional diversity, using trait-based classification of planktonic crustaceans. Salinity, and to a lesser extent turbidity and temperature, were found to be the main predictors of the spatial patterns and functional diversity of the zooplankton community. Occurrence of cyclopoid copepods, as well as abundances of the calanoid copepod genus Acartia and the rotifer genus Keratella were found to be key factors in differentiating sites along the gradient. As far as we know, this is the first extensive study of functional diversity in Baltic Sea coastal zooplankton communities.

  4. Spatial and temporal fish diversity patterns from Santa Catarina Island, Brazil

    Directory of Open Access Journals (Sweden)

    André Cattani

    2015-11-01

    Full Text Available The Santa Catarina Island has a mosaic of ecosystems, with great importance for the fishes. There is the presence of estuaries, lagoons, mangroves and sandy beaches in the same island. Thus, the objectives of this study were to evaluate the spatio and temporal fish diversity patterns in estuaries, lagoons and beach systems of Santa Catarina Island, Santa Catarina, Brazil. Fish data collected between 1983 to 2011 in the baía Norte, saco dos Limões, Itacorubi and Ratones mangroves, Conceição lagoon and Índio beach was analyzed. Fish were sampled with different gear techniques. In the North Bay and saco dos Limões individuals were caught by trawl, but in the mangroves and lagoon were used gillnets, cast nets and dip nets. In the Índio beach the fishes were collected using fyke nets. For each local, species accumulation curves were plotted to compare the observed pattern with modelled data, using first order Jackknife estimator. Species richness differences among locals and seasons were tested using PERMANOVA, followed by a canonical analysis of principal coordinates (CAP. To assess the taxonomic structures at each location, the average taxonomic distinctness (AvTD and the variation in taxonomic distinctness (VarTD were also used. Higher average species richness was found in the saco dos Limões (mean ± SE; 59.8 ± 2.5, followed by Índio Beach (55.7 ± 2.7, Conceição lagoon (52.3 ± 6.4, North bay (45.0 ± 2.5, mangrove Itacorubi (34.5 ± 3.2 and mangrove Ratones (30.8 ± 3.8. No significate differences for the taxonomic patterns were observed between seasons. Furthermore the hereby data suggest that the fish assemblages of the inner portion of the island of Santa Catarina are mainly formed by estuarine and marine fish, but differing in species richness among locals.

  5. Determining the Diversity and Species Abundance Patterns in Arctic Soils using Rational Methods for Exploring Microbial Diversity

    Science.gov (United States)

    Ovreas, L.; Quince, C.; Sloan, W.; Lanzen, A.; Davenport, R.; Green, J.; Coulson, S.; Curtis, T.

    2012-12-01

    Arctic microbial soil communities are intrinsically interesting and poorly characterised. We have inferred the diversity and species abundance distribution of 6 Arctic soils: new and mature soil at the foot of a receding glacier, Arctic Semi Desert, the foot of bird cliffs and soil underlying Arctic Tundra Heath: all near Ny-Ålesund, Spitsbergen. Diversity, distribution and sample sizes were estimated using the rational method of Quince et al., (Isme Journal 2 2008:997-1006) to determine the most plausible underlying species abundance distribution. A log-normal species abundance curve was found to give a slightly better fit than an inverse Gaussian curve if, and only if, sequencing error was removed. The median estimates of diversity of operational taxonomic units (at the 3% level) were 3600-5600 (lognormal assumed) and 2825-4100 (inverse Gaussian assumed). The nature and origins of species abundance distributions are poorly understood but may yet be grasped by observing and analysing such distributions in the microbial world. The sample size required to observe the distribution (by sequencing 90% of the taxa) varied between ~ 106 and ~105 for the lognormal and inverse Gaussian respectively. We infer that between 5 and 50 GB of sequencing would be required to capture 90% or the metagenome. Though a principle components analysis clearly divided the sites into three groups there was a high (20-45%) degree of overlap in between locations irrespective of geographical proximity. Interestingly, the nearest relatives of the most abundant taxa at a number of most sites were of alpine or polar origin. Samples plotted on first two principal components together with arbitrary discriminatory OTUs

  6. Fine and Coarse-Scale Patterns of Vegetation Diversity on Reclaimed Surface Mine-land Over a 40-Year Chronosequence.

    Science.gov (United States)

    Bohrer, Stefanie L; Limb, Ryan F; Daigh, Aaron L; Volk, Jay M; Wick, Abbey F

    2017-03-01

    Rangelands are described as heterogeneous, due to patterning in species assemblages and productivity that arise from species dispersal and interactions with environmental gradients and disturbances across multiple scales. The objectives of rangeland reclamation are typically vegetation establishment, plant community productivity, and soil stability. However, while fine-scale diversity is often promoted through species-rich seed mixes, landscape heterogeneity and coarse-scale diversity are largely overlooked. Our objectives were to evaluate fine and coarse-scale vegetation patterns across a 40-year reclamation chronosequence on reclaimed surface coalmine lands. We hypothesized that both α-diversity and β-diversity would increase and community patch size and species dissimilarity to reference sites would decrease on independent sites over 40 years. Plant communities were surveyed on 19 post-coalmine reclaimed sites and four intact native reference sites in central North Dakota mixed-grass prairie. Our results showed no differences in α or β-diversity and plant community patch size over the 40-year chronosequence. However, both α-diversity and β-diversity on reclaimed sites was similar to reference sites. Native species establishment was limited due to the presence of non-native species such as Kentucky bluegrass (Poa pratensis) on both the reclaimed and reference sites. Species composition was different between reclaimed and reference sites and community dissimilarity increased on reclaimed sites over the 40-year chronosequence. Plant communities resulting from reclamation followed non-equilibrium succession, even with consistent seeds mixes established across all reclaimed years. This suggests post-reclamation management strategies influence species composition outcomes and land management strategies applied uniformly may not increase landscape-level diversity.

  7. Obesity induced by a pair-fed high fat sucrose diet: methylation and expression pattern of genes related to energy homeostasis

    Directory of Open Access Journals (Sweden)

    Campión Javier

    2010-06-01

    Full Text Available Abstract Background The expression of some genes controlling energy homeostasis could be regulated by epigenetic mechanisms that may play a role in body weight regulation. Thus, it is known that various nutritional factors affect DNA methylation. In order to assess whether the macronutrient composition of the diet could be related to the epigenetic regulation of gene expression and with obesity development, we investigated the effects on methylation and expression patterns of two pair-fed isocaloric diets in rats: control (rich in starch and HFS (rich in fat and sucrose. Results The pair-fed HFS diet induced higher weight gain and adiposity as compared to the controls as well as liver triglyceride accumulation and oxidative stress. Feeding the HFS diet impaired glucose tolerance and serum triglycerides and cholesterol. Liver glucokinase expression, a key glycolytic gene, remained unaltered, as well as the mRNA values of fatty acid synthase and NADH dehydrogenase (ubiquinone 1 beta subcomplex, 6 (NDUFB6 in liver and visceral adipocytes, which regulate lipogenesis and mitochondrial oxidative metabolism, respectively. Liver expression of hydroxyacyl-coenzyme A dehydrogenase (HADHB, a key gene of β-oxidation pathway, was higher in the HFS-fed animals. However, the methylation status of CpG islands in HADHB and glucokinase genes remained unchanged after feeding the HFS diet. Conclusions These results confirm that the distribution and type of macronutrients (starch vs. sucrose, and percent of fat influence obesity onset and the associated metabolic complications. HFS diets produce obesity independently of total energy intake, although apparently no epigenetic (DNA methylation changes accompanied the modifications observed in gene expression.

  8. Epigenome-wide DNA methylation analysis in siblings and monozygotic twins discordant for sporadic Parkinson's disease revealed different epigenetic patterns in peripheral blood mononuclear cells.

    Science.gov (United States)

    Kaut, Oliver; Schmitt, Ina; Tost, Jörg; Busato, Florence; Liu, Yi; Hofmann, Per; Witt, Stephanie H; Rietschel, Marcella; Fröhlich, Holger; Wüllner, Ullrich

    2017-01-01

    Numerous studies have elucidated the genetics of Parkinson's disease; however, the aetiology of the majority of sporadic cases has not yet been resolved. We hypothesized that epigenetic variations could be associated with PD and evaluated the DNA methylation pattern in PD patients compared to brothers or twins without PD. The methylation of DNA from peripheral blood mononuclear cells of 62 discordant siblings including 24 monozygotic twins was characterized with Illumina DNA Methylation 450K bead arrays and subsequently validated in two independent cohorts: 221 PD vs. 227 healthy individuals (cohort 1) applying Illumina's VeraCode and 472 PD patients vs. 487 controls (cohort 2) using pyrosequencing. We choose a delta beta of >15 % and selected 62 differentially methylated CpGs in 51 genes from the discordant siblings. Among them, three displayed multiple CpGs per gene: microRNA 886 (MIR886, 10 CpGs), phosphodiesterase 4D (PDE4D, 2 CpGs) and tripartite motif-containing 34 (TRIM34, 2 CpGs). PDE4D was confirmed in both cohorts (p value 2.44e-05). In addition, for biomarker construction, we used the penalized logistic regression model, resulting in a signature of eight CpGs with an AUC of 0.77. Our findings suggest that a distinct level of PD susceptibility stems from individual, epigenetic modifications of specific genes. We identified a signature of CpGs in blood cells that could separate control from disease with a reasonable discriminatory power, holding promise for future epigenetically based biomarker development.

  9. Mapping of the methylation pattern of the hMSH2 promoter in colon cancer, using bisulfite genomic sequencing

    Directory of Open Access Journals (Sweden)

    Zhang Hua

    2006-08-01

    Full Text Available Abstract The detailed methylation status of CpG sites in the promoter region of hMSH2 gene has yet not to be reported. We have mapped the complete methylation status of the hMSH2 promoter, a region that contains 75 CpG sites, using bisulfite genomic sequencing in 60 primary colorectal cancers. And the expression of hMSH2 was detected by immunohistochemistry. The hypermethylation of hMSH2 was detected in 18.33% (11/60 of tumor tissues. The protein of hMSH2 was detected in 41.67% (25/60 of tumor tissues. No hypermethylation of hMSH2 was detected in normal tissues. The protein of hMSH2 was detected in all normal tissues. Our study demonstrated that hMSH2 hypermethylation and protein expression were associated with the development of colorectal cancer.

  10. Patterns of diversity of the Rissoidae (Mollusca: Gastropoda) in the Atlantic and the Mediterranean region.

    Science.gov (United States)

    Ávila, Sérgio P; Goud, Jeroen; de Frias Martins, António M

    2012-01-01

    The geographical distribution of the Rissoidae in the Atlantic Ocean and Mediterranean Sea was compiled and is up-to-date until July 2011. All species were classified according to their mode of larval development (planktotrophic and nonplanktotrophic), and bathymetrical zonation (shallow species--those living between the intertidal and 50 m depth, and deep species--those usually living below 50 m depth). 542 species of Rissoidae are presently reported to the Atlantic Ocean and the Mediterranean Sea, belonging to 33 genera. The Mediterranean Sea is the most diverse site, followed by Canary Islands, Caribbean, Portugal, and Cape Verde. The Mediterranean and Cape Verde Islands are the sites with higher numbers of endemic species, with predominance of Alvania spp. in the first site, and of Alvania and Schwartziella at Cape Verde. In spite of the large number of rissoids at Madeira archipelago, a large number of species are shared with Canaries, Selvagens, and the Azores, thus only about 8% are endemic to the Madeira archipelago. Most of the 542-rissoid species that live in the Atlantic and in the Mediterranean are shallow species (323), 110 are considered as deep species, and 23 species are reported in both shallow and deep waters. There is a predominance of nonplanktotrophs in islands, seamounts, and at high and medium latitudes. This pattern is particularly evident in the genera Crisilla, Manzonia, Onoba, Porosalvania, Schwartziella, and Setia. Planktotrophic species are more abundant in the eastern Atlantic and in the Mediterranean Sea. The results of the analysis of the probable directions of faunal flows support the patterns found by both the Parsimony Analysis of Endemicity and the geographical distribution. Four main source areas for rissoids emerge: Mediterranean, Caribbean, Canaries/Madeira archipelagos, and the Cape Verde archipelago. We must stress the high percentage of endemics that occurs in the isolated islands of Saint Helena, Tristan da Cunha, Cape

  11. Diversity and aggregation patterns of plant species in a grass community

    Directory of Open Access Journals (Sweden)

    Ran Li

    2014-09-01

    Full Text Available Both composition and aggregation patterns of species in a community are the outcome of community self-organizing. In this paper we conducted analysis on species diversity and aggregation patterns of plant species in a grass community, Zhuhai, China. According to the sampling survey, in total of 47 plant species, belonging to 16 families, were found. Compositae had 10 species (21.3%, seconded by Gramineae (9 species, 19.1%, Leguminosae (6 species, 12.8%, Cyperaceae (4 species, 8.5%, and Malvaceae (3 species, 6.4%. The results revealed that the means of aggregation indices Iδ, I and m*/m were 21.71, 15.71 and 19.89 respectively and thus individuals of most of plant species strongly followed aggregative distribution. Iwao analysis indicated that both individuals of all species and clumps of all individuals of all species followed aggregative distribution. Taylor's power law indicated that individuals of all species followed aggregative distribution and aggregation intensity strengthened as the increase of mean density. We held that the strong aggregation intensity of a species has been resulted from the strong adaptation ability to the environment, the strong interspecific competition ability and the earlier establishment of the species. Fitting goodness of the mean, I, Iδ, m*/m with probability distributions demonstrated that the mean (density, I, Iδ, and m*/m over all species followed Weibull distribution rather than normal distribution. Lophatherum gracile, Paederia scandens (Lour. Merr., Eleusine indica, and Alternanthera philoxeroides (Mart. Griseb. were mostly aggregative, and Oxalis sp., Eleocharis plantagineiformis, Vernonia cinerea (L. Less., and Sapium sebiferum (L. Roxb, were mostly uniform in the spatial distribution. Importance values (IV showed that Cynodon dactylon was the most important species, seconded by Desmodium triflorum (L. DC., Cajanus scarabaeoides (L. Benth., Paspalum scrobiculatum L., and Rhynchelytrum repens. Oxalis

  12. Patterns of Diversity of the Rissoidae (Mollusca: Gastropoda) in the Atlantic and the Mediterranean Region

    Science.gov (United States)

    Ávila, Sérgio P.; Goud, Jeroen; de Frias Martins, António M.

    2012-01-01

    The geographical distribution of the Rissoidae in the Atlantic Ocean and Mediterranean Sea was compiled and is up-to-date until July 2011. All species were classified according to their mode of larval development (planktotrophic and nonplanktotrophic), and bathymetrical zonation (shallow species—those living between the intertidal and 50 m depth, and deep species—those usually living below 50 m depth). 542 species of Rissoidae are presently reported to the Atlantic Ocean and the Mediterranean Sea, belonging to 33 genera. The Mediterranean Sea is the most diverse site, followed by Canary Islands, Caribbean, Portugal, and Cape Verde. The Mediterranean and Cape Verde Islands are the sites with higher numbers of endemic species, with predominance of Alvania spp. in the first site, and of Alvania and Schwartziella at Cape Verde. In spite of the large number of rissoids at Madeira archipelago, a large number of species are shared with Canaries, Selvagens, and the Azores, thus only about 8% are endemic to the Madeira archipelago. Most of the 542-rissoid species that live in the Atlantic and in the Mediterranean are shallow species (323), 110 are considered as deep species, and 23 species are reported in both shallow and deep waters. There is a predominance of nonplanktotrophs in islands, seamounts, and at high and medium latitudes. This pattern is particularly evident in the genera Crisilla, Manzonia, Onoba, Porosalvania, Schwartziella, and Setia. Planktotrophic species are more abundant in the eastern Atlantic and in the Mediterranean Sea. The results of the analysis of the probable directions of faunal flows support the patterns found by both the Parsimony Analysis of Endemicity and the geographical distribution. Four main source areas for rissoids emerge: Mediterranean, Caribbean, Canaries/Madeira archipelagos, and the Cape Verde archipelago. We must stress the high percentage of endemics that occurs in the isolated islands of Saint Helena, Tristan da Cunha

  13. Genomic patterns of nucleotide diversity in divergent populations of U.S. weedy rice

    Directory of Open Access Journals (Sweden)

    Olsen Kenneth M

    2010-06-01

    Full Text Available Abstract Background Weedy rice (red rice, a conspecific weed of cultivated rice (Oryza sativa L., is a significant problem throughout the world and an emerging threat in regions where it was previously absent. Despite belonging to the same species complex as domesticated rice and its wild relatives, the evolutionary origins of weedy rice remain unclear. We use genome-wide patterns of single nucleotide polymorphism (SNP variation in a broad geographic sample of weedy, domesticated, and wild Oryza samples to infer the origin and demographic processes influencing U.S. weedy rice evolution. Results We find greater population structure than has been previously reported for U.S. weedy rice, and that the multiple, genetically divergent populations have separate origins. The two main U.S. weedy rice populations share genetic backgrounds with cultivated O. sativa varietal groups not grown commercially in the U.S., suggesting weed origins from domesticated ancestors. Hybridization between weedy groups and between weedy rice and local crops has also led to the evolution of distinct U.S. weedy rice populations. Demographic simulations indicate differences among the main weedy groups in the impact of bottlenecks on their establishment in the U.S., and in the timing of divergence from their cultivated relatives. Conclusions Unlike prior research, we did not find unambiguous evidence for U.S. weedy rice originating via hybridization between cultivated and wild Oryza species. Our results demonstrate the potential for weedy life-histories to evolve directly from within domesticated lineages. The diverse origins of U.S. weedy rice populations demonstrate the multiplicity of evolutionary forces that can influence the emergence of weeds from a single species complex.

  14. Common Distribution Patterns of Marsupials Related to Physiographical Diversity in Venezuela

    Science.gov (United States)

    Ventura, Jacint; Bagaria, Guillem; Sans-Fuentes, Maria Assumpció; Pérez-Hernández, Roger

    2014-01-01

    The aim of this study is to identify significant biotic regions (groups of areas with similar biotas) and biotic elements (groups of taxa with similar distributions) for the marsupial fauna in a part of northern South America using physiographical areas as Operational Geographical Units (OGUs). We considered Venezuela a good model to elucidate this issue because of its high diversity in landscapes and the relatively vast amount of information available on the geographical distribution of marsupial species. Based on the presence-absence of 33 species in 15 physiographical sub-regions (OGUs) we identified Operational Biogeographical Units (OBUs) and chorotypes using a quantitative analysis that tested statistical significance of the resulting groups. Altitudinal and/or climatic trends in the OBUs and chorotypes were studied using a redundancy analysis. The classification method revealed four OBUs. Strong biotic boundaries separated: i) the xerophytic zone of the Continental coast (OBU I); ii) the sub-regions north of the Orinoco River (OBU III and IV); and those south to the river (OBU II). Eleven chorotypes were identified, four of which included a single species with a restricted geographic distribution. As for the other chorotypes, three main common distribution patterns have been inferred: i) species from the Llanos and/or distributed south of the Orinoco River; ii) species exclusively from the Andes; and iii) species that either occur exclusively north of the Orinoco River or that show a wide distribution throughout Venezuela. Mean altitude, evapotranspiration and precipitation of the driest month, and temperature range allowed us to characterize environmentally most of the OBUs and chorotypes obtained. PMID:24806452

  15. Common distribution patterns of marsupials related to physiographical diversity in Venezuela.

    Directory of Open Access Journals (Sweden)

    Jacint Ventura

    Full Text Available The aim of this study is to identify significant biotic regions (groups of areas with similar biotas and biotic elements (groups of taxa with similar distributions for the marsupial fauna in a part of northern South America using physiographical areas as Operational Geographical Units (OGUs. We considered Venezuela a good model to elucidate this issue because of its high diversity in landscapes and the relatively vast amount of information available on the geographical distribution of marsupial species. Based on the presence-absence of 33 species in 15 physiographical sub-regions (OGUs we identified Operational Biogeographical Units (OBUs and chorotypes using a quantitative analysis that tested statistical significance of the resulting groups. Altitudinal and/or climatic trends in the OBUs and chorotypes were studied using a redundancy analysis. The classification method revealed four OBUs. Strong biotic boundaries separated: i the xerophytic zone of the Continental coast (OBU I; ii the sub-regions north of the Orinoco River (OBU III and IV; and those south to the river (OBU II. Eleven chorotypes were identified, four of which included a single species with a restricted geographic distribution. As for the other chorotypes, three main common distribution patterns have been inferred: i species from the Llanos and/or distributed south of the Orinoco River; ii species exclusively from the Andes; and iii species that either occur exclusively north of the Orinoco River or that show a wide distribution throughout Venezuela. Mean altitude, evapotranspiration and precipitation of the driest month, and temperature range allowed us to characterize environmentally most of the OBUs and chorotypes obtained.

  16. Unexpected pattern of pearl millet genetic diversity among ethno-linguistic groups in the Lake Chad Basin.

    Science.gov (United States)

    Naino Jika, A K; Dussert, Y; Raimond, C; Garine, E; Luxereau, A; Takvorian, N; Djermakoye, R S; Adam, T; Robert, T

    2017-05-01

    Despite of a growing interest in considering the role of sociological factors in seed exchanges and their consequences on the evolutionary dynamics of agro-biodiversity, very few studies assessed the link between ethno-linguistic diversity and genetic diversity patterns in small-holder farming systems. This is key for optimal improvement and conservation of crop genetic resources. Here, we investigated genetic diversity at 17 SSR markers of pearl millet landraces (varieties named by farmers) in the Lake Chad Basin. 69 pearl millet populations, representing 27 landraces collected in eight ethno-linguistic farmer groups, were analyzed. We found that the farmers' local taxonomy was not a good proxy for population's genetic differentiation as previously shown at smaller scales. Our results show the existence of a genetic structure of pearl millet mainly associated with ethno-linguistic diversity in the western side of the lake Chad. It suggests there is a limit to gene flow between landraces grown by different ethno-linguistic groups. This result was rather unexpected, because of the highly outcrossing mating system of pearl millet, the high density of pearl millet fields all along the green belt of this Sahelian area and the fact that seed exchanges among ethno-linguistic groups are known to occur. In the eastern side of the Lake, the pattern of genetic diversity suggests a larger efficient circulation of pearl millet genes between ethno-linguistic groups that are less numerous, spatially intermixed and, for some of them, more prone to exogamy. Finally, other historical and environmental factors which may contribute to the observed diversity patterns are discussed.

  17. Regional patterns of genetic diversity in swine influenza A viruses in the United States from 2010 to 2016.

    Science.gov (United States)

    Walia, Rasna R; Anderson, Tavis K; Vincent, Amy L

    2018-04-06

    Regular spatial and temporal analyses of the genetic diversity and evolutionary patterns of influenza A virus (IAV) in swine informs control efforts and improves animal health. Initiated in 2009, the USDA passively surveils IAV in U.S. swine, with a focus on subtyping clinical respiratory submissions, sequencing at minimum the hemagglutinin (HA) and neuraminidase (NA) genes, and sharing these data publicly. In this study, our goal was to quantify and describe regional and national patterns in the genetic diversity and evolution of IAV in U.S. swine from 2010 to 2016. A comprehensive phylogenetic and epidemiological analysis of publicly available HA and NA genes generated by the USDA surveillance system collected from January 2010 to December 2016 was conducted. The dominant subtypes and genetic clades detected during the study period were H1N1 (H1-γ/1A.3.3.3, N1-classical, 29%), H1N2 (H1-δ1/1B.2.2, N2-2002, 27%), and H3N2 (H3-IV-A, N2-2002, 15%), but many other minor clades were also maintained. Year-round circulation was observed, with a primary epidemic peak in October-November and a secondary epidemic peak in March-April. Partitioning these data into 5 spatial zones revealed that genetic diversity varied regionally and was not correlated with aggregated national patterns of HA/NA diversity. These data suggest that vaccine composition and control efforts should consider IAV diversity within swine production regions in addition to aggregated national patterns. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  18. Elevational Gradients in Bird Diversity in the Eastern Himalaya: An Evaluation of Distribution Patterns and Their Underlying Mechanisms

    Science.gov (United States)

    Acharya, Bhoj Kumar; Sanders, Nathan J.; Vijayan, Lalitha; Chettri, Basundhara

    2011-01-01

    Background Understanding diversity patterns and the mechanisms underlying those patterns along elevational gradients is critically important for conservation efforts in montane ecosystems, especially those that are biodiversity hotspots. Despite recent advances, consensus on the underlying causes, or even the relative influence of a suite of factors on elevational diversity patterns has remained elusive. Methods and Principal Findings We examined patterns of species richness, density and range size distribution of birds, and the suite of biotic and abiotic factors (primary productivity, habitat variables, climatic factors and geometric constraints) that governs diversity along a 4500-m elevational gradient in the Eastern Himalayan region, a biodiversity hotspot within the world's tallest mountains. We used point count methods for sampling birds and quadrats for estimating vegetation at 22 sites along the elevational gradient. We found that species richness increased to approximately 2000 m, then declined. We found no evidence that geometric constraints influenced this pattern, whereas actual evapotranspiration (a surrogate for primary productivity) and various habitat variables (plant species richness, shrub density and basal area of trees) accounted for most of the variation in bird species richness. We also observed that ranges of most bird species were narrow along the elevation gradient. We find little evidence to support Rapoport's rule for the birds of Sikkim region of the Himalaya. Conclusions and Significance This study in the Eastern Himalaya indicates that species richness of birds is highest at intermediate elevations along one of the most extensive elevational gradients ever examined. Additionally, primary productivity and factors associated with habitat accounted for most of the variation in avian species richness. The diversity peak at intermediate elevations and the narrow elevational ranges of most species suggest important conservation implications

  19. Patterns of tree species diversity and composition in old-field successional forests in central Illinois

    Science.gov (United States)

    Scott M. Bretthauer; George Z. Gertner; Gary L. Rolfe; Jeffery O. Dawson

    2003-01-01

    Tree species diversity increases and dominance decreases with proximity to forest border in two 60-year-old successional forest stands developed on abandoned agricultural land in Piatt County, Illinois. A regression equation allowed us to quantify an increase in diversity with closeness to forest border for one of the forest stands. Shingle oak is the most dominant...

  20. Invasive exotic plants in the tropical Pacific Islands: Patterns of Diversity

    Science.gov (United States)

    J.S. Denslow; J.C. Space; P.A. Thomas

    2009-01-01

    Oceanic islands are good model systems with which to explore factors affecting exotic species diversity. Islands vary in size, topography, substrate type, degree of isolation, native species diversity, history, human population characteristics, and economic development. Moreover, islands are highly vulnerable to exotic species establishment. We used AICc analyses of...

  1. Evolutionary and demographic processes shaping geographic patterns of genetic diversity in a keystone species, the African forest elephant (Loxodonta cyclotis).

    Science.gov (United States)

    Ishida, Yasuko; Gugala, Natalie A; Georgiadis, Nicholas J; Roca, Alfred L

    2018-05-01

    The past processes that have shaped geographic patterns of genetic diversity may be difficult to infer from current patterns. However, in species with sex differences in dispersal, differing phylogeographic patterns between mitochondrial (mt) and nuclear (nu) DNA may provide contrasting insights into past events. Forest elephants ( Loxodonta cyclotis ) were impacted by climate and habitat change during the Pleistocene, which likely shaped phylogeographic patterns in mitochondrial (mt) DNA that have persisted due to limited female dispersal. By contrast, the nuclear (nu) DNA phylogeography of forest elephants in Central Africa has not been determined. We therefore examined the population structure of Central African forest elephants by genotyping 94 individuals from six localities at 21 microsatellite loci. Between forest elephants in western and eastern Congolian forests, there was only modest genetic differentiation, a pattern highly discordant with that of mtDNA. Nuclear genetic patterns are consistent with isolation by distance. Alternatively, male-mediated gene flow may have reduced the previous regional differentiation in Central Africa suggested by mtDNA patterns, which likely reflect forest fragmentation during the Pleistocene. In species like elephants, male-mediated gene flow erases the nuclear genetic signatures of past climate and habitat changes, but these continue to persist as patterns in mtDNA because females do not disperse. Conservation implications of these results are discussed.

  2. Elevational gradients in fish diversity in the Himalaya: water discharge is the key driver of distribution patterns.

    Science.gov (United States)

    Bhatt, Jay P; Manish, Kumar; Pandit, Maharaj K

    2012-01-01

    Studying diversity and distribution patterns of species along elevational gradients and understanding drivers behind these patterns is central to macroecology and conservation biology. A number of studies on biogeographic gradients are available for terrestrial ecosystems, but freshwater ecosystems remain largely neglected. In particular, we know very little about the species richness gradients and their drivers in the Himalaya, a global biodiversity hotspot. We collated taxonomic and distribution data of fish species from 16 freshwater Himalayan rivers and carried out empirical studies on environmental drivers and fish diversity and distribution in the Teesta river (Eastern Himalaya). We examined patterns of fish species richness along the Himalayan elevational gradients (50-3800 m) and sought to understand the drivers behind the emerging patterns. We used generalized linear models (GLM) and generalized additive models (GAM) to examine the richness patterns; GLM was used to investigate relationship between fish species richness and various environmental variables. Regression modelling involved stepwise procedures, including elimination of collinear variables, best model selection, based on the least Akaike's information criterion (AIC) and the highest percentage of deviance explained (D(2)). This maiden study on the Himalayan fishes revealed that total and non-endemic fish species richness monotonously decrease with increasing elevation, while endemics peaked around mid elevations (700-1500 m). The best explanatory model (synthetic model) indicated that water discharge is the best predictor of fish species richness patterns in the Himalayan rivers. This study, carried out along one of the longest bioclimatic elevation gradients of the world, lends support to Rapoport's elevational rule as opposed to mid domain effect hypothesis. We propose a species-discharge model and contradict species-area model in predicting fish species richness. We suggest that drivers of

  3. Patterns of microbial diversity along a salinity gradient in the Guerrero Negro solar saltern, Baja CA Sur, Mexico

    Directory of Open Access Journals (Sweden)

    Jesse G Dillon

    2013-12-01

    Full Text Available The goal of this study was to use environmental sequencing of 16S rRNA and bop genes to compare the diversity of planktonic bacteria and archaea across ponds with increasing salinity in the Exportadora de Sal (ESSA evaporative saltern in Guerrero Negro, Baja CA S., Mexico. We hypothesized that diverse communities of heterotrophic bacteria and archaea would be found in the ESSA ponds, but that bacterial diversity would decrease relative to archaea at the highest salinities. Archaeal 16S rRNA diversity was higher in Ponds 11 and 12 (370 & 380 g l-1 total salts respectively compared to Pond 9 (180 g l-1 total salts. Both Pond 11 and 12 communities had high representation (47 and 45% of clones respectively by Haloquadratum walsbyi-like (99% similarity lineages. The archaeal community in Pond 9 was dominated (79% by a single uncultured phylotype with 99% similarity to sequences recovered from the Sfax saltern in Tunisia. This pattern was mirrored in bop gene diversity with greater numbers of highly supported phylotypes including many Haloquadratum-like sequences from the two highest salinity ponds. In Pond 9, most bop sequences, were not closely related to sequences in databases. Bacterial 16S rRNA diversity was higher than archaeal in both Pond 9 and Pond 12 samples, but not Pond 11, where a non-Salinibacter lineage within the Bacteroidetes >98% similar to environmental clones recovered from Lake Tuz in Turkey and a saltern in Chula Vista, CA was most abundant (69% of community. This OTU was also the most abundant in Pond 12, but only represented 14% of clones in the more diverse pond. The most abundant OTU in Pond 9 (33% of community was 99% similar to an uncultured gammaproteobacterial clone from the Salton Sea. Results suggest that the communities of saltern bacteria and archaea vary even in ponds with similar salinity and further investigation into the ecology of diverse, uncultured halophile communities is warranted.

  4. Linking diverse nutrient patterns to different water masses within anticyclonic eddies in the upwelling system off Peru

    Science.gov (United States)

    Saranga José, Yonss; Dietze, Heiner; Oschlies, Andreas

    2017-03-01

    Ocean eddies can both trigger mixing (during their formation and decay) and effectively shield water encompassed from being exchanged with ambient water (throughout their lifetimes). These antagonistic effects of eddies complicate the interpretation of synoptic snapshots typically obtained by ship-based oceanographic measurement campaigns. Here we use a coupled physical-biogeochemical model to explore biogeochemical dynamics within anticyclonic eddies in the eastern tropical South Pacific Ocean. The goal is to understand the diverse biogeochemical patterns that have been observed at the subsurface layers of the anticyclonic eddies in this region. Our model results suggest that the diverse subsurface nutrient patterns within eddies are associated with the presence of water masses of different origins at different depths.

  5. Diversity patterns amongst herbivorous dinosaurs and plants during the Cretaceous: implications for hypotheses of dinosaur/angiosperm co-evolution.

    Science.gov (United States)

    Butler, R J; Barrett, P M; Kenrick, P; Penn, M G

    2009-03-01

    Palaeobiologists frequently attempt to identify examples of co-evolutionary interactions over extended geological timescales. These hypotheses are often intuitively appealing, as co-evolution is so prevalent in extant ecosystems, and are easy to formulate; however, they are much more difficult to test than their modern analogues. Among the more intriguing deep time co-evolutionary scenarios are those that relate changes in Cretaceous dinosaur faunas to the primary radiation of flowering plants. Demonstration of temporal congruence between the diversifications of co-evolving groups is necessary to establish whether co-evolution could have occurred in such cases, but is insufficient to prove whether it actually did take place. Diversity patterns do, however, provide a means for falsifying such hypotheses. We have compiled a new database of Cretaceous dinosaur and plant distributions from information in the primary literature. This is used as the basis for plotting taxonomic diversity and occurrence curves for herbivorous dinosaurs (Sauropodomorpha, Stegosauria, Ankylosauria, Ornithopoda, Ceratopsia, Pachycephalosauria and herbivorous theropods) and major groups of plants (angiosperms, Bennettitales, cycads, cycadophytes, conifers, Filicales and Ginkgoales) that co-occur in dinosaur-bearing formations. Pairwise statistical comparisons were made between various floral and faunal groups to test for any significant similarities in the shapes of their diversity curves through time. We show that, with one possible exception, diversity patterns for major groups of herbivorous dinosaurs are not positively correlated with angiosperm diversity. In other words, at the level of major clades, there is no support for any diffuse co-evolutionary relationship between herbivorous dinosaurs and flowering plants. The diversification of Late Cretaceous pachycephalosaurs (excluding the problematic taxon Stenopelix) shows a positive correlation, but this might be spuriously related to

  6. A comparison of alpha and beta diversity patterns of ferns, bryophytes and macrolichens in tropical montane forests of southern Ecuador

    OpenAIRE

    Mandl, N A; Lehnert, M; Kessler, M; Gradstein, S R

    2010-01-01

    We present a first comparison of patterns of alpha and beta diversity of ferns, mosses, liverworts and macrolichens in neotropical montane rainforests, and explore the question whether specific taxa may be used as surrogates for others. In three localities in southern Ecuador, we surveyed terrestrial and epiphytic species assemblages in ridge and slope forests in 28 plots of 400 m² each. The epiphytic habitat was significantly richer in ferns, liverworts, and macrolichens than the terrestrial...

  7. Impacts of weather on long-term patterns of plant richness and diversity vary with location and management.

    Science.gov (United States)

    Jonas, Jayne L; Buhl, Deborah A; Symstad, Amy J

    2015-09-01

    Better understanding the influence of precipitation and temperature on plant assemblages is needed to predict the effects of climate change. Many studies have examined the relationship between plant productivity and weather (primarily precipitation), but few have directly assessed the relationship between plant richness or diversity and weather despite their increased use as metrics of ecosystem condition. We focus on the grasslands of central North America, which are characterized by high temporal climatic variability. Over the next 100 years, these grasslands are predicted to experience further increased variability in growing season precipitation, as well as increased temperatures, due to global climate change. We assess the portion of interannual variability of richness and diversity explained by weather, how relationships between these metrics and weather vary among plant assemblages, and which aspects of weather best explain temporal variability. We used an information-theoretic approach to assess relationships between long-term plant richness and diversity patterns and a priori weather covariates using six data sets from four grasslands. Weather explained up to 49% and 63% of interannual variability in total plant species richness and diversity, respectively. However, richness and diversity responses to specific weather variables varied both among sites and among experimental treatments within sites. In general, we found many instances in which temperature was of equal or greater importance as precipitation, as well as evidence of the importance of lagged effects and precipitation or temperature variability. Although precipitation has been shown to be a key driver of productivity in grasslands, our results indicate that increasing temperatures alone, without substantial changes in precipitation patterns, could have measurable effects on Great Plains grassland plant assemblages and biodiversity metrics. Our results also suggest that richness and diversity

  8. Phylogenetic diversity and ecological pattern of ammonia-oxidizing archaea in the surface sediments of the western Pacific.

    Science.gov (United States)

    Cao, Huiluo; Hong, Yiguo; Li, Meng; Gu, Ji-Dong

    2011-11-01

    The phylogenetic diversity of ammonia-oxidizing archaea (AOA) was surveyed in the surface sediments from the northern part of the South China Sea (SCS). The distribution pattern of AOA in the western Pacific was discussed through comparing the SCS with other areas in the western Pacific including Changjiang Estuary and the adjacent East China Sea where high input of anthropogenic nitrogen was evident, the tropical West Pacific Continental Margins close to the Philippines, the deep-sea methane seep sediments in the Okhotsk Sea, the cold deep sea of Northeastern Japan Sea, and the hydrothermal field in the Southern Okinawa Trough. These various environments provide a wide spectrum of physical and chemical conditions for a better understanding of the distribution pattern and diversities of AOA in the western Pacific. Under these different conditions, the distinct community composition between shallow and deep-sea sediments was clearly delineated based on the UniFrac PCoA and Jackknife Environmental Cluster analyses. Phylogenetic analyses showed that a few ammonia-oxidizing archaeal subclades in the marine water column/sediment clade and endemic lineages were indicative phylotypes for some environments. Higher phylogenetic diversity was observed in the Philippines while lower diversity in the hydrothermal vent habitat. Water depth and possibly with other environmental factors could be the main driving forces to shape the phylogenetic diversity of AOA observed, not only in the SCS but also in the whole western Pacific. The multivariate regression tree analysis also supported this observation consistently. Moreover, the functions of current and other climate factors were also discussed in comparison of phylogenetic diversity. The information collectively provides important insights into the ecophysiological requirements of uncultured ammonia-oxidizing archaeal lineages in the western Pacific Ocean.

  9. Predicting plant diversity patterns in Madagascar: understanding the effects of climate and land cover change in a biodiversity hotspot.

    Directory of Open Access Journals (Sweden)

    Kerry A Brown

    Full Text Available Climate and land cover change are driving a major reorganization of terrestrial biotic communities in tropical ecosystems. In an effort to understand how biodiversity patterns in the tropics will respond to individual and combined effects of these two drivers of environmental change, we use species distribution models (SDMs calibrated for recent climate and land cover variables and projected to future scenarios to predict changes in diversity patterns in Madagascar. We collected occurrence records for 828 plant genera and 2186 plant species. We developed three scenarios, (i.e., climate only, land cover only and combined climate-land cover based on recent and future climate and land cover variables. We used this modelling framework to investigate how the impacts of changes to climate and land cover influenced biodiversity across ecoregions and elevation bands. There were large-scale climate- and land cover-driven changes in plant biodiversity across Madagascar, including both losses and gains in diversity. The sharpest declines in biodiversity were projected for the eastern escarpment and high elevation ecosystems. Sharp declines in diversity were driven by the combined climate-land cover scenarios; however, there were subtle, region-specific differences in model outputs for each scenario, where certain regions experienced relatively higher species loss under climate or land cover only models. We strongly caution that predicted future gains in plant diversity will depend on the development and maintenance of dispersal pathways that connect current and future suitable habitats. The forecast for Madagascar's plant diversity in the face of future environmental change is worrying: regional diversity will continue to decrease in response to the combined effects of climate and land cover change, with habitats such as ericoid thickets and eastern lowland and sub-humid forests particularly vulnerable into the future.

  10. Consistent patterns of high alpha and low beta diversity in tropical parasitic and free-living protists.

    Science.gov (United States)

    Lentendu, Guillaume; Mahé, Frédéric; Bass, David; Rueckert, Sonja; Stoeck, Thorsten; Dunthorn, Micah

    2018-05-30

    Tropical animals and plants are known to have high alpha diversity within forests, but low beta diversity between forests. By contrast, it is unknown whether microbes inhabiting the same ecosystems exhibit similar biogeographic patterns. To evaluate the biogeographies of tropical protists, we used metabarcoding data of species sampled in the soils of three lowland Neotropical rainforests. Taxa-area and distance-decay relationships for three of the dominant protist taxa and their subtaxa were estimated at both the OTU and phylogenetic levels, with presence-absence and abundance-based measures. These estimates were compared to null models. High local alpha and low regional beta diversity patterns were consistently found for both the parasitic Apicomplexa and the largely free-living Cercozoa and Ciliophora. Similar to animals and plants, the protists showed spatial structures between forests at the OTU and phylogenetic levels, and only at the phylogenetic level within forests. These results suggest that the biogeographies of macro- and micro-organismal eukaryotes in lowland Neotropical rainforests are partially structured by the same general processes. However, and unlike the animals and plants, the protist OTUs did not exhibit spatial structures within forests, which hinders our ability to estimate the local and regional diversity of protists in tropical forests. © 2018 John Wiley & Sons Ltd.

  11. Cross-shelf investigation of coral reef cryptic benthic organisms reveals diversity patterns of the hidden majority

    KAUST Repository

    Pearman, John K.

    2018-05-18

    Coral reefs harbor diverse assemblages of organisms yet the majority of this diversity is hidden within the three dimensional structure of the reef and neglected using standard visual surveys. This study uses Autonomous Reef Monitoring Structures (ARMS) and amplicon sequencing methodologies, targeting mitochondrial cytochrome oxidase I and 18S rRNA genes, to investigate changes in the cryptic reef biodiversity. ARMS, deployed at 11 sites across a near- to off-shore gradient in the Red Sea were dominated by Porifera (sessile fraction), Arthropoda and Annelida (mobile fractions). The two primer sets detected different taxa lists, but patterns in community composition and structure were similar. While the microhabitat of the ARMS deployment affected the community structure, a clear cross-shelf gradient was observed for all fractions investigated. The partitioning of beta-diversity revealed that replacement (i.e. the substitution of species) made the highest contribution with richness playing a smaller role. Hence, different reef habitats across the shelf are relevant to regional diversity, as they harbor different communities, a result with clear implications for the design of Marine Protected Areas. ARMS can be vital tools to assess biodiversity patterns in the generally neglected but species-rich cryptic benthos, providing invaluable information for the management and conservation of hard-bottomed habitats over local and global scales.

  12. Population genomic analysis reveals differential evolutionary histories and patterns of diversity across subgenomes and subpopulations of Brassica napus L.

    Directory of Open Access Journals (Sweden)

    Elodie eGazave

    2016-04-01

    Full Text Available The allotetraploid species Brassica napus L. is a global crop of major economic importance, providing canola oil (seed and vegetables for human consumption and fodder and meal for livestock feed. Characterizing the genetic diversity present in the extant germplasm pool of B. napus is fundamental to better conserve, manage and utilize the genetic resources of this species. We used sequence-based genotyping to identify and genotype 30,881 SNPs in a diversity panel of 782 B. napus accessions, representing samples of winter and spring growth habits originating from 33 countries across Europe, Asia and America. We detected strong population structure broadly concordant with growth habit and geography, and identified three major genetic groups: spring (SP, winter Europe (WE, and winter Asia (WA. Subpopulation-specific polymorphism patterns suggest enriched genetic diversity within the WA group and a smaller effective breeding population for the SP group compared to WE. Interestingly, the two subgenomes of B. napus appear to have different geographic origins, with phylogenetic analysis placing WE and WA as basal clades for the other subpopulations in the C and A subgenomes, respectively. Finally, we identified 16 genomic regions where the patterns of diversity differed markedly from the genome-wide average, several of which are suggestive of genomic inversions. The results obtained in this study constitute a valuable resource for worldwide breeding efforts and the genetic dissection and prediction of complex B. napus traits.

  13. Detection of temporal behaviour patterns of free-ranging cattle by means of diversity spectra

    Directory of Open Access Journals (Sweden)

    de Miguel, J. M.

    1991-06-01

    Full Text Available The aim of this paper is to detect temporal patterns of cattle behaviour. The method, diversity spectra, provides, on the one hand, the number of parts into which a temporary transect should be divided in order to understand the maximum segregation of cattle activities and, on the other, the clarity with which each segregation is defined. In the case under study (a 'dehesa' pasture-land in central Spain the maximum segregation of fundamental activities in cattle behaviour is reached by considering the year as divided into two periods: spring-summer and autumn-winter. Cattle behaviour shows an annual "coarse grain" pattern, which is associated with management activities and with the meteorological seasonality of the Mediterranean climate. However, within each of the two annual periods, maximum segregation is reached considering separately the days of observation. This "fine grain" pattern indicates within each season, a certain capacity for response to a fluctuating environment and determines very different behaviour on close days. During autumn-winter period cattle show seasonal and daily activity segregations which are clearer than during spring-summer. In the former period, the lack of grass, more severe climatic conditions and management would seem to be determining factors of this temporal behaviour pattern.

    [es] El objetivo del trabajo es identificar patrones temporales de comportamiento del ganado. El procedimiento utilizado, espectros de diversidad, permite apreciar, por un lado, el número de partes en que debe dividirse un transecto temporal para detectar la máxima segregación de las actividades del ganado y, por otro, el grado de definición con que se manifiesta dicha segregación. En el caso estudiado (una dehesa del centro de España la máxima segregación de las actividades fundamentales de comportamiento del ganado se produce al considerar el año dividido en dos periodos: primavera-verano y otoño-invierno. El

  14. Trophic diversity, size and biomass spectrum of Bay of Bengal nematodes: A study case on depth and latitudinal patterns

    Science.gov (United States)

    Ansari, Kapuli Gani Mohamed Thameemul; Lyla, Somasundharanair; Khan, Syed Ajmal; Bhadury, Punyasloke

    2017-09-01

    Depth and latitudinal patterns of nematode functional attributes were investigated from 35 stations of Bay of Bengal (BoB) continental shelf. We aim to address whether depth and latitudinal variations can modify nematode community structure and their functional attributes (trophic diversity, size and biomass spectra). Global trend of depth and latitudinal related variations have also been noticed from BoB shelf in terms of nematode abundance and species richness, albeit heterogeneity patterns were encountered in functional attributes. Index of trophic diversity values revealed higher trophic diversity across the BoB shelf and suggested variety of food resource availability. However, downstream analysis of trophic status showed depth and latitude specific patterns but not reflected in terms of size and biomass spectrum. The peaks at different positions clearly visualized heterogeneity in distribution patterns for both size and biomass spectrum and also there was evidence of availability of diversified food resources. Nematode biomass spectra (NBS) constructed for nematode communities showed shift in peak biomass values towards lower to moderate size classes particularly in shallower depth but did not get reflected in latitudes. However, Chennai and Parangipettai transects demonstrated shift in peak biomass values towards higher biomass classes explaining the representation of higher nematode abundance. Our findings concluded that depth and latitudes are physical variables; they may not directly affect nematode community structure and functional attributes but they might influence the other factors such as food availability, sediment deposition and settlement rate. Our observations suggest that the local factors (seasonal character) of phytodetrital food flux can be very important for shaping the nematode community structure and success of nematode functional heterogeneity patterns across the Bay of Bengal shelf.

  15. Emergent Patterns of Diversity and Dynamics in Natural Populations of Planktonic Vibrio Bacteria

    National Research Council Canada - National Science Library

    Thompson, Janelle R

    2005-01-01

    ... an environmental condition into a system-level response. Prerequisite to developing such a framework is an understanding of how microbial diversity is partitioned into functional groups of organisms...

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

    International Nuclear Information System (INIS)

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

    2017-01-01

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

  17. Identification of regioisomers of methylated kaempferol and quercetin by ultra high performance liquid chromatography quadrupole time-of-flight (UHPLC–QTOF) tandem mass spectrometry combined with diagnostic fragmentation pattern analysis

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Chengying; Lv, Haipeng; Zhang, Xinzhong; Chen, Zongmao; Shi, Jiang [Tea Research Institute, Chinese Academy of Agricultural Sciences, 9 Meiling South Road, Hangzhou, Zhejiang 310008 (China); Lu, Meiling, E-mail: meilinglu@hotmail.com [Chemical Analysis Group, Agilent Technologies, No. 3 Wangjing North Road, Chaoyang Distr., Beijing 100102 (China); Lin, Zhi, E-mail: linz@mail.tricaas.com [Tea Research Institute, Chinese Academy of Agricultural Sciences, 9 Meiling South Road, Hangzhou, Zhejiang 310008 (China)

    2013-09-17

    Highlights: •Found methane elimination is position-specific for methylated flavonols. •Found retro Diels–Alder fragments retained methoxy at original ring of flavonols. •Proposed a diagnostic pattern for discriminating regioisomers of flavonols. •Identified the specificity of three novel flavonol O-methyltransferases. •Identified six biologically active compounds and four new compounds. -- Abstract: The O-methylation of active flavonoids can enhance their antiallergic, anticancerous, and cardioprotective effects depending on the methylation position. Thus, it is biologically and pharmacologically important to differentiate methylated flavonoid regioisomers. In this study, we examined the regioisomers of methylated kaempferol and quercetin using ultra high performance liquid chromatography quadrupole time-of-flight tandem mass spectrometry. The methyl groups on the flavonoids can generally be cleaved as methyl radicals in a position-independent manner. We found that methyl groups can be cleaved as methane. If there are protons adjacent the methoxy on the flavonol rings, intra-molecule proton transfer can occur via collision-induced dissociation, and one molecule of methane can then be eliminated. The remaining charged fragment ([M+H−CH{sub 4}]{sup +}) reflects the adjacent structure and is specific to the methoxy position. Furthermore, the retro Diels–Alder (RDA) fragmentation of methylated flavonols can generate fragments with the methoxy at the original methylated ring. Combining the position-specific [M+H−CH{sub 4}]{sup +} fragment with the RDA fragments provides a diagnostic pattern for rapidly identifying methylated regioisomeric flavonols. Along with their retention behaviour, we have successfully identified ten regioisomers of methylated kaempferol and quercetin, which include six compounds previously reported in plants and shown to be biologically active. The developed approach is sensitive, rapid, reliable, and requires few standard

  18. Fish assemblage in a semi-arid Neotropical reservoir: composition, structure and patterns of diversity and abundance.

    Science.gov (United States)

    Novaes, J L C; Moreira, S I L; Freire, C E C; Sousa, M M O; Costa, R S

    2014-05-01

    The aim of this study was to analyse the composition, structure and spatial and temporal patterns of diversity and abundance of the ichthyofauna of the Santa Cruz Reservoir in semi-arid Brazil. Data were collected quarterly at eight sampling locations on the reservoir between February 2010 and November 2011 using gillnets from 12- to 70-mm mesh that were left in the water for 12h00min during the night. We evaluated the composition, structure and assemblage descriptors (Shannon-Wiener diversity index and equitability, respectively) and catch per unit effort by the number (CPUEn) and biomass (CPUEb) of the ichthyofauna. The 6,047 individuals (399,211.6 g) captured represented three orders, ten families and 20 species, of which four belonged to introduced species. The family Characidae was the most abundant with a total of 2,772 (45.8%) individuals captured. The species-abundance curve fit the log-normal model. In the spatial analysis of diversity, there were significant differences between sampling sites in the lacustrine and fluvial regions, and the highest values were found in the lacustrine region. In the temporal analysis of diversity, significant differences were also observed between the rainy and dry seasons, and the higher values were found during the dry season. Equitability followed the same spatiotemporal pattern as diversity. The Spearman correlation was significantly negative between diversity and rainfall. A cluster analysis spatially separated the ichthyofauna into two groups: one group formed by sampling sites in the fluvial region and another group formed by the remainder of the points in the lacustrine region. Both the CPUEn and CPUEb values were higher at point 8 (fluvial region) and during the rainy season. A two-way ANOVA showed that the CPUEn and CPUEb values were spatially and temporally significant. We conclude that the spatial and temporal trends of diversity in the Santa Cruz reservoir differ from those of other Brazilian reservoirs but that

  19. High variability of dung beetle diversity patterns at four mountains of the Trans-Mexican Volcanic Belt

    Directory of Open Access Journals (Sweden)

    Alfonsina Arriaga-Jiménez

    2018-02-01

    Full Text Available Insect diversity patterns of high mountain ecosystems remain poorly studied in the tropics. Sampling dung beetles of the subfamilies Aphodiinae, Scarabaeinae, and Geotrupinae was carried out at four volcanoes in the Trans-Mexican Volcanic Belt (TMVB in the Mexican transition zone at 2,700 and 3,400 MASL, and on the windward and leeward sides. Sampling units represented a forest–shrubland–pasture (FSP mosaic typical of this mountain region. A total of 3,430 individuals of 29 dung beetle species were collected. Diversity, abundance and compositional similarity (CS displayed a high variability at all scales; elevation, cardinal direction, or FSP mosaics did not show any patterns of higher or lower values of those measures. The four mountains were different regarding dispersion patterns and taxonomic groups, both for species and individuals. Onthophagus chevrolati dominated all four mountains with an overall relative abundance of 63%. CS was not related to distance among mountains, but when O. chevrolati was excluded from the analysis, CS values based on species abundance decreased with increasing distance. Speciation, dispersion, and environmental instability are suggested as the main drivers of high mountain diversity patterns, acting together at different spatial and temporal scales. Three species new to science were collected (>10% of all species sampled. These discoveries may indicate that speciation rate is high among these volcanoes—a hypothesis that is also supported by the elevated number of collected species with a restricted montane distribution. Dispersion is an important factor in driving species composition, although naturally limited between high mountains; horizontal colonization events at different time scales may best explain the observed species composition in the TMVB, complemented by vertical colonization events to a lesser extent. Environmental instability may be the main factor causing the high variability of diversity

  20. High variability of dung beetle diversity patterns at four mountains of the Trans-Mexican Volcanic Belt.

    Science.gov (United States)

    Arriaga-Jiménez, Alfonsina; Rös, Matthias; Halffter, Gonzalo

    2018-01-01

    Insect diversity patterns of high mountain ecosystems remain poorly studied in the tropics. Sampling dung beetles of the subfamilies Aphodiinae, Scarabaeinae, and Geotrupinae was carried out at four volcanoes in the Trans-Mexican Volcanic Belt (TMVB) in the Mexican transition zone at 2,700 and 3,400 MASL, and on the windward and leeward sides. Sampling units represented a forest-shrubland-pasture (FSP) mosaic typical of this mountain region. A total of 3,430 individuals of 29 dung beetle species were collected. Diversity, abundance and compositional similarity (CS) displayed a high variability at all scales; elevation, cardinal direction, or FSP mosaics did not show any patterns of higher or lower values of those measures. The four mountains were different regarding dispersion patterns and taxonomic groups, both for species and individuals. Onthophagus chevrolati dominated all four mountains with an overall relative abundance of 63%. CS was not related to distance among mountains, but when O. chevrolati was excluded from the analysis, CS values based on species abundance decreased with increasing distance. Speciation, dispersion, and environmental instability are suggested as the main drivers of high mountain diversity patterns, acting together at different spatial and temporal scales. Three species new to science were collected (>10% of all species sampled). These discoveries may indicate that speciation rate is high among these volcanoes-a hypothesis that is also supported by the elevated number of collected species with a restricted montane distribution. Dispersion is an important factor in driving species composition, although naturally limited between high mountains; horizontal colonization events at different time scales may best explain the observed species composition in the TMVB, complemented by vertical colonization events to a lesser extent. Environmental instability may be the main factor causing the high variability of diversity and abundance patterns

  1. Attending to Communication and Patterns of Interaction: Culturally Sensitive Mental Health Care for Groups of Urban, Ethnically Diverse, Impoverished, and Underserved Women.

    Science.gov (United States)

    Molewyk Doornbos, Mary; Zandee, Gail Landheer; DeGroot, Joleen

    2014-07-01

    The United States is ethnically diverse. This diversity presents challenges to nurses, who, without empirical evidence to design culturally congruent interventions, may contribute to mental health care disparities. Using Leininger's theory of culture care diversity and universality, this study documented communication and interaction patterns of ethnically diverse, urban, impoverished, and underserved women. Using a community-based participatory research framework, 61 Black, Hispanic, and White women participated in focus groups around their experiences with anxiety/depression. Researchers recorded verbal communication, nonverbal behavior, and patterns of interaction. The women's communication and interaction patterns gave evidence of three themes that were evident across all focus groups and five subthemes that emerged along ethnic lines. The results suggest cultural universalities and cultural uniquenesses relative to the communication and interaction patterns of urban, ethnically diverse, impoverished, and underserved women that may assist in the design of culturally sensitive mental health care. © The Author(s) 2014.

  2. Crystal Structure of the N-Benzyloxycarbonyl-alanyl-phenylalanyl-methyl Ester: The Importance of the H-Bonding Pattern

    Directory of Open Access Journals (Sweden)

    Ignacio Alfonso

    2011-08-01

    Full Text Available Large crystals of the methyl ester of the N-a-benzyloxycarbonyl protected Ala-Phe dipeptide (Z-AF-OMe were obtained after the very slow evaporation of a solution of the corresponding carboxylic acid (Z-AF-OH in methanol containing an excess of HCl. The structure was confirmed by single crystal X-ray diffraction data. It crystallizes in the orthorhombic space group P212121 with unit cell dimensions a = 5.0655(6 Å, b = 8.4614(8 Å, c = 46.856(5 Å, V = 2008.3(4 Å3, Z = 4. In the crystal, the molecules form hydrogen bonded chains running along the a axis of the unit cell. Other secondary interactions are also discussed.

  3. Patterns of Phylogenetic Diversity of Subtropical Rainforest of the Great Sandy Region, Australia Indicate Long Term Climatic Refugia.

    Science.gov (United States)

    Howard, Marion G; McDonald, William J F; Forster, Paul I; Kress, W John; Erickson, David; Faith, Daniel P; Shapcott, Alison

    2016-01-01

    Australia's Great Sandy Region is of international significance containing two World Heritage areas and patches of rainforest growing on white sand. Previous broad-scale analysis found the Great Sandy biogeographic subregion contained a significantly more phylogenetically even subset of species than expected by chance contrasting with rainforest on white sand in Peru. This study aimed to test the patterns of rainforest diversity and relatedness at a finer scale and to investigate why we may find different patterns of phylogenetic evenness compared with rainforests on white sands in other parts of the world. This study focussed on rainforest sites within the Great Sandy and surrounding areas in South East Queensland (SEQ), Australia. We undertook field collections, expanded our three-marker DNA barcode library of SEQ rainforest plants and updated the phylogeny to 95% of the SEQ rainforest flora. We sampled species composition of rainforest in fixed area plots from 100 sites. We calculated phylogenetic diversity (PD) measures as well as species richness (SR) for each rainforest community. These combined with site variables such as geology, were used to evaluate patterns and relatedness. We found that many rainforest communities in the Great Sandy area were significantly phylogenetically even at the individual site level consistent with a broader subregion analysis. Sites from adjacent areas were either not significant or were significantly phylogenetically clustered. Some results in the neighbouring areas were consistent with historic range expansions. In contrast with expectations, sites located on the oldest substrates had significantly lower phylogenetic diversity (PD). Fraser Island was once connected to mainland Australia, our results are consistent with a region geologically old enough to have continuously supported rainforest in refugia. The interface of tropical and temperate floras in part also explains the significant phylogenetic evenness and higher than

  4. Patterns of Phylogenetic Diversity of Subtropical Rainforest of the Great Sandy Region, Australia Indicate Long Term Climatic Refugia.

    Directory of Open Access Journals (Sweden)

    Marion G Howard

    Full Text Available Australia's Great Sandy Region is of international significance containing two World Heritage areas and patches of rainforest growing on white sand. Previous broad-scale analysis found the Great Sandy biogeographic subregion contained a significantly more phylogenetically even subset of species than expected by chance contrasting with rainforest on white sand in Peru. This study aimed to test the patterns of rainforest diversity and relatedness at a finer scale and to investigate why we may find different patterns of phylogenetic evenness compared with rainforests on white sands in other parts of the world. This study focussed on rainforest sites within the Great Sandy and surrounding areas in South East Queensland (SEQ, Australia. We undertook field collections, expanded our three-marker DNA barcode library of SEQ rainforest plants and updated the phylogeny to 95% of the SEQ rainforest flora. We sampled species composition of rainforest in fixed area plots from 100 sites. We calculated phylogenetic diversity (PD measures as well as species richness (SR for each rainforest community. These combined with site variables such as geology, were used to evaluate patterns and relatedness. We found that many rainforest communities in the Great Sandy area were significantly phylogenetically even at the individual site level consistent with a broader subregion analysis. Sites from adjacent areas were either not significant or were significantly phylogenetically clustered. Some results in the neighbouring areas were consistent with historic range expansions. In contrast with expectations, sites located on the oldest substrates had significantly lower phylogenetic diversity (PD. Fraser Island was once connected to mainland Australia, our results are consistent with a region geologically old enough to have continuously supported rainforest in refugia. The interface of tropical and temperate floras in part also explains the significant phylogenetic evenness

  5. Species turnover drives β-diversity patterns across multiple spatial scales of plant-galling interactions in mountaintop grasslands.

    Science.gov (United States)

    Coelho, Marcel Serra; Carneiro, Marco Antônio Alves; Branco, Cristina Alves; Borges, Rafael Augusto Xavier; Fernandes, Geraldo Wilson

    2018-01-01

    This study describes differences in species richness and composition of the assemblages of galling insects and their host plants at different spatial scales. Sampling was conducted along altitudinal gradients composed of campos rupestres and campos de altitude of two mountain complexes in southeastern Brazil: Espinhaço Range and Mantiqueira Range. The following hypotheses were tested: i) local and regional richness of host plants and galling insects are positively correlated; ii) beta diversity is the most important component of regional diversity of host plants and galling insects; and iii) Turnover is the main mechanism driving beta diversity of both host plants and galling insects. Local richness of galling insects and host plants increased with increasing regional richness of species, suggesting a pattern of unsaturated communities. The additive partition of regional richness (γ) into local and beta components shows that local richnesses (α) of species of galling insects and host plants are low relative to regional richness; the beta (β) component incorporates most of the regional richness. The multi-scale analysis of additive partitioning showed similar patterns for galling insects and host plants with the local component (α) incorporated a small part of regional richness. Beta diversity of galling insects and host plants were mainly the result of turnover, with little contribution from nesting. Although the species composition of galling insects and host plant species varied among sample sites, mountains and even mountain ranges, local richness remained relatively low. In this way, the addition of local habitats with different landscapes substantially affects regional richness. Each mountain contributes fundamentally to the composition of regional diversity of galling insects and host plants, and so the design of future conservation strategies should incorporate multiple scales.

  6. Diversity in work: The heterogeneity of women's labour market participation patterns

    NARCIS (Netherlands)

    Yerkes, M.

    2006-01-01

    Employment patterns are gender-driven, yet analyses of women’s employment often fail to recognize the heterogeneous patterns evident within women’s labour market participation itself. This article examines the variation in women’s labour market participation in light of Hakim’s heterogeneity

  7. Explaining bathymetric diversity patterns in marine benthic invertebrates and demersal fishes: physiological contributions to adaptation of life at depth.

    Science.gov (United States)

    Brown, Alastair; Thatje, Sven

    2014-05-01

    Bathymetric biodiversity patterns of marine benthic invertebrates and demersal fishes have been identified in the extant fauna of the deep continental margins. Depth zonation is widespread and evident through a transition between shelf and slope fauna from the shelf break to 1000 m, and a transition between slope and abyssal fauna from 2000 to 3000 m; these transitions are characterised by high species turnover. A unimodal pattern of diversity with depth peaks between 1000 and 3000 m, despite the relatively low area represented by these depths. Zonation is thought to result from the colonisation of the deep sea by shallow-water organisms following multiple mass extinction events throughout the Phanerozoic. The effects of low temperature and high pressure act across hierarchical levels of biological organisation and appear sufficient to limit the distributions of such shallow-water species. Hydrostatic pressures of bathyal depths have consistently been identified experimentally as the maximum tolerated by shallow-water and upper bathyal benthic invertebrates at in situ temperatures, and adaptation appears required for passage to deeper water in both benthic invertebrates and demersal fishes. Together, this suggests that a hyperbaric and thermal physiological bottleneck at bathyal depths contributes to bathymetric zonation. The peak of the unimodal diversity-depth pattern typically occurs at these depths even though the area represented by these depths is relatively low. Although it is recognised that, over long evolutionary time scales, shallow-water diversity patterns are driven by speciation, little consideration has been given to the potential implications for species distribution patterns with depth. Molecular and morphological evidence indicates that cool bathyal waters are the primary site of adaptive radiation in the deep sea, and we hypothesise that bathymetric variation in speciation rates could drive the unimodal diversity-depth pattern over time. Thermal

  8. Diethylstilbestrol (DES)-stimulated hormonal toxicity is mediated by ERα alteration of target gene methylation patterns and epigenetic modifiers (DNMT3A, MBD2, and HDAC2) in the mouse seminal vesicle.

    Science.gov (United States)

    Li, Yin; Hamilton, Katherine J; Lai, Anne Y; Burns, Katherine A; Li, Leping; Wade, Paul A; Korach, Kenneth S

    2014-03-01

    Diethylstilbestrol (DES) is a synthetic estrogen associated with adverse effects on reproductive organs. DES-induced toxicity of the mouse seminal vesicle (SV) is mediated by estrogen receptor α (ERα), which alters expression of seminal vesicle secretory protein IV (Svs4) and lactoferrin (Ltf) genes. We examined a role for nuclear receptor activity in association with DNA methylation and altered gene expression. We used the neonatal DES exposure mouse model to examine DNA methylation patterns via bisulfite conversion sequencing in SVs of wild-type (WT) and ERα-knockout (αERKO) mice. The DNA methylation status at four specific CpGs (-160, -237, -306, and -367) in the Svs4 gene promoter changed during mouse development from methylated to unmethylated, and DES prevented this change at 10 weeks of age in WT SV. At two specific CpGs (-449 and -459) of the Ltf gene promoter, DES altered the methylation status from methylated to unmethylated. Alterations in DNA methylation of Svs4 and Ltf were not observed in αERKO SVs, suggesting that changes of methylation status at these CpGs are ERα dependent. The methylation status was associated with the level of gene expression. In addition, gene expression of three epigenetic modifiers-DNMT3A, MBD2, and HDAC2-increased in the SV of DES-exposed WT mice. DES-induced hormonal toxicity resulted from altered gene expression of Svs4 and Ltf associated with changes in DNA methylation that were mediated by ERα. Alterations in gene expression of DNMT3A, MBD2, and HDAC2 in DES-exposed male mice may be involved in mediating the changes in methylation status in the SV. Li Y, Hamilton KJ, Lai AY, Burns KA, Li L, Wade PA, Korach KS. 2014. Diethylstilbestrol (DES)-stimulated hormonal toxicity is mediated by ERα alteration of target gene methylation patterns and epigenetic modifiers (DNMT3A, MBD2, and HDAC2) in the mouse seminal vesicle. Environ Health Perspect 122:262-268; http://dx.doi.org/10.1289/ehp.1307351.

  9. Patterns of ancestry and genetic diversity in reintroduced populations of the slimy sculpin: Implications for conservation

    Science.gov (United States)

    Huff, David D.; Miller, Loren M.; Vondracek, Bruce C.

    2010-01-01

    Reintroductions are a common approach for preserving intraspecific biodiversity in fragmented landscapes. However, they may exacerbate the reduction in genetic diversity initially caused by population fragmentation because the effective population size of reintroduced populations is often smaller and reintroduced populations also tend to be more geographically isolated than native populations. Mixing genetically divergent sources for reintroduction purposes is a practice intended to increase genetic diversity. We documented the outcome of reintroductions from three mixed sources on the ancestral composition and genetic variation of a North American fish, the slimy sculpin (Cottus cognatus). We used microsatellite markers to evaluate allelic richness and heterozygosity in the reintroduced populations relative to computer simulated expectations. Sculpins in reintroduced populations exhibited higher levels of heterozygosity and allelic richness than any single source, but only slightly higher than the single most genetically diverse source population. Simulations intended to mimic an ideal scenario for maximizing genetic variation in the reintroduced populations also predicted increases, but they were only moderately greater than the most variable source population. We found that a single source contributed more than the other two sources at most reintroduction sites. We urge caution when choosing whether to mix source populations in reintroduction programs. Genetic characteristics of candidate source populations should be evaluated prior to reintroduction if feasible. When combined with knowledge of the degree of genetic distinction among sources, simulations may allow the genetic diversity benefits of mixing populations to be weighed against the risks of outbreeding depression in reintroduced and nearby populations.

  10. PATTERNS OF ALLOZYME DIVERSITY IN THE THREATENED PLANT ERIGERON PARISHII (ASTERACEAE). (R826102)

    Science.gov (United States)

    Thirty-one occurrences of Erigeron parishii, a narrowly endemic plant threatened by mining, were sampled for allozyme diversity. This taxon held considerable genetic variation at the [4 allozyme loci surveyed. Species (e.g., alleles per locus [A] = 4.3 and proportion of polymorph...

  11. Diversity patterns in macrobenthos across a continental slope in the NE Atlantic

    NARCIS (Netherlands)

    Flach, E.; De Bruin, W.

    1999-01-01

    Different estimates were used to assess the diversity of the total macrofauna and its major taxonomic groups separately from a broad bathymetric range at a site in the NE Atlantic. In the Goban Spur region, a transect was sampled from the shelf to the abyssal plain over a depth range from similar to

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

    NARCIS (Netherlands)

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

    2009-01-01

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

  13. Genetic and genomic diversity studies of Acacia symbionts in Senegal reveal new species of Mesorhizobium with a putative geographical pattern.

    Directory of Open Access Journals (Sweden)

    Fatou Diouf

    Full Text Available Acacia senegal (L Willd. and Acacia seyal Del. are highly nitrogen-fixing and moderately salt tolerant species. In this study we focused on the genetic and genomic diversity of Acacia mesorhizobia symbionts from diverse origins in Senegal and investigated possible correlations between the genetic diversity of the strains, their soil of origin, and their tolerance to salinity. We first performed a multi-locus sequence analysis on five markers gene fragments on a collection of 47 mesorhizobia strains of A. senegal and A. seyal from 8 localities. Most of the strains (60% clustered with the M. plurifarium type strain ORS 1032T, while the others form four new clades (MSP1 to MSP4. We sequenced and assembled seven draft genomes: four in the M. plurifarium clade (ORS3356, ORS3365, STM8773 and ORS1032T, one in MSP1 (STM8789, MSP2 (ORS3359 and MSP3 (ORS3324. The average nucleotide identities between these genomes together with the MLSA analysis reveal three new species of Mesorhizobium. A great variability of salt tolerance was found among the strains with a lack of correlation between the genetic diversity of mesorhizobia, their salt tolerance and the soils samples characteristics. A putative geographical pattern of A. senegal symbionts between the dryland north part and the center of Senegal was found, reflecting adaptations to specific local conditions such as the water regime. However, the presence of salt does not seem to be an important structuring factor of Mesorhizobium species.

  14. Genetic and genomic diversity studies of Acacia symbionts in Senegal reveal new species of Mesorhizobium with a putative geographical pattern.

    Science.gov (United States)

    Diouf, Fatou; Diouf, Diegane; Klonowska, Agnieszka; Le Queré, Antoine; Bakhoum, Niokhor; Fall, Dioumacor; Neyra, Marc; Parrinello, Hugues; Diouf, Mayecor; Ndoye, Ibrahima; Moulin, Lionel

    2015-01-01

    Acacia senegal (L) Willd. and Acacia seyal Del. are highly nitrogen-fixing and moderately salt tolerant species. In this study we focused on the genetic and genomic diversity of Acacia mesorhizobia symbionts from diverse origins in Senegal and investigated possible correlations between the genetic diversity of the strains, their soil of origin, and their tolerance to salinity. We first performed a multi-locus sequence analysis on five markers gene fragments on a collection of 47 mesorhizobia strains of A. senegal and A. seyal from 8 localities. Most of the strains (60%) clustered with the M. plurifarium type strain ORS 1032T, while the others form four new clades (MSP1 to MSP4). We sequenced and assembled seven draft genomes: four in the M. plurifarium clade (ORS3356, ORS3365, STM8773 and ORS1032T), one in MSP1 (STM8789), MSP2 (ORS3359) and MSP3 (ORS3324). The average nucleotide identities between these genomes together with the MLSA analysis reveal three new species of Mesorhizobium. A great variability of salt tolerance was found among the strains with a lack of correlation between the genetic diversity of mesorhizobia, their salt tolerance and the soils samples characteristics. A putative geographical pattern of A. senegal symbionts between the dryland north part and the center of Senegal was found, reflecting adaptations to specific local conditions such as the water regime. However, the presence of salt does not seem to be an important structuring factor of Mesorhizobium species.

  15. Spatial patterns of diversity at local and regional scales in a tropical lagoon

    Directory of Open Access Journals (Sweden)

    José Adán Caballero-Vázquez

    Full Text Available The present study reports estimates of alpha (α, beta (β and gamma (Γ diversity for the fish community of Chacmochuch Lagoon (SE Mexico, a natural protected area located in the northern portion of the Mesoamerican Barrier Reef System. Fish specimens were sampled in 2004 and 2006. Field work was carried out at three climatic peaks: at 13 stations using a 70 m-long beach seine. The collected data were supplemented with information obtained from a previous work conducted in 2002 and were then analyzed with multivariate statistical methods. In addition, fish composition results from this study were compared to those reported for other similar ecosystems of the region. A total of 68 fish species were recorded, determined as peripheral (high-salinity species, usually marine affinity most of them. Most of the fish species collected were determined as rare, and a few number of species were determined as common and dominant. Salinity, TSD, temperature, dissolved oxygen and other variables were measured to determine the influence over the fish communities, four groups of sites where determined. Results indicated a gradual decrease in the degree of species replacement towards the interior of the system (away from the coast. The estimated value of gamma diversity was high compared to that reported for other coastal systems of the region and, due to the high degree of habitat heterogeneity found in this system; beta diversity had a greater contribution to gamma diversity than alpha diversity. This lagoon acts as a nursing area for many of the fish species collected in this study as indicated by the presence of juvenile stages.

  16. Identification of Differentially Methylated Sites with Weak Methylation Effects

    Directory of Open Access Journals (Sweden)

    Hong Tran

    2018-02-01

    Full Text Available Deoxyribonucleic acid (DNA methylation is an epigenetic alteration crucial for regulating stress responses. Identifying large-scale DNA methylation at single nucleotide resolution is made possible by whole genome bisulfite sequencing. An essential task following the generation of bisulfite sequencing data is to detect differentially methylated cytosines (DMCs among treatments. Most statistical methods for DMC detection do not consider the dependency of methylation patterns across the genome, thus possibly inflating type I error. Furthermore, small sample sizes and weak methylation effects among different phenotype categories make it difficult for these statistical methods to accurately detect DMCs. To address these issues, the wavelet-based functional mixed model (WFMM was introduced to detect DMCs. To further examine the performance of WFMM in detecting weak differential methylation events, we used both simulated and empirical data and compare WFMM performance to a popular DMC detection tool methylKit. Analyses of simulated data that replicated the effects of the herbicide glyphosate on DNA methylation in Arabidopsis thaliana show that WFMM results in higher sensitivity and specificity in detecting DMCs compared to methylKit, especially when the methylation differences among phenotype groups are small. Moreover, the performance of WFMM is robust with respect to small sample sizes, making it particularly attractive considering the current high costs of bisulfite sequencing. Analysis of empirical Arabidopsis thaliana data under varying glyphosate dosages, and the analysis of monozygotic (MZ twins who have different pain sensitivities—both datasets have weak methylation effects of <1%—show that WFMM can identify more relevant DMCs related to the phenotype of interest than methylKit. Differentially methylated regions (DMRs are genomic regions with different DNA methylation status across biological samples. DMRs and DMCs are essentially the same

  17. Well-ordered "tooth-shaped" silver-microstructures on poly(methyl methacrylate) patterned by laser writing

    Czech Academy of Sciences Publication Activity Database

    Tůma, J.; Lyutakov, O.; Šimek, P.; Hnatowicz, Vladimír; Švorčík, V.

    2015-01-01

    Roč. 158, NOV (2015), s. 388-391 ISSN 0167-577X R&D Projects: GA ČR(CZ) GBP108/12/G108 Institutional support: RVO:61389005 Keywords : polymer laser writing * patterning * porphyrine absorber * silver microstructures Subject RIV: JJ - Other Materials Impact factor: 2.437, year: 2015

  18. Heterogeneous genetic diversity pattern in Plasmodium vivax genes encoding merozoite surface proteins (MSP) -7E, -7F and -7L.

    Science.gov (United States)

    Garzón-Ospina, Diego; Forero-Rodríguez, Johanna; Patarroyo, Manuel A

    2014-12-13

    The msp-7 gene has become differentially expanded in the Plasmodium genus; Plasmodium vivax has the highest copy number of this gene, several of which encode antigenic proteins in merozoites. DNA sequences from thirty-six Colombian clinical isolates from P. vivax (pv) msp-7E, -7F and -7L genes were analysed for characterizing and studying the genetic diversity of these pvmsp-7 members which are expressed during the intra-erythrocyte stage; natural selection signals producing the variation pattern so observed were evaluated. The pvmsp-7E gene was highly polymorphic compared to pvmsp-7F and pvmsp-7L which were seen to have limited genetic diversity; pvmsp-7E polymorphism was seen to have been maintained by different types of positive selection. Even though these copies seemed to be species-specific duplications, a search in the Plasmodium cynomolgi genome (P. vivax sister taxon) showed that both species shared the whole msp-7 repertoire. This led to exploring the long-term effect of natural selection by comparing the orthologous sequences which led to finding signatures for lineage-specific positive selection. The results confirmed that the P. vivax msp-7 family has a heterogeneous genetic diversity pattern; some members are highly conserved whilst others are highly diverse. The results suggested that the 3'-end of these genes encode MSP-7 proteins' functional region whilst the central region of pvmsp-7E has evolved rapidly. The lineage-specific positive selection signals found suggested that mutations occurring in msp-7s genes during host switch may have succeeded in adapting the ancestral P. vivax parasite population to humans.

  19. Tree diversity patterns along the latitudinal gradient in the northwestern Russia

    Directory of Open Access Journals (Sweden)

    Elena Tikhonova

    2017-12-01

    Full Text Available Background One of the key forest characteristics is the biodiversity, particularly the diversity of trees which are forest ecosystem engineers. Nowadays the most worldwide common approach for assessment of forest conditions and dynamics is based on the systematic monitoring, performed at a set of regularly structured plots. To fulfill the existing gap in this sort of knowledge on the Russian forests, an extensive study of tree species diversity on a regular network was conducted in north-west of Russia. Methods The study used the ICP Forests monitoring network that spans over 1700 km along the western Russian border from forest-tundra in the north to broadleaved-coniferous forests in the south. Tree data were collected at 710 sites that were assigned along a regular grid. We performed series of statistical analyses of the tree species distribution and diversity in relation to environmental and anthropogenic factors. Results According to the Maxent species distribution modelling results only Pinus sylvestris, Betula sp. and Picea abies have the potential to grow throughout the study area. The locally maximum tree species diversity varies along the latitudinal gradient from 1 to 3 species in the north to 5–7 species in the south. Monocultural stands are relatively abundant across the study area, being especially common in the south taiga. The prevailing part of the monocultural stands is represented by Scots pine (72%. The age distribution of dominant trees has a clear connection with the intensity of forest use. We found that recent wildfire events had only little effect on tree diversity in the study area. Conclusions We demonstrated that ICP Forests monitoring network enables to successfully establish the main qualitative and quantitative relations of the spatial variation of tree species diversity to climatic, landscape, soil and anthropogenic factors. Analysis of the influence of these factors on tree species distribution allowed us to

  20. Comparative Analysis of the Pattern of Population Genetic Diversity in Three Indo-West Pacific Rhizophora Mangrove Species.

    Science.gov (United States)

    Yan, Yu-Bin; Duke, Norm C; Sun, Mei

    2016-01-01

    Rhizophora species are the most widely distributed mangrove trees in the Indo-West Pacific (IWP) region. Comparative studies of these species with shared life history traits can help identify evolutionary factors that have played most important roles in determining genetic diversity within and between populations in ocean-current dispersed mangrove tree species. We sampled 935 individuals from 54 natural populations for genotyping with 13 microsatellite markers to investigate the level of genetic variation, population structure, and gene flow on a broad geographic scale in Rhizophora apiculata, Rhizophora mucronata , and Rhizophora stylosa across the IWP region. In contrast to the pattern expected of long-lived woody plants with predominant wind-pollination, water-dispersed seeds and wide geographic range, genetic variation within populations was generally low in all the three species, especially in those peripheral populations from geographic range limits. Although the large water-buoyant propagules of Rhizophora have capacity for long distance dispersal, such events might be rare in reality, as reflected by the low level of gene flow and high genetic differentiation between most of population pairs within each species. Phylogeographic separation of Australian and Pacific island populations from SE Asian lineages previously revealed with DNA sequence data was still detectable in R. apiculata based on genetic distances, but this pattern of disjunction was not always evident in R. mucronata and R. stylosa , suggesting that fast-evolving molecular markers could be more suitable for detecting contemporary genetic structure but not deep evolutionary divergence caused by historical vicariance. Given that mangrove species generally have small effective population sizes, we conclude that genetic drift coupled with limited gene flow have played a dominant role in producing the current pattern of population genetic diversity in the IWP Rhizophora species, overshadowing the

  1. Comparative Analysis of the Pattern of Population Genetic Diversity in Three Indo-West Pacific Rhizophora Mangrove Species

    Directory of Open Access Journals (Sweden)

    Yu-Bin Yan

    2016-09-01

    Full Text Available Rhizophora species are the most widely distributed mangrove trees in the Indo-West Pacific (IWP region. Comparative studies of these species with shared life history traits can help identify evolutionary factors that have played most important roles in determining genetic diversity within and between populations in ocean-current dispersed mangrove tree species. We sampled 935 individuals from 54 natural populations for genotyping with 13 microsatellite markers to investigate the level of genetic variation, population structure, and gene flow on a broad geographic scale in Rhizophora apiculata, R. mucronata, and R. stylosa across the IWP region. In contrast to the pattern expected of long-lived woody plants with predominant wind-pollination, water-dispersed seeds and wide geographic range, genetic variation within populations was generally low in all the three species, especially in those peripheral populations from geographic range limits. Although the large water-buoyant propagules of Rhizophora have capacity for long distance dispersal, such events might be rare in reality, as reflected by the low level of gene flow and high genetic differentiation between most of population pairs within each species. Phylogeographic separation of Australian and Pacific island populations from SE Asian lineages previously revealed with DNA sequence data was still detectable in R. apiculata based on genetic distances, but this pattern of disjunction was not always evident in R. mucronata and R. stylosa, suggesting that fast-evolving molecular markers could be more suitable for detecting contemporary genetic structure but not deep evolutionary divergence caused by historical vicariance. Given that mangrove species generally have small effective population sizes, we conclude that genetic drift coupled with limited gene flow have played a dominant role in producing the current pattern of population genetic diversity in the IWP Rhizophora species, overshadowing the

  2. The Gut Microbiota of Rural Papua New Guineans: Composition, Diversity Patterns, and Ecological Processes

    Directory of Open Access Journals (Sweden)

    Inés Martínez

    2015-04-01

    Full Text Available Although recent research revealed an impact of westernization on diversity and composition of the human gut microbiota, the exact consequences on metacommunity characteristics are insufficiently understood, and the underlying ecological mechanisms have not been elucidated. Here, we have compared the fecal microbiota of adults from two non-industrialized regions in Papua New Guinea (PNG with that of United States (US residents. Papua New Guineans harbor communities with greater bacterial diversity, lower inter-individual variation, vastly different abundance profiles, and bacterial lineages undetectable in US residents. A quantification of the ecological processes that govern community assembly identified bacterial dispersal as the dominant process that shapes the microbiome in PNG but not in the US. These findings suggest that the microbiome alterations detected in industrialized societies might arise from modern lifestyle factors limiting bacterial dispersal, which has implications for human health and the development of strategies aimed to redress the impact of westernization.

  3. Correlating Microbial Diversity Patterns with Geochemistry in an Extreme and Heterogeneous Environment of Mine Tailings

    Science.gov (United States)

    Liu, Jun; Hua, Zheng-Shuang; Chen, Lin-Xing; Kuang, Jia-Liang; Li, Sheng-Jin; Shu, Wen-Sheng

    2014-01-01

    Recent molecular surveys have advanced our understanding of the forces shaping the large-scale ecological distribution of microbes in Earth's extreme habitats, such as hot springs and acid mine drainage. However, few investigations have attempted dense spatial analyses of specific sites to resolve the local diversity of these extraordinary organisms and how communities are shaped by the harsh environmental conditions found there. We have applied a 16S rRNA gene-targeted 454 pyrosequencing approach to explore the phylogenetic differentiation among 90 microbial communities from a massive copper tailing impoundment generating acidic drainage and coupled these variations in community composition with geochemical parameters to reveal ecological interactions in this extreme environment. Our data showed that the overall microbial diversity estimates and relative abundances of most of the dominant lineages were significantly correlated with pH, with the simplest assemblages occurring under extremely acidic conditions and more diverse assemblages associated with neutral pHs. The consistent shifts in community composition along the pH gradient indicated that different taxa were involved in the different acidification stages of the mine tailings. Moreover, the effect of pH in shaping phylogenetic structure within specific lineages was also clearly evident, although the phylogenetic differentiations within the Alphaproteobacteria, Deltaproteobacteria, and Firmicutes were attributed to variations in ferric and ferrous iron concentrations. Application of the microbial assemblage prediction model further supported pH as the major factor driving community structure and demonstrated that several of the major lineages are readily predictable. Together, these results suggest that pH is primarily responsible for structuring whole communities in the extreme and heterogeneous mine tailings, although the diverse microbial taxa may respond differently to various environmental conditions

  4. Patterns of functional diversity of two trophic groups after canopy thinning in an abandoned coppice

    Czech Academy of Sciences Publication Activity Database

    Šipoš, Jan; Hédl, Radim; Hula, V.; Chudomelová, Markéta; Košulič, O.; Niedobová, J.; Riedl, Vladan

    2017-01-01

    Roč. 52, č. 1 (2017), s. 45-58 ISSN 1211-9520 R&D Projects: GA AV ČR IAA600050812; GA MŠk(CZ) EE2.3.20.0267 EU Projects: European Commission(XE) 278065 - LONGWOOD Institutional support: RVO:67985939 Keywords : coppice restoration * functional diversity * trophic groups Subject RIV: EH - Ecology, Behaviour OBOR OECD: Ecology Impact factor: 1.017, year: 2016

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

    Directory of Open Access Journals (Sweden)

    Jihong Huang

    2018-06-01

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

  6. Malagasy bats shelter a considerable genetic diversity of pathogenic Leptospira suggesting notable host-specificity patterns.

    Science.gov (United States)

    Gomard, Yann; Dietrich, Muriel; Wieseke, Nicolas; Ramasindrazana, Beza; Lagadec, Erwan; Goodman, Steven M; Dellagi, Koussay; Tortosa, Pablo

    2016-04-01

    Pathogenic Leptospira are the causative agents of leptospirosis, a disease of global concern with major impact in tropical regions. Despite the importance of this zoonosis for human health, the evolutionary and ecological drivers shaping bacterial communities in host reservoirs remain poorly investigated. Here, we describe Leptospira communities hosted by Malagasy bats, composed of mostly endemic species, in order to characterize host-pathogen associations and investigate their evolutionary histories. We screened 947 individual bats (representing 31 species, 18 genera and seven families) for Leptospira infection and subsequently genotyped positive samples using three different bacterial loci. Molecular identification showed that these Leptospira are notably diverse and include several distinct lineages mostly belonging to Leptospira borgpetersenii and L. kirschneri. The exploration of the most probable host-pathogen evolutionary scenarios suggests that bacterial genetic diversity results from a combination of events related to the ecology and the evolutionary history of their hosts. Importantly, based on the data set presented herein, the notable host-specificity we have uncovered, together with a lack of geographical structuration of bacterial genetic diversity, indicates that the Leptospira community at a given site depends on the co-occurring bat species assemblage. The implications of such tight host-specificity on the epidemiology of leptospirosis are discussed. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  7. Altitudinal patterns of diversity and functional traits of metabolically active microorganisms in stream biofilms

    Science.gov (United States)

    Wilhelm, Linda; Besemer, Katharina; Fragner, Lena; Peter, Hannes; Weckwerth, Wolfram; Battin, Tom J

    2015-01-01

    Resources structure ecological communities and potentially link biodiversity to energy flow. It is commonly believed that functional traits (generalists versus specialists) involved in the exploitation of resources depend on resource availability and environmental fluctuations. The longitudinal nature of stream ecosystems provides changing resources to stream biota with yet unknown effects on microbial functional traits and community structure. We investigated the impact of autochthonous (algal extract) and allochthonous (spruce extract) resources, as they change along alpine streams from above to below the treeline, on microbial diversity, community composition and functions of benthic biofilms. Combining bromodeoxyuridine labelling and 454 pyrosequencing, we showed that diversity was lower upstream than downstream of the treeline and that community composition changed along the altitudinal gradient. We also found that, especially for allochthonous resources, specialisation by biofilm bacteria increased along that same gradient. Our results suggest that in streams below the treeline biofilm diversity, specialisation and functioning are associated with increasing niche differentiation as potentially modulated by divers allochthonous and autochthonous constituents contributing to resources. These findings expand our current understanding on biofilm structure and function in alpine streams. PMID:25978543

  8. [Correlative analysis of the diversity patterns of regional surface water, NDVI and thermal environment].

    Science.gov (United States)

    Duan, Jin-Long; Zhang, Xue-Lei

    2012-10-01

    Taking Zhengzhou City, the capital of Henan Province in Central China, as the study area, and by using the theories and methodologies of diversity, a discreteness evaluation on the regional surface water, normalized difference vegetation index (NDVI), and land surface temperature (LST) distribution was conducted in a 2 km x 2 km grid scale. Both the NDVI and the LST were divided into 4 levels, their spatial distribution diversity indices were calculated, and their connections were explored. The results showed that it was of operability and practical significance to use the theories and methodologies of diversity in the discreteness evaluation of the spatial distribution of regional thermal environment. There was a higher overlap of location between the distributions of surface water and the lowest temperature region, and the high vegetation coverage was often accompanied by low land surface temperature. In 1988-2009, the discreteness of the surface water distribution in the City had an obvious decreasing trend. The discreteness of the surface water distribution had a close correlation with the discreteness of the temperature region distribution, while the discreteness of the NDVI classification distribution had a more complicated correlation with the discreteness of the temperature region distribution. Therefore, more environmental factors were needed to be included for a better evaluation.

  9. Genetic diversity and distribution patterns of host insects of Caterpillar Fungus Ophiocordyceps sinensis in the Qinghai-Tibet Plateau.

    Science.gov (United States)

    Quan, Qing-Mei; Chen, Ling-Ling; Wang, Xi; Li, Shan; Yang, Xiao-Ling; Zhu, Yun-Guo; Wang, Mu; Cheng, Zhou

    2014-01-01

    The caterpillar fungus Ophiocordyceps sinensis is one of the most valuable medicinal fungi in the world, and it requires host insects in family Hepialidae (Lepidoptera) to complete its life cycle. However, the genetic diversity and phylogeographic structures of the host insects remain to be explored. We analyzed the genetic diversity and temporal and spatial distribution patterns of genetic variation of the host insects throughout the O. sinensis distribution. Abundant haplotype and nucleotide diversity mainly existed in the areas of Nyingchi, ShangriLa, and around the edge of the Qinghai-Tibet Plateau, where are considered as the diversity center or micro-refuges of the host insects of O. sinensis. However, there was little genetic variation among host insects from 72.1% of all populations, indicating that the host species composition might be relatively simple in large-scale O. sinensis populations. All host insects are monophyletic except for those from four O. sinensis populations around Qinghai Lake. Significant phylogeographic structure (NST>GST, Pinsects, and the three major phylogenetic groups corresponded with specific geographical areas. The divergence of most host insects was estimated to have occurred at ca. 3.7 Ma, shortly before the rapid uplift of the QTP. The geographical distribution and star-like network of the haplotypes implied that most host insects were derived from the relicts of a once-widespread host that subsequently became fragmented. Neutrality tests, mismatch distribution analysis, and expansion time estimation confirmed that most host insects presented recent demographic expansions that began ca. 0.118 Ma in the late Pleistocene. Therefore, the genetic diversity and distribution of the present-day insects should be attributed to effects of the Qinghai-Tibet Plateau uplift and glacial advance/retreat cycles during the Quaternary ice age. These results provide valuable information to guide the protection and sustainable use of these host

  10. Analysis of Genetic Diversity and Structure Pattern of Indigofera Pseudotinctoria in Karst Habitats of the Wushan Mountains Using AFLP Markers.

    Science.gov (United States)

    Fan, Yan; Zhang, Chenglin; Wu, Wendan; He, Wei; Zhang, Li; Ma, Xiao

    2017-10-16

    Indigofera pseudotinctoria Mats is an agronomically and economically important perennial legume shrub with a high forage yield, protein content and strong adaptability, which is subject to natural habitat fragmentation and serious human disturbance. Until now, our knowledge of the genetic relationships and intraspecific genetic diversity for its wild collections is still poor, especially at small spatial scales. Here amplified fragment length polymorphism (AFLP) technology was employed for analysis of genetic diversity, differentiation, and structure of 364 genotypes of I. pseudotinctoria from 15 natural locations in Wushan Montain, a highly structured mountain with typical karst landforms in Southwest China. We also tested whether eco-climate factors has affected genetic structure by correlating genetic diversity with habitat features. A total of 515 distinctly scoreable bands were generated, and 324 of them were polymorphic. The polymorphic information content (PIC) ranged from 0.694 to 0.890 with an average of 0.789 per primer pair. On species level, Nei's gene diversity ( H j ), the Bayesian genetic diversity index ( H B ) and the Shannon information index ( I ) were 0.2465, 0.2363 and 0.3772, respectively. The high differentiation among all sampling sites was detected ( F ST = 0.2217, G ST = 0.1746, G' ST = 0.2060, θ B = 0.1844), and instead, gene flow among accessions ( N m = 1.1819) was restricted. The population genetic structure resolved by the UPGMA tree, principal coordinate analysis, and Bayesian-based cluster analyses irrefutably grouped all accessions into two distinct clusters, i.e., lowland and highland groups. The population genetic structure resolved by the UPGMA tree, principal coordinate analysis, and Bayesian-based cluster analyses irrefutably grouped all accessions into two distinct clusters, i.e., lowland and highland groups. This structure pattern may indicate joint effects by the neutral evolution and natural selection. Restricted N m was

  11. Genetic diversity and distribution patterns of host insects of Caterpillar Fungus Ophiocordyceps sinensis in the Qinghai-Tibet Plateau.

    Directory of Open Access Journals (Sweden)

    Qing-Mei Quan

    Full Text Available The caterpillar fungus Ophiocordyceps sinensis is one of the most valuable medicinal fungi in the world, and it requires host insects in family Hepialidae (Lepidoptera to complete its life cycle. However, the genetic diversity and phylogeographic structures of the host insects remain to be explored. We analyzed the genetic diversity and temporal and spatial distribution patterns of genetic variation of the host insects throughout the O. sinensis distribution. Abundant haplotype and nucleotide diversity mainly existed in the areas of Nyingchi, ShangriLa, and around the edge of the Qinghai-Tibet Plateau, where are considered as the diversity center or micro-refuges of the host insects of O. sinensis. However, there was little genetic variation among host insects from 72.1% of all populations, indicating that the host species composition might be relatively simple in large-scale O. sinensis populations. All host insects are monophyletic except for those from four O. sinensis populations around Qinghai Lake. Significant phylogeographic structure (NST>GST, P<0.05 was revealed for the monophyletic host insects, and the three major phylogenetic groups corresponded with specific geographical areas. The divergence of most host insects was estimated to have occurred at ca. 3.7 Ma, shortly before the rapid uplift of the QTP. The geographical distribution and star-like network of the haplotypes implied that most host insects were derived from the relicts of a once-widespread host that subsequently became fragmented. Neutrality tests, mismatch distribution analysis, and expansion time estimation confirmed that most host insects presented recent demographic expansions that began ca. 0.118 Ma in the late Pleistocene. Therefore, the genetic diversity and distribution of the present-day insects should be attributed to effects of the Qinghai-Tibet Plateau uplift and glacial advance/retreat cycles during the Quaternary ice age. These results provide valuable

  12. Spatial gradients in freshwater fish diversity, abundance and current pattern in the Himalayan region of Upper Ganges Basin, India

    Directory of Open Access Journals (Sweden)

    AJEY KUMAR PATHAK

    2014-10-01

    Full Text Available Pathak AK, Sarkar UK, Singh SP. 2014. Spatial gradients in freshwater fish diversity, abundance and current pattern in the Himalayan region of Upper Ganges Basin, India. Biodiversitas 15: 186-194.The present study describes the analysis and mapping of the different measurements of freshwater fish biodiversity of the Upper Ganges basin in the Himalayan region using spatial interpolation methods of Geographical Information System. The diversity, richness and abundance of fishes for each sampling location were determined and Kriging interpolation was applied on each fisheries measurement to predict and produce semivariogram. The semivariogarms produced were cross validated and reclassified. The reclassified maps for richness, abundance and diversity of fishes, occurrence of cold water threatened fish and abundance of important genera like Tor, Schziothorax and species were produced. The result of the Kriging produced good results and overall error in the estimation process was found significant. The cross validation of semovariograms also provided a better result with the observed data sets. Moreover, weighted overlay analysis of the reclassified raster maps of richness and abundance of fishes produced the classified raster map at different evaluation scale (0-10 qualitatively describing the gradient of species richness and abundance compositely. Similarly, the classified raster map at same evaluation scale qualitatively describing the gradient of species abundance and diversity compositely was produced and published. Further, basin wise analysis between Alaknanda/Pindar and Ganga1 sub basins showed 0.745 disparities at 0.745 distances in 2 dimensional spaces. The richness, diversity and abundance of threatened fishes among the different sampling locations were not significant (p = 0.9.

  13. The use of protein patterns in genetic diversity analysis in some Brassica napus cultivars

    Directory of Open Access Journals (Sweden)

    Roya Razavizadeh

    2013-11-01

    Full Text Available In this study, protein variations of seeds and five-day old cotyledonal leaves of four selected Brassica napus cultivars including Elite, Ocapy, Tasilo and Zarfam were analyzed by SDS-PAGE to identify protein markers. The amount of total soluble protein of seed storage proteins did not show significant differences in all cultivars whereas it was different in cotyledonal leaves. Protein patterns of seeds and cotyledonal leaves showed significant differences using SDS-PAGE and consequence analysis of bands by ImageJ program. Relative expression of six protein bands in seeds and five-day old cotyledonal leaves were significantly different. Three protein markers were identified by protein patterns of seed and cotyledonal leaves. The results of relationship analysis based on presence and absence of the specific protein bands in protein pattern of seed storage proteins showed that Tasilo and Elite cultivars had the highest similarities.

  14. Diversity of dietary patterns observed in the European Prospective Investigation into Cancer and Nutrition (EPIC) project

    DEFF Research Database (Denmark)

    Slimani, N.; Fahey, M.; Welch, A.A.

    2002-01-01

    differences were observed across centres, the countries participating in EPIC are characterised by specific dietary patterns. Overall, Italy and Greece have a dietary pattern characterised by plant foods (except potatoes) and a lower consumption of animal and processed foods, compared with the other EPIC...... countries. France and particularly Spain have more heterogeneous dietary patterns, with a relatively high consumption of both plant foods and animal products. Apart from characteristics specific to vegetarian groups, the UK 'health-conscious' group shares with the UK general population a relatively high...... consumption of tea, sauces, cakes, soft drinks (women), margarine and butter. In contrast, the diet in the Nordic countries, The Netherlands, Germany and the UK general population is relatively high in potatoes and animal, processed and sweetened/refined foods, with proportions varying across countries...

  15. Diversity of dietary patterns observed in the European Prospective Investigation into Cancer and Nutrition (EPIC) project

    DEFF Research Database (Denmark)

    Slimani, N.; Fahey, M.; Welch, A.A.

    2002-01-01

    countries. France and particularly Spain have more heterogeneous dietary patterns, with a relatively high consumption of both plant foods and animal products. Apart from characteristics specific to vegetarian groups, the UK 'health-conscious' group shares with the UK general population a relatively high....../centres. In these countries, consumption of vegetables and fruit is similar to, or below, the overall EPIC means, and is low for legumes and vegetable oils. Overall, dietary patterns were similar for men and women, although there were large gender differences for certain food groups. CONCLUSIONS: There are considerable...

  16. Spatial Patterns of Species Diversity and Phylogenetic Structure of Plant Communities in the Tianshan Mountains, Arid Central Asia

    Directory of Open Access Journals (Sweden)

    Hong-Xiang Zhang

    2017-12-01

    Full Text Available The Tianshan Mountains, located in arid Central Asia, have a humid climate and are biodiversity hotspots. Here, we aimed to clarify whether the pattern of species diversity and the phylogenetic structure of plant communities is affected by environmental variables and glacial refugia. In this study, plant community assemblies of 17 research sites with a total of 35 sample plots were investigated at the grassland/woodland boundaries on the Tianshan Mountains. Community phylogeny of these plant communities was constructed based on two plant DNA barcode regions. The indices of phylogenetic diversity and phylogenetic community structure were calculated for these sample plots. We first estimated the correlation coefficients between species richness (SR and environmental variables as well as the presence of glacial refugia. We then mapped the significant values of indices of community phylogeny (PD, RPD, NRI, and NTI to investigate the correlation between community phylogeny and environmental structure or macrozones in the study area. The results showed that a significantly higher value of SR was obtained for the refugial groups than for the colonizing groups (P < 0.05; presence of refugia and environmental variables were highly correlated to the pattern of variation in SR. Indices of community phylogeny were not significantly different between refugial and colonizing regions. Comparison with the humid western part showed that plant communities in the arid eastern part of the Tianshan Mountains tended to display more significant phylogenetic overdispersion. The variation tendency of the PhyloSor index showed that the increase in macro-geographical and environmental distance did not influence obvious phylogenetic dissimilarities between different sample plots. In conclusion, glacial refugia and environmental factors profoundly influenced the pattern of SR, but community phylogenetic structure was not affected by glacial refugia among different plant

  17. The Vasodilator Effect of a Cream Containing 10% Menthol and 15% Methyl Salicylate on Random-Pattern Skin Flaps in Rats.

    Science.gov (United States)

    Dölen, Utku Can; Sungur, Nezih; Koca, Gökhan; Ertunç, Onur; Bağcı Bosi, Ayşe Tülay; Koçer, Uğur; Korkmaz, Meliha

    2015-11-01

    It is still difficult to prevent partial or full-thickness flap necrosis. In this study, the effects of a cream containing menthol and methyl salicylate on the viability of randompattern skin flaps were studied. Forty female Sprague-Dawley rats were divided into two equal groups. Caudally based dorsal random-pattern skin flaps were elevated, including the panniculus carnosus. In the study group, 1.5 mL of a cream containing menthol and methyl salicylate was applied to the skin of the flap, and saline solution (0.9%) was used in the control group. Upon completion of the experiment, flap necrosis was analyzed with imaging software and radionuclide scintigraphy. Histopathological measurements were made of the percentage of viable flaps, the number of vessels, and the width of the panniculus carnosus muscle. According to the photographic analysis, the mean viable flap surface area in the study group was larger than that in the control group (P=0.004). According to the scintigrams, no change in radioactivity uptake was seen in the study group (P>0.05). However, a significant decrease was observed in the control group (P=0.006). No statistically significant differences were observed between the groups in terms of the percentage of viable flaps, the number of vessels, or the width of the panniculus carnosus muscle (P>0.05). Based on these results, it is certain that the cream did not reduce the viability of the flaps. Due to its vasodilatory effect, it can be used as a component of the dressing in reconstructive operations where skin perfusion is compromised.

  18. The Vasodilator Effect of a Cream Containing 10% Menthol and 15% Methyl Salicylate on Random-Pattern Skin Flaps in Rats

    Directory of Open Access Journals (Sweden)

    Utku Can Dölen

    2015-11-01

    Full Text Available BackgroundIt is still difficult to prevent partial or full-thickness flap necrosis. In this study, the effects of a cream containing menthol and methyl salicylate on the viability of randompattern skin flaps were studied.MethodsForty female Sprague-Dawley rats were divided into two equal groups. Caudally based dorsal random-pattern skin flaps were elevated, including the panniculus carnosus. In the study group, 1.5 mL of a cream containing menthol and methyl salicylate was applied to the skin of the flap, and saline solution (0.9% was used in the control group. Upon completion of the experiment, flap necrosis was analyzed with imaging software and radionuclide scintigraphy. Histopathological measurements were made of the percentage of viable flaps, the number of vessels, and the width of the panniculus carnosus muscle.ResultsAccording to the photographic analysis, the mean viable flap surface area in the study group was larger than that in the control group (P=0.004. According to the scintigrams, no change in radioactivity uptake was seen in the study group (P>0.05. However, a significant decrease was observed in the control group (P=0.006. No statistically significant differences were observed between the groups in terms of the percentage of viable flaps, the number of vessels, or the width of the panniculus carnosus muscle (P>0.05.ConclusionsBased on these results, it is certain that the cream did not reduce the viability of the flaps. Due to its vasodilatory effect, it can be used as a component of the dressing in reconstructive operations where skin perfusion is compromised.

  19. Interracial and Intraracial Patterns of Mate Selection among America's Diverse Black Populations

    Science.gov (United States)

    Batson, Christie D.; Qian, Zhenchao; Lichter, Daniel T.

    2006-01-01

    Despite recent immigration from Africa and the Caribbean, Blacks in America are still viewed as a monolith in many previous studies. In this paper, we use newly released 2000 census data to estimate log-linear models that highlight patterns of interracial and intraracial marriage and cohabitation among African Americans, West Indians, Africans,…

  20. [Effects of topography on the diversity and distribution pattern of ground plants in karst montane forests in Southwest Guangxi, China].

    Science.gov (United States)

    Yuan, Tie-Xiang; Zhang, He-Ping; Ou, Zhi-Yang; Tan, Yi-Bo

    2014-10-01

    Covariance analysis, curve-fitting, and canonical correspondence analysis (CCA) were used to explore the effects of topographic factors on the plant diversity and distribution patterns of ground flora with different growth forms in the karst mountains of Southwest Guangxi, China. A total of 152 ground plants were recorded. Among them, 37 species were ferns, 44 species herbs, 9 species lianas, and 62 species shrubs. Covariance analysis revealed that altitude significantly correlated with the individual number and richness of ground plants, and slope aspect had a significant effect on richness. Statistical analyses showed a highly significant nonlinear correlation between the individual number or richness of ground plants and altitude. Results of CCA revealed that slope aspect had a significant effect on the distribution pattern of ferns, and slope had a significant effect on the distribution patterns of herbs, lianas and shrubs. Ferns were more sensitive than herbs, lianas and shrubs to changes in heat and soil water caused by aspect. The effect of slope was stronger than that of elevation on soil water and nutrients, and it was the most important topographic factor that affected the distribution patterns of herbs, lianas and shrubs in this region.

  1. Diversity of chimera-like patterns from a model of 2D arrays of neurons with nonlocal coupling

    Science.gov (United States)

    Tian, Chang-Hai; Zhang, Xi-Yun; Wang, Zhen-Hua; Liu, Zong-Hua

    2017-06-01

    Chimera states have been studied in 1D arrays, and a variety of different chimera states have been found using different models. Research has recently been extended to 2D arrays but only to phase models of them. Here, we extend it to a nonphase model of 2D arrays of neurons and focus on the influence of nonlocal coupling. Using extensive numerical simulations, we find, surprisingly, that this system can show most types of previously observed chimera states, in contrast to previous models, where only one or a few types of chimera states can be observed in each model. We also find that this model can show some special chimera-like patterns such as gridding and multicolumn patterns, which were previously observed only in phase models. Further, we present an effective approach, i.e., removing some of the coupling links, to generate heterogeneous coupling, which results in diverse chimera-like patterns and even induces transformations from one chimera-like pattern to another.

  2. A cross-study analysis of prenatal exposures to environmental contaminants and the epigenome: support for stress-responsive transcription factor occupancy as a mediator of gene-specific CpG methylation patterning

    Science.gov (United States)

    Martin, Elizabeth M.; Fry, Rebecca C.

    2016-01-01

    Abstract A biological mechanism by which exposure to environmental contaminants results in gene-specific CpG methylation patterning is currently unknown. We hypothesize that gene-specific CpG methylation is related to environmentally perturbed transcription factor occupancy. To test this hypothesis, a database of 396 genes with altered CpG methylation either in cord blood leukocytes or placental tissue was compiled from 14 studies representing assessments of six environmental contaminants. Subsequently, an in silico approach was used to identify transcription factor binding sites enriched among the genes with altered CpG methylation in relationship to the suite of environmental contaminants. For each study, the sequences of the promoter regions (representing −1000 to +500 bp from the transcription start site) of all genes with altered CpG methylation were analyzed for enrichment of transcription factor binding sites. Binding sites for a total of 56 unique transcription factors were identified to be enriched within the promoter regions of the genes. Binding sites for the Kidney-Enriched Krupple-like Factor 15, a known responder to endogenous stress, were enriched ( P  contaminants. These data support the transcription factor occupancy theory as a potential mechanism underlying environmentally-induced gene-specific CpG methylation. PMID:27066266

  3. Molecular diversity patterns among various phytoplankton size-fractions in West Greenland in late summer

    Science.gov (United States)

    Elferink, Stephanie; Neuhaus, Stefan; Wohlrab, Sylke; Toebe, Kerstin; Voß, Daniela; Gottschling, Marc; Lundholm, Nina; Krock, Bernd; Koch, Boris P.; Zielinski, Oliver; Cembella, Allan; John, Uwe

    2017-03-01

    Arctic regions have experienced pronounced biological and biophysical transformations as a result of global change processes over the last several decades. Current hypotheses propose an elevated impact of those environmental changes on the biodiversity, community composition and metabolic processes of species. The effects on ecosystem function and services, particularly when invasive or toxigenic harmful species become dominant, can be expressed over a wide range of temporal and spatial scales in plankton communities. Our study focused on the comparison of molecular biodiversity of three size-fractions (micro-, nano-, picoplankton) in the coastal pelagic zone of West Greenland and their association with environmental parameters. Molecular diversity was assessed via parallel amplicon sequencing the 28S rRNA hypervariable D1/D2 region. We showed that biodiversity distribution within the area of Uummannaq Fjord, Vaigat Strait and Disko Bay differed markedly within and among size-fractions. In general, we observed a higher diversity within the picoplankton size fraction compared to the nano- and microplankton. In multidimensional scaling analysis, community composition of all three size fractions correlated with cell size, silicate and phosphate, chlorophyll a (chl a) and dinophysistoxin (DTX). Individually, each size fraction community composition also correlated with other different environmental parameters, i.e. temperature and nitrate. We observed a more homogeneous community of the picoplankton across all stations compared to the larger size classes, despite different prevailing environmental conditions of the sampling areas. This suggests that habitat niche occupation for larger-celled species may lead to higher functional trait plasticity expressed as an enhanced range of phenotypes, whereas smaller organisms may compensate for lower potential plasticity with higher diversity. The presence of recently identified toxigenic harmful algal bloom (HAB) species (such

  4. Patterns of genetic diversity at the nine forensically approved STR loci in the Indian populations.

    Science.gov (United States)

    Dutta, Ranjan; Reddy, B Mohan; Chattopadhyay, P; Kashyap, V K; Sun, Guangyun; Deka, Ranjan

    2002-02-01

    Genetic diversity at the nine short tandem repeat (STR) loci, which are universally approved and widely used for forensic investigations, has been studied among nine Indian populations with diverse ethnic, linguistic, and geographic backgrounds. The nine STR loci were profiled on 902 individuals using fluorescent detection methods on an ABI377 System, with the aid of an Amp-F1 Profiler Plus Kit. The studied populations include two upper castes, Brahmin and Kayastha; a tribe, Garo, from West Bengal; a Hindu caste, Meitei, with historical links to Bengal Brahmins; a migrant group of Muslims; three tribal groups, Naga, Kuki and Hmar, from Manipur in northeast India; and a middle-ranking caste, Golla, who are seminomadic herders from Andhra Pradesh. Gene diversity analysis suggests that the average heterozygosity is uniformly high (>0.8) in the studied populations, with the coefficient of gene differentiation at 0.050 +/- 0.0054. Both neighbor-joining (NJ) and unweighted pair group method with arithmetic mean (UPGMA) trees based on DA distances bring out distinct clusters that are consistent with ethnic, linguistic, and/or geographic backgrounds of the populations. The fit of the Harpending and Ward model of regression of average heterozygosity on the gene frequency centroid is found to be good, and the observed outliers are consistent with the population structure and history of the studied populations. Our study suggests that the nine STR loci, used so far mostly for forensic investigations, can be used fruitfully for microevolutionary studies as well, and for reconstructing the phylogenetic history of human populations, at least at the local level.

  5. Patterns of genetic diversity and differentiation in resistance gene clusters of two hybridizing European Populus species

    OpenAIRE

    Casey, Céline; Stölting, Kai N.; Barbará, Thelma; González-Martínez, Santiago C.; Lexer, Christian

    2015-01-01

    Resistance genes (R-genes) are essential for long-lived organisms such as forest trees, which are exposed to diverse herbivores and pathogens. In short-lived model species, R-genes have been shown to be involved in species isolation. Here, we studied more than 400 trees from two natural hybrid zones of the European Populus species Populus alba and Populus tremula for microsatellite markers located in three R-gene clusters, including one cluster situated in the incipient sex chromosome region....

  6. Spatial pattern affects diversity-productivity relationships in experimental meadow communities

    Czech Academy of Sciences Publication Activity Database

    Lamošová, T.; Doležal, Jiří; Lanta, V.; Lepš, Jan

    2010-01-01

    Roč. 36, č. 3 (2010), s. 325-332 ISSN 1146-609X R&D Projects: GA AV ČR IAA600050802; GA ČR GA526/09/0963; GA ČR GA206/09/1642; GA ČR GA526/07/0808 Institutional research plan: CEZ:AV0Z60050516; CEZ:AV0Z50070508 Keywords : functional-groups richness * species-diversity * experimental plant-communities Subject RIV: EF - Botanics Impact factor: 1.460, year: 2010

  7. Anti-leucine rich glioma inactivated 1 protein and anti-N-methyl-D-aspartate receptor encephalitis show distinct patterns of brain glucose metabolism in 18F-fluoro-2-deoxy-d-glucose positron emission tomography.

    Science.gov (United States)

    Wegner, Florian; Wilke, Florian; Raab, Peter; Tayeb, Said Ben; Boeck, Anna-Lena; Haense, Cathleen; Trebst, Corinna; Voss, Elke; Schrader, Christoph; Logemann, Frank; Ahrens, Jörg; Leffler, Andreas; Rodriguez-Raecke, Rea; Dengler, Reinhard; Geworski, Lilli; Bengel, Frank M; Berding, Georg; Stangel, Martin; Nabavi, Elham

    2014-06-20

    Pathogenic autoantibodies targeting the recently identified leucine rich glioma inactivated 1 protein and the subunit 1 of the N-methyl-D-aspartate receptor induce autoimmune encephalitis. A comparison of brain metabolic patterns in 18F-fluoro-2-deoxy-d-glucose positron emission tomography of anti-leucine rich glioma inactivated 1 protein and anti-N-methyl-D-aspartate receptor encephalitis patients has not been performed yet and shall be helpful in differentiating these two most common forms of autoimmune encephalitis. The brain 18F-fluoro-2-deoxy-d-glucose uptake from whole-body positron emission tomography of six anti-N-methyl-D-aspartate receptor encephalitis patients and four patients with anti-leucine rich glioma inactivated 1 protein encephalitis admitted to Hannover Medical School between 2008 and 2012 was retrospectively analyzed and compared to matched controls. Group analysis of anti-N-methyl-D-aspartate encephalitis patients demonstrated regionally limited hypermetabolism in frontotemporal areas contrasting an extensive hypometabolism in parietal lobes, whereas the anti-leucine rich glioma inactivated 1 protein syndrome was characterized by hypermetabolism in cerebellar, basal ganglia, occipital and precentral areas and minor frontomesial hypometabolism. This retrospective 18F-fluoro-2-deoxy-d-glucose positron emission tomography study provides novel evidence for distinct brain metabolic patterns in patients with anti-leucine rich glioma inactivated 1 protein and anti-N-methyl-D-aspartate receptor encephalitis.

  8. In silico prediction of Tetrahymena pyriformis toxicity for diverse industrial chemicals with substructure pattern recognition and machine learning methods.

    Science.gov (United States)

    Cheng, Feixiong; Shen, Jie; Yu, Yue; Li, Weihua; Liu, Guixia; Lee, Philip W; Tang, Yun

    2011-03-01

    There is an increasing need for the rapid safety assessment of chemicals by both industries and regulatory agencies throughout the world. In silico techniques are practical alternatives in the environmental hazard assessment. It is especially true to address the persistence, bioaccumulative and toxicity potentials of organic chemicals. Tetrahymena pyriformis toxicity is often used as a toxic endpoint. In this study, 1571 diverse unique chemicals were collected from the literature and composed of the largest diverse data set for T. pyriformis toxicity. Classification predictive models of T. pyriformis toxicity were developed by substructure pattern recognition and different machine learning methods, including support vector machine (SVM), C4.5 decision tree, k-nearest neighbors and random forest. The results of a 5-fold cross-validation showed that the SVM method performed better than other algorithms. The overall predictive accuracies of the SVM classification model with radial basis functions kernel was 92.2% for the 5-fold cross-validation and 92.6% for the external validation set, respectively. Furthermore, several representative substructure patterns for characterizing T. pyriformis toxicity were also identified via the information gain analysis methods. Copyright © 2010 Elsevier Ltd. All rights reserved.

  9. Mitochondrial diversity patterns and the Magdalenian resettlement of Europe: new insights from the edge of the Franco-Cantabrian refuge.

    Science.gov (United States)

    Pardiñas, Antonio F; Roca, Agustín; Garcia-Vazquez, Eva; Lopez, Belen

    2012-11-26

    Phylogeography of the mitochondrial lineages commonly found in Western Europe can be interpreted in the light of a postglacial resettlement of the continent. The center of this proposal lies in the Franco-Cantabrian glacial refuge, located in the northern Iberian Peninsula and Southwestern France. Recently, this interpretation has been confronted by the unexpected patterns of diversity found in some European haplogroups. To shed new lights on this issue, research on Iberian populations is crucial if events behind the actual genetics of the European continent are to be untangled. In this regard, the region of Asturias has not been extensively studied, despite its convoluted history with prolonged periods of isolation. As mitochondrial DNA is a kind of data that has been commonly used in human population genetics, we conducted a thorough regional study in which we collected buccal swabs from 429 individuals with confirmed Asturian ancestry. The joint analysis of these sequences with a large continent-wide database and previously published diversity patterns allowed us to discuss a new explanation for the population dynamics inside the Franco-Cantabrian area, based on range expansion theory. This approximation to previously contradictory findings has made them compatible with most proposals about the postglacial resettlement of Western Europe.

  10. Comparative Phylogeography Reveals Cryptic Diversity and Repeated Patterns of Cladogenesis for Amphibians and Reptiles in Northwestern Ecuador

    Science.gov (United States)

    Pyron, R. Alexander; Peñafiel, Nicolás; Romero-Barreto, Paulina; Culebras, Jaime; Bustamante, Lucas; Yánez-Muñoz, Mario H.; Guayasamin, Juan M.

    2016-01-01

    Comparative phylogeography allow us to understand how shared historical circumstances have shaped the formation of lineages, by examining a broad spectrum of co-distributed populations of different taxa. However, these types of studies are scarce in the Neotropics, a region that is characterized by high diversity, complex geology, and poorly understood biogeography. Here, we investigate the diversification patterns of five lineages of amphibians and reptiles, co-distributed across the Choco and Andes ecoregions in northwestern Ecuador. Mitochondrial DNA and occurrence records were used to determine the degree of geographic genetic divergence within species. Our results highlight congruent patterns of parapatric speciation and common geographical barriers for distantly related taxa. These comparisons indicate similar biological and demographic characteristics for the included clades, and reveal the existence of two new species of Pristimantis previously subsumed under P. walkeri, which we describe herein. Our data supports the hypothesis that widely distributed Chocoan taxa may generally experience their greatest opportunities for isolation and parapatric speciation across thermal elevational gradients. Finally, our study provides critical information to predict which unstudied lineages may harbor cryptic diversity, and how geology and climate are likely to have shaped their evolutionary history. PMID:27120100

  11. Comparative Phylogeography Reveals Cryptic Diversity and Repeated Patterns of Cladogenesis for Amphibians and Reptiles in Northwestern Ecuador.

    Science.gov (United States)

    Arteaga, Alejandro; Pyron, R Alexander; Peñafiel, Nicolás; Romero-Barreto, Paulina; Culebras, Jaime; Bustamante, Lucas; Yánez-Muñoz, Mario H; Guayasamin, Juan M

    2016-01-01

    Comparative phylogeography allow us to understand how shared historical circumstances have shaped the formation of lineages, by examining a broad spectrum of co-distributed populations of different taxa. However, these types of studies are scarce in the Neotropics, a region that is characterized by high diversity, complex geology, and poorly understood biogeography. Here, we investigate the diversification patterns of five lineages of amphibians and reptiles, co-distributed across the Choco and Andes ecoregions in northwestern Ecuador. Mitochondrial DNA and occurrence records were used to determine the degree of geographic genetic divergence within species. Our results highlight congruent patterns of parapatric speciation and common geographical barriers for distantly related taxa. These comparisons indicate similar biological and demographic characteristics for the included clades, and reveal the existence of two new species of Pristimantis previously subsumed under P. walkeri, which we describe herein. Our data supports the hypothesis that widely distributed Chocoan taxa may generally experience their greatest opportunities for isolation and parapatric speciation across thermal elevational gradients. Finally, our study provides critical information to predict which unstudied lineages may harbor cryptic diversity, and how geology and climate are likely to have shaped their evolutionary history.

  12. Local climatic conditions constrain soil yeast diversity patterns in Mediterranean forests, woodlands and scrub biome.

    Science.gov (United States)

    Yurkov, Andrey M; Röhl, Oliver; Pontes, Ana; Carvalho, Cláudia; Maldonado, Cristina; Sampaio, José Paulo

    2016-02-01

    Soil yeasts represent a poorly known fraction of the soil microbiome due to limited ecological surveys. Here, we provide the first comprehensive inventory of cultivable soil yeasts in a Mediterranean ecosystem, which is the leading biodiversity hotspot for vascular plants and vertebrates in Europe. We isolated and identified soil yeasts from forested sites of Serra da Arrábida Natural Park (Portugal), representing the Mediterranean forests, woodlands and scrub biome. Both cultivation experiments and the subsequent species richness estimations suggest the highest species richness values reported to date, resulting in a total of 57 and 80 yeast taxa, respectively. These values far exceed those reported for other forest soils in Europe. Furthermore, we assessed the response of yeast diversity to microclimatic environmental factors in biotopes composed of the same plant species but showing a gradual change from humid broadleaf forests to dry maquis. We observed that forest properties constrained by precipitation level had strong impact on yeast diversity and on community structure and lower precipitation resulted in an increased number of rare species and decreased evenness values. In conclusion, the structure of soil yeast communities mirrors the environmental factors that affect aboveground phytocenoses, aboveground biomass and plant projective cover. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  13. Patterns of nucleotide diversity at photoperiod related genes in Norway spruce [Picea abies (L.) Karst].

    Science.gov (United States)

    Källman, Thomas; De Mita, Stéphane; Larsson, Hanna; Gyllenstrand, Niclas; Heuertz, Myriam; Parducci, Laura; Suyama, Yoshihisa; Lagercrantz, Ulf; Lascoux, Martin

    2014-01-01

    The ability of plants to track seasonal changes is largely dependent on genes assigned to the photoperiod pathway, and variation in those genes is thereby important for adaptation to local day length conditions. Extensive physiological data in several temperate conifer species suggest that populations are adapted to local light conditions, but data on the genes underlying this adaptation are more limited. Here we present nucleotide diversity data from 19 genes putatively involved in photoperiodic response in Norway spruce (Picea abies). Based on similarity to model plants the genes were grouped into three categories according to their presumed position in the photoperiod pathway: photoreceptors, circadian clock genes, and downstream targets. An HKA (Hudson, Kreitman and Aquade) test showed a significant excess of diversity at photoreceptor genes, but no departure from neutrality at circadian genes and downstream targets. Departures from neutrality were also tested with Tajima's D and Fay and Wu's H statistics under three demographic scenarios: the standard neutral model, a population expansion model, and a more complex population split model. Only one gene, the circadian clock gene PaPRR3 with a highly positive Tajima's D value, deviates significantly from all tested demographic scenarios. As the PaPRR3 gene harbours multiple non-synonymous variants it appears as an excellent candidate gene for control of photoperiod response in Norway spruce.

  14. Mapping Diversity of Publication Patterns in the Social Sciences and Humanities: An Approach Making Use of Fuzzy Cluster Analysis

    Directory of Open Access Journals (Sweden)

    Frederik T. Verleysen

    2016-11-01

    Full Text Available Purpose: To present a method for systematically mapping diversity of publication patterns at the author level in the social sciences and humanities in terms of publication type, publication language and co-authorship. Design/methodology/approach: In a follow-up to the hard partitioning clustering by Verleysen and Weeren in 2016, we now propose the complementary use of fuzzy cluster analysis, making use of a membership coefficient to study gradual differences between publication styles among authors within a scholarly discipline. The analysis of the probability density function of the membership coefficient allows to assess the distribution of publication styles within and between disciplines. Findings: As an illustration we analyze 1,828 productive authors affiliated in Flanders, Belgium. Whereas a hard partitioning previously identified two broad publication styles, an international one vs. a domestic one, fuzzy analysis now shows gradual differences among authors. Internal diversity also varies across disciplines and can be explained by researchers' specialization and dissemination strategies. Research limitations: The dataset used is limited to one country for the years 2000-2011; a cognitive classification of authors may yield a different result from the affiliation-based classification used here. Practical implications: Our method is applicable to other bibliometric and research evaluation contexts, especially for the social sciences and humanities in non-Anglophone countries. Originality/value: The method proposed is a novel application of cluster analysis to the field of bibliometrics. Applied to publication patterns at the author level in the social sciences and humanities, for the first time it systematically documents intra-disciplinary diversity.

  15. Anthropogenic fragmentation may not alter pre-existing patterns of genetic diversity and differentiation in perennial shrubs.

    Science.gov (United States)

    Llorens, Tanya M; Ayre, David J; Whelan, Robert J

    2018-04-01

    Many plant species have pollination and seed dispersal systems and evolutionary histories that have produced strong genetic structuring. These genetic patterns may be consistent with expectations following recent anthropogenic fragmentation, making it difficult to detect fragmentation effects if no prefragmentation genetic data are available. We used microsatellite markers to investigate whether severe habitat fragmentation may have affected the structure and diversity of populations of the endangered Australian bird-pollinated shrub Grevillea caleyi R.Br., by comparing current patterns of genetic structure and diversity with those of the closely related G. longifolia R.Br. that has a similar life history but has not experienced anthropogenic fragmentation. Grevillea caleyi and G. longifolia showed similar and substantial population subdivision at all spatial levels (global F' ST  = 0.615 and 0.454; S p  = 0.039 and 0.066), marked isolation by distance and large heterozygous deficiencies. These characteristics suggest long-term effects of inbreeding in self-compatible species that have poor seed dispersal, limited connectivity via pollen flow and undergo population bottlenecks because of periodic fires. Highly structured allele size distributions, most notably in G. caleyi, imply historical processes of drift and mutation were important in isolated subpopulations. Genetic diversity did not vary with population size but was lower in more isolated populations for both species. Through this comparison, we reject the hypothesis that anthropogenic fragmentation has impacted substantially on the genetic composition or structure of G. caleyi populations. Our results suggest that highly self-compatible species with limited dispersal may be relatively resilient to the genetic changes predicted to follow habitat fragmentation. © 2018 John Wiley & Sons Ltd.

  16. High diversity in neuropeptide immunoreactivity patterns among three closely related species of Dinophilidae (Annelida)

    DEFF Research Database (Denmark)

    Kerbl, Alexandra; Conzelmann, Markus; Jékely, Gáspár

    2017-01-01

    Neuropeptides are conserved metazoan signaling molecules, and represent useful markers for comparative investigations on the morphology and function of the nervous system. However, little is known about the variation of neuropeptide expression patterns across closely related species in invertebrate...... groups other than insects. In this study, we compare the immunoreactivity patterns of 14 neuropeptides in three closely related microscopic dinophilid annelids (Dinophilus gyrociliatus, D. taeniatus and Trilobodrilus axi). The brains of all three species were found to consist of around 700 somata...... species. FMRFamide, MLD/pedal peptide, allatotropin, RNamide, excitatory peptide, and FVRIamide showed a broad localization within the brain, while calcitonin, SIFamide, vasotocin, RGWamide, DLamide, FLamide, FVamide, MIP, and serotonin were present in fewer cells in demarcated regions. The different...

  17. Patterns of change in the size spectra of numbers and diversity of the North Sea fish assemblage, as reflected in surveys and models

    DEFF Research Database (Denmark)

    Rice, J.; Gislason, Henrik

    1996-01-01

    data. The shape showed no overall trend, but diversity of smaller size classes showed a different temporal pattern from the diversity of intermediate and large size classes. The patterns in modelled output are consistent with, but do not prove, the hypothesis that trophic interactions are an important...... were very similar. Annual abundance spectra were linear and slopes increased significantly and fairly smoothly over the 20 years? indicating significant effects of fishing on the size composition of the exploited fish assemblage. The annual diversity spectra were more dome-shaped than in the survey...... factor in the fish community structure in the North Sea. (C) 1996 International Council for the Exploration of the Sea....

  18. Global diversity patterns of freshwater fishes - potential victims of their own success

    OpenAIRE

    Pelayo-Villamil, P.; Guisande, C.; Vari, R. P.; Manjarres-Hernandez, A.; Garcia-Rosello, E.; Gonzalez-Dacosta, J.; Heine, J.; Vilas, L. G.; Patti, B.; Quinci, E. M.; Jimenez, L. F.; Granado-Lorencio, C.; Tedesco, Pablo; Lobo, J. M.

    2015-01-01

    AimTo examine the pattern and cumulative curve of descriptions of freshwater fishes world-wide, the geographical biases in the available information on that fauna, the relationship between species richness and geographical rarity of such fishes, as well as to assess the relative contributions of different environmental factors on these variables. LocationGlobal. MethodsModestR was used to summarize the geographical distribution of freshwater fish species using information available from data-...

  19. Patterns of species diversity and phylogenetic structure of vascular plants on the Qinghai-Tibetan Plateau.

    Science.gov (United States)

    Yan, Yujing; Yang, Xian; Tang, Zhiyao

    2013-11-01

    Large-scale patterns of species richness and the underlying mechanisms regulating these patterns have long been the central issues in biogeography and macroecology. Phylogenetic community structure is a result of combined effects of contemporary ecological interactions, environmental filtering, and evolutionary history, and it links community ecology with biogeography and trait evolution. The Qinghai-Tibetan Plateau provides a good opportunity to test the influence of contemporary climate on shaping species richness because of its unique geological history, cold climate, and high biodiversity. In this study, based on high-resolution distributions of ˜9000 vascular plant species, we explored how species richness and phylogenetic structure of vascular plants correlate with climates on the highest (and species rich) plateau on the Earth. The results showed that most of the vascular plants were distributed on the eastern part of the plateau; there was a strong association between species richness and climate, even after the effects of habitat heterogeneity were controlled. However, the responses of richness to climate remarkably depended on life-forms. Richness of woody plants showed stronger climatic associations than that of herbaceous plants; energy and water availability together regulated richness pattern of woody plants; whereas water availability predominantly regulated richness pattern of herbaceous plants. The phylogenetic structure of vascular species clustered in most areas of the plateau, suggesting that rapid speciation and environment filtering dominated the assembly of communities on the plateau. We further propose that biodiversity conservation in this area should better take into account ecological features for different life-forms and phylogenetic lineages.

  20. Bryophyte diversity patterns in flooded and tierra firme forests in the Araracuara Region, Colombian Amazonia

    OpenAIRE

    Benavides, Juan C.; Idarraga, Alvaro; Alvarez, Esteban

    2004-01-01

    We investigated patterns of bryophyte species richness and composition in two forest types of Colombian Amazonia, non-flooded tierra firme forest and floodplain forest of the Caquetá River. A total of 109 bryophyte species were recorded from 14 0.2 ha plots. Bryophyte life forms and habitats were analyzed, including the canopy and epiphylls. Bryophyte species did not show significant differences between landscapes but mosses and liverworts were different and with opposite responses balancing ...

  1. Phytogeographic patterns and cryptic diversity in an aposematic toad from NW Argentina.

    Science.gov (United States)

    Clemente-Carvalho, Rute B; Vaira, Marcos; King, Laura E; Koscinski, Daria; Bonansea, Maria I; Lougheed, Stephen C

    2017-11-01

    The Yungas Redbelly Toad, Melanophryniscus rubriventris, is patchily distributed in Argentina, confined to the upland portion (1000-2000m above sea level) of the montane forests of northern and central regions of Salta, and in central-eastern and south-eastern Jujuy. This species is known for its striking aposematic color variation across its geographic distribution, and was once treated as a complex of three subspecies based on distinctive color patterns. Here we assess the geographical genetic variation within M. rubriventris and quantify divergence in color and pattern among individuals sampled from Northwestern Argentina. We compare multi-gene phylogeography of M. rubriventris to patterns of dorsal and ventral coloration to test whether evolutionary affinities predict variation in warning color. Our results reveal two well-supported species lineages: one confined to the extreme northern portion of our sampling area, and the other extending over most of the Argentine portion of the species' range, within which there are two populations. However, these well-supported evolutionary relationships do not mirror the marked variation in warning coloration. This discordance between DNA genealogy and warning color variation may reflect selection brought about by differences in local predation pressures, potentially coupled with effects of sexual selection and thermoregulation. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Diversity of fecal coliforms and their antimicrobial resistance patterns in wastewater treatment model plant.

    Science.gov (United States)

    Luczkiewicz, A; Fudala-Ksiazek, S; Jankowska, K; Quant, B; Olańczuk-Neyman, K

    2010-01-01

    The occurrence of resistance patterns among wastewater fecal coliforms was determined in the study. Susceptibility of the isolates was tested against 19 antimicrobial agents: aminoglycosides, aztreonam, carbapenems, cephalosporines, beta-lactam/beta-lactamase inhibitors, penicillines, tetracycline, trimethoprim/sulfamethoxazole, and fluoroquinolones. Additionally the removal of resistant isolates was evaluated in the laboratory-scale wastewater treatment model plant (M-WWTP), continuously supplied with the wastewater obtained from the full-scale WWTP. Number of fecal coliforms in raw (after mechanical treatment) and treated wastewater, as well as in aerobic chamber effluent was determined using selective medium. The selected strains were identified and examined for antibiotic resistance using Phoenix Automated Microbiology System (BD Biosciences, USA). The strains were identified as Escherichia coli (n=222), Klebsiella pneumoniae ssp. ozaenae (n=9), and Pantoea agglomerans (n=1). The isolate of P. agglomerans as well as 48% of E. coli isolates were sensitive to all antimicrobials tested. The most frequent resistance patterns were found for ampicillin: 100% of K. pneumoniae ssp. ozaenae and 41% of E. coli isolates. Among E. coli isolates 12% was regarded as multiple antimicrobial resistant (MAR). In the studied M-WWTP, the applied activated sludge processes reduced considerably the number of fecal coliforms, but increased the ratio of antimicrobial-resistant E. coli isolates to sensitive ones, especially among strains with MAR patterns.

  3. Geographical diversity of cause-of-death patterns and trends in Russia

    Directory of Open Access Journals (Sweden)

    Vladimir Shkolnikov

    2005-06-01

    Full Text Available This paper performs a systematic analysis of all currently available Russian data on mortality by region, census year (1970, 1979, 1989, and 1994 and cause of death. It investigates what links may be found between these geographical variations in cause-specific mortality, the negative general trends observed since 1965, and the wide fluctuations of the last two decades. For that, four two-year periods of observation were selected where it was possible to calculate fairly reliable mortality indicators by geographic units using census data for 1970, 1979, 1989, and micro-census data for 1994, and used a clustering model. Behind the complexity of the studied universe, three main conclusions appeared. Firstly, in European Russia, there is a stark contrast between south-west and north-east, both in terms of total mortality and of cause-of-death patterns. Secondly, analysis of overall cause-of-death patterns for all periods combined clearly confirms that contrast at the whole country level by the prolongation of the southern part of European Russia through the continuation of the black soil ("chernoziom" belt along the Kazakhstan border, while the rest of Siberia presents a radically different picture to European Russia. Thirdly, while it is difficult to infer any permanent geographical pattern of mortality from that very fluctuating piece of history, 1988-89 appears to be a base period for at least the entire period from 1969-1994.

  4. Diversity and antibiotic resistance patterns of Sphingomonadaceae isolates from drinking water.

    Science.gov (United States)

    Vaz-Moreira, Ivone; Nunes, Olga C; Manaia, Célia M

    2011-08-15

    Sphingomonadaceae (n = 86) were isolated from a drinking water treatment plant (n = 6), tap water (n = 55), cup fillers for dental chairs (n = 21), and a water demineralization filter (n = 4). The bacterial isolates were identified based on analysis of the 16S rRNA gene sequence, and intraspecies variation was assessed on the basis of atpD gene sequence analysis. The isolates were identified as members of the genera Sphingomonas (n = 27), Sphingobium (n = 28), Novosphingobium (n = 12), Sphingopyxis (n = 7), and Blastomonas (n = 12). The patterns of susceptibility to five classes of antibiotics were analyzed and compared for the different sites of isolation and taxonomic groups. Colistin resistance was observed to be intrinsic (92%). The highest antibiotic resistance prevalence values were observed in members of the genera Sphingomonas and Sphingobium and for beta-lactams, ciprofloxacin, and cotrimoxazole. In tap water and in water from dental chairs, antibiotic resistance was more prevalent than in the other samples, mainly due to the predominance of isolates of the genera Sphingomonas and Sphingobium. These two genera presented distinct patterns of association with antibiotic resistance, suggesting different paths of resistance development. Antibiotic resistance patterns were often related to the species rather than to the site or strain, suggesting the importance of vertical resistance transmission in these bacteria. This is the first study demonstrating that members of the family Sphingomonadaceae are potential reservoirs of antibiotic resistance in drinking water.

  5. Diversity and Antibiotic Resistance Patterns of Sphingomonadaceae Isolates from Drinking Water▿

    Science.gov (United States)

    Vaz-Moreira, Ivone; Nunes, Olga C.; Manaia, Célia M.

    2011-01-01

    Sphingomonadaceae (n = 86) were isolated from a drinking water treatment plant (n = 6), tap water (n = 55), cup fillers for dental chairs (n = 21), and a water demineralization filter (n = 4). The bacterial isolates were identified based on analysis of the 16S rRNA gene sequence, and intraspecies variation was assessed on the basis of atpD gene sequence analysis. The isolates were identified as members of the genera Sphingomonas (n = 27), Sphingobium (n = 28), Novosphingobium (n = 12), Sphingopyxis (n = 7), and Blastomonas (n = 12). The patterns of susceptibility to five classes of antibiotics were analyzed and compared for the different sites of isolation and taxonomic groups. Colistin resistance was observed to be intrinsic (92%). The highest antibiotic resistance prevalence values were observed in members of the genera Sphingomonas and Sphingobium and for beta-lactams, ciprofloxacin, and cotrimoxazole. In tap water and in water from dental chairs, antibiotic resistance was more prevalent than in the other samples, mainly due to the predominance of isolates of the genera Sphingomonas and Sphingobium. These two genera presented distinct patterns of association with antibiotic resistance, suggesting different paths of resistance development. Antibiotic resistance patterns were often related to the species rather than to the site or strain, suggesting the importance of vertical resistance transmission in these bacteria. This is the first study demonstrating that members of the family Sphingomonadaceae are potential reservoirs of antibiotic resistance in drinking water. PMID:21705522

  6. Patterns of benthic bacterial diversity in coastal areas contaminated by heavy metals, Polycyclic Aromatic Hydrocarbons (PAHs and Polychlorinated Biphenyls (PCBs

    Directory of Open Access Journals (Sweden)

    Grazia Marina eQuero

    2015-10-01

    Full Text Available Prokaryotes in coastal sediments are fundamental players in the ecosystem functioning and regulate processes relevant in the global biogeochemical cycles. Nevertheless, knowledge on benthic microbial diversity patterns across spatial scales, or as function to anthropogenic influence, is still limited. We investigated the microbial diversity in two of the most chemically polluted sites along the coast of Italy. One site is the Po River Prodelta (Northern Adriatic Sea, which receives contaminant discharge from one of the largest rivers in Europe. The other site, the Mar Piccolo of Taranto (Ionian Sea, is a chronically-polluted area due to steel production plants, oil refineries, and intense maritime traffic. We collected sediments from 30 stations along gradients of contamination, and studied prokaryotic diversity using Illumina sequencing of amplicons of a 16S rDNA gene fragment. The main sediment variables and the concentration of eleven metals, PCBs and PAHs were measured. Chemical analyses confirmed the high contamination in both sites, with concentrations of PCBs particularly high and often exceeding the sediment guidelines. The analysis of more than 3 millions 16S rDNA sequences showed that richness decreased with higher contamination levels. Multivariate analyses showed that contaminants significantly shaped community composition. Assemblages differed significantly between the two sites, but showed wide within-site variations related with spatial gradients in the chemical contamination, and the presence of a core set of OTUs shared by the two geographically distant sites. A larger importance of PCB-degrading taxa was observed in the Mar Piccolo, suggesting their potential selection in this historically-polluted site. Our results indicate that sediment contamination by multiple contaminants significantly alter benthic prokaryotic diversity in coastal areas, and suggests considering the potential contribution of the resident microbes to

  7. Phylogeny and patterns of diversity of goat mtDNA haplogroup A revealed by resequencing complete mitogenomes.

    Directory of Open Access Journals (Sweden)

    Maria Grazia Doro

    Full Text Available We sequenced to near completion the entire mtDNA of 28 Sardinian goats, selected to represent the widest possible diversity of the most widespread mitochondrial evolutionary lineage, haplogroup (Hg A. These specimens were reporters of the diversity in the island but also elsewhere, as inferred from their affiliation to each of 11 clades defined by D-loop variation. Two reference sequences completed the dataset. Overall, 206 variations were found in the full set of 30 sequences, of which 23 were protein-coding non-synonymous single nucleotide substitutions. Many polymorphic sites within Hg A were informative for the reconstruction of its internal phylogeny. Bayesian and network clustering revealed a general similarity over the entire molecule of sequences previously assigned to the same D-loop clade, indicating evolutionarily meaningful lineages. Two major sister groupings emerged within Hg A, which parallel distinct geographical distributions of D-loop clades in extant stocks. The pattern of variation in protein-coding genes revealed an overwhelming role of purifying selection, with the quota of surviving variants approaching neutrality. However, a simple model of relaxation of selection for the bulk of variants here reported should be rejected. Non-synonymous diversity of Hg's A, B and C denoted that a proportion of variants not greater than that allowed in the wild was given the opportunity to spread into domesticated stocks. Our results also confirmed that a remarkable proportion of pre-existing Hg A diversity became incorporated into domestic stocks. Our results confirm clade A11 as a well differentiated and ancient lineage peculiar of Sardinia.

  8. Patterns of fish diversity and assemblage structure and water quality in the longest Asian tropical river (Mekong)

    Science.gov (United States)

    Chea, R.; Lek, S.; Grenouillet, G.

    2016-12-01

    Although the Mekong River is one of the world's 35 biodiversity hotspots, the large-scale patterns of fish diversity and assemblage structure remain poorly addressed. The present study aimed to investigate the spatial variability of water quality in the Lower Mekong Basin and the fish distribution patterns in the Lower Mekong River (LMR) and to identify their environmental determinants. Daily fish catch data at 38 sites distributed along the LMR were related to 15 physicochemical and 19 climatic variables. As a result, four different clusters were defined according to the similarity in assemblage composition and 80 indicator species were identified. While fish species richness was highest in the Mekong delta and lowest in the upper part of the LMR, the diversity index was highest in the middle part of the LMR and lowest in the delta. We found that fish assemblages changed along the environmental gradients and that the main drivers affecting the fish assemblage structure were the seasonal variation of temperature, precipitation, dissolved oxygen, pH, and total phosphorus. Specifically, upstream assemblages were characterized by cyprinids and Pangasius catfish, well suited to low temperature, high dissolved oxygen and high pH. Fish assemblages in the delta were dominated by perch-like fish and clupeids, more tolerant to high temperatures, and high levels of nutrients (nitrates and total phosphorus) and salinity. Overall, the patterns were consistent between seasons. Our study contributes to establishing the first holistic fish community study in the LMR. Overall of the LMR water quality, we found that the water in the mainstream was less polluted than its tributaries; eutrophication and salinity could be key factors affecting water quality in LMR. Moreover, the seasonal variation of water quality seemed to be less marked than spatial variation occurring along the longitudinal gradient of Mekong River. Significant degradations were mainly associated with human

  9. Genetic diversity and biogeographical patterns of Caulerpa prolifera across the Mediterranean and Mediterranean/Atlantic transition zone

    KAUST Repository

    Varela-Á lvarez, Elena; Balau, Ana C.; Marbà , Nú rià N.; Afonso-Carrillo, Julio; Duarte, Carlos M.; Serrã o, Ester Á lvares

    2015-01-01

    Knowledge of spatial patterns of genetic differentiation between populations is key to understanding processes in evolutionary history of biological species. Caulerpa is a genus of marine green algae, which has attracted much public attention, mainly because of the impacts of invasive species in the Mediterranean. However, very little is known about the ecological and evolutionary history of the Mediterranean native Caulerpa prolifera, a species which is currently found at sites distributed worldwide. C. prolifera provides a good model to explore the patterns of genetic diversity at different scales across the Mediterranean and Atlantic area. This study aims to investigate the biogeographical patterns of diversity and differentiation of C. prolifera in the Mediterranean, with special focus on the Mediterranean/Atlantic transition zone. We used two nuclear (ITS rDNA and the hypervariable microsatellite locus CaPr_J2) and one chloroplast (tufA) DNA markers on samples of C. prolifera from its entire range. Analyses of 51 sequences of the cpDNA tufA of C. prolifera, 87 ITS2 sequences and genotypes of 788 ramets of C. prolifera for the locus CaPr_J2 revealed three different biogeographical areas: West Atlantic, East Atlantic and a larger area representing the Mediterranean, the Mediterranean/Atlantic transition zone and a Pacific site (Bali). It was found out that the Mediterranean/Atlantic transition zone is a biogeographical boundary for C. prolifera. A lack of connectivity was revealed between Atlantic and Mediterranean types, and identical sequences found in the Mediterranean and Indo-Pacific suggest either recent gene flow along the Red Sea connection or a possible ancient Indo-Pacific origin.

  10. Genetic diversity and biogeographical patterns of Caulerpa prolifera across the Mediterranean and Mediterranean/Atlantic transition zone

    KAUST Repository

    Varela-Álvarez, Elena

    2015-01-11

    Knowledge of spatial patterns of genetic differentiation between populations is key to understanding processes in evolutionary history of biological species. Caulerpa is a genus of marine green algae, which has attracted much public attention, mainly because of the impacts of invasive species in the Mediterranean. However, very little is known about the ecological and evolutionary history of the Mediterranean native Caulerpa prolifera, a species which is currently found at sites distributed worldwide. C. prolifera provides a good model to explore the patterns of genetic diversity at different scales across the Mediterranean and Atlantic area. This study aims to investigate the biogeographical patterns of diversity and differentiation of C. prolifera in the Mediterranean, with special focus on the Mediterranean/Atlantic transition zone. We used two nuclear (ITS rDNA and the hypervariable microsatellite locus CaPr_J2) and one chloroplast (tufA) DNA markers on samples of C. prolifera from its entire range. Analyses of 51 sequences of the cpDNA tufA of C. prolifera, 87 ITS2 sequences and genotypes of 788 ramets of C. prolifera for the locus CaPr_J2 revealed three different biogeographical areas: West Atlantic, East Atlantic and a larger area representing the Mediterranean, the Mediterranean/Atlantic transition zone and a Pacific site (Bali). It was found out that the Mediterranean/Atlantic transition zone is a biogeographical boundary for C. prolifera. A lack of connectivity was revealed between Atlantic and Mediterranean types, and identical sequences found in the Mediterranean and Indo-Pacific suggest either recent gene flow along the Red Sea connection or a possible ancient Indo-Pacific origin.

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

    Science.gov (United States)

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

    2016-09-23

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

  12. Cope's Rule and Romer's theory: patterns of diversity and gigantism in eurypterids and Palaeozoic vertebrates

    Science.gov (United States)

    Lamsdell, James C.; Braddy, Simon J.

    2010-01-01

    Gigantism is widespread among Palaeozoic arthropods, yet causal mechanisms, particularly the role of (abiotic) environmental factors versus (biotic) competition, remain unknown. The eurypterids (Arthropoda: Chelicerata) include the largest arthropods; gigantic predatory pterygotids (Eurypterina) during the Siluro-Devonian and bizarre sweep-feeding hibbertopterids (Stylonurina) from the Carboniferous to end-Permian. Analysis of family-level originations and extinctions among eurypterids and Palaeozoic vertebrates show that the diversity of Eurypterina waned during the Devonian, while the Placodermi radiated, yet Stylonurina remained relatively unaffected; adopting a sweep-feeding strategy they maintained their large body size by avoiding competition, and persisted throughout the Late Palaeozoic while the predatory nektonic Eurypterina (including the giant pterygotids) declined during the Devonian, possibly out-competed by other predators including jawed vertebrates. PMID:19828493

  13. Histone Lysine Methylation and Neurodevelopmental Disorders

    Directory of Open Access Journals (Sweden)

    Jeong-Hoon Kim

    2017-06-01

    Full Text Available Methylation of several lysine residues of histones is a crucial mechanism for relatively long-term regulation of genomic activity. Recent molecular biological studies have demonstrated that the function of histone methylation is more diverse and complex than previously thought. Moreover, studies using newly available genomics techniques, such as exome sequencing, have identified an increasing number of histone lysine methylation-related genes as intellectual disability-associated genes, which highlights the importance of accurate control of histone methylation during neurogenesis. However, given the functional diversity and complexity of histone methylation within the cell, the study of the molecular basis of histone methylation-related neurodevelopmental disorders is currently still in its infancy. Here, we review the latest studies that revealed the pathological implications of alterations in histone methylation status in the context of various neurodevelopmental disorders and propose possible therapeutic application of epigenetic compounds regulating histone methylation status for the treatment of these diseases.

  14. Longitudinal shifts in bacterial diversity and fermentation pattern in the rumen of steers grazing wheat pasture.

    Science.gov (United States)

    Pitta, D W; Pinchak, W E; Dowd, S; Dorton, K; Yoon, I; Min, B R; Fulford, J D; Wickersham, T A; Malinowski, D P

    2014-12-01

    Grazing steers on winter wheat forage is routinely practiced in the Southern Great Plains of the US. Here, we investigated the dynamics in bacterial populations of both solid and liquid ruminal fractions of steers grazing on maturing wheat forage of changing nutritive quality. The relationship between bacterial diversity and fermentation parameters in the liquid fraction was also investigated. During the first 28 days, the wheat was in a vegetative phase with a relatively high crude protein content (CP; 21%), which led to the incidence of mild cases of frothy bloat among steers. Rumen samples were collected on days 14, 28, 56 and 76, separated into solid and liquid fractions and analyzed for bacterial diversity using 16S pyrotag technology. The predominant phyla identified were Bacteroidetes (59-77%) and Firmicutes (20-33%) across both ruminal fractions. Very few differences were observed in the rumen bacterial communities within solid and liquid fractions on day 14. However, by day 28, the relatively high CP content complemented a distinct bacterial and chemical composition of the rumen fluid that was characterized by a higher ratio (4:1) of Bacteroidetes:Firmicutes and a corresponding lower acetate:propionate (3:1) ratio. Further, a greater accumulation of biofilm (mucopolysaccharide complex) on day 28 was strongly associated with the abundance of Firmicutes lineages such as Clostridium, Ruminococcus, Oscillospira and Moryella (Prumen microbiome and their association with fermentation activity in the rumen of steers during the vegetative (bloat-prone) and reproductive stages of wheat forage. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. Whole-genome methylation caller designed for methyl- DNA ...

    African Journals Online (AJOL)

    etchie

    2013-02-20

    Feb 20, 2013 ... Key words: Methyl-DNA immunoprecipitation, next-generation sequencing, Hidden ... its response to environmental cues. .... have a great potential to become the most cost-effective ... hg18 reference genome (set to 0 if not present in retrieved reads). ..... DNA methylation patterns and epigenetic memory.

  16. Estimating Common Growth Patterns in Juvenile Chinook Salmon (Oncorhynchus tshawytscha from Diverse Genetic Stocks and a Large Spatial Extent.

    Directory of Open Access Journals (Sweden)

    Pascale A L Goertler

    Full Text Available Life history variation in Pacific salmon (Oncorhynchus spp. supports species resilience to natural disturbances and fishery exploitation. Within salmon species, life-history variation often manifests during freshwater and estuarine rearing, as variation in growth. To date, however, characterizing variability in growth patterns within and among individuals has been difficult via conventional sampling methods because of the inability to obtain repeated size measurements. In this study we related otolith microstructures to growth rates of individual juvenile Chinook salmon (O. tshawytscha from the Columbia River estuary over a two-year period (2010-2012. We used dynamic factor analysis to determine whether there were common patterns in growth rates within juveniles based on their natal region, capture location habitat type, and whether they were wild or of hatchery origin. We identified up to five large-scale trends in juvenile growth rates depending on month and year of capture. We also found that hatchery fish had a narrower range of trend loadings for some capture groups, suggesting that hatchery fish do not express the same breadth of growth variability as wild fish. However, we were unable to resolve a relationship between specific growth patterns and habitat transitions. Our study exemplifies how a relatively new statistical analysis can be applied to dating or aging techniques to summarize individual variation, and characterize aspects of life history diversity.

  17. Pattern of morphological variation and diversity of Cocos nucifera (Arecaceae) in Mexico.

    Science.gov (United States)

    Zizumbo-Villarreal, D; Piñero, D

    1998-06-01

    The pattern of morphological variation of Cocos nucifera in Mexico was statistically and numerically evaluated. Forty-one populations were analyzed, using 17 morphological fruit characters. Principal components and cluster analyses indicated four main groups of coconut populations that showed high similarity with four different genotypes recently imported into Mexico from areas that could be the origin of Mexican coconut populations. These four genotypes were evaluated with regard to the lethal yellowing disease in Jamaica and showed a differential susceptibility. Therefore it is possible to speculate upon a difference in susceptibility of the Mexican genotypes. The analysis of correlation between morphological and geographical distances showed a high positive correlation that supports: (1) historical evidence that indicates early introductions of coconut from different regions of the world, (2) that on both coasts of Mexico two different patterns of dispersal were involved: continuous and in jumps. Collectively these results suggest that the impact of the lethal yellowing disease on coconut populations will vary depending on the specific area and the origin of its coconuts.

  18. Diversity and evolutionary patterns of immune genes in free-ranging Namibian leopards (Panthera pardus pardus).

    Science.gov (United States)

    Castro-Prieto, Aines; Wachter, Bettina; Melzheimer, Joerg; Thalwitzer, Susanne; Sommer, Simone

    2011-01-01

    The genes of the major histocompatibility complex (MHC) are a key component of the mammalian immune system and have become important molecular markers for fitness-related genetic variation in wildlife populations. Currently, no information about the MHC sequence variation and constitution in African leopards exists. In this study, we isolated and characterized genetic variation at the adaptively most important region of MHC class I and MHC class II-DRB genes in 25 free-ranging African leopards from Namibia and investigated the mechanisms that generate and maintain MHC polymorphism in the species. Using single-stranded conformation polymorphism analysis and direct sequencing, we detected 6 MHC class I and 6 MHC class II-DRB sequences, which likely correspond to at least 3 MHC class I and 3 MHC class II-DRB loci. Amino acid sequence variation in both MHC classes was higher or similar in comparison to other reported felids. We found signatures of positive selection shaping the diversity of MHC class I and MHC class II-DRB loci during the evolutionary history of the species. A comparison of MHC class I and MHC class II-DRB sequences of the leopard to those of other felids revealed a trans-species mode of evolution. In addition, the evolutionary relationships of MHC class II-DRB sequences between African and Asian leopard subspecies are discussed.

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

    Science.gov (United States)

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

    2012-03-01

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

  20. Patterns of cultural consensus and intracultural diversity in Ghanaian complementary feeding practices.

    Science.gov (United States)

    Kalra, Nikhila; Pelto, Gretel; Tawiah, Charlotte; Zobrist, Stephanie; Milani, Peiman; Manu, Grace; Laar, Amos; Parker, Megan

    2018-01-01

    Designing effective interventions to improve infant and young child (IYC) feeding requires knowledge about determinants of current practices, including cultural factors. Current approaches to obtaining and using research on culture tend to assume cultural homogeneity within a population. The purpose of this study was to examine the extent of cultural consensus (homogeneity) in communities where interventions to improve IYC feeding practices are needed to address undernutrition during the period of complementary feeding. A second, related objective was to identify the nature of intracultural variation, if such variation was evident. Selected protocols from the Focused Ethnographic Study for Infant and Young Child Feeding Manual were administered to samples of key informants and caregivers in a peri-urban and a rural area in Brong-Ahafo, Ghana. Cultural domain analysis techniques (free listing, caregiver assessment of culturally significant dimensions, and food ratings on these dimensions), as well as open-ended questions with exploratory probing, were used to obtain data on beliefs and related practices. Results reveal generally high cultural consensus on the 5 dimensions that were assessed (healthiness, appeal, child acceptance, convenience, and modernity) for caregiver decisions and on their ratings of individual foods. However, thematic analysis of caregiver narratives indicates that the meanings and content of the constructs connoted by the dimensions differed widely among individual mothers. These findings suggest that research on cultural factors that affect IYC practices, particularly cultural beliefs, should consider the nature and extent of cultural consensus and intracultural diversity, rather than assuming cultural homogeneity. © 2017 John Wiley & Sons Ltd.

  1. The diversity of polyprenol pattern in leaves of fruit trees belonging to Rosaceae and Cornaceae.

    Science.gov (United States)

    Wanke, M; Chojnacki, T; Swiezewska, E

    1998-01-01

    The polyprenol pattern in leaves of fruit trees belonging to the Rosaceae (genera: Prunus, Malus) and Cornaceae (genus: Cornus) families is presented. The content of polyprenyl acetates varied within plant species between 10-50 mg per gram of dry weight. In genus Prunus, Cornus and in representatives of species Malus domestica, a mixture of polyprenols composed of 18, 19, 20, 21 isoprene units was found. In six species of genus Prunus (sour-cherry): P. serrulata-spontanea, P. yedoensis, P. fruticosa. P. kurilensis, P. subhirtella and P. incisa the presence of a second polyprenol family, i.e. the group of prenologues consisting of prenol -35, -36, -37, etc. up to -42 was detected.

  2. Establishing the common patterns of future tropospheric ozone under diverse climate change scenarios

    Science.gov (United States)

    Jimenez-Guerrero, Pedro; Gómez-Navarro, Juan J.; Jerez, Sonia; Lorente-Plazas, Raquel; Baro, Rocio; Montávez, Juan P.

    2013-04-01

    The impacts of climate change on air quality may affect long-term air quality planning. However, the policies aimed at improving air quality in the EU directives have not accounted for the variations in the climate. Climate change alone influences future air quality through modifications of gas-phase chemistry, transport, removal, and natural emissions. As such, the aim of this work is to check whether the projected changes in gas-phase air pollution over Europe depends on the scenario driving the regional simulation. For this purpose, two full-transient regional climate change-air quality projections for the first half of the XXI century (1991-2050) have been carried out with MM5+CHIMERE system, including A2 and B2 SRES scenarios. Experiments span the periods 1971-2000, as a reference, and 2071-2100, as future enhanced greenhouse gas and aerosol scenarios (SRES A2 and B2). The atmospheric simulations have a horizontal resolution of 25 km and 23 vertical layers up to 100 mb, and were driven by ECHO-G global climate model outputs. The analysis focuses on the connection between meteorological and air quality variables. Our simulations suggest that the modes of variability for tropospheric ozone and their main precursors hardly change under different SRES scenarios. The effect of changing scenarios has to be sought in the intensity of the changing signal, rather than in the spatial structure of the variation patterns, since the correlation between the spatial patterns of variability in A2 and B2 simulation is r > 0.75 for all gas-phase pollutants included in this study. In both cases, full-transient simulations indicate an enhanced enhanced chemical activity under future scenarios. The causes for tropospheric ozone variations have to be sought in a multiplicity of climate factors, such as increased temperature, different distribution of precipitation patterns across Europe, increased photolysis of primary and secondary pollutants due to lower cloudiness, etc

  3. Patterns of plant diversity in seven temperate forest types of Western Himalaya, India

    Directory of Open Access Journals (Sweden)

    Javid Ahmad Dar

    2016-09-01

    Full Text Available Plant biodiversity patterns were analyzed in seven temperate forest types [Populus deltoides (PD, Juglans regia, Cedrus deodara, Pinus wallichiana, mixed coniferous, Abies pindrow (AP and Betula utilis (BU] of Kashmir Himalaya. A total of 177 plant species (158 genera, 66 families were recorded. Most of the species are herbs (82.5%, while shrubs account for 9.6% and trees represent 7.9%. Species richness ranged from 24 (PD to 96 (AP. Shannon, Simpson, and Fisher α indices varied: 0.17–1.06, 0.46–1.22, and 2.01–2.82 for trees; 0.36–0.94, 0.43–0.75, and 0.08–0.35 for shrubs; and 0.35–1.41, 0.27–0.95, and 5.61–39.98 for herbs, respectively. A total of five species were endemic. The total stems and basal area of trees were 35,794 stems (stand mean 330 stems/ha and 481.1 m2 (stand mean 40.2 m2/ha, respectively. The mean density and basal area ranged from 103 stems/ha (BU to 1,201 stems/ha (PD, and from 19.4 m2/ha (BU to 51.9 m2/ha (AP, respectively. Tree density decreased with increase in diameter class. A positive relationship was obtained between elevation and species richness and between elevation and evenness (R2 = 0.37 and 0.19, respectively. Tree and shrub communities were homogenous in nature across the seven forest types, while herbs showed heterogeneous distribution pattern.

  4. Diversity patterns and composition of native and exotic floras in central Chile

    Science.gov (United States)

    Figueroa, Javier A.; Teillier, Sebastián; Castro, Sergio A.

    2011-03-01

    Floristic changes in the Mediterranean region of central Chile brought about by human impact appear to be shared with other climatic regions, although there is a notable absence of empirical studies and available quantitative evidence for the central Chile region. This study examines the cover, richness and composition of native and exotic plant species in a representative area of central Chile. Through floristic characterization of 33 sites sampled using 40 × 40 m plots distributed along transect on which the two farthest sites were separated by 50 km, the floristic richness and cover patterns, as well as the general land use characteristics were evaluated (native matorral, espinal, abandoned farming field, forest plantations, periurban sites, road sites, river bank, and burnt site). We recorded 327 species of plants; 213 species were native and 114 were exotic. The average number of species was heterogeneous in all sites, showing a greater relative native frequency in those sites with a lower level of anthropic intervention. Except for the matorral, the cover of exotic species was greater than that of native species. No relation was found between richness and cover in relation to the different types of land use. The relationship between cover of native and exotic was negative, although for richness did not show relationship. Results show that the exotic species are limited by resources, although they have not completely displaced the native species. The native and exotic floras respond to different spatial distribution patterns, so their presence makes it possible to establish two facts rarely quantified in central Chile: first, that the exotic flora replaces (but does not necessarily displace) the native flora, and second, that at the same time, because of its greater geographic ubiquity and the abundance levels that it achieves, it contributes to the taxonomic and physiognomic homogenization of central Chile.

  5. The South-to-North Water Diversion Project: effect of the water diversion pattern on transmission of Oncomelania hupensis, the intermediate host of Schistosoma japonicum in China.

    Science.gov (United States)

    Liang, You-Sheng; Wang, Wei; Li, Hong-Jun; Shen, Xue-Hui; Xu, Yong-Liang; Dai, Jian-Rong

    2012-03-20

    The South-to-North Water Diversion Project (SNWDP) is the largest national water conservancy project in China. However, the Eastern Route Project (ERP) of SNWDP will refer to the habitats of Oncomelania hupensis, the intermediate host of Schistosoma japonicum. The present study was aimed at investigating the effects of some factors relating to the water diversion pattern on the spread north of O. hupensis and transmission of S. japonicum. Marked snails were attached to the floating debris, and then placed on the water surface, the passage of snails through water pumps was observed. Some marked living adult snails were placed under water in the 5 spots, 15, 30, 60, 90 and 120 days later, their survival and transfer under water were investigated. 2, 4, 8, 16, 32, 64 and 128 juvenile snails, with a male: female ratio of about 1, were caged, 1 year later, their reproductions were calculated. The snails attached on the floating debris at 100-, 50- and 20-cm-distance from the inlet pipe of the big pump (with a diameter of 80 cm), could be absorbed into the pumps, with passing rates of 2.45%, 3.93% and 43.46%, respectively, compared with 72.07% and 91.00% for the snails at 20 cm and 10 cm-distance from the inlet pipe of the small pump (with a diameter of 20 cm). A total of 36,600 marked living snails were put into 5 ponds and ditches, with the water depths of 1-1.6 m, 15-120 days later, no marked ones were found along the ponds and ditches or in the straw packages. The juvenile snails did not reproduce until their density reached up to 8 snails (ratio of male: female of 1)/0.16 m2. During the construction of ERP of SNWDP, the risk of northward spread of schistosomiasis japonica will be decreased or eliminated as long as long-term reliable interventions for snail control are implemented.

  6. Neighborhood diversity of large trees shows independent species patterns in a mixed dipterocarp forest in Sri Lanka.

    Science.gov (United States)

    Punchi-Manage, Ruwan; Wiegand, Thorsten; Wiegand, Kerstin; Getzin, Stephan; Huth, Andreas; Gunatilleke, C V Savitri; Gunatilleke, I A U Nimal

    2015-07-01

    Interactions among neighboring individuals influence plant performance and should create spatial patterns in local community structure. In order to assess the role of large trees in generating spatial patterns in local species richness, we used the individual species-area relationship (ISAR) to evaluate the species richness of trees of different size classes (and dead trees) in circular neighborhoods with varying radius around large trees of different focal species. To reveal signals of species interactions, we compared the ISAR function of the individuals of focal species with that of randomly selected nearby locations. We expected that large trees should strongly affect the community structure of smaller trees in their neighborhood, but that these effects should fade away with increasing size class. Unexpectedly, we found that only few focal species showed signals of species interactions with trees of the different size classes and that this was less likely for less abundant focal species. However, the few and relatively weak departures from independence were consistent with expectations of the effect of competition for space and the dispersal syndrome on spatial patterns. A noisy signal of competition for space found for large trees built up gradually with increasing life stage; it was not yet present for large saplings but detectable for intermediates. Additionally, focal species with animal-dispersed seeds showed higher species richness in their neighborhood than those with gravity- and gyration-dispersed seeds. Our analysis across the entire ontogeny from recruits to large trees supports the hypothesis that stochastic effects dilute deterministic species interactions in highly diverse communities. Stochastic dilution is a consequence of the stochastic geometry of biodiversity in species-rich communities where the identities of the nearest neighbors of a given plant are largely unpredictable. While the outcome of local species interactions is governed for each

  7. Nuclear distributions of NUP62 and NUP214 suggest architectural diversity and spatial patterning among nuclear pore complexes.

    Directory of Open Access Journals (Sweden)

    Yayoi Kinoshita

    Full Text Available The shape of nuclei in many adherent cultured cells approximates an oblate ellipsoid, with contralateral flattened surfaces facing the culture plate or the medium. Observations of cultured cell nuclei from orthogonal perspectives revealed that nucleoporin p62 (NUP62 and nucleoporin 214 (NUP214 are differentially distributed between nuclear pore complexes on the flattened surfaces and peripheral rim of the nucleus. High resolution stimulated emission depletion (STED immunofluorescence microscopy resolved individual NPCs, and suggested both heterogeneity and microheterogeneity in NUP62 and NUP214 immunolabeling among in NPC populations. Similar to nuclear domains and interphase chromosome territories, architectural diversity and spatial patterning of NPCs may be an intrinsic property of the nucleus that is linked to the functions and organization of underlying chromatin.

  8. Prokaryotic caspase homologs: phylogenetic patterns and functional characteristics reveal considerable diversity.

    Directory of Open Access Journals (Sweden)

    Johannes Asplund-Samuelsson

    Full Text Available Caspases accomplish initiation and execution of apoptosis, a programmed cell death process specific to metazoans. The existence of prokaryotic caspase homologs, termed metacaspases, has been known for slightly more than a decade. Despite their potential connection to the evolution of programmed cell death in eukaryotes, the phylogenetic distribution and functions of these prokaryotic metacaspase sequences are largely uncharted, while a few experiments imply involvement in programmed cell death. Aiming at providing a more detailed picture of prokaryotic caspase homologs, we applied a computational approach based on Hidden Markov Model search profiles to identify and functionally characterize putative metacaspases in bacterial and archaeal genomes. Out of the total of 1463 analyzed genomes, merely 267 (18% were identified to contain putative metacaspases, but their taxonomic distribution included most prokaryotic phyla and a few archaea (Euryarchaeota. Metacaspases were particularly abundant in Alphaproteobacteria, Deltaproteobacteria and Cyanobacteria, which harbor many morphologically and developmentally complex organisms, and a distinct correlation was found between abundance and phenotypic complexity in Cyanobacteria. Notably, Bacillus subtilis and Escherichia coli, known to undergo genetically regulated autolysis, lacked metacaspases. Pfam domain architecture analysis combined with operon identification revealed rich and varied configurations among the metacaspase sequences. These imply roles in programmed cell death, but also e.g. in signaling, various enzymatic activities and protein modification. Together our data show a wide and scattered distribution of caspase homologs in prokaryotes with structurally and functionally diverse sub-groups, and with a potentially intriguing evolutionary role. These features will help delineate future characterizations of death pathways in prokaryotes.

  9. Patterns of ecological specialization among microbial populations in the Red Sea and diverse oligotrophic marine environments.

    Science.gov (United States)

    Thompson, Luke R; Field, Chris; Romanuk, Tamara; Ngugi, David; Siam, Rania; El Dorry, Hamza; Stingl, Ulrich

    2013-06-01

    Large swaths of the nutrient-poor surface ocean are dominated numerically by cyanobacteria (Prochlorococcus), cyanobacterial viruses (cyanophage), and alphaproteobacteria (SAR11). How these groups thrive in the diverse physicochemical environments of different oceanic regions remains poorly understood. Comparative metagenomics can reveal adaptive responses linked to ecosystem-specific selective pressures. The Red Sea is well-suited for studying adaptation of pelagic-microbes, with salinities, temperatures, and light levels at the extreme end for the surface ocean, and low nutrient concentrations, yet no metagenomic studies have been done there. The Red Sea (high salinity, high light, low N and P) compares favorably with the Mediterranean Sea (high salinity, low P), Sargasso Sea (low P), and North Pacific Subtropical Gyre (high light, low N). We quantified the relative abundance of genetic functions among Prochlorococcus, cyanophage, and SAR11 from these four regions. Gene frequencies indicate selection for phosphorus acquisition (Mediterranean/Sargasso), DNA repair and high-light responses (Red Sea/Pacific Prochlorococcus), and osmolyte C1 oxidation (Red Sea/Mediterranean SAR11). The unexpected connection between salinity-dependent osmolyte production and SAR11 C1 metabolism represents a potentially major coevolutionary adaptation and biogeochemical flux. Among Prochlorococcus and cyanophage, genes enriched in specific environments had ecotype distributions similar to nonenriched genes, suggesting that inter-ecotype gene transfer is not a major source of environment-specific adaptation. Clustering of metagenomes using gene frequencies shows similarities in populations (Red Sea with Pacific, Mediterranean with Sargasso) that belie their geographic distances. Taken together, the genetic functions enriched in specific environments indicate competitive strategies for maintaining carrying capacity in the face of physical stressors and low nutrient availability.

  10. Ecological and social patterns of child dietary diversity in India: a population-based study.

    Science.gov (United States)

    Gausman, Jewel; Perkins, Jessica M; Lee, Hwa-Young; Mejia-Guevara, Ivan; Nam, You-Seon; Lee, Jong-Koo; Oh, Juhwan; Subramanian, S V

    2018-02-13

    Dietary diversity (DD) measures dietary variation in children. Factors at the child, community, and state levels may be associated with poor child nutritional outcomes. However, few studies have examined the role of macro-level factors on child DD. This study seeks to 1) describe the distribution of child DD in India, 2) examine the variation in DD attributable to the child, community and state levels, and 3) explore the relationship between community socioeconomic context and child DD. Using nationally representative data from children aged 6-23 months in India, multilevel models were used to determine the associations between child DD and individual- and community-level factors. There was substantial variation in child DD score across demographic and socioeconomic characteristics. In an age and sex-only adjusted regression model, the largest portion of variation in child DD was attributable to the child level (75%) while the portions of variance attributable to the community-level and state level were similar to each other (15% and 11%). Including individual-level socioeconomic factors explained 35.6 percent of the total variation attributed to child DD at the community level and 24.8 percent of the total variation attributed to child DD at the state level. Finally, measures of community disadvantage were associated with child DD in when added to the fully adjusted model. This study suggests that both individual and contextual factors are associated with child DD. These results suggest that a population-based approach combined with a targeted intervention for at-risk children may be needed to improve child DD in India. Copyright © 2018 Elsevier Inc. All rights reserved.

  11. Patterns of ecological specialization among microbial populations in the Red Sea and diverse oligotrophic marine environments

    KAUST Repository

    Thompson, Luke R

    2013-05-11

    Large swaths of the nutrient-poor surface ocean are dominated numerically by cyanobacteria (Prochlorococcus), cyanobacterial viruses (cyanophage), and alphaproteobacteria (SAR11). How these groups thrive in the diverse physicochemical environments of different oceanic regions remains poorly understood. Comparative metagenomics can reveal adaptive responses linked to ecosystem-specific selective pressures. The Red Sea is well-suited for studying adaptation of pelagic-microbes, with salinities, temperatures, and light levels at the extreme end for the surface ocean, and low nutrient concentrations, yet no metagenomic studies have been done there. The Red Sea (high salinity, high light, low N and P) compares favorably with the Mediterranean Sea (high salinity, low P), Sargasso Sea (low P), and North Pacific Subtropical Gyre (high light, low N). We quantified the relative abundance of genetic functions among Prochlorococcus, cyanophage, and SAR11 from these four regions. Gene frequencies indicate selection for phosphorus acquisition (Mediterranean/Sargasso), DNA repair and high-light responses (Red Sea/Pacific Prochlorococcus), and osmolyte C1 oxidation (Red Sea/Mediterranean SAR11). The unexpected connection between salinity-dependent osmolyte production and SAR11 C1 metabolism represents a potentially major coevolutionary adaptation and biogeochemical flux. Among Prochlorococcus and cyanophage, genes enriched in specific environments had ecotype distributions similar to nonenriched genes, suggesting that inter-ecotype gene transfer is not a major source of environment-specific adaptation. Clustering of metagenomes using gene frequencies shows similarities in populations (Red Sea with Pacific, Mediterranean with Sargasso) that belie their geographic distances. Taken together, the genetic functions enriched in specific environments indicate competitive strategies for maintaining carrying capacity in the face of physical stressors and low nutrient availability. 2013 The

  12. Patterns of species richness and diversity of insects associated with cucurbit fruits in the southern part of Cameroon.

    Science.gov (United States)

    Mokam, Didi Gaëlle; Djiéto-Lordon, Champlain; Bilong Bilong, Charles-Félix

    2014-01-01

    Patterns of species diversity and community structure of insects associated with fruits of domesticated cucurbits were investigated from January 2009 to 2011 in three localities from two agroecological zones in the southern part of Cameroon. Rarefaction curves combined with nonparametric estimators of species richness were used to extrapolate species richness beyond our own data. Sampling efforts of over 92% were reached in each of the three study localities. Data collected revealed a total of 66 insect morphospecies belonging to 37 families and five orders, identified from a set of 57,510 insects. The orders Diptera (especially Tephritidae and Lonchaeidae) and Hymenoptera (mainly Braconidae and Eulophidae) were the most important, in terms of both abundance and species richness on the one hand, and effects on agronomic performance on the other. Values for both the species diversity (Shannon and Simpson) and the species richness indices (Margalef and Berger-Parker) calculated showed that the insect communities were species-rich but dominated, all to a similar extent, by five main species (including four fruit fly species and one parasitoid). Species abundance distributions in these communities ranged from the Zipf-Mandelbrot to Mandelbrot models. The communities are structured as tritrophic networks, including cucurbit fruits, fruit-feeding species (fruit flies) and carnivorous species (parasitoids). Within the guild of the parasitoids, about 30% of species, despite their low abundance, may potentially be of use in biological control of important pests. Our field data contribute in important ways to basic knowledge of biodiversity patterns in agrosystems and constitute baseline data for the planned implementation of biological control in Integrated Pest Management. © The Author 2014. Published by Oxford University Press on behalf of the Entomological Society of America.

  13. Patterns of adaptive and neutral diversity identify the Xiaoxiangling mountains as a refuge for the giant panda.

    Directory of Open Access Journals (Sweden)

    Yi-Yan Chen

    Full Text Available Genetic variation plays a significant role in maintaining the evolutionary potential of a species. Comparing the patterns of adaptive and neutral diversity in extant populations is useful for understanding the local adaptations of a species. In this study, we determined the fine-scale genetic structure of 6 extant populations of the giant panda (Ailuropoda melanoleuca using mtDNA and DNA fingerprints, and then overlaid adaptive variations in 6 functional Aime-MHC class II genes (DRA, DRB3, DQA1, DQA2, DQB1, and DQB2 on this framework. We found that: (1 analysis of the mtDNA and DNA fingerprint-based networks of the 6 populations identified the independent evolutionary histories of the 2 panda subspecies; (2 the basal (ancestral branches of the fingerprint-based Sichuan-derived network all originated from the smallest Xiaoxiangling (XXL population, suggesting the status of a glacial refuge in XXL; (3 the MHC variations among the tested populations showed that the XXL population exhibited extraordinary high levels of MHC diversity in allelic richness, which is consistent with the diversity characteristics of a glacial refuge; (4 the phylogenetic tree showed that the basal clades of giant panda DQB sequences were all occupied by XXL-specific sequences, providing evidence for the ancestor-resembling traits of XXL. Finally, we found that the giant panda had many more DQ alleles than DR alleles (33∶13, contrary to other mammals, and that the XXL refuge showed special characteristics in the DQB loci, with 7 DQB members of 9 XXL-unique alleles. Thus, this study identified XXL as a glacial refuge, specifically harboring the most number of primitive DQB alleles.

  14. Heterogeneous Patterns of Genetic Diversity and Differentiation in European and Siberian Chiffchaff (Phylloscopus collybita abietinus/P. tristis)

    Science.gov (United States)

    Talla, Venkat; Kalsoom, Faheema; Shipilina, Daria; Marova, Irina; Backström, Niclas

    2017-01-01

    Identification of candidate genes for trait variation in diverging lineages and characterization of mechanistic underpinnings of genome differentiation are key steps toward understanding the processes underlying the formation of new species. Hybrid zones provide a valuable resource for such investigations, since they allow us to study how genomes evolve as species exchange genetic material and to associate particular genetic regions with phenotypic traits of interest. Here, we use whole-genome resequencing of both allopatric and hybridizing populations of the European (Phylloscopus collybita abietinus) and the Siberian chiffchaff (P. tristis)—two recently diverged species which differ in morphology, plumage, song, habitat, and migration—to quantify the regional variation in genome-wide genetic diversity and differentiation, and to identify candidate regions for trait variation. We find that the levels of diversity, differentiation, and divergence are highly heterogeneous, with significantly reduced global differentiation, and more pronounced differentiation peaks in sympatry than in allopatry. This pattern is consistent with regional differences in effective population size and recurrent background selection or selective sweeps reducing the genetic diversity in specific regions prior to lineage divergence, but the data also suggest that postdivergence selection has resulted in increased differentiation and fixed differences in specific regions. We find that hybridization and backcrossing is common in sympatry, and that phenotype is a poor predictor of the genomic composition of sympatric birds. The combination of a differentiation scan approach with identification of fixed differences pinpoint a handful of candidate regions that might be important for trait variation between the two species. PMID:29054864

  15. Distribution of Escherichia coli in a coastal lagoon (Venice, Italy): Temporal patterns, genetic diversity and the role of tidal forcing.

    Science.gov (United States)

    Perini, L; Quero, G M; García, E Serrano; Luna, G M

    2015-12-15

    Despite its worldwide importance as fecal indicator in aquatic systems, little is known about the diversity of Escherichia coli in the environment and the factors driving its spatial distribution. The city of Venice (Italy), lying at the forefront of a large European lagoon, is an ideal site to study the mechanisms driving the fate of fecal bacteria, due to the huge fluxes of tourists, the city's unique architecture (causing poor efficiency of sewages treatment), and the long branching network of canals crossing the city. We summarize the results of a multi-year investigation to study the temporal dynamics of E. coli around the city, describe the population structure (by assigning isolates to their phylogenetic group) and the genotypic diversity, and explore the role of environmental factors in determining its variability. E. coli abundance in water was highly variable, ranging from being undetectable up to 10(4) Colony Forming Units (CFU) per 100 ml. Abundance did not display significant relationships with the water physico-chemical variables. The analysis of the population structure showed the presence of all known phylogroups, including extra-intestinal and potentially pathogenic ones. The genotypic diversity was very high, as likely consequence of the heterogeneous input of fecal bacteria from the city, and showed site-specific patterns. Intensive sampling during the tidal fluctuations highlighted the prominent role of tides, rather than environmental variables, as source of spatial variation, with a more evident influence in water than sediments. These results, the first providing information on the genetic properties, spatial heterogeneity and influence of tides on E. coli populations around Venice, have implications to manage the fecal pollution, and the associated waterborne disease risks, in coastal cities lying in front of lagoons and semi-enclosed basins. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

    Science.gov (United States)

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

    2015-10-13

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

  17. Assessing the diversity, host-specificity and infection patterns of apicomplexan parasites in reptiles from Oman, Arabia.

    Science.gov (United States)

    Maia, João P; Harris, D James; Carranza, Salvador; Goméz-Díaz, Elena

    2016-11-01

    Understanding the processes that shape parasite diversification, their distribution and abundance provides valuable information on the dynamics and evolution of disease. In this study, we assessed the diversity, distribution, host-specificity and infection patterns of apicomplexan parasites in amphibians and reptiles from Oman, Arabia. Using a quantitative PCR approach we detected three apicomplexan parasites (haemogregarines, lankesterellids and sarcocystids). A total of 13 haemogregarine haplotypes were identified, which fell into four main clades in a phylogenetic framework. Phylogenetic analysis of six new lankesterellid haplotypes revealed that these parasites were distinct from, but phylogenetically related to, known Lankesterella species and might represent new taxa. The percentage of infected hosts (prevalence) and the number of haemogregarines in the blood (parasitaemia) varied significantly between gecko species. We also found significant differences in parasitaemia between haemogregarine parasite lineages (defined by phylogenetic clustering of haplotypes), suggesting differences in host-parasite compatibility between these lineages. For Pristurus rupestris, we found significant differences in haemogregarine prevalence between geographical areas. Our results suggest that host ecology and host relatedness may influence haemogregarine distributions and, more generally, highlight the importance of screening wild hosts from remote regions to provide new insights into parasite diversity.

  18. Epigenetic Loss of MLH1 Expression in Normal Human Hematopoietic Stem Cell Clones is Defined by the Promoter CpG Methylation Pattern Observed by High-Throughput Methylation Specific Sequencing.

    Science.gov (United States)

    Kenyon, Jonathan; Nickel-Meester, Gabrielle; Qing, Yulan; Santos-Guasch, Gabriela; Drake, Ellen; PingfuFu; Sun, Shuying; Bai, Xiaodong; Wald, David; Arts, Eric; Gerson, Stanton L

    Normal human hematopoietic stem and progenitor cells (HPC) lose expression of MLH1 , an important mismatch repair (MMR) pathway gene, with age. Loss of MMR leads to replication dependent mutational events and microsatellite instability observed in secondary acute myelogenous leukemia and other hematologic malignancies. Epigenetic CpG methylation upstream of the MLH1 promoter is a contributing factor to acquired loss of MLH1 expression in tumors of the epithelia and proximal mucosa. Using single molecule high-throughput bisulfite sequencing we have characterized the CpG methylation landscape from -938 to -337 bp upstream of the MLH1 transcriptional start site (position +0), from 30 hematopoietic colony forming cell clones (CFC) either expressing or not expressing MLH1 . We identify a correlation between MLH1 promoter methylation and loss of MLH1 expression. Additionally, using the CpG site methylation frequencies obtained in this study we were able to generate a classification algorithm capable of sorting the expressing and non-expressing CFC. Thus, as has been previously described for many tumor cell types, we report for the first time a correlation between the loss of MLH1 expression and increased MLH1 promoter methylation in CFC derived from CD34 + selected hematopoietic stem and progenitor cells.

  19. The eastern Asian and eastern and western North American floristic disjunction: congruent phylogenetic patterns in seven diverse genera.

    Science.gov (United States)

    Xiang, Q Y; Soltis, D E; Soltis, P S

    1998-10-01

    One of the most remarkable examples of intercontinental disjunction of the North Temperate Flora involves eastern Asia and eastern and western North America. Although there has been considerable interest in this phytogeographic pattern for over 150 years (e.g., Gray, 1859; Li, 1952; Graham, 1972; Boufford and Spongberg, 1983; Wu, 1983; Tiffney, 1985a, 1985b), relationships among taxa displaying the disjunction remain obscure. Understanding phylogenetic relationships is, however, a prerequisite for historical biogeographic analyses of this distributional pattern. To understand better the relationships of taxa displaying this intercontinental disjunction, phylogenetic analyses were conducted using a variety of DNA data sets for species of four genera (Cornus, Boykinia, Tiarella, and Trautvetteria) that occur in eastern Asia, eastern North America, and western North America. An area cladogram was constructed for each of the four genera, all of which show a similar pattern of relationship: the eastern Asian species are sister to all North American species. An identical phylogenetic pattern is also found in three other taxa exhibiting this disjunction (Aralia sect. Aralia, Calycanthus, and Adiantum pedatum). The congruent phylogenetic pattern found in these seven diverse genera raises the possibility of a common origin of the eastern Asia, eastern and western North America disjunction. The data are in agreement with the long-standing hypothesis that this well-known floristic disjunction represents the fragmentation of a once continuous Mixed Mesophytic forest community and suggest that the disjunction may have involved only two major vicariance events: an initial split between Eurasia and North America, followed by the isolation of floras between eastern and western North America. However, congruence between phylogenies and geographic distributions does not necessarily indicate an identical phytogeographic history. Taxa exhibiting the same phylogenetic pattern may have

  20. Methylated β-Cyclodextrins

    DEFF Research Database (Denmark)

    Schönbeck, Jens Christian Sidney; Westh, Peter; Madsen, Jens Christian

    2011-01-01

    The complexation of 6 bile salts with various methylated β-cyclodextrins was studied to elucidate how the degree and pattern of substitution affects the binding. The structures of the CDs were determined by mass spectrometry and NMR techniques, and the structures of the inclusion complexes were...

  1. Patterns of genetic diversity in Hepatozoon spp. infecting snakes from North Africa and the Mediterranean Basin.

    Science.gov (United States)

    Tomé, Beatriz; Maia, João P; Salvi, Daniele; Brito, José C; Carretero, Miguel A; Perera, Ana; Meimberg, Harald; Harris, David James

    2014-03-01

    Species of Hepatozoon Miller, 1908 are blood parasites most commonly found in snakes but some have been described from all tetrapod groups and a wide variety of hematophagous invertebrates. Previous studies have suggested possible associations between Hepatozoon spp. found in predators and prey. Particularly, some saurophagous snakes from North Africa and the Mediterranean region have been found to be infected with Hepatozoon spp. similar to those of various sympatric lizard hosts. In this study, we have screened tissue samples of 111 North African and Mediterranean snakes, using specific primers for the 18S rRNA gene. In the phylogenetic analysis, the newly-generated Hepatozoon spp. sequences grouped separately into five main clusters. Three of these clusters were composed by Hepatozoon spp. also found in snakes and other reptiles from the Mediterranean Basin and North Africa. In the other two clusters, the new sequences were not closely related to geographically proximate known sequences. The phylogeny of Hepatozoon spp. inferred here was not associated with intermediate host taxonomy or geographical distribution. From the other factors that could explain these evolutionary patterns, the most likely seems series of intermediate hosts providing similar ribotypes of Hepatozoon and a high prevalence of host shifts for Hepatozoon spp. This is indicated by ribotypes of high similarity found in different reptile families, as well as by divergent ribotypes found in the same host species. This potentially low host specificity has profound implications for the systematics of Hepatozoon spp.

  2. Reliable and rapid characterization of functional FCN2 gene variants reveals diverse geographical patterns

    Directory of Open Access Journals (Sweden)

    Ojurongbe Olusola

    2012-05-01

    Full Text Available Abstract Background Ficolin-2 coded by FCN2 gene is a soluble serum protein and an innate immune recognition element of the complement system. FCN2 gene polymorphisms reveal distinct geographical patterns and are documented to alter serum ficolin levels and modulate disease susceptibility. Methods We employed a real-time PCR based on Fluorescence Resonance Energy Transfer (FRET method to genotype four functional SNPs including -986 G > A (#rs3124952, -602 G > A (#rs3124953, -4A > G (#rs17514136 and +6424 G > T (#rs7851696 in the ficolin-2 (FCN2 gene. We characterized the FCN2 variants in individuals representing Brazilian (n = 176, Nigerian (n = 180, Vietnamese (n = 172 and European Caucasian ethnicity (n = 165. Results We observed that the genotype distribution of three functional SNP variants (−986 G > A, -602 G > A and -4A > G differ significantly between the populations investigated (p p  Conclusions The observed distribution of the FCN2 functional SNP variants may likely contribute to altered serum ficolin levels and this may depend on the different disease settings in world populations. To conclude, the use of FRET based real-time PCR especially for FCN2 gene will benefit a larger scientific community who extensively depend on rapid, reliable method for FCN2 genotyping.

  3. Alteration in Methylation Pattern of Retinoblastoma 1 Gene Promotor Region in Intestinal Metaplasia with or without Helicobacter pylori and Gastric Cancer Patients.

    Science.gov (United States)

    Boyacioglu, Seda Orenay; Kasap, Elmas; Yuceyar, Hakan; Korkmaz, Mehmet

    2016-01-01

    Helicobacter pylori, intestinal metaplasia (IM), and gene methylation play important roles in gastric carcinogenesis. However, the association among H. pylori infection, IM, gastric cancer (GC), and gene methylation is not fully understood. Cell cycle control involving retinoblastoma 1 (RB1) gene is one of the main regulatory pathways reported to be altered in gastric carcinogenesis. The purpose of this research is to assess the methylation status of RB1 gene in GC and IM with or without H. pylori infection, and to discuss the possible role of H. pylori-induced RB1 gene methylation in the mechanism of gastric carcinogenesis. The methylation profile of RB1 gene was analyzed by sodium bisulfite modification and methylation-specific PCR in GC (n = 24), IM patients with H. pylori positive (n = 20) and negative (n = 20), and control subjects (n = 20). According to methylation levels in RB1 gene; the high correlation values were detected between H. pylori positive-IM group and GC group, and between H. pylori positive-IM and H. pylori negative-IM groups (p gene. High methylation levels in RB1 gene in H. pylori positive individuals may suggest an elevated risk of gastric cancer occurrence.

  4. Patterns and predictors of β-diversity in the fragmented Brazilian Atlantic forest: a multiscale analysis of forest specialist and generalist birds.

    Science.gov (United States)

    Morante-Filho, José Carlos; Arroyo-Rodríguez, Víctor; Faria, Deborah

    2016-01-01

    Biodiversity maintenance in human-altered landscapes (HALs) depends on the species turnover among localities, but the patterns and determinants of β-diversity in HALs are poorly known. In fact, declines, increases and neutral shifts in β-diversity have all been documented, depending on the landscape, ecological group and spatial scale of analysis. We shed some light on this controversy by assessing the patterns and predictors of bird β-diversity across multiple spatial scales considering forest specialist and habitat generalist bird assemblages. We surveyed birds from 144 point counts in 36 different forest sites across two landscapes with different amount of forest cover in the Brazilian Atlantic forest. We analysed β-diversity among points, among sites and between landscapes with multiplicative diversity partitioning of Hill numbers. We tested whether β-diversity among points was related to within-site variations in vegetation structure, and whether β-diversity among sites was related to site location and/or to differences among sites in vegetation structure and landscape composition (i.e. per cent forest and pasture cover surrounding each site). β-diversity between landscapes was lower than among sites and among points in both bird assemblages. In forest specialist birds, the landscape with less forest cover showed the highest β-diversity among sites (bird differentiation among sites), but generalist birds showed the opposite pattern. At the local scale, however, the less forested landscape showed the lowest β-diversity among points (bird homogenization within sites), independently of the bird assemblage. β-diversity among points was weakly related to vegetation structure, but higher β-diversity values were recorded among sites that were more isolated from each other, and among sites with higher differences in landscape composition, particularly in the less forested landscape. Our findings indicate that patterns of bird β-diversity vary across scales

  5. DNA methylation and memory formation.

    Science.gov (United States)

    Day, Jeremy J; Sweatt, J David

    2010-11-01

    Memory formation and storage require long-lasting changes in memory-related neuronal circuits. Recent evidence indicates that DNA methylation may serve as a contributing mechanism in memory formation and storage. These emerging findings suggest a role for an epigenetic mechanism in learning and long-term memory maintenance and raise apparent conundrums and questions. For example, it is unclear how DNA methylation might be reversed during the formation of a memory, how changes in DNA methylation alter neuronal function to promote memory formation, and how DNA methylation patterns differ between neuronal structures to enable both consolidation and storage of memories. Here we evaluate the existing evidence supporting a role for DNA methylation in memory, discuss how DNA methylation may affect genetic and neuronal function to contribute to behavior, propose several future directions for the emerging subfield of neuroepigenetics, and begin to address some of the broader implications of this work.

  6. Bathymetric patterns in standing stock and diversity of deep-sea nematodes at the long-term ecological research observatory HAUSGARTEN (Fram Strait)

    Science.gov (United States)

    Grzelak, Katarzyna; Kotwicki, Lech; Hasemann, Christiane; Soltwedel, Thomas

    2017-08-01

    Bathymetric patterns in standing stocks and diversity are a major topic of investigation in deep-sea biology. From the literature, responses of metazoan meiofauna and nematodes to bathymetric gradients are well studied, with a general decrease in biomass and abundance with increasing water depth, while bathymetric diversity gradients often, although it is not a rule, show a unimodal pattern. Spatial distribution patterns of nematode communities along bathymetric gradients are coupled with surface-water processes and interacting physical and biological factors within the benthic system. We studied the nematode communities at the Long-Term Ecological Research (LTER) observatory HAUSGARTEN, located in the Fram Strait at the Marginal Ice Zone, with respect to their standing stocks as well as structural and functional diversity. We evaluated whether nematode density, biomass and diversity indices, such as H0, Hinf, EG(50), Θ- 1, are linked with environmental conditions along a bathymetric transect spanning from 1200 m to 5500 m water depth. Nematode abundance, biomass and diversity, as well as food availability from phytodetritus sedimentation (indicated by chloroplastic pigments in the sediments), were higher at the stations located at upper bathyal depths (1200-2000 m) and tended to decrease with increasing water depth. A faunal shift was found below 3500 m water depth, where genus composition and trophic structure changed significantly and structural diversity indices markedly decreased. A strong dominance of very few genera and its high turnover particularly at the abyssal stations (4000-5500 m) suggests that environmental conditions were rather unfavorable for most genera. Despite the high concentrations of sediment-bound chloroplastic pigments and elevated standing stocks found at the deepest station (5500 m), nematode genus diversity remained the lowest compared to all other stations. This study provides a further insight into the knowledge of deep-sea nematodes

  7. Nucleosomes correlate with in vivo progression pattern of de novo methylation of p16 CpG islands in human gastric carcinogenesis.

    Directory of Open Access Journals (Sweden)

    Zhe-Ming Lu

    Full Text Available BACKGROUND: The exact relationship between nucleosome positioning and methylation of CpG islands in human pathogenesis is unknown. METHODOLOGY/PRINCIPAL FINDINGS: In the present study, we characterized the nucleosome position within the p16 CpG island and established a seeding methylation-specific PCR (sMSP assay based on bisulfite modification to enrich the p16 alleles containing methylated-CpG at the methylation "seeding" sites within its intron-1 in gastric carcinogenesis. The sMSP-positive rate in primary gastric carcinoma (GC samples (36/40 was significantly higher than that observed in gastritis (19/45 or normal samples (7/13 (P<0.01. Extensive clone sequencing of these sMSP products showed that the density of methylated-CpGs in p16 CpG islands increased gradually along with the severity of pathological changes in gastric tissues. In gastritis lesions the methylation was frequently observed in the region corresponding to the exon-1 coding-nucleosome and the 5'UTR-nucleosome; the methylation was further extended to the region corresponding to the promoter-nucleosome in GC samples. Only few methylated-CpG sites were randomly detected within p16 CpG islands in normal tissues. The significantly inversed relationship between the p16 exon-1 methylation and its transcription was observed in GC samples. An exact p16 promoter-specific 83 bp-MSP assay confirms the result of sMSP (33/55 vs. 1/6, P<0.01. In addition, p16 methylation in chronic gastritis lesions significantly correlated with H. pylori infection; however, such correlation was not observed in GC specimens. CONCLUSIONS/SIGNIFICANCE: It was determined that de novo methylation was initiated in the coding region of p16 exon-1 in gastritis, then progressed to its 5'UTR, and ultimately to the proximal promoter in GCs. Nucleosomes may function as the basic extension/progression unit of de novo methylation of p16 CpG islands in vivo.

  8. Experimental designs for modeling retention patterns and separation efficiency in analysis of fatty acid methyl esters by gas chromatography-mass spectrometry.

    Science.gov (United States)

    Skartland, Liv Kjersti; Mjøs, Svein A; Grung, Bjørn

    2011-09-23

    The retention behavior of components analyzed by chromatography varies with instrumental settings. Being able to predict how changes in these settings alter the elution pattern is useful, both with regards to component identification, as well as with regards to optimization of the chromatographic system. In this work, it is shown how experimental designs can be used for this purpose. Different experimental designs for response surface modeling of the separation of fatty acid methyl esters (FAME) as function of chromatographic conditions in GC have been evaluated. Full factorial, central composite, Doehlert and Box-Behnken designs were applied. A mixture of 38 FAMEs was separated on a polar cyanopropyl substituted polysilphenylene-siloxane phase capillary column. The temperature gradient, the start temperature of the gradient, and the carrier gas velocity were varied in the experiments. The modeled responses, as functions of chromatographic conditions, were retention time, retention indices, peak widths, separation efficiency and resolution between selected peak pairs. The designs that allowed inclusion of quadratic terms among the predictors performed significantly better than factorial design. Box-Behnken design provided the best results for prediction of retention, but the differences between the central composite, Doehlert and Box-Behnken designs were small. Retention indices could be modeled with much better accuracy than retention times. However, because the errors of predicted tR of closely eluting peaks were highly correlated, models of resolution (Rs) that were based on retention time had errors in the same range as corresponding models based on ECL. Copyright © 2011 Elsevier B.V. All rights reserved.

  9. Biogeographic and diversification patterns of Neotropical Troidini butterflies (Papilionidae support a museum model of diversity dynamics for Amazonia

    Directory of Open Access Journals (Sweden)

    Condamine Fabien L

    2012-06-01

    Full Text Available Abstract Background The temporal and geographical diversification of Neotropical insects remains poorly understood because of the complex changes in geological and climatic conditions that occurred during the Cenozoic. To better understand extant patterns in Neotropical biodiversity, we investigated the evolutionary history of three Neotropical swallowtail Troidini genera (Papilionidae. First, DNA-based species delimitation analyses were conducted to assess species boundaries within Neotropical Troidini using an enlarged fragment of the standard barcode gene. Molecularly delineated species were then used to infer a time-calibrated species-level phylogeny based on a three-gene dataset and Bayesian dating analyses. The corresponding chronogram was used to explore their temporal and geographical diversification through distinct likelihood-based methods. Results The phylogeny for Neotropical Troidini was well resolved and strongly supported. Molecular dating and biogeographic analyses indicate that the extant lineages of Neotropical Troidini have a late Eocene (33–42 Ma origin in North America. Two independent lineages (Battus and Euryades + Parides reached South America via the GAARlandia temporary connection, and later became extinct in North America. They only began substantive diversification during the early Miocene in Amazonia. Macroevolutionary analysis supports the “museum model” of diversification, rather than Pleistocene refugia, as the best explanation for the diversification of these lineages. Conclusions This study demonstrates that: (i current Neotropical biodiversity may have originated ex situ; (ii the GAARlandia bridge was important in facilitating invasions of South America; (iii colonization of Amazonia initiated the crown diversification of these swallowtails; and (iv Amazonia is not only a species-rich region but also acted as a sanctuary for the dynamics of this diversity. In particular, Amazonia probably allowed

  10. Biogeographic and diversification patterns of Neotropical Troidini butterflies (Papilionidae) support a museum model of diversity dynamics for Amazonia.

    Science.gov (United States)

    Condamine, Fabien L; Silva-Brandão, Karina L; Kergoat, Gael J; Sperling, Felix A H

    2012-06-12

    The temporal and geographical diversification of Neotropical insects remains poorly understood because of the complex changes in geological and climatic conditions that occurred during the Cenozoic. To better understand extant patterns in Neotropical biodiversity, we investigated the evolutionary history of three Neotropical swallowtail Troidini genera (Papilionidae). First, DNA-based species delimitation analyses were conducted to assess species boundaries within Neotropical Troidini using an enlarged fragment of the standard barcode gene. Molecularly delineated species were then used to infer a time-calibrated species-level phylogeny based on a three-gene dataset and Bayesian dating analyses. The corresponding chronogram was used to explore their temporal and geographical diversification through distinct likelihood-based methods. The phylogeny for Neotropical Troidini was well resolved and strongly supported. Molecular dating and biogeographic analyses indicate that the extant lineages of Neotropical Troidini have a late Eocene (33-42 Ma) origin in North America. Two independent lineages (Battus and Euryades+Parides) reached South America via the GAARlandia temporary connection, and later became extinct in North America. They only began substantive diversification during the early Miocene in Amazonia. Macroevolutionary analysis supports the "museum model" of diversification, rather than Pleistocene refugia, as the best explanation for the diversification of these lineages. This study demonstrates that: (i) current Neotropical biodiversity may have originated ex situ; (ii) the GAARlandia bridge was important in facilitating invasions of South America; (iii) colonization of Amazonia initiated the crown diversification of these swallowtails; and (iv) Amazonia is not only a species-rich region but also acted as a sanctuary for the dynamics of this diversity. In particular, Amazonia probably allowed the persistence of old lineages and contributed to the steady

  11. Re-patterning of H3K27me3, H3K4me3 and DNA methylation during fibroblast conversion into induced cardiomyocytes

    Directory of Open Access Journals (Sweden)

    Ziqing Liu

    2016-03-01

    Full Text Available Direct conversion of fibroblasts into induced cardiomyocytes (iCMs offers an alternative strategy for cardiac disease modeling and regeneration. During iCM reprogramming, the starting fibroblasts must overcome existing epigenetic barriers to acquire the CM-like chromatin pattern. However, epigenetic dynamics along this reprogramming process have not been studied. Here, we took advantage of our recently generated polycistronic system and determined the dynamics of two critical histone marks, H3K27me3 and H3K4me3, in parallel with gene expression at a set of carefully selected cardiac and fibroblast loci during iCM reprogramming. We observed reduced H3K27me3 and increased H3K4me3 at cardiac promoters as early as day 3, paralleled by a rapid significant increase in their mRNA expression. In contrast, H3K27me3 at loci encoding fibroblast marker genes did not increase until day 10 and H3K4me3 progressively decreased along the reprogramming process; these changes were accompanied by a gradual decrease in the mRNA expression of fibroblast marker genes. Further analyses of fibroblast-enriched transcription factors revealed a similarly late deposition of H3K27me3 and decreased mRNA expression of Sox9, Twist1 and Twist2, three important players in epithelial−mesenchymal transition. Our data suggest early rapid activation of the cardiac program and later progressive suppression of fibroblast fate at both epigenetic and transcriptional levels. Additionally, we determined the DNA methylation states of representative cardiac promoters and found that not every single CpG was equally demethylated during early stages of iCM reprogramming. Rather, there are specific CpGs, whose demethylation states correlated tightly with transcription activation, that we propose are the major contributing CpGs. Our work thus reveals a differential re-patterning of H3K27me3, H3K4me3 at cardiac and fibroblast loci during iCM reprogramming and could provide future genome

  12. Spatial Patterns in the Distribution, Diversity and Abundance of Benthic Foraminifera around Moorea (Society Archipelago, French Polynesia).

    Science.gov (United States)

    Fajemila, Olugbenga T; Langer, Martin R; Lipps, Jere H

    2015-01-01

    Coral reefs are now subject to global threats and influences from numerous anthropogenic sources. Foraminifera, a group of unicellular shelled organisms, are excellent indicators of water quality and reef health. Thus we studied a set of samples taken in 1992 to provide a foraminiferal baseline for future studies of environmental change. Our study provides the first island-wide analysis of shallow benthic foraminifera from around Moorea (Society Archipelago). We analyzed the composition, species richness, patterns of distribution and abundance of unstained foraminiferal assemblages from bays, fringing reefs, nearshore and back- and fore-reef environments. A total of 380 taxa of foraminifera were recorded, a number that almost doubles previous species counts. Spatial patterns of foraminiferal assemblages are characterized by numerical abundances of individual taxa, cluster groups and gradients of species richness, as documented by cluster, Fisher α, ternary plot and Principal Component Analyses (PCA). The inner bay inlets are dominated by stress-tolerant, mostly thin-shelled taxa of Bolivina, Bolivinella, Nonionoides, Elongobula, and Ammonia preferring low-oxygen and/or nutrient-rich habitats influenced by coastal factors such as fresh-water runoff and overhanging mangroves. The larger symbiont-bearing foraminifera (Borelis, Amphistegina, Heterostegina, Peneroplis) generally live in the oligotrophic, well-lit back- and fore-reef environments. Amphisteginids and peneroplids were among the few taxa found in the bay environments, probably due to their preferences for phytal substrates and tolerance to moderate levels of eutrophication. The fringing reef environments along the outer bay are characterized by Borelis schlumbergeri, Heterostegina depressa, Textularia spp. and various miliolids which represent a hotspot of diversity within the complex reef-lagoon system of Moorea. The high foraminiferal Fisher α and species richness diversity in outer bay fringing reefs

  13. Spatial Patterns in the Distribution, Diversity and Abundance of Benthic Foraminifera around Moorea (Society Archipelago, French Polynesia.

    Directory of Open Access Journals (Sweden)

    Olugbenga T Fajemila

    Full Text Available Coral reefs are now subject to global threats and influences from numerous anthropogenic sources. Foraminifera, a group of unicellular shelled organisms, are excellent indicators of water quality and reef health. Thus we studied a set of samples taken in 1992 to provide a foraminiferal baseline for future studies of environmental change. Our study provides the first island-wide analysis of shallow benthic foraminifera from around Moorea (Society Archipelago. We analyzed the composition, species richness, patterns of distribution and abundance of unstained foraminiferal assemblages from bays, fringing reefs, nearshore and back- and fore-reef environments. A total of 380 taxa of foraminifera were recorded, a number that almost doubles previous species counts. Spatial patterns of foraminiferal assemblages are characterized by numerical abundances of individual taxa, cluster groups and gradients of species richness, as documented by cluster, Fisher α, ternary plot and Principal Component Analyses (PCA. The inner bay inlets are dominated by stress-tolerant, mostly thin-shelled taxa of Bolivina, Bolivinella, Nonionoides, Elongobula, and Ammonia preferring low-oxygen and/or nutrient-rich habitats influenced by coastal factors such as fresh-water runoff and overhanging mangroves. The larger symbiont-bearing foraminifera (Borelis, Amphistegina, Heterostegina, Peneroplis generally live in the oligotrophic, well-lit back- and fore-reef environments. Amphisteginids and peneroplids were among the few taxa found in the bay environments, probably due to their preferences for phytal substrates and tolerance to moderate levels of eutrophication. The fringing reef environments along the outer bay are characterized by Borelis schlumbergeri, Heterostegina depressa, Textularia spp. and various miliolids which represent a hotspot of diversity within the complex reef-lagoon system of Moorea. The high foraminiferal Fisher α and species richness diversity in outer bay

  14. Patterns and Drivers of Egg Pigment Intensity and Colour Diversity in the Ocean: A Meta-Analysis of Phylum Echinodermata.

    Science.gov (United States)

    Montgomery, E M; Hamel, J-F; Mercier, A

    Egg pigmentation is proposed to serve numerous ecological, physiological, and adaptive functions in egg-laying animals. Despite the predominance and taxonomic diversity of egg layers, syntheses reviewing the putative functions and drivers of egg pigmentation have been relatively narrow in scope, centring almost exclusively on birds. Nonvertebrate and aquatic species are essentially overlooked, yet many of them produce maternally provisioned eggs in strikingly varied colours, from pale yellow to bright red or green. We explore the ways in which these colour patterns correlate with behavioural, morphological, geographic and phylogenetic variables in extant classes of Echinodermata, a phylum that has close phylogenetic ties with chordates and representatives in nearly all marine environments. Results of multivariate analyses show that intensely pigmented eggs are characteristic of pelagic or external development whereas pale eggs are commonly brooded internally. Of the five egg colours catalogued, orange and yellow are the most common. Yellow eggs are a primitive character, associated with all types of development (predominant in internal brooders), whereas green eggs are always pelagic, occur in the most derived orders of each class and are restricted to the Indo-Pacific Ocean. Orange eggs are geographically ubiquitous and may represent a 'universal' egg pigment that functions well under a diversity of environmental conditions. Finally, green occurs chiefly in the classes Holothuroidea and Ophiuroidea, orange in Asteroidea, yellow in Echinoidea, and brown in Holothuroidea. By examining an unprecedented combination of egg colours/intensities and reproductive strategies, this phylum-wide study sheds new light on the role and drivers of egg pigmentation, drawing parallels with theories developed from the study of more derived vertebrate taxa. The primary use of pigments (of any colour) to protect externally developing eggs from oxidative damage and predation is

  15. Genome-wide Differences in DNA Methylation Changes in Two Contrasting Rice Genotypes in Response to Drought Conditions

    Directory of Open Access Journals (Sweden)

    Wensheng Wang

    2016-11-01

    Full Text Available Differences in drought stress tolerance within diverse rice genotypes have been attributed to genetic diversity and epigenetic alterations. DNA methylation is an important epigenetic modification that influences diverse biological processes, but its effects on rice drought stress tolerance are poorly understood. In this study, methylated DNA immunoprecipitation sequencing and an Affymetrix GeneChip rice genome array were used to profile the DNA methylation patterns and transcriptomes of the drought-tolerant introgression line DK151 and its drought-sensitive recurrent parent IR64 under drought and control conditions. The introgression of donor genomic DNA induced genome-wide DNA methylation changes in DK151 plants. A total of 1190 differentially methylated regions (DMRs were detected between the two genotypes under normal growth conditions, and the DMR-associated genes in DK151 plants were mainly related to stress response, programmed cell death, and nutrient reservoir activity, which are implicated to constitutive drought stress tolerance. A comparison of the DNA methylation changes in the two genotypes under drought conditions indicated that DK151 plants have a more stable methylome, with only 92 drought-induced DMRs, than IR64 plants with 506 DMRs. Gene ontology analyses of the DMR-associated genes in drought-stressed plants revealed that changes to the DNA methylation status of genotype-specific genes are associated with the epigenetic regulation of drought stress responses. Transcriptome analysis further helped to identify a set of 12 and 23 DMR-associated genes that were differentially expressed in DK151 and IR64, respectively, under drought stress compared with respective controls. Correlation analysis indicated that DNA methylation has various effects on gene expression, implying that it affects gene expression directly or indirectly through diverse regulatory pathways. Our results indicate that drought-induced alterations to DNA

  16. Temporal and spatial regulation of anthocyanin biosynthesis provide diverse flower colour intensities and patterning in Cymbidium orchid.

    Science.gov (United States)

    Wang, Lei; Albert, Nick W; Zhang, Huaibi; Arathoon, Steve; Boase, Murray R; Ngo, Hanh; Schwinn, Kathy E; Davies, Kevin M; Lewis, David H

    2014-11-01

    This study confirmed pigment profiles in different colour groups, isolated key anthocyanin biosynthetic genes and established a basis to examine the regulation of colour patterning in flowers of Cymbidium orchid. Cymbidium orchid (Cymbidium hybrida) has a range of flower colours, often classified into four colour groups; pink, white, yellow and green. In this study, the biochemical and molecular basis for the different colour types was investigated, and genes involved in flavonoid/anthocyanin synthesis were identified and characterised. Pigment analysis across selected cultivars confirmed cyanidin 3-O-rutinoside and peonidin 3-O-rutinoside as the major anthocyanins detected; the flavonols quercetin and kaempferol rutinoside and robinoside were also present in petal tissue. β-carotene was the major carotenoid in the yellow cultivars, whilst pheophytins were the major chlorophyll pigments in the green cultivars. Anthocyanin pigments were important across all eight cultivars because anthocyanin accumulated in the flower labellum, even if not in the other petals/sepals. Genes encoding the flavonoid biosynthetic pathway enzymes chalcone synthase, flavonol synthase, flavonoid 3' hydroxylase (F3'H), dihydroflavonol 4-reductase (DFR) and anthocyanidin synthase (ANS) were isolated from petal tissue of a Cymbidium cultivar. Expression of these flavonoid genes was monitored across flower bud development in each cultivar, confirming that DFR and ANS were only expressed in tissues where anthocyanin accumulated. Phylogenetic analysis suggested a cytochrome P450 sequence as that of the Cymbidium F3'H, consistent with the accumulation of di-hydroxylated anthocyanins and flavonols in flower tissue. A separate polyketide synthase, identified as a bibenzyl synthase, was isolated from petal tissue but was not associated with pigment accumulation. Our analyses show the diversity in flower colour of Cymbidium orchid derives not from different individual pigments but from subtle

  17. Regional patterns and controlling factors in plant species composition and diversity in Canadian lowland coastal bogs and laggs

    Directory of Open Access Journals (Sweden)

    S.A. Howie

    2016-11-01

    Full Text Available Inventories of natural assemblages of plant species are critical when planning ecological restoration of bogs. However, little is known about the regional variation in plant communities at the margins (laggs of bogs, even though they are an integral element of raised bog ecosystems. Therefore, we investigated the regional patterns in the plant communities of bogs and laggs, and the factors that control them, for thirteen bogs in coastal British Columbia, Canada. Species richness was significantly higher in the bogs and laggs of the cooler, wetter Pacific Oceanic wetland region. Beta Diversity analyses showed that bogs in the Pacific Oceanic wetland region often shared species with their respective laggs, whereas half of the laggs in the warmer, drier Pacific Temperate wetland region had no species in common with the adjacent bogs and were thus more ecologically distinct from the bog. Primary climatic variables, such as mean annual precipitation, mean annual temperature and latitude, as well as climate-influenced variables, such as pH, peat depth, and Na+ concentrations were the main correlates of plant species composition in the studied bogs. Site-specific factors, particularly depth to water table, and fraction of inorganic material in peat samples, were as strongly related to lagg plant communities as climate, while hydrochemistry appeared to have less influence.

  18. Regionally and climatically restricted patterns of distribution of genetic diversity in a migratory bat species, Miniopterus schreibersii (Chiroptera: Vespertilionidae

    Directory of Open Access Journals (Sweden)

    Çoraman Emrah

    2008-07-01

    Full Text Available Abstract Background Various mechanisms such as geographic barriers and glacial episodes have been proposed as determinants of intra-specific and inter-specific differentiation of populations, and the distribution of their genetic diversity. More recently, habitat and climate differences, and corresponding adaptations have been shown to be forces influencing the phylogeographic evolution of some vertebrates. In this study, we examined the contribution of these various factors on the genetic differentiation of the bent-winged bat, Miniopterus schreibersii, in southeastern Europe and Anatolia. Results and conclusion Our results showed differentiation in mitochondrial DNA coupled with weaker nuclear differentiation. We found evidence for restriction of lineages to geographical areas for hundreds of generations. The results showed that the most likely ancestral haplotype was restricted to the same geographic area (the Balkans for at least 6,000 years. We were able to delineate the migration routes during the population expansion process, which followed the coasts and the inland for different nested mitochondrial clades. Hence, we were able to describe a scenario showing how multiple biotic and abiotic events including glacial periods, climate and historical dispersal patterns complemented each other in causing regional and local differentiation within a species.

  19. A 25 million year macrofloral record (Carboniferous-Permian) in the Czech part of the Intra-Sudetic Basin, biostratigraphy, plant diversity and vegetation patterns

    Czech Academy of Sciences Publication Activity Database

    Opluštil, S.; Šimůnek, Z.; Pšenička, J.; Bek, Jiří; Libertín, M.

    2017-01-01

    Roč. 244, SEP 2017 (2017), s. 241-307 ISSN 0034-6667 R&D Projects: GA ČR GAP210/12/2053 Institutional support: RVO:67985831 Keywords : Early Permian * floral zonation * Intra-Sudetic Basin * Pennsylvanian * plant diversity * plant taphonomy * vegetation patterns Subject RIV: DB - Geology ; Mineralogy OBOR OECD: Paleontology Impact factor: 1.817, year: 2016

  20. Spatial patterns of diversity and genetic erosion of traditional cassava (Manihot esculenta Crantz) cultivation in the Peruvian Amazon: an evaluation of socio-economic and environmental indicators

    NARCIS (Netherlands)

    Willemen, L.; Scheldeman, X.; Soto Cabellos, V.; Salazar, S.R.; Guarino, L.

    2007-01-01

    This study evaluates quantitatively the suitability of the use of site-specific socio-economic and environmental data as indicators to rapidly assess patterns of diversity and genetic erosion risk in cassava. Socio-economic data as well as farmers¿ estimation of genetic erosion were collected in the

  1. Genetic diversity in a Colombian bean (Phaseolus vulgaris L. collection as assessed by phaseolin patterns and isoenzymatic markers

    Directory of Open Access Journals (Sweden)

    Gustavo Ligarreto

    2012-08-01

    Full Text Available The knowledge of genetic diversity patterns increase the efficiency of the conservation and the enrichment of the genetic resourses. This study allowed the discrimination of the existing genetic variability in a Colombian collection of shrub bean by phaseolin patterns and isoenzymatic markers. Bean seed proteins revelated that the phaseolin patterns types T and C are predominant in the Andean pool, type S in the Meso-American pool and type B in Colombian and Central American accessions, with a predominance of 81% of phaseolin T in the Andean pool, and 78% of phaseolin B in the Meso-American pool. The accessions of cultivated and wild beans showed variation in 10 of the studied enzymatic systems: αβ-EST , GOT, αβ-ACP, DIA , PRX, AS D, 6-PGDH, MDH, IDH and ME; and monomorphism in the PGI and PGM systems. The isozyme systems presented 19 bands of activity, of which 74% were polymorphic loci. Both in the Andean and Meso-American genetic pools, the loci Mdh-1, Mdh-2, β-Est-1, Skdh and Me exhibited polymorphisms. Single alleles in the Meso-American pool were found in 6-Pgdh-2(103, Mdh-1(100, Idh100, α-Est-1(100, α-Est-2(100, and Dia-195; and in the Andean pool, in 6-Pgdh-1(100, and Acp-2(100. For degree of domestication, the wild and cultivated accessions presented polymorphisms in 58 and 47% of the lOCi, respectively. The enzymatic relationship cluster analysis of the studied bean collection revealed three distinct groups of accessions; namely the Meso-American pool, including its cultivated and wild accessions; the Andean pool, which is mainly comprised of cultivated accessions, plus the wild DGD-626; and finally, featured by a high degree of enzymatic polymorphism and by the presence of the type I phaseolin, a third group that contains only a wild accession from the northern, Peruvian Andes

  2. AN UPWARD TREND IN DNA P16INK4A METHYLATION PATTERN AND HIGH RISK HPV INFECTION ACCORDING TO THE SEVERITY OF THE CERVICAL LESION

    Directory of Open Access Journals (Sweden)

    Fernanda Nahoum Carestiato

    2013-09-01

    Full Text Available SUMMARY High-risk human papillomavirus (hr-HPV infection is necessary but not sufficient for cervical cancer development. Recently, P16INK4A gene silencing through hypermethylation has been proposed as an important cofactor in cervical carcinogenesis due to its tumor suppressor function. We aimed to investigate P16INK4A methylation status in normal and neoplastic epithelia and evaluate an association with HPV infection and genotype. This cross-sectional study was performed with 141 cervical samples from patients attending Hospital Moncorvo Filho, Rio de Janeiro. HPV detection and genotyping were performed through PCR and P16INK4A methylation by nested-methylation specific PCR (MSP. HPV frequency was 62.4% (88/141. The most common HPV were HPV16 (37%, HPV18 (16.3% and HPV33/45(15.2%. An upward trend was observed concerning P16INK4A methylation and lesion degree: normal epithelia (10.7%, low grade lesions (22.9%, high grade (57.1% and carcinoma (93.1% (p < 0.0001. A multivariate analysis was performed to evaluate an association between methylation, age, tobacco exposure, HPV infection and genotyping. A correlation was found concerning methylation with HPV infection (p < 0.0001, hr-HPV (p = 0.01, HSIL (p < 0.0007 and malignant lesions (p < 0.0001. Since viral infection and epigenetic alterations are related to cervical carcinoma, we suggest that P16INK4A methylation profile maybe thoroughly investigated as a biomarker to identify patients at risk of cancer.

  3. Genome-wide identification of blood DNA methylation patterns associated with early-onset hepatocellular carcinoma development in hepatitis B carriers.

    Science.gov (United States)

    Kao, Wei-Yi; Yang, Shu-Han; Liu, Wen-Jie; Yeh, Meng-Yin; Lin, Chih-Lin; Liu, Chun-Jen; Huang, Chi-Jung; Lin, Shi-Ming; Lee, Shou-Dong; Chen, Pei-Jer; Yu, Ming-Whei

    2017-02-01

    The etiology of early-onset hepatocellular carcinoma (HCC) among hepatitis B virus (HBV) carriers remains unclear. DNA methylation levels in peripheral leukocytes have been associated with different environmental exposures and immune or inflammatory response. We aimed to identify methylation signatures of peripheral leukocytes that could track hepatitis B progression to HCC, especially for early-onset HCC. We first performed an epigenome-wide association analysis on 48 matched case-control pairs in a nested case-control study within a 22-yr follow-up cohort of HBV carriers. Through this analysis we found that progression to early-onset HCC involved methylation variable positions across the genome, in which a substantial proportion displayed significant variation due to HBV viral load, chronic hepatitis status, and/or leukocyte subtype composition, and these associations were significantly enriched among genes in immune pathways. Methylation at probes cg00300879, cg06872964, and cg07080864, that are located within the proximal promoter of CNKSR1, IFI44L, and PENK, respectively, was validated by bisulfite pyrosequencing and findings were replicated in a case-sibling study of early-onset HCC (134 cases vs. 174 sibling controls). Furthermore, a high methylation score, constructed using the three probes, was predictive for the risk of early-onset HCC in two datasets (adjusted-odds ratios = 0.21-0.32, P ≤ 0.0206). This association was also observed for late-onset HCC (adjusted-odds ratio = 0.42-0.47, P ≤ 0.0194) in a nested case-control study (120 cases vs. 178 controls). In prospective analysis, change in the score was detected 5-9 yr before HCC onset. Blood-based methylation profiling provides new insights into the complexity of virus-host interaction underlying HBV-related HCC, holding promise for the disease risk management. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  4. Barcoding the butterflies of southern South America: Species delimitation efficacy, cryptic diversity and geographic patterns of divergence.

    Directory of Open Access Journals (Sweden)

    Pablo D Lavinia

    Full Text Available Because the tropical regions of America harbor the highest concentration of butterfly species, its fauna has attracted considerable attention. Much less is known about the butterflies of southern South America, particularly Argentina, where over 1,200 species occur. To advance understanding of this fauna, we assembled a DNA barcode reference library for 417 butterfly species of Argentina, focusing on the Atlantic Forest, a biodiversity hotspot. We tested the efficacy of this library for specimen identification, used it to assess the frequency of cryptic species, and examined geographic patterns of genetic variation, making this study the first large-scale genetic assessment of the butterflies of southern South America. The average sequence divergence to the nearest neighbor (i.e. minimum interspecific distance was 6.91%, ten times larger than the mean distance to the furthest conspecific (0.69%, with a clear barcode gap present in all but four of the species represented by two or more specimens. As a consequence, the DNA barcode library was extremely effective in the discrimination of these species, allowing a correct identification in more than 95% of the cases. Singletons (i.e. species represented by a single sequence were also distinguishable in the gene trees since they all had unique DNA barcodes, divergent from those of the closest non-conspecific. The clustering algorithms implemented recognized from 416 to 444 barcode clusters, suggesting that the actual diversity of butterflies in Argentina is 3%-9% higher than currently recognized. Furthermore, our survey added three new records of butterflies for the country (Eurema agave, Mithras hannelore, Melanis hillapana. In summary, this study not only supported the utility of DNA barcoding for the identification of the butterfly species of Argentina, but also highlighted several cases of both deep intraspecific and shallow interspecific divergence that should be studied in more detail.

  5. Phylogenetic and population genetic analyses of diploid Leucaena (Leguminosae; Mimosoideae) reveal cryptic species diversity and patterns of divergent allopatric speciation.

    Science.gov (United States)

    Govindarajulu, Rajanikanth; Hughes, Colin E; Bailey, C Donovan

    2011-12-01

    Leucaena comprises 17 diploid species, five tetraploid species, and a complex series of hybrids whose evolutionary histories have been influenced by human seed translocation, cultivation, and subsequent spontaneous hybridization. Here we investigated patterns of evolutionary divergence among diploid Leucaena through comprehensively sampled multilocus phylogenetic and population genetic approaches to address species delimitation, interspecific relationships, hybridization, and the predominant mode of speciation among diploids. Parsimony- and maximum-likelihood-based phylogenetic approaches were applied to 59 accessions sequenced for six SCAR-based nuclear loci, nrDNA ITS, and four cpDNA regions. Population genetic comparisons included 1215 AFLP loci representing 42 populations and 424 individuals. Phylogenetic results provided a well-resolved hypothesis of divergent species relationships, recovering previously recognized clades of diploids as well as newly resolved relationships. Phylogenetic and population genetic assessments identified two cryptic species that are consistent with geography and morphology. Findings from this study highlight the importance and utility of multilocus data in the recovery of complex evolutionary histories. The results are consistent with allopatric divergence representing the predominant mode of speciation among diploid Leucaena. These findings contrast with the potential hybrid origin of several tetraploid species and highlight the importance of human translocation of seed to the origin of these tetraploids. The recognition of one previously unrecognized species (L. cruziana) and the elevation of another taxon (L. collinsii subsp. zacapana) to specific status (L. zacapana) is consistent with a growing number of newly diagnosed species from neotropical seasonally dry forests, suggesting these communities harbor greater species diversity than previously recognized.

  6. Barcoding the butterflies of southern South America: Species delimitation efficacy, cryptic diversity and geographic patterns of divergence.

    Science.gov (United States)

    Lavinia, Pablo D; Núñez Bustos, Ezequiel O; Kopuchian, Cecilia; Lijtmaer, Darío A; García, Natalia C; Hebert, Paul D N; Tubaro, Pablo L

    2017-01-01

    Because the tropical regions of America harbor the highest concentration of butterfly species, its fauna has attracted considerable attention. Much less is known about the butterflies of southern South America, particularly Argentina, where over 1,200 species occur. To advance understanding of this fauna, we assembled a DNA barcode reference library for 417 butterfly species of Argentina, focusing on the Atlantic Forest, a biodiversity hotspot. We tested the efficacy of this library for specimen identification, used it to assess the frequency of cryptic species, and examined geographic patterns of genetic variation, making this study the first large-scale genetic assessment of the butterflies of southern South America. The average sequence divergence to the nearest neighbor (i.e. minimum interspecific distance) was 6.91%, ten times larger than the mean distance to the furthest conspecific (0.69%), with a clear barcode gap present in all but four of the species represented by two or more specimens. As a consequence, the DNA barcode library was extremely effective in the discrimination of these species, allowing a correct identification in more than 95% of the cases. Singletons (i.e. species represented by a single sequence) were also distinguishable in the gene trees since they all had unique DNA barcodes, divergent from those of the closest non-conspecific. The clustering algorithms implemented recognized from 416 to 444 barcode clusters, suggesting that the actual diversity of butterflies in Argentina is 3%-9% higher than currently recognized. Furthermore, our survey added three new records of butterflies for the country (Eurema agave, Mithras hannelore, Melanis hillapana). In summary, this study not only supported the utility of DNA barcoding for the identification of the butterfly species of Argentina, but also highlighted several cases of both deep intraspecific and shallow interspecific divergence that should be studied in more detail.

  7. Seasonal and spatial patterns of microbial diversity along a trophic gradient in the interconnected lakes of the Osterseen Lake District, Bavaria

    Science.gov (United States)

    Zwirglmaier, Katrin; Keiz, Katharina; Engel, Marion; Geist, Juergen; Raeder, Uta

    2015-01-01

    The Osterseen Lake District in Bavaria consists of 19 small interconnected lakes that exhibit a pronounced trophic gradient from eutrophic to oligotrophic. It therefore presents a unique model system to address ecological questions regarding niche adaptation and Baas Becking's long standing hypothesis of “everything is everywhere, but the environment selects.” Here, we present the first assessment of the microbial diversity in these lakes. We sampled the lakes in August and December and used 454 pyrosequencing of 16S rRNA amplicons to analyze the microbial diversity. The diversity patterns between lakes and seasons were compared and the bacterial community composition was correlated with key chemical and physical parameters. Distinct patterns of bacterial diversity only emerged at the level of individual OTUs (operational taxonomic units), but not at the level of the major bacterial phyla. This emphasizes the high functional and physiological diversity among bacterial species within a phylum and calls for analysis of biodiversity at the level of OTUs in order to understand fine-scale biogeography. We were able to identify a number of cosmopolitan OTUs as well as specialist OTUs that were restricted to certain lakes or seasons, suggesting adaptation to specific ecological niches. PMID:26579082

  8. Postglacial recolonization in a cold climate specialist in western Europe: patterns of genetic diversity in the adder (Vipera berus) support the central-marginal hypothesis.

    Science.gov (United States)

    Ursenbacher, Sylvain; Guillon, Michaël; Cubizolle, Hervé; Dupoué, Andréaz; Blouin-Demers, Gabriel; Lourdais, Olivier

    2015-07-01

    Understanding the impact of postglacial recolonization on genetic diversity is essential in explaining current patterns of genetic variation. The central-marginal hypothesis (CMH) predicts a reduction in genetic diversity from the core of the distribution to peripheral populations, as well as reduced connectivity between peripheral populations. While the CMH has received considerable empirical support, its broad applicability is still debated and alternative hypotheses predict different spatial patterns of genetic diversity. Using microsatellite markers, we analysed the genetic diversity of the adder (Vipera berus) in western Europe to reconstruct postglacial recolonization. Approximate Bayesian Computation (ABC) analyses suggested a postglacial recolonization from two routes: a western route from the Atlantic Coast up to Belgium and a central route from the Massif Central to the Alps. This cold-adapted species likely used two isolated glacial refugia in southern France, in permafrost-free areas during the last glacial maximum. Adder populations further from putative glacial refugia had lower genetic diversity and reduced connectivity; therefore, our results support the predictions of the CMH. Our study also illustrates the utility of highly variable nuclear markers, such as microsatellites, and ABC to test competing recolonization hypotheses. © 2015 John Wiley & Sons Ltd.

  9. Contrasting Patterns of Genomic Diversity Reveal Accelerated Genetic Drift but Reduced Directional Selection on X-Chromosome in Wild and Domestic Sheep Species.

    Science.gov (United States)

    Chen, Ze-Hui; Zhang, Min; Lv, Feng-Hua; Ren, Xue; Li, Wen-Rong; Liu, Ming-Jun; Nam, Kiwoong; Bruford, Michael W; Li, Meng-Hua

    2018-04-01

    Analyses of genomic diversity along the X chromosome and of its correlation with autosomal diversity can facilitate understanding of evolutionary forces in shaping sex-linked genomic architecture. Strong selective sweeps and accelerated genetic drift on the X-chromosome have been inferred in primates and other model species, but no such insight has yet been gained in domestic animals compared with their wild relatives. Here, we analyzed X-chromosome variability in a large ovine data set, including a BeadChip array for 943 ewes from the world's sheep populations and 110 whole genomes of wild and domestic sheep. Analyzing whole-genome sequences, we observed a substantially reduced X-to-autosome diversity ratio (∼0.6) compared with the value expected under a neutral model (0.75). In particular, one large X-linked segment (43.05-79.25 Mb) was found to show extremely low diversity, most likely due to a high density of coding genes, featuring highly conserved regions. In general, we observed higher nucleotide diversity on the autosomes, but a flat diversity gradient in X-linked segments, as a function of increasing distance from the nearest genes, leading to a decreased X: autosome (X/A) diversity ratio and contrasting to the positive correlation detected in primates and other model animals. Our evidence suggests that accelerated genetic drift but reduced directional selection on X chromosome, as well as sex-biased demographic events, explain low X-chromosome diversity in sheep species. The distinct patterns of X-linked and X/A diversity we observed between Middle Eastern and non-Middle Eastern sheep populations can be explained by multiple migrations, selection, and admixture during the domestic sheep's recent postdomestication demographic expansion, coupled with natural selection for adaptation to new environments. In addition, we identify important novel genes involved in abnormal behavioral phenotypes, metabolism, and immunity, under selection on the sheep X-chromosome.

  10. Contrasting land uses in Mediterranean agro-silvo-pastoral systems generated patchy diversity patterns of vascular plants and below-ground microorganisms.

    Science.gov (United States)

    Bagella, Simonetta; Filigheddu, Rossella; Caria, Maria Carmela; Girlanda, Mariangela; Roggero, Pier Paolo

    2014-12-01

    The aims of this paper were (i) to define how contrasting land uses affected plant biodiversity in Mediterranean agro-silvo-pastoral-systems across a gradient of disturbance regimes: cork oak forests, secondary grasslands, hay crops, grass covered vineyards, tilled vineyards; (ii) to determine whether these patterns mirrored those of below-ground microorganisms and whether the components of γ-diversity followed a similar model. The disturbance regimes affected plant assemblage composition. Species richness decreased with increasing land use intensity, the Shannon index showed the highest values in grasslands and hay crops. Plant assemblage composition patterns mirrored those of Basidiomycota and Ascomycota. Richness in Basidiomycota, denitrifying bacteria and microbial biomass showed the same trend as that observed for vascular plant richness. The Shannon index pattern of below-ground microorganisms was different from that of plants. The plant γ-diversity component model weakly mirrored those of Ascomycota. Patchy diversity patterns suggest that the maintenance of contrasting land uses associated with different productions typical of agro-silvo-pastoral-systems can guarantee the conservation of biodiversity. Copyright © 2014 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  11. Characterization of in vitro haploid and doubled haploid Chrysanthemum morifolium plants via unfertilized ovule culture for phenotypical traits and DNA methylation pattern.

    Directory of Open Access Journals (Sweden)

    Haibin eWang

    2014-12-01

    Full Text Available Chrysanthemum is one of important ornamental species in the world. Its highly heterozygous state complicates molecular analysis, so it is of interest to derive haploid forms. A total of 2,579 non-fertilized chrysanthemum ovules pollinated by Argyranthemum frutescens were cultured in vitro to isolate haploid progeny. One single regenerant emerged from each of three of the 105 calli produced. Chromosome counts and microsatellite fingerprinting showed that only one of the regenerants was a true haploid. Nine doubled haploid derivatives were subsequently generated by colchicine treatment of 80 in vitro cultured haploid nodal segments. Morphological screening showed that the haploid plant was shorter than the doubled haploids, and developed smaller leaves, flowers and stomata. An in vitro pollen germination test showed that few of the haploid's pollen were able to germinate and those which did so were abnormal. Both the haploid and the doubled haploids produced yellow flowers, whereas those of the maternal parental cultivar were mauve. Methylation-sensitive amplification polymorphism (MSAP profiling was further used to detect alterations in cytosine methylation caused by the haploidization and/or the chromosome doubling processes. While 52.2% of the resulting amplified fragments were cytosine methylated in the maternal parent's genome, the corresponding proportions for the haploid's and doubled haploids' genomes were, respectively, 47.0% and 51.7%, demonstrating a reduction in global cytosine methylation caused by haploidization and a partial recovery following chromosome doubling.

  12. Effect of Anthropogenic Activities on Patterns of Genetic Diversity in Symplocos racemosa Roxb. from Western Ghats, India

    Directory of Open Access Journals (Sweden)

    Sofia Banu

    2014-01-01

    Full Text Available The Western Ghats (WG in India is recognized as one of the global biodiversity hotspots which have high proportion of endemic species and the medicinally important tree species. Due to medicinal importance and being found on the forest fringes, Symplocos racemosa Roxb. is highly susceptible to anthropogenic activities. The present study was undertaken to systematically analyze the effects of anthropogenic activities on the genetic diversity and population structure of S. racemosa and to generate preliminary data for conservation purposes. We analyzed the variation in intergenic sequences of chloroplast and mitochondrial genomes from seven sites of S. racemosa sampled from protected, semiprotected, and disturbed areas of WG. Total diversity was high although within-sites diversity was low. The protected sites were highly diverse, while the disturbed areas possessed less genetic diversity indicating the effect of anthropogenic activities.

  13. Modeling spatiotemporal dynamics of DNA methylation

    DEFF Research Database (Denmark)

    Lövkvist, Cecilia Elisabet

    into how epigenetic marks are distributed in the human genome. In the first part of the thesis, we investigate DNA methylation and maintenance of methylation patterns throughout cell division. We argue that collaborative models, those where the methylation of CpG sites depends on the methylation status...... into the game more explicitly in another type of model that speaks out the duality of the two aspects. Using statistical analysis of experimental data, this thesis further explores a link between DNA methylation and nucleosome occupancy. By comparing the patterns on promoters to regions with similar Cp...... division. The patterns of epigentic marks depend on enzymes that ensure their maintenance and introduction. Using theoretical models, this thesis proposes new mechanisms for how enzymes operate to maintain patterns of epigenetic marks. Through analysis of experimental data this work gives new insight...

  14. Present spatial diversity patterns of Theobroma cacao L. in the neotropics reflect genetic differentiation in pleistocene refugia followed by human-influenced dispersal.

    Science.gov (United States)

    Thomas, Evert; van Zonneveld, Maarten; Loo, Judy; Hodgkin, Toby; Galluzzi, Gea; van Etten, Jacob

    2012-01-01

    Cacao (Theobroma cacao L.) is indigenous to the Amazon basin, but is generally believed to have been domesticated in Mesoamerica for the production of chocolate beverage. However, cacao's distribution of genetic diversity in South America is also likely to reflect pre-Columbian human influences that were superimposed on natural processes of genetic differentiation. Here we present the results of a spatial analysis of the intra-specific diversity of cacao in Latin America, drawing on a dataset of 939 cacao trees genotypically characterized by means of 96 SSR markers. To assess continental diversity patterns we performed grid-based calculations of allelic richness, Shannon diversity and Nei gene diversity, and distinguished different spatially coherent genetic groups by means of cluster analysis. The highest levels of genetic diversity were observed in the Upper Amazon areas from southern Peru to the Ecuadorian Amazon and the border areas between Colombia, Peru and Brazil. On the assumption that the last glaciation (22,000-13,000 BP) had the greatest pre-human impact on the current distribution and diversity of cacao, we modeled the species' Pleistocene niche suitability and overlaid this with present-day diversity maps. The results suggest that cacao was already widely distributed in the Western Amazon before the onset of glaciation. During glaciations, cacao populations were likely to have been restricted to several refugia where they probably underwent genetic differentiation, resulting in a number of genetic clusters which are representative for, or closest related to, the original wild cacao populations. The analyses also suggested that genetic differentiation and geographical distribution of a number of other clusters seem to have been significantly affected by processes of human management and accompanying genetic bottlenecks. We discuss the implications of these results for future germplasm collection and in situ, on farm and ex situ conservation of cacao.

  15. Quantitative proteome-level analysis of paulownia witches’ broom disease with methyl methane sulfonate assistance reveals diverse metabolic changes during the infection and recovery processes

    Directory of Open Access Journals (Sweden)

    Zhe Wang

    2017-07-01

    Full Text Available Paulownia witches’ broom (PaWB disease caused by phytoplasma is a fatal disease that leads to considerable economic losses. Although there are a few reports describing studies of PaWB pathogenesis, the molecular mechanisms underlying phytoplasma pathogenicity in Paulownia trees remain uncharacterized. In this study, after building a transcriptome database containing 67,177 sequences, we used isobaric tags for relative and absolute quantification (iTRAQ to quantify and analyze the proteome-level changes among healthy P. fortunei (PF, PaWB-infected P. fortunei (PFI, and PaWB-infected P. fortunei treated with 20 mg L−1 or 60 mg L−1 methyl methane sulfonate (MMS (PFI-20 and PFI-60, respectively. A total of 2,358 proteins were identified. We investigated the proteins profiles in PF vs. PFI (infected process and PFI-20 vs. PFI-60 (recovered process, and further found that many of the MMS-response proteins mapped to “photosynthesis” and “ribosome” pathways. Based on our comparison scheme, 36 PaWB-related proteins were revealed. Among them, 32 proteins were classified into three functional groups: (1 carbohydrate and energy metabolism, (2 protein synthesis and degradation, and (3 stress resistance. We then investigated the PaWB-related proteins involved in the infected and recovered processes, and discovered that carbohydrate and energy metabolism was inhibited, and protein synthesis and degradation decreased, as the plant responded to PaWB. Our observations may be useful for characterizing the proteome-level changes that occur at different stages of PaWB disease. The data generated in this study may serve as a valuable resource for elucidating the pathogenesis of PaWB disease during phytoplasma infection and recovery stages.

  16. Consistent variability in beta-diversity patterns contrasts with changes in alpha-diversity along an onshore to offshore environmental gradient: the case of Red Sea soft-bottom macrobenthos

    KAUST Repository

    Alsaffar, Zahra Hassan Ali

    2017-09-30

    Patterns of variability in diversity (alpha and beta), abundance, and community structure of soft-bottom macrobenthic assemblages were investigated across an inshore/offshore environmental gradient in the central Red Sea. A total of three distinct soft-substrate biotopes were identified through multivariate techniques: seagrass meadows, nearshore, and offshore. While the seagrass biotope was associated with higher organic matter content, the two coastal biotopes presented higher redox potential in the sediments and dissolved oxygen in the water. Depth and medium sand increased toward the offshore, while the percentage of fine particles was a determinant of nearshore communities. Regardless of the prevailing environmental conditions, the three biotopes were characterized by high numbers of exclusive taxa, most of which were singletons. Changes in species richness were not related to depth or organic matter, peaking at intermediate depths (nearshore). However, the number of taxa increased exponentially with abundance. On the other hand, density decreased logarithmically with depth and organic matter in sediments, probably linked to a reduced availability of food. One of the most conspicuous features of the macrobenthic assemblages inhabiting soft substrates in the central oligotrophic Red Sea is the low level of dominance resulting from a high species richness: abundance ratio. Despite the differences observed for alpha-diversity across the three biotopes, beta-diversity patterns were rather consistent. These findings suggest that mechanisms driving biodiversity are similar across the depth gradient. The partitioning of beta-diversity also show that assemblages are mainly driven by the substitution of species (turnover or replacement), most likely as a result of environmental filtering. The heterogeneity of the seafloor in shallow waters of the Red Sea promoted by the co-existence of coral reefs inter-spaced by sedimentary habitats may increase the regional pool of

  17. Two colonisation stages generate two different patterns of genetic diversity within native and invasive ranges of Ulex europaeus.

    Science.gov (United States)

    Hornoy, B; Atlan, A; Roussel, V; Buckley, Y M; Tarayre, M

    2013-11-01

    Genetic diversity and the way a species is introduced influence the capacity of populations of invasive species to persist in, and adapt to, their new environment. The diversity of introduced populations affects their evolutionary potential, which is particularly important for species that have invaded a wide range of habitats and climates, such as European gorse, Ulex europaeus. This species originated in the Iberian peninsula and colonised Europe in the Neolithic; over the course of the past two centuries it was introduced to, and has become invasive in, other continents. We characterised neutral genetic diversity and its structure in the native range and in invaded regions. By coupling these results with historical data, we have identified the way in which gorse populations were introduced and the consequences of introduction history on genetic diversity. Our study is based on the genotyping of individuals from 18 populations at six microsatellite loci. As U. europaeus is an allohexaploid species, we used recently developed tools that take into account genotypic ambiguity. Our results show that genetic diversity in gorse is very high and mainly contained within populations. We confirm that colonisation occurred in two stages. During the first stage, gorse spread out naturally from Spain towards northern Europe, losing some genetic diversity. During the second stage, gorse was introduced by humans into different regions of the world, from northern Europe. These introductions resulted in the loss of rare alleles but did not significantly reduce genetic diversity and thus the evolutionary potential of this invasive species.

  18. Contrasting patterns of diversity and population differentiation at the innate immunity gene toll-like receptor 2 (TLR2) in two sympatric rodent species.

    Science.gov (United States)

    Tschirren, Barbara; Andersson, Martin; Scherman, Kristin; Westerdahl, Helena; Råberg, Lars

    2012-03-01

    Comparing patterns of diversity and divergence between populations at immune genes and neutral markers can give insights into the nature and geographic scale of parasite-mediated selection. To date, studies investigating such patterns of selection in vertebrates have primarily focused on the acquired branch of the immune system, whereas it remains largely unknown how parasite-mediated selection shapes innate immune genes both within and across vertebrate populations. Here, we present a study on the diversity and population differentiation at the innate immune gene Toll-like receptor 2 (TLR2) across nine populations of yellow-necked mice (Apodemus flavicollis) and bank voles (Myodes glareolus) in southern Sweden. In yellow-necked mice, TLR2 diversity was very low, as was TLR2 population differentiation compared to neutral loci. In contrast, several TLR2 haplotypes co-occurred at intermediate frequencies within and across bank vole populations, and pronounced isolation by distance between populations was observed. The diversity and differentiation at neutral loci was similar in the two species. These results indicate that parasite-mediated selection has been acting in dramatically different ways on a given immune gene in ecologically similar and sympatric species. Furthermore, the finding of TLR2 population differentiation at a small geographical scale in bank voles highlights that vertebrate innate immune defense may be evolutionarily more dynamic than has previously been appreciated. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

  19. Common DNA methylation alterations in multiple brain regions in autism.

    Science.gov (United States)

    Ladd-Acosta, C; Hansen, K D; Briem, E; Fallin, M D; Kaufmann, W E; Feinberg, A P

    2014-08-01

    Autism spectrum disorders (ASD) are increasingly common neurodevelopmental disorders defined clinically by a triad of features including impairment in social interaction, impairment in communication in social situations and restricted and repetitive patterns of behavior and interests, with considerable phenotypic heterogeneity among individuals. Although heritability estimates for ASD are high, conventional genetic-based efforts to identify genes involved in ASD have yielded only few reproducible candidate genes that account for only a small proportion of ASDs. There is mounting evidence to suggest environmental and epigenetic factors play a stronger role in the etiology of ASD than previously thought. To begin to understand the contribution of epigenetics to ASD, we have examined DNA methylation (DNAm) in a pilot study of postmortem brain tissue from 19 autism cases and 21 unrelated controls, among three brain regions including dorsolateral prefrontal cortex, temporal cortex and cerebellum. We measured over 485,000 CpG loci across a diverse set of functionally relevant genomic regions using the Infinium HumanMethylation450 BeadChip and identified four genome-wide significant differentially methylated regions (DMRs) using a bump hunting approach and a permutation-based multiple testing correction method. We replicated 3/4 DMRs identified in our genome-wide screen in a different set of samples and across different brain regions. The DMRs identified in this study represent suggestive evidence for commonly altered methylation sites in ASD and provide several promising new candidate genes.

  20. Genetic diversity of Ralstonia solanacearum strains from China assessed by PCR-based fingerprints to unravel host plant- and site-dependent distribution patterns.

    Science.gov (United States)

    Xue, Qing-Yun; Yin, Yan-Ni; Yang, Wei; Heuer, Holger; Prior, Philippe; Guo, Jian-Hua; Smalla, Kornelia

    2011-03-01

    Bacterial wilt caused by Ralstonia solanacearum is a serious threat to crop production in China. A collection of 319 R. solanacearum strains isolated from 14 different diseased host plants collected in 15 Chinese provinces was investigated by BOX fingerprints in order to test the influence of the site and the host plant on their genetic diversity. Phylotype, fliC-RFLP patterns and biovar were determined for all strains and the sequevar for 39 representative strains. The majority of strains belonged to the Asian phylotype I, shared identical fliC-RFLP patterns and were assigned to four biovars (bv3:123; bv4:162; bv5:3; and bv6:11). Twenty strains were phylotype II, assigned to biovar 2, and had distinct fliC-RFLP patterns. BOX-PCR fingerprints generated from the genomic DNA of each strain revealed a high diversity of the phylotype I strains, where 28 types of BOX fingerprints could be distinguished. While many BOX clusters comprised isolates from different provinces and several host plants, some groups contained isolates that were plant or site specific. All phylotype II isolates originating from 10 provinces belonged to sequevar 1 and displayed identical BOX patterns as the potato brown rot strains from various regions of the world. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  1. Genetic and DNA methylation changes in cotton (Gossypium genotypes and tissues.

    Directory of Open Access Journals (Sweden)

    Kenji Osabe

    Full Text Available In plants, epigenetic regulation is important in normal development and in modulating some agronomic traits. The potential contribution of DNA methylation mediated gene regulation to phenotypic diversity and development in cotton was investigated between cotton genotypes and various tissues. DNA methylation diversity, genetic diversity, and changes in methylation context were investigated using methylation-sensitive amplified polymorphism (MSAP assays including a methylation insensitive enzyme (BsiSI, and the total DNA methylation level was measured by high-performance liquid chromatography (HPLC. DNA methylation diversity was greater than the genetic diversity in the selected cotton genotypes and significantly different levels of DNA methylation were identified between tissues, including fibre. The higher DNA methylation diversity (CHG methylation being more diverse than CG methylation in cotton genotypes suggest epigenetic regulation may be important for cotton, and the change in DNA methylation between fibre and other tissues hints that some genes may be epigenetically regulated for fibre development. The novel approach using BsiSI allowed direct comparison between genetic and epigenetic diversity, and also measured CC methylation level that cannot be detected by conventional MSAP.

  2. Genetic and DNA methylation changes in cotton (Gossypium) genotypes and tissues.

    Science.gov (United States)

    Osabe, Kenji; Clement, Jenny D; Bedon, Frank; Pettolino, Filomena A; Ziolkowski, Lisa; Llewellyn, Danny J; Finnegan, E Jean; Wilson, Iain W

    2014-01-01

    In plants, epigenetic regulation is important in normal development and in modulating some agronomic traits. The potential contribution of DNA methylation mediated gene regulation to phenotypic diversity and development in cotton was investigated between cotton genotypes and various tissues. DNA methylation diversity, genetic diversity, and changes in methylation context were investigated using methylation-sensitive amplified polymorphism (MSAP) assays including a methylation insensitive enzyme (BsiSI), and the total DNA methylation level was measured by high-performance liquid chromatography (HPLC). DNA methylation diversity was greater than the genetic diversity in the selected cotton genotypes and significantly different levels of DNA methylation were identified between tissues, including fibre. The higher DNA methylation diversity (CHG methylation being more diverse than CG methylation) in cotton genotypes suggest epigenetic regulation may be important for cotton, and the change in DNA methylation between fibre and other tissues hints that some genes may be epigenetically regulated for fibre development. The novel approach using BsiSI allowed direct comparison between genetic and epigenetic diversity, and also measured CC methylation level that cannot be detected by conventional MSAP.

  3. Diversity patterns and isolation of Planctomycetes associated with metalliferous deposits from hydrothermal vent fields along the Valu Fa Ridge (SW Pacific).

    Science.gov (United States)

    Storesund, Julia Endresen; Lanzèn, Anders; García-Moyano, Antonio; Reysenbach, Anna-Louise; Øvreås, Lise

    2018-02-08

    The microbial diversity associated with diffuse venting deep-sea hydrothermal deposits is tightly coupled to the geochemistry of the hydrothermal fluids. Previous 16S rRNA gene amplicon sequencing (metabarcoding) of marine iron-hydroxide deposits along the Arctic Mid Ocean Ridge, revealed the presence of diverse bacterial communities associated with these deposits (Storesund and Øvreås in Antonie van Leeuwenhoek 104:569-584, 2013). One of the most abundant and diverse phyla detected was the enigmatic Planctomycetes. Here we report on the comparative analyses of the diversity and distribution patterns of Planctomycetes associated with metalliferous deposits from two diffuse-flow hydrothermal vent fields (Mariner and Vai Lili) from the Valu Fa Ridge in the Southwestern Pacific. Metabarcoding of 16S rRNA genes showed that the major prokaryotic phyla were Proteobacteria (51-73% of all 16S rRNA gene reads), Epsilonbacteraeota (0.5-19%), Bacteriodetes (5-17%), Planctomycetes (0.4-11%), Candidatus Latescibacteria (0-5%) and Marine Benthic Group E (Hydrothermarchaeota) (0-5%). The two different sampling sites differed considerably in overall community composition. The abundance of Planctomycetes also varied substantially between the samples and the sites, with the majority of the sequences affiliated with uncultivated members of the classes Planctomycetacia and Phycisphaerae, and other deep branching lineages. Seven different strains affiliated with the order Planctomycetales were isolated, mostly from the Vai Lili samples, where also the highest Planctomycetales diversity was seen. Most of the isolates were affiliated with the genera Gimesia, Rhodopirellula and Blastopirellula. One isolate was only distantly related to known cultured, but uncharacterized species within the Pir4 group. This study shows that the deep-sea Planctomycetes represent a very heterogeneous group with a high phylogenetic diversity and a substantial potential for novel organism discovery in these

  4. Community level patterns in diverse systems: A case study of litter fauna in a Mexican pine-oak forest using higher taxa surrogates and re-sampling methods

    Science.gov (United States)

    Moreno, Claudia E.; Guevara, Roger; Sánchez-Rojas, Gerardo; Téllez, Dianeis; Verdú, José R.

    2008-01-01

    Environmental assessment at the community level in highly diverse ecosystems is limited by taxonomic constraints and statistical methods requiring true replicates. Our objective was to show how diverse systems can be studied at the community level using higher taxa as biodiversity surrogates, and re-sampling methods to allow comparisons. To illustrate this we compared the abundance, richness, evenness and diversity of the litter fauna in a pine-oak forest in central Mexico among seasons, sites and collecting methods. We also assessed changes in the abundance of trophic guilds and evaluated the relationships between community parameters and litter attributes. With the direct search method we observed differences in the rate of taxa accumulation between sites. Bootstrap analysis showed that abundance varied significantly between seasons and sampling methods, but not between sites. In contrast, diversity and evenness were significantly higher at the managed than at the non-managed site. Tree regression models show that abundance varied mainly between seasons, whereas taxa richness was affected by litter attributes (composition and moisture content). The abundance of trophic guilds varied among methods and seasons, but overall we found that parasitoids, predators and detrivores decreased under management. Therefore, although our results suggest that management has positive effects on the richness and diversity of litter fauna, the analysis of trophic guilds revealed a contrasting story. Our results indicate that functional groups and re-sampling methods may be used as tools for describing community patterns in highly diverse systems. Also, the higher taxa surrogacy could be seen as a preliminary approach when it is not possible to identify the specimens at a low taxonomic level in a reasonable period of time and in a context of limited financial resources, but further studies are needed to test whether the results are specific to a system or whether they are general

  5. Genome-Wide Maps of m6A circRNAs Identify Widespread and Cell-Type-Specific Methylation Patterns that Are Distinct from mRNAs

    Directory of Open Access Journals (Sweden)

    Chan Zhou

    2017-08-01

    Full Text Available N6-methyladenosine (m6A is the most abundant internal modification of mRNAs and is implicated in all aspects of post-transcriptional RNA metabolism. However, little is known about m6A modifications to circular (circ RNAs. We developed a computational pipeline (AutoCirc that, together with depletion of ribosomal RNA and m6A immunoprecipitation, defined thousands of m6A circRNAs with cell-type-specific expression. The presence of m6A circRNAs is corroborated by interaction between circRNAs and YTHDF1/YTHDF2, proteins that read m6A sites in mRNAs, and by reduced m6A levels upon depletion of METTL3, the m6A writer. Despite sharing m6A readers and writers, m6A circRNAs are frequently derived from exons that are not methylated in mRNAs, whereas mRNAs that are methylated on the same exons that compose m6A circRNAs exhibit less stability in a process regulated by YTHDF2. These results expand our understanding of the breadth of m6A modifications and uncover regulation of circRNAs through m6A modification.

  6. Patterns of genetic diversity and differentiation in the tsetse fly Glossina morsitans morsitans Westwood populations in East and southern Africa

    International Nuclear Information System (INIS)

    Ouma, J.O.; Marquez, J.G.; Krafsur, E.S

    2007-01-01

    Genetic diversity and differentiation within and among nine G. morsitans morsitans populations from East and southern Africa was assessed by examining variation at seven microsatellite loci and a mitochondrial locus, cytochrome oxidase (COI). Mean COI diversity within populations was 0.63 ± 0.33 and 0.81 taken over all populations. Diversities averaged over microsatellite loci were high (mean number of alleles/locus ≥7.4; mean HE ≥ 65%) in all populations. Diversities averaged across populations were greater in East Africa (mean number of alleles = 22 ± 2.6; mean he = 0.773 ± 0.033) than in southern Africa (mean number of alleles = 18.7 ± 4.0; mean he = 0.713 ± 0.072). Differentiation among all populations was highly significant (RST = 0.25, FST = 0.132). Nei’s Gij statistics were 0.09 and 0.19 within regions for microsatellites and mitochondria, respectively; between regions, Gij was 0.14 for microsatellites and 0.23 for mitochondria. GST among populations was 0.23 for microsatellite loci and 0.40 for mitochondria. The F, G and R statistics indicate highly restricted gene flow among G. m. morsitans populations separated over geographic scales of 12–917 km. (author)

  7. Diversity, distribution pattern and seasonal variation in moth assemblages along altitudinal gradient in Gangotri landscape area, Western Himalaya, Uttarakhand, India

    Directory of Open Access Journals (Sweden)

    A.K. Sanyal

    2013-02-01

    Full Text Available Field survey was conducted at different altitudes and land-use areas in the two protected areas, viz., Gangotri National Park and Govind National Park of Uttarkashi District, Uttarakhand, India. A total of 475 specimens of moth representing 436 morphospecies were collected using light trap method during the survey conducted between September 2008-May 2010. Preliminary findings show a decreasing diversity with increasing altitude. Subalpine areas were least diverse and subtropical areas had the highest diversity of moths. The greatest number of specimens were collected during the summer and post-monsoon period. The lunar phase had a significant effect on catch success with new moon days resulting in the largest catches and full moon days resulting in the least number of species as well as individuals. Of the thirty two species mentioned in Appendix 1, nine species are first time record from the state Uttarakhand. Four species are new record from Western Himalaya within Indian Territory, and also first time recorded from entire Himalayan landscape. As there was no previous comprehensive study on the moth diversity of Gangotri landscape area, all the 32 species described could be regarded as new record from these two protected areas.

  8. Discordant genetic diversity and geographic patterns between Crassicutis cichlasomae (Digenea: Apocreadiidae) and its cichlid host, "Cichlasoma" urophthalmus (Osteichthyes: Cichlidae), in Middle-America.

    Science.gov (United States)

    Razo-Mendivil, Ulises; Vázquez-Domínguez, Ella; de León, Gerardo Pérez-Ponce

    2013-12-01

    Genetic analyses of hosts and their parasites are key to understand the evolutionary patterns and processes that have shaped host-parasite associations. We evaluated the genetic structure of the digenean Crassicutis cichlasomae and its most common host, the Mayan cichlid "Cichlasoma" urophthalmus, encompassing most of their geographical range in Middle-America (river basins in southeastern Mexico, Belize, and Guatemala together with the Yucatan Peninsula). Genetic diversity and structure analyses were done based on 167 cytochrome c oxidase subunit 1 sequences (330 bp) for C. cichlasomae from 21 populations and 161 cytochrome b sequences (599 bp) for "C." urophthalmus from 26 populations. Analyses performed included phylogenetic tree estimation under Bayesian inference and maximum likelihood analysis, genetic diversity, distance and structure estimates, haplotype networks, and demographic evaluations. Crassicutis cichlasomae showed high genetic diversity values and genetic structuring, corresponding with 4 groups clearly differentiated and highly divergent. Conversely, "C." urophthalmus showed low levels of genetic diversity and genetic differentiation, defined as 2 groups with low divergence and with no correspondence with geographical distribution. Our results show that species of cichlids parasitized by C. cichlasomae other than "C." urophthalmus, along with multiple colonization events and subsequent isolation in different basins, are likely factors that shaped the genetic structure of the parasite. Meanwhile, historical long-distance dispersal and drought periods during the Holocene, with significant population size reductions and fragmentations, are factors that could have shaped the genetic structure of the Mayan cichlid.

  9. Time-location patterns of a diverse population of older adults: the Multi-Ethnic Study of Atherosclerosis and Air Pollution (MESA Air).

    Science.gov (United States)

    Spalt, Elizabeth W; Curl, Cynthia L; Allen, Ryan W; Cohen, Martin; Adar, Sara D; Stukovsky, Karen H; Avol, Ed; Castro-Diehl, Cecilia; Nunn, Cathy; Mancera-Cuevas, Karen; Kaufman, Joel D

    2016-06-01

    The primary aim of this analysis was to present and describe questionnaire data characterizing time-location patterns of an older, multiethnic population from six American cities. We evaluated the consistency of results from repeated administration of this questionnaire and between this questionnaire and other questionnaires collected from participants of the Multi-Ethnic Study of Atherosclerosis and Air Pollution (MESA Air). Participants reported spending most of their time inside their homes (average: 121 h/week or 72%). More than 50% of the participants reported spending no time in several of the location options, including at home outdoors, at work/volunteer/school locations indoors or outdoors, or in "other" locations outdoors. We observed consistency between self-reported time-location patterns from repeated administration of the time-location questionnaire and compared with other survey instruments. Comparisons with national cohorts demonstrated the differences in time-location patterns in the MESA Air cohort due to differences in demographics, but the data showed similar trends in patterns by age, gender, season, and employment status. This study was the first to explicitly examine the time-location patterns in an older, multiethnic population and the first to add data on Chinese participants. These data can be used to inform future epidemiological research of MESA Air and other studies that include diverse populations.

  10. Diversity and above-ground biomass patterns of vascular flora induced by flooding in the drawdown area of China's Three Gorges Reservoir.

    Directory of Open Access Journals (Sweden)

    Qiang Wang

    Full Text Available Hydrological alternation can dramatically influence riparian environments and shape riparian vegetation zonation. However, it was difficult to predict the status in the drawdown area of the Three Gorges Reservoir (TGR, because the hydrological regime created by the dam involves both short periods of summer flooding and long-term winter impoundment for half a year. In order to examine the effects of hydrological alternation on plant diversity and biomass in the drawdown area of TGR, twelve sites distributed along the length of the drawdown area of TGR were chosen to explore the lateral pattern of plant diversity and above-ground biomass at the ends of growing seasons in 2009 and 2010. We recorded 175 vascular plant species in 2009 and 127 in 2010, indicating that a significant loss of vascular flora in the drawdown area of TGR resulted from the new hydrological regimes. Cynodon dactylon and Cyperus rotundus had high tolerance to short periods of summer flooding and long-term winter flooding. Almost half of the remnant species were annuals. Species richness, Shannon-Wiener Index and above-ground biomass of vegetation exhibited an increasing pattern along the elevation gradient, being greater at higher elevations subjected to lower submergence stress. Plant diversity, above-ground biomass and species distribution were significantly influenced by the duration of submergence relative to elevation in both summer and previous winter. Several million tonnes of vegetation would be accumulated on the drawdown area of TGR in every summer and some adverse environmental problems may be introduced when it was submerged in winter. We conclude that vascular flora biodiversity in the drawdown area of TGR has dramatically declined after the impoundment to full capacity. The new hydrological condition, characterized by long-term winter flooding and short periods of summer flooding, determined vegetation biodiversity and above-ground biomass patterns along the

  11. Genetic diversity and differentiation patterns in Micromeria from the Canary Islands are congruent with multiple colonization dynamics and the establishment of species syngameons.

    Science.gov (United States)

    Curto, M; Puppo, P; Kratschmer, S; Meimberg, H

    2017-08-22

    Especially on islands closer to the mainland, such as the Canary Islands, different lineages that originated by multiple colonization events could have merged by hybridization, which then could have promoted radiation events (Herben et al., J Ecol 93: 572-575, 2005; Saunders and Gibson, J Ecol 93: 649-652, 2005; Caujapé-Castells, Jesters, red queens, boomerangs and surfers: a molecular outlook on the diversity of the Canarian endemic flora, 2011). This is an alternative to the scenario where evolution is mostly driven by drift (Silvertown, J Ecol 92: 168-173, 2004; Silvertown et al., J Ecol 93: 653-657, 2005). In the former case hybridization should be reflected in the genetic structure and diversity patterns of island species. In the present work we investigate Micromeria from the Canary Islands by extensively studying their phylogeographic pattern based on 15 microsatellite loci and 945 samples. These results are interpreted according to the hypotheses outlined above. Genetic structure assessment allowed us to genetically differentiate most Micromeria species and supported their current classification. We found that populations on younger islands were significantly more genetically diverse and less differentiated than those on older islands. Moreover, we found that genetic distance on younger islands was in accordance with an isolation-by-distance pattern, while on the older islands this was not the case. We also found evidence of introgression among species and islands. These results are congruent with a scenario of multiple colonizations during the expansion onto new islands. Hybridization contributes to the grouping of multiple lineages into highly diverse populations. Thus, in our case, islands receive several colonization events from different sources, which are combined into sink populations. This mechanism is in accordance with the surfing syngameon hypothesis. Contrary to the surfing syngameon current form, our results may reflect a slightly different

  12. Patterns of diversity and regeneration in unmanaged moist deciduous forests in response to disturbance in Shiwalik Himalayas, India

    Directory of Open Access Journals (Sweden)

    Mukesh Kumar Gautam

    2016-06-01

    Full Text Available We studied vegetation attributes in Indian tropical moist deciduous unmanaged forests to determine the influence of forest disturbances on them. We enumerated 89 species: 72 under moderate disturbance and 54 under least disturbance. The data from 3399 stems [>5 cm diameter at breast height (dbh] decreased linearly along the disturbance gradient. The basal area was largest in least disturbed forests (61 m2/ha and smallest in intensely disturbed forest (41 m2/ha. Under least and moderate disturbance, tree density-diameter distribution had negative exponential curves, whereas highly disturbed forests had unimodal-shaped curves where a few trees 5–10 cm and >50 cm in diameter were recorded. Most tree and shrub layer species under heavy and intense disturbance had impaired regeneration. Moderate disturbance intensity thus apparently benefits species diversity, stand density, and regeneration. Decline in seedlings and saplings, especially tree species, threaten forest regeneration and the maintenance of species diversity of unmanaged tropical forests.

  13. Accurate Determination of Leucine and Valine Side-chain Conformations using U-[15N/13C/2H]/[1H-(methine/methyl)-Leu/Val] Isotope Labeling, NOE Pattern Recognition, and Methine Cγ-Hγ/Cβ-Hβ Residual Dipolar Couplings

    International Nuclear Information System (INIS)

    Tang, Chun; Iwahara, Junji; Clore, G. Marius

    2005-01-01

    An isotope labeling scheme is described in which specific protonation of methine and methyl protons of leucine and valine is obtained on a 15 N/ 13 C labeled background with uniform deuteration of all other non-exchangeable protons. The presence of a protonated methine group has little effect on the favorable relaxation properties of the methyl protons of Leu and Val. This labeling scheme permits the rotameric state of leucine side-chains to be readily determined by simple inspection of the pattern of Hγ(i)-H N (i) and Hγ(i)-H N (i+1) NOEs in a 3D 15 N-separated NOE spectrum free of complications arising from spectral overlap and spin-diffusion. In addition, one-bond residual dipolar couplings for the methine 13 C- 1 H bond vectors of Leu and Val can be accurately determined from an intensity J-modulated constant-time HCCH-COSY experiment and used to accurately orient the side-chains of Leu and Val. Incorporation of these data into structure refinement improves the accuracy with which the conformations of Leu and Val side-chains can be established. This is important to ensure optimal packing both within the protein core and at intermolecular interfaces. The impact of the method on protein structure determination is illustrated by application to enzyme IIA Chitobiose , a 34 kDa homotrimeric phosphotransferase protein

  14. Global patterns of workplace productivity for people with depression: absenteeism and presenteeism costs across eight diverse countries

    OpenAIRE

    Evans-Lacko, S.; Knapp, M.

    2016-01-01

    Purpose Depression is a leading cause of disability worldwide. Research suggests that by far, the greatest contributor to the overall economic impact of depression is loss in productivity; however, there is very little research on the costs of depression outside of Western high-income countries. Thus, this study examines the impact of depression on workplace productivity across eight diverse countries. Methods We estimated the extent and costs of depression-related absenteeism and presenteeis...

  15. Selection, diversity and evolutionary patterns of the MHC class II DAB in free-ranging Neotropical marsupials

    Directory of Open Access Journals (Sweden)

    Otten Celine

    2008-06-01

    Full Text Available Abstract Background Research on the genetic architecture and diversity of the MHC has focused mainly on eutherian mammals, birds and fish. So far, studies on model marsupials used in laboratory investigations indicated very little or even no variation in MHC class II genes. However, natural levels of diversity and selection are unknown in marsupials as studies on wild populations are virtually absent. We used two endemic South American mouse opossums, Gracilinanus microtarsus and Marmosops incanus, to investigate characteristic features of MHC selection. This study is the first investigation of MHC selection in free-ranging Neotropical marsupials. In addition, the evolutionary history of MHC lineages within the group of marsupials was examined. Results G. microtarsus showed extensive levels of MHC diversity within and among individuals as 47 MHC-DAB alleles and high levels of sequence divergence were detected at a minimum of four loci. Positively selected codon sites were identified, of which most were congruent with human antigen binding sites. The diversity in M. incanus was rather low with only eight observed alleles at presumably two loci. However, these alleles also revealed high sequence divergence. Again, positive selection was identified on specific codon sites, all congruent with human ABS and with positively selected sites observed in G. microtarsus. In a phylogenetic comparison alleles of M. incanus interspersed widely within alleles of G. microtarsus with four alleles being present in both species. Conclusion Our investigations revealed extensive MHC class II polymorphism in a natural marsupial population, contrary to previous assumptions. Furthermore, our study confirms for the first time in marsupials the presence of three characteristic features common at MHC loci of eutherian mammals, birds and fish: large allelic sequence divergence, positive selection on specific sites and trans-specific polymorphism.

  16. Measuring networks for environmental radioactivity monitoring in the European Community, - a pattern of diversity as varying as the peoples?

    International Nuclear Information System (INIS)

    Maushart, R.

    1991-01-01

    A new study entitled 'Monitoring of Environmental Radioactivity in the European Community', (RAES, 90), shows a survey of the methods currently applied in every country. The study compiles available quality assurance programs and makes suggestions for CEC initiatives. The study refers to the current practice of monitoring in European countries as 'enormous diversity of methods' in member countries. Further suggestions for standardization of the data measuring networks are put forward by a manufacturer of monitoring equipment. (orig./DG) [de

  17. How coastal upwelling influences spatial patterns of size-structured diversity of copepods off central-southern Chile (summer 2009)

    Science.gov (United States)

    Hidalgo, Pamela; Escribano, Ruben; Fuentes, Marcelo; Jorquera, Erika; Vergara, Odette

    2012-01-01

    This study assessed the structure of the copepod community in the upper 20