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Sample records for sampling nucleotide diversity

  1. Sampling nucleotide diversity in cotton

    Directory of Open Access Journals (Sweden)

    Yu John Z

    2009-10-01

    Full Text Available Abstract Background Cultivated cotton is an annual fiber crop derived mainly from two perennial species, Gossypium hirsutum L. or upland cotton, and G. barbadense L., extra long-staple fiber Pima or Egyptian cotton. These two cultivated species are among five allotetraploid species presumably derived monophyletically between G. arboreum and G. raimondii. Genomic-based approaches have been hindered by the limited variation within species. Yet, population-based methods are being used for genome-wide introgression of novel alleles from G. mustelinum and G. tomentosum into G. hirsutum using combinations of backcrossing, selfing, and inter-mating. Recombinant inbred line populations between genetics standards TM-1, (G. hirsutum × 3-79 (G. barbadense have been developed to allow high-density genetic mapping of traits. Results This paper describes a strategy to efficiently characterize genomic variation (SNPs and indels within and among cotton species. Over 1000 SNPs from 270 loci and 279 indels from 92 loci segregating in G. hirsutum and G. barbadense were genotyped across a standard panel of 24 lines, 16 of which are elite cotton breeding lines and 8 mapping parents of populations from six cotton species. Over 200 loci were genetically mapped in a core mapping population derived from TM-1 and 3-79 and in G. hirsutum breeding germplasm. Conclusion In this research, SNP and indel diversity is characterized for 270 single-copy polymorphic loci in cotton. A strategy for SNP discovery is defined to pre-screen loci for copy number and polymorphism. Our data indicate that the A and D genomes in both diploid and tetraploid cotton remain distinct from each such that paralogs can be distinguished. This research provides mapped DNA markers for intra-specific crosses and introgression of exotic germplasm in cotton.

  2. Mitochondrial DNA analysis reveals a low nucleotide diversity of ...

    African Journals Online (AJOL)

    Mitochondrial DNA analysis reveals a low nucleotide diversity of Caligula japonica in China. ... Mitochondrial DNA analysis reveals a low nucleotide diversity of Caligula japonica in China. Y Li, B Yang, H Wang, R Xia, L Wang, Z Zhang, L Qin, Y Liu ...

  3. Nucleotide diversity and phylogenetic relationships among ...

    Indian Academy of Sciences (India)

    Navya

    The genus Gladilous L. is comprised of about 265 species in the world, and is one of the largest genera of family Iridaceae. The Cape of Good Hope (South Africa) is considered to be the centre of diversity for the genus Gladiolus. It is distributed throughout tropical Africa,. Madagascar, Arabian Peninsula, the Mediterranean ...

  4. Nucleotide diversity and phylogenetic relationships among ...

    Indian Academy of Sciences (India)

    2017-03-03

    Mar 3, 2017 ... of Good Hope (South Africa) is considered to be the centre of diversity for the genus Gladiolus. It is distributed throughout the region of tropical Africa, Madagascar, Arabian Peninsula, the Mediterranean basin, Europe and Asia, including Iran and Afghanistan (Goldblatt and Manning 1998; Goldblatt et al.

  5. Nucleotide diversity and linkage disequilibrium in 11 expressed resistance candidate genes in Lolium perenne

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    Asp Torben

    2007-08-01

    Full Text Available Abstract Background Association analysis is an alternative way for QTL mapping in ryegrass. So far, knowledge on nucleotide diversity and linkage disequilibrium in ryegrass is lacking, which is essential for the efficiency of association analyses. Results 11 expressed disease resistance candidate (R genes including 6 nucleotide binding site and leucine rich repeat (NBS-LRR like genes and 5 non-NBS-LRR genes were analyzed for nucleotide diversity. For each of the genes about 1 kb genomic fragments were isolated from 20 heterozygous genotypes in ryegrass. The number of haplotypes per gene ranged from 9 to 27. On average, one single nucleotide polymorphism (SNP was present per 33 bp between two randomly sampled sequences for the 11 genes. NBS-LRR like gene fragments showed a high degree of nucleotide diversity, with one SNP every 22 bp between two randomly sampled sequences. NBS-LRR like gene fragments showed very high non-synonymous mutation rates, leading to altered amino acid sequences. Particularly LRR regions showed very high diversity with on average one SNP every 10 bp between two sequences. In contrast, non-NBS LRR resistance candidate genes showed a lower degree of nucleotide diversity, with one SNP every 112 bp. 78% of haplotypes occurred at low frequency ( Conclusion Substantial LD decay was found within a distance of 500 bp for most resistance candidate genes in this study. Hence, LD based association analysis is feasible and promising for QTL fine mapping of resistance traits in ryegrass.

  6. Diversity and evolutionary relationship of nucleotide binding site ...

    Indian Academy of Sciences (India)

    Degenerate primers based on the conserved motif (P-loop and GLPL) of the NBS domain from -genes were used to isolate RGAs from the genomic DNA of sweet potato cultivar Qingnong no. 2. Five distinct clusters of RGAs (22 sequences) with the characteristic NBS representing a highly diverse sample were identified in ...

  7. Nucleotide diversity and linkage disequilibrium in wild avocado (Persea americana Mill.).

    Science.gov (United States)

    Chen, Haofeng; Morrell, Peter L; de la Cruz, Marlene; Clegg, Michael T

    2008-01-01

    Resequencing studies provide the ultimate resolution of genetic diversity because they identify all mutations in a gene that are present within the sampled individuals. We report a resequencing study of Persea americana, a subtropical tree species native to Meso- and Central America and the progenitor of cultivated avocado. The sample includes 21 wild accessions from Mexico, Costa Rica, Ecuador, and the Dominican Republic. Estimated levels of nucleotide polymorphism and linkage disequilibrium (LD) are obtained from fully resolved haplotype data from 4 nuclear loci that span 5960 nucleotide sites. Results show that, although avocado is a subtropical tree crop and a predominantly outcrossing plant, the overall level of genetic variation is not exceptionally high (nucleotide diversity at silent sites, pi(sil) = 0.0102) compared with available estimates from temperate plant species. Intralocus LD decays rapidly to half the initial value within about 1 kb. Estimates of recombination rate (based on the sequence data) show that the rate is not exceptionally high when compared with annual plants such as wild barley or maize. Interlocus LD is significant owing to substantial population structure induced by mixing of the 3 botanical races of avocado.

  8. Single nucleotide polymorphisms for assessing genetic diversity in castor bean (Ricinus communis

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    Rabinowicz Pablo D

    2010-01-01

    Full Text Available Abstract Background Castor bean (Ricinus communis is an agricultural crop and garden ornamental that is widely cultivated and has been introduced worldwide. Understanding population structure and the distribution of castor bean cultivars has been challenging because of limited genetic variability. We analyzed the population genetics of R. communis in a worldwide collection of plants from germplasm and from naturalized populations in Florida, U.S. To assess genetic diversity we conducted survey sequencing of the genomes of seven diverse cultivars and compared the data to a reference genome assembly of a widespread cultivar (Hale. We determined the population genetic structure of 676 samples using single nucleotide polymorphisms (SNPs at 48 loci. Results Bayesian clustering indicated five main groups worldwide and a repeated pattern of mixed genotypes in most countries. High levels of population differentiation occurred between most populations but this structure was not geographically based. Most molecular variance occurred within populations (74% followed by 22% among populations, and 4% among continents. Samples from naturalized populations in Florida indicated significant population structuring consistent with local demes. There was significant population differentiation for 56 of 78 comparisons in Florida (pairwise population ϕPT values, p Conclusion Low levels of genetic diversity and mixing of genotypes have led to minimal geographic structuring of castor bean populations worldwide. Relatively few lineages occur and these are widely distributed. Our approach of determining population genetic structure using SNPs from genome-wide comparisons constitutes a framework for high-throughput analyses of genetic diversity in plants, particularly in species with limited genetic diversity.

  9. Mango (Mangifera indica L.) germplasm diversity based on single nucleotide polymorphisms derived from the transcriptome.

    Science.gov (United States)

    Sherman, Amir; Rubinstein, Mor; Eshed, Ravit; Benita, Miri; Ish-Shalom, Mazal; Sharabi-Schwager, Michal; Rozen, Ada; Saada, David; Cohen, Yuval; Ophir, Ron

    2015-11-14

    Germplasm collections are an important source for plant breeding, especially in fruit trees which have a long duration of juvenile period. Thus, efforts have been made to study the diversity of fruit tree collections. Even though mango is an economically important crop, most of the studies on diversity in mango collections have been conducted with a small number of genetic markers. We describe a de novo transcriptome assembly from mango cultivar 'Keitt'. Variation discovery was performed using Illumina resequencing of 'Keitt' and 'Tommy Atkins' cultivars identified 332,016 single-nucleotide polymorphisms (SNPs) and 1903 simple-sequence repeats (SSRs). Most of the SSRs (70.1%) were of trinucleotide with the preponderance of motif (GGA/AAG)n and only 23.5% were di-nucleotide SSRs with the mostly of (AT/AT)n motif. Further investigation of the diversity in the Israeli mango collection was performed based on a subset of 293 SNPs. Those markers have divided the Israeli mango collection into two major groups: one group included mostly mango accessions from Southeast Asia (Malaysia, Thailand, Indonesia) and India and the other with mainly of Floridian and Israeli mango cultivars. The latter group was more polymorphic (FS=-0.1 on the average) and was more of an admixture than the former group. A slight population differentiation was detected (FST=0.03), suggesting that if the mango accessions of the western world apparently was originated from Southeast Asia, as has been previously suggested, the duration of cultivation was not long enough to develop a distinct genetic background. Whole-transcriptome reconstruction was used to significantly broaden the mango's genetic variation resources, i.e., SNPs and SSRs. The set of SNP markers described in this study is novel. A subset of SNPs was sampled to explore the Israeli mango collection and most of them were polymorphic in many mango accessions. Therefore, we believe that these SNPs will be valuable as they recapitulate and

  10. Diverse nucleotide compositions and sequence fluctuation in Rubisco protein genes

    Science.gov (United States)

    Holden, Todd; Dehipawala, S.; Cheung, E.; Bienaime, R.; Ye, J.; Tremberger, G., Jr.; Schneider, P.; Lieberman, D.; Cheung, T.

    2011-10-01

    The Rubisco protein-enzyme is arguably the most abundance protein on Earth. The biology dogma of transcription and translation necessitates the study of the Rubisco genes and Rubisco-like genes in various species. Stronger correlation of fractal dimension of the atomic number fluctuation along a DNA sequence with Shannon entropy has been observed in the studied Rubisco-like gene sequences, suggesting a more diverse evolutionary pressure and constraints in the Rubisco sequences. The strategy of using metal for structural stabilization appears to be an ancient mechanism, with data from the porphobilinogen deaminase gene in Capsaspora owczarzaki and Monosiga brevicollis. Using the chi-square distance probability, our analysis supports the conjecture that the more ancient Rubisco-like sequence in Microcystis aeruginosa would have experienced very different evolutionary pressure and bio-chemical constraint as compared to Bordetella bronchiseptica, the two microbes occupying either end of the correlation graph. Our exploratory study would indicate that high fractal dimension Rubisco sequence would support high carbon dioxide rate via the Michaelis- Menten coefficient; with implication for the control of the whooping cough pathogen Bordetella bronchiseptica, a microbe containing a high fractal dimension Rubisco-like sequence (2.07). Using the internal comparison of chi-square distance probability for 16S rRNA (~ E-22) versus radiation repair Rec-A gene (~ E-05) in high GC content Deinococcus radiodurans, our analysis supports the conjecture that high GC content microbes containing Rubisco-like sequence are likely to include an extra-terrestrial origin, relative to Deinococcus radiodurans. Similar photosynthesis process that could utilize host star radiation would not compete with radiation resistant process from the biology dogma perspective in environments such as Mars and exoplanets.

  11. High-throughput nucleotide sequence analysis of diverse bacterial communities in leachates of decomposing pig carcasses

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    Seung Hak Yang

    2015-09-01

    Full Text Available The leachate generated by the decomposition of animal carcass has been implicated as an environmental contaminant surrounding the burial site. High-throughput nucleotide sequencing was conducted to investigate the bacterial communities in leachates from the decomposition of pig carcasses. We acquired 51,230 reads from six different samples (1, 2, 3, 4, 6 and 14 week-old carcasses and found that sequences representing the phylum Firmicutes predominated. The diversity of bacterial 16S rRNA gene sequences in the leachate was the highest at 6 weeks, in contrast to those at 2 and 14 weeks. The relative abundance of Firmicutes was reduced, while the proportion of Bacteroidetes and Proteobacteria increased from 3–6 weeks. The representation of phyla was restored after 14 weeks. However, the community structures between the samples taken at 1–2 and 14 weeks differed at the bacterial classification level. The trend in pH was similar to the changes seen in bacterial communities, indicating that the pH of the leachate could be related to the shift in the microbial community. The results indicate that the composition of bacterial communities in leachates of decomposing pig carcasses shifted continuously during the study period and might be influenced by the burial site.

  12. Nucleotide diversity analysis of three major bacterial blight resistance genes in rice.

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    Waikhom Bimolata

    Full Text Available Nucleotide sequence polymorphisms among R gene alleles influence the process of co-evolutionary interaction between host and pathogen by shaping the response of host plants towards invading pathogens. Here, we present the DNA sequence polymorphisms and diversities present among natural alleles of three rice bacterial blight resistance genes, Xa21, Xa26 and xa5. The diversity was examined across different wild relatives and cultivars of Oryza species. Functional significance of selected alleles was evaluated through semi-quantitative reverse transcription polymerase chain reaction and real time PCR. The greatest nucleotide diversity and singleton variable sites (SVS were present in Xa26 (π = 0.01958; SVS = 182 followed by xa5 and Xa21 alleles. The highest frequency of single nucleotide polymorphisms were observed in Xa21 alleles and least in xa5. Transition bias was observed in all the genes and 'G' to 'A' transitions were more favored than other form of transitions. Neutrality tests failed to show the presence of selection at these loci, though negative Tajima's D values indicate the presence of a rare form of polymorphisms. At the interspecies level, O. nivara exhibited more diversity than O. sativa. We have also identified two nearly identical resistant alleles of xa5 and two sequentially identical alleles of Xa21. The alleles of xa5 showed basal levels of expression while Xa21 alleles were functionally not expressed.

  13. A multilocus assay reveals high nucleotide diversity and limited differentiation among Scandinavian willow grouse (Lagopus lagopus

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    Quintela Maria

    2008-12-01

    Full Text Available Abstract Background There is so far very little data on autosomal nucleotide diversity in birds, except for data from the domesticated chicken and some passerines species. Estimates of nucleotide diversity reported so far in birds have been high (~10-3 and a likely explanation for this is the generally higher effective population sizes compared to mammals. In this study, the level of nucleotide diversity has been examined in the willow grouse, a non-domesticated bird species from the order Galliformes, which also holds the chicken. The willow grouse (Lagopus lagopus has an almost circumpolar distribution but is absent from Greenland and the north Atlantic islands. It primarily inhabits tundra, forest edge habitats and sub-alpine vegetation. Willow grouse are hunted throughout its range, and regionally it is a game bird of great cultural and economical importance. Results We sequenced 18 autosomal protein coding loci from approximately 15–18 individuals per population. We found a total of 127 SNP's, which corresponds to 1 SNP every 51 bp. 26 SNP's were amino acid replacement substitutions. Total nucleotide diversity (πt was between 1.30 × 10-4 and 7.66 × 10-3 (average πt = 2.72 × 10-3 ± 2.06 × 10-3 and silent nucleotide diversity varied between 4.20 × 10-4and 2.76 × 10-2 (average πS = 9.22 × 10-3 ± 7.43 × 10-4. The synonymous diversity is approximately 20 times higher than in humans and two times higher than in chicken. Non-synonymous diversity was on average 18 times lower than the synonymous diversity and varied between 0 and 4.90 × 10-3 (average πa = 5.08 × 10-4 ± 7.43 × 103, which suggest that purifying selection is strong in these genes. FST values based on synonymous SNP's varied between -5.60 × 10-4 and 0.20 among loci and revealed low levels of differentiation among the four localities, with an overall value of FST = 0.03 (95% CI: 0.006 – 0.057 over 60 unlinked loci. Non-synonymous SNP's gave similar results. Low

  14. Nucleotide polymorphisms and haplotype diversity of RTCS gene in China elite maize inbred lines.

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    Enying Zhang

    Full Text Available The maize RTCS gene, encoding a LOB domain transcription factor, plays important roles in the initiation of embryonic seminal and postembryonic shoot-borne root. In this study, the genomic sequences of this gene in 73 China elite inbred lines, including 63 lines from 5 temperate heteroric groups and 10 tropic germplasms, were obtained, and the nucleotide polymorphisms and haplotype diversity were detected. A total of 63 sequence variants, including 44 SNPs and 19 indels, were identified at this locus, and most of them were found to be located in the regions of UTR and intron. The coding region of this gene in all tested inbred lines carried 14 haplotypes, which encoding 7 deferring RTCS proteins. Analysis of the polymorphism sites revealed that at least 6 recombination events have occurred. Among all 6 groups tested, only the P heterotic group had a much lower nucleotide diversity than the whole set, and selection analysis also revealed that only this group was under strong negative selection. However, the set of Huangzaosi and its derived lines possessed a higher nucleotide diversity than the whole set, and no selection signal were identified.

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

    Science.gov (United States)

    2010-01-01

    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. PMID:20550656

  16. Nucleotide diversity of the Chlamydomonas reinhardtii plastid genome: addressing the mutational-hazard hypothesis.

    Science.gov (United States)

    Smith, David Roy; Lee, Robert W

    2009-05-27

    The mutational-hazard hypothesis argues that the noncoding-DNA content of a genome is a consequence of the mutation rate (mu) and the effective number of genes per locus in the population (N(g)). The hypothesis predicts that genomes with a high N(g)mu will be more compact than those with a small N(g)mu. Approximations of N(g)mu can be gained by measuring the nucleotide diversity at silent sites (pi(silent)). We addressed the mutation-hazard hypothesis apropos plastid-genome evolution by measuring pi(silent) of the Chlamydomonas reinhardtii plastid DNA (ptDNA), the most noncoding-DNA-dense plastid genome observed to date. The data presented here in conjunction with previously published values of pi(silent) for the C. reinhardtii mitochondrial and nuclear genomes, which are respectively compact and bloated, allow for a complete analysis of nucleotide diversity and genome compactness in all three genetic compartments of this model organism. In C. reinhardtii, the mean estimate of pi(silent) for the ptDNA (14.5 x 10(-3)) is less than that of the nuclear DNA (32 x 10(-3)) and greater than that of the mitochondrial DNA (8.5 x 10(-3)). On average, C. reinhardtii has approximately 4 times more silent-site ptDNA diversity than the mean value reported for land plants, which have more compact plastid genomes. The silent-site nucleotide diversity of the different ptDNA loci that were studied varied significantly: from 0 to 71 x 10(-3) for synonymous sites and from 0 to 42 x 10(-3) for intergenic regions. Our findings on silent-site ptDNA diversity are inconsistent with what would be expected under the mutational-hazard hypothesis and go against the documented trend in other systems of pi(silent) positively correlating with genome compactness. Overall, we highlight the lack of reliable nucleotide-diversity measurements for ptDNA and hope that the values presented here will act as sound data for future research concerning the mutational-hazard hypothesis and plastid evolution in

  17. A new supervised over-sampling algorithm with application to protein-nucleotide binding residue prediction.

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    Jun Hu

    Full Text Available Protein-nucleotide interactions are ubiquitous in a wide variety of biological processes. Accurately identifying interaction residues solely from protein sequences is useful for both protein function annotation and drug design, especially in the post-genomic era, as large volumes of protein data have not been functionally annotated. Protein-nucleotide binding residue prediction is a typical imbalanced learning problem, where binding residues are extremely fewer in number than non-binding residues. Alleviating the severity of class imbalance has been demonstrated to be a promising means of improving the prediction performance of a machine-learning-based predictor for class imbalance problems. However, little attention has been paid to the negative impact of class imbalance on protein-nucleotide binding residue prediction. In this study, we propose a new supervised over-sampling algorithm that synthesizes additional minority class samples to address class imbalance. The experimental results from protein-nucleotide interaction datasets demonstrate that the proposed supervised over-sampling algorithm can relieve the severity of class imbalance and help to improve prediction performance. Based on the proposed over-sampling algorithm, a predictor, called TargetSOS, is implemented for protein-nucleotide binding residue prediction. Cross-validation tests and independent validation tests demonstrate the effectiveness of TargetSOS. The web-server and datasets used in this study are freely available at http://www.csbio.sjtu.edu.cn/bioinf/TargetSOS/.

  18. Characterization of polyploid wheat genomic diversity using a high‐density 90 000 single nucleotide polymorphism array

    National Research Council Canada - National Science Library

    Wang, Shichen; Wong, Debbie; Forrest, Kerrie; Allen, Alexandra; Chao, Shiaoman; Huang, Bevan E; Maccaferri, Marco; Salvi, Silvio; Milner, Sara G; Cattivelli, Luigi; Mastrangelo, Anna M; Whan, Alex; Stephen, Stuart; Barker, Gary; Wieseke, Ralf; Plieske, Joerg; Lillemo, Morten; Mather, Diane; Appels, Rudi; Dolferus, Rudy; Brown‐Guedira, Gina; Korol, Abraham; Akhunova, Alina R; Feuillet, Catherine; Salse, Jerome; Morgante, Michele; Pozniak, Curtis; Luo, Ming‐Cheng; Dvorak, Jan; Morell, Matthew; Dubcovsky, Jorge; Ganal, Martin; Tuberosa, Roberto; Lawley, Cindy; Mikoulitch, Ivan; Cavanagh, Colin; Edwards, Keith J; Hayden, Matthew; Akhunov, Eduard

    2014-01-01

    High‐density single nucleotide polymorphism ( SNP ) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker...

  19. Genetic Diversity Revealed by Single Nucleotide Polymorphism Markers in a Worldwide Germplasm Collection of Durum Wheat

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    Ming-Cheng Luo

    2013-03-01

    Full Text Available Evaluation of genetic diversity and genetic structure in crops has important implications for plant breeding programs and the conservation of genetic resources. Newly developed single nucleotide polymorphism (SNP markers are effective in detecting genetic diversity. In the present study, a worldwide durum wheat collection consisting of 150 accessions was used. Genetic diversity and genetic structure were investigated using 946 polymorphic SNP markers covering the whole genome of tetraploid wheat. Genetic structure was greatly impacted by multiple factors, such as environmental conditions, breeding methods reflected by release periods of varieties, and gene flows via human activities. A loss of genetic diversity was observed from landraces and old cultivars to the modern cultivars released during periods of the Early Green Revolution, but an increase in cultivars released during the Post Green Revolution. Furthermore, a comparative analysis of genetic diversity among the 10 mega ecogeographical regions indicated that South America, North America, and Europe possessed the richest genetic variability, while the Middle East showed moderate levels of genetic diversity.

  20. Genetic Diversity Revealed by Single Nucleotide Polymorphism Markers in a Worldwide Germplasm Collection of Durum Wheat

    Science.gov (United States)

    Ren, Jing; Sun, Daokun; Chen, Liang; You, Frank M.; Wang, Jirui; Peng, Yunliang; Nevo, Eviatar; Sun, Dongfa; Luo, Ming-Cheng; Peng, Junhua

    2013-01-01

    Evaluation of genetic diversity and genetic structure in crops has important implications for plant breeding programs and the conservation of genetic resources. Newly developed single nucleotide polymorphism (SNP) markers are effective in detecting genetic diversity. In the present study, a worldwide durum wheat collection consisting of 150 accessions was used. Genetic diversity and genetic structure were investigated using 946 polymorphic SNP markers covering the whole genome of tetraploid wheat. Genetic structure was greatly impacted by multiple factors, such as environmental conditions, breeding methods reflected by release periods of varieties, and gene flows via human activities. A loss of genetic diversity was observed from landraces and old cultivars to the modern cultivars released during periods of the Early Green Revolution, but an increase in cultivars released during the Post Green Revolution. Furthermore, a comparative analysis of genetic diversity among the 10 mega ecogeographical regions indicated that South America, North America, and Europe possessed the richest genetic variability, while the Middle East showed moderate levels of genetic diversity. PMID:23538839

  1. Diverse size approach to incorporate and extend highly fluorescent unnatural nucleotides into DNA.

    Science.gov (United States)

    Le, Binh Huy; Koo, Ja Choon; Joo, Han Na; Seo, Young Jun

    2017-07-15

    We have prepared a series of size-diverse unnatural nucleotides containing fluorescent (dApyrTP, dUpyrTP, dUantTP, dUthiTP) and quencher (dUazoTP) units, as well as nucleotides presenting small functional groups (dAethTP, dAoctTP, dUethTP, dUiodTP), all based on deoxyadenosine and deoxyuridine, and examined their suitability for use in enzymatic incorporation and extension into DNA. We observed a size-dependence of the incorporation and extension capability (following the order dUiodTP=dUethTP=dUthiTP>dUazoTP>dUpyrTP>dUantTP) during primer extension. This result was supported by circular dichroism (CD) spectra, which revealed a trend in the different B-form DNA structures depending on the size of the unit at the 5-position of the deoxyuridine (dUiodTP>dUethTP>dUthiTP>dUpyrTP), obtained from the PCR products. Interestingly, dUthiTP could be incorporated and extended into long DNA strands during primer extension and even PCR amplification, with CD spectroscopy confirming a stable secondary B-form duplex DNA structure. We observed full-length extension products even when combining dUthiTP with a template containing 24 continuous dA units during the primer extension. Thus, we believe that dUthiTP is a promising fluorescent nucleotide for a diverse range of biological applications requiring multiple incorporation and extension directly without disruption of B-form DNA structures. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. Nucleotide diversity of the melanocortin 1 receptor gene (MC1R) in the gayal (Bos frontalis).

    Science.gov (United States)

    Xi, Dongmei; Liu, Qing; Huo, Yinqiang; Sun, Yongke; Leng, Jing; Gou, Xiao; Mao, Huaming; Deng, Weidong

    2012-07-01

    The melanocortin 1 receptor gene (MC1R) plays a crucial role in determining coat colour of mammals. To investigate the relationship of polymorphism of the MC1R with coat colour in gayal, the coding sequence (CDS), and the 5'- and 3'-untranslated regions (UTR) of the MC1R were sequenced from 63 samples from the gayal and compared with the sequences of the MC1R from other ruminant species. A sequence of 1,136 bp including the whole CDS (954 bp) and parts of the 5'- and 3'-UTR (164 and 18 bp, respectively) of the gayal MC1R was obtained. A total of nine single nucleotide polymorphisms (SNPs) including four SNPs (c.-129T>C, c.-127A>C, c.-106C>T, c.-1G>A) in the 5'-UTR and five SNPs (c.201C>T, c.583C>T, c.663T>C, c.871A>G and c.876T>C) in the CDS were detected, revealing high genetic diversity. Three novel coding SNPs including c.201C>T, c.583C>T and c.876T>C, which have not been reported previously in bovid species, were retrieved. Within five coding SNPs, c.201C>T, c.663T>C and c.876T>C were silent mutations, while c.583C>T and c.871A>G were mis-sense mutations, resulting in changes in the amino acids located in the fifth (p.L195F) and seventh (p.T291A) transmembrane regions, respectively. The alignment of amino acid sequences was found to be very similar to those for other bovid species. It was demonstrated, using the functional effect prediction, that the p.T291A amino acid replacement could have an effect on MC1R protein function but not for the p.L195F substitution. Using phylogenetic analyses it was revealed that the gayal has a close genetic relationship with the yak. However, three classical bovine MC1R loci the E (D), E (+) and e were not retrieved in the gayal, indicating other genes or factors could affect coat colour in this species.

  3. Nucleotide diversity and population differentiation of the Melanocortin 1 Receptor gene, MC1R

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    Peris Ketty

    2008-04-01

    Full Text Available Abstract Background The melanocortin 1 receptor gene (MC1R is responsible for normal pigment variation in humans and is highly polymorphic with numerous population-specific alleles. Some MC1R variants have been associated with skin cancer risk. Results Allele frequency data were compiled on 55 single nucleotide polymorphisms from seven geographically distinct human populations (n = 2306 individuals. MC1R nucleotide diversity, π, was much higher (10.1 × 10-4 than in other genes for all subjects. A large degree of population differentiation, determined by FST, was also present, particularly between Asia and all other populations, due to the p.R163Q (c.488 G>A polymorphism. The least amount of differentiation was between the United States, Northern Europe, and Southern Europe. Tajima's D statistic suggested the presence of positive selection in individuals from Europe. Conclusion This study further quantifies the degree of population-specific genetic variation and suggests that positive selection may be present in European populations in MC1R.

  4. Single Nucleotide Polymorphism Genotyping and Distribution of Coxiella burnetii Strains from Field Samples in Belgium

    Science.gov (United States)

    Dal Pozzo, Fabiana; Renaville, Bénédicte; Martinelle, Ludovic; Renaville, Robert; Thys, Christine; Smeets, François; Kirschvink, Nathalie; Grégoire, Fabien; Delooz, Laurent; Czaplicki, Guy

    2015-01-01

    The genotypic characterization of Coxiella burnetii provides useful information about the strains circulating at the farm, region, or country level and may be used to identify the source of infection for animals and humans. The aim of the present study was to investigate the strains of C. burnetii circulating in caprine and bovine Belgian farms using a single nucleotide polymorphism (SNP) technique. Direct genotyping was applied to different samples (bulk tank milk, individual milk, vaginal swab, fetal product, and air sample). Besides the well-known SNP genotypes, unreported ones were found in bovine and caprine samples, increasing the variability of the strains found in the two species in Belgium. Moreover, multiple genotypes were detected contemporarily in caprine farms at different years of sampling and by using different samples. Interestingly, certain SNP genotypes were detected in both bovine and caprine samples, raising the question of interspecies transmission of the pathogen. PMID:26475104

  5. Exploring the diversity of Gardnerella vaginalis in the genitourinary tract microbiota of monogamous couples through subtle nucleotide variation.

    Directory of Open Access Journals (Sweden)

    A Murat Eren

    Full Text Available BACKGROUND: Bacterial vaginosis (BV is an enigmatic disease of unknown origin that affects a large percentage of women. The vaginal microbiota of women with BV is associated with serious sequelae, including abnormal pregnancies. The etiology of BV is not fully understood, however, it has been suggested that it is transmissible, and that G. vaginalis may be an etiological agent. Studies using enzymatic assays to define G. vaginalis biotypes, as well as more recent genomic comparisons of G. vaginalis isolates from symptomatic and asymptomatic women, suggest that particular G. vaginalis strains may play a key role in the pathogenesis of BV. METHODOLOGY/PRINCIPAL FINDINGS: To explore G. vaginalis diversity, distribution and sexual transmission, we developed a Shannon entropy-based method to analyze low-level sequence variation in 65,710 G. vaginalis 16S rRNA gene segments that were PCR-amplified from vaginal samples of 53 monogamous women and from urethral and penile skin samples of their male partners. We observed a high degree of low-level diversity among G. vaginalis sequences with a total of 46 unique sequence variants (oligotypes, and also found strong correlations of these oligotypes between sexual partners. Even though Gram stain-defined normal and some Gram stain-defined intermediate oligotype profiles clustered together in UniFrac analysis, no single G. vaginalis oligotype was found to be specific to BV or normal vaginal samples. CONCLUSIONS: This study describes a novel method for investigating G. vaginalis diversity at a low level of taxonomic discrimination. The findings support cultivation-based studies that indicate sexual partners harbor the same strains of G. vaginalis. This study also highlights the fact that a few, reproducible nucleotide variations within the 16S rRNA gene can reveal clinical or epidemiological associations that would be missed by genus-level or species-level categorization of 16S rRNA data.

  6. The SUPERMAN gene family in Populus: nucleotide diversity and gene expression in a dioecious plant.

    Science.gov (United States)

    Song, Yuepeng; Ma, Kaifeng; Ci, Dong; Tian, Xueyuan; Zhang, Zhiyi; Zhang, Deqiang

    2013-08-01

    SUP gene family expression and regulation patterns reported in dioecious woody plant. Phylogenetic and nucleotide diversity analysis indicated PtoSUP1 is highly conserved and has undergone strong purifying selection. The molecular basis of SUPERMAN (SUP) regulation during floral development in monoecious plants has been extensively studied, but little is known of the SUP gene family in dioecious woody plants. In this study, we systematically examined the diversification of the SUP gene family in Populus, integrating genomic organization, expression, and phylogeny data. SUP family members showed sex-specific expression throughout flower development. Transcript profiling of rare gynomonoecious poplar flowers revealed that a significant reduction in PtoSUP1 mRNA might be important for stamen development in gynomonoecious poplar flowers. We found that the coding regions of Populus SUP genes are very highly conserved and that synonymous sites in exon regions have undergone strong purifying selection during SUP evolution in Populus. These results indicate that SUP genes play an important role in floral development of dioecious plants. Expression analysis of SUP suggested possible regulatory mechanisms for gynomonoecious poplar flower development. These findings provide an important insight into the mechanisms of the evolution of SUP function and may help enable engineered regulation of flower development for breeding improved tree varieties.

  7. Prevalence of single nucleotide polymorphism among 27 diverse alfalfa genotypes as assessed by transcriptome sequencing

    Directory of Open Access Journals (Sweden)

    Li Xuehui

    2012-10-01

    Full Text Available Abstract Background Alfalfa, a perennial, outcrossing species, is a widely planted forage legume producing highly nutritious biomass. Currently, improvement of cultivated alfalfa mainly relies on recurrent phenotypic selection. Marker assisted breeding strategies can enhance alfalfa improvement efforts, particularly if many genome-wide markers are available. Transcriptome sequencing enables efficient high-throughput discovery of single nucleotide polymorphism (SNP markers for a complex polyploid species. Result The transcriptomes of 27 alfalfa genotypes, including elite breeding genotypes, parents of mapping populations, and unimproved wild genotypes, were sequenced using an Illumina Genome Analyzer IIx. De novo assembly of quality-filtered 72-bp reads generated 25,183 contigs with a total length of 26.8 Mbp and an average length of 1,065 bp, with an average read depth of 55.9-fold for each genotype. Overall, 21,954 (87.2% of the 25,183 contigs represented 14,878 unique protein accessions. Gene ontology (GO analysis suggested that a broad diversity of genes was represented in the resulting sequences. The realignment of individual reads to the contigs enabled the detection of 872,384 SNPs and 31,760 InDels. High resolution melting (HRM analysis was used to validate 91% of 192 putative SNPs identified by sequencing. Both allelic variants at about 95% of SNP sites identified among five wild, unimproved genotypes are still present in cultivated alfalfa, and all four US breeding programs also contain a high proportion of these SNPs. Thus, little evidence exists among this dataset for loss of significant DNA sequence diversity from either domestication or breeding of alfalfa. Structure analysis indicated that individuals from the subspecies falcata, the diploid subspecies caerulea, and the tetraploid subspecies sativa (cultivated tetraploid alfalfa were clearly separated. Conclusion We used transcriptome sequencing to discover large numbers of SNPs

  8. Molecular detection and nucleotide sequence analysis of a new Aichi virus closely related to canine kobuvirus in sewage samples.

    Science.gov (United States)

    Yamashita, Teruo; Adachi, Hirokazu; Hirose, Emi; Nakamura, Noriko; Ito, Miyabi; Yasui, Yoshihiro; Kobayashi, Shinichi; Minagawa, Hiroko

    2014-05-01

    Between 2001 and 2005, 207 raw sewage samples were collected at the inflow of a sewage treatment plant in Aichi Prefecture, Japan. Of the 207 sewage samples, 137 (66.2 %) were found to be positive for amplification of Aichi virus (AiV) nucleotide using reverse transcription (RT)-PCR with 10 forward and 10 reverse primers in the 3D region corresponding to the nucleotide sequence of all kobuviruses. AiV genotype A sequences were detected in all 137 samples. New sequences of AiV were detected in nine samples, exhibiting 83 % similarity with AiV A846/88, but 95 % similarity with canine kobuvirus (CKV) US-PC0082 in this region. The nucleotide sequences from the VP3 region to the 3' untranslated region (UTR) of sewage sample Y12/2004 were determined. The number of nucleotides in each region was the same as that of CKV. The similarity of the nucleotide (amino acid) identity of a complete VP1 region was 90.5 % (94.8 %) between Y12/2004 and CKV US-PC0082. The phylogenic analyses based on the nucleotide and the deduced amino acid sequences of VP1 and 3D showed that Y12/2004 was independent from AiV, but closely related to CKV. These results suggested that CKV is present in Aichi Prefecture, Japan.

  9. Nucleotide diversity and linkage disequilibrium in five Lolium perenne genes with putative role in shoot branching

    DEFF Research Database (Denmark)

    Brazauskas, Gintaras; Pašakinskienė, Izolda; Asp, Torben

    2010-01-01

    Knowledge on nucleotide diversity and linkage disequilibrium (LD) patterns is prerequisite for association analyses. However, little is known about the nucleotide diversity in the evolutionary important ryegrass shoot morphology genes. Five candidate genes, LpIAA1, LpRUB1, LpBRI1, LpSHOOT1 and Lp...... substitutions were detected in LpTB1. A negative and significant (P IAA......1 to 16 in both LpRUB1 and LpTB1, with an average of 14 alleles per gene. Low intragenic linkage disequilibrium (LD) (average r2 = 0.21–0.26) was observed for three genes, LpIAA1, LpRUB1 and LpSHOOT1, while LpTB1 and LpBRI1 showed substantially higher average LD levels of r2 = 0.56 and r2 = 0...

  10. Sampling wild species to conserve genetic diversity

    Science.gov (United States)

    Sampling seed from natural populations of crop wild relatives requires choice of the locations to sample from and the amount of seed to sample. While this may seem like a simple choice, in fact careful planning of a collector’s sampling strategy is needed to ensure that a crop wild collection will ...

  11. Genetic diversity in domesticated soybean (Glycine max) and its wild progenitor (Glycine soja) for simple sequence repeat and single-nucleotide polymorphism loci.

    Science.gov (United States)

    Li, Ying-Hui; Li, Wei; Zhang, Chen; Yang, Liang; Chang, Ru-Zhen; Gaut, Brandon S; Qiu, Li-Juan

    2010-10-01

    • The study of genetic diversity between a crop and its wild relatives may yield fundamental insights into evolutionary history and the process of domestication. • In this study, we genotyped a sample of 303 accessions of domesticated soybean (Glycine max) and its wild progenitor Glycine soja with 99 microsatellite markers and 554 single-nucleotide polymorphism (SNP) markers. • The simple sequence repeat (SSR) loci averaged 21.5 alleles per locus and overall Nei's gene diversity of 0.77. The SNPs had substantially lower genetic diversity (0.35) than SSRs. A SSR analyses indicated that G. soja exhibited higher diversity than G. max, but SNPs provided a slightly different snapshot of diversity between the two taxa. For both marker types, the primary division of genetic diversity was between the wild and domesticated accessions. Within taxa, G. max consisted of four geographic regions in China. G. soja formed six subgroups. Genealogical analyses indicated that cultivated soybean tended to form a monophyletic clade with respect to G. soja. • G. soja and G. max represent distinct germplasm pools. Limited evidence of admixture was discovered between these two species. Overall, our analyses are consistent with the origin of G. max from regions along the Yellow River of China.

  12. Nucleotide diversity and linkage disequilibrium in cold-hardiness- and wood quality-related candidate genes in Douglas fir.

    Science.gov (United States)

    Krutovsky, Konstantin V; Neale, David B

    2005-12-01

    Nuclear sequence variation and linkage disequilibrium (LD) were studied in 15 cold-hardiness- and 3 wood quality-related candidate genes in Douglas fir [Pseudotsuga menziesii (Mirb.) Franco]. This set of genes was selected on the basis of its function in other plants and collocation with cold-hardiness-related quantitative trait loci (QTL). The single-nucleotide polymorphism (SNP) discovery panel represented 24 different trees from six regions in Washington and Oregon plus parents of a segregating population used in the QTL study. The frequency of SNPs was one SNP per 46 bp across coding and noncoding regions on average. Haplotype and nucleotide diversities were also moderately high with H(d) = 0.827 +/- 0.043 and pi = 0.00655 +/- 0.00082 on average, respectively. The nonsynonymous (replacement) nucleotide substitutions were almost five times less frequent than synonymous ones and substitutions in noncoding regions. LD decayed relatively slowly but steadily within genes. Haploblock analysis was used to define haplotype tag SNPs (htSNPs). These data will help to select SNPs for association mapping, which is already in progress.

  13. Nucleotide diversity of the colorless green alga Polytomella parva (Chlorophyceae, Chlorophyta): high for the mitochondrial telomeres, surprisingly low everywhere else.

    Science.gov (United States)

    Smith, David Roy; Lee, Robert W

    2011-01-01

    Silent-site nucleotide diversity data (π(silent)) can provide insights into the forces driving genome evolution. Here we present π(silent) statistics for the mitochondrial and nuclear DNAs of Polytomella parva, a nonphotosynthetic green alga with a highly reduced, linear fragmented mitochondrial genome. We show that this species harbors very little genetic diversity, with the exception of the mitochondrial telomeres, which have an excess of polymorphic sites. These data are compared with previously published π(silent) values from the mitochondrial and nuclear genomes of the model species Chlamydomonas reinhardtii and Volvox carteri, which are close relatives of P. parva, and are used to understand the modes and tempos of genome evolution within green algae. © 2011 The Author(s). Journal of Eukaryotic Microbiology © 2011 International Society of Protistologists.

  14. Sequence analysis of single-copy genes in two wild olive subspecies: nucleotide diversity and potential use for testing admixture.

    Science.gov (United States)

    Besnard, G; El Bakkali, A

    2014-03-01

    The wild olive distribution extends from the Mediterranean region to south Asia and Austral Africa. The species is also invasive, particularly in Australia. Here, we investigated the sequence variation at five nuclear single-copy genes in 41 native and invasive accessions of the Mediterranean and African olive subspecies. The nucleotide diversity was assessed and the phylogenetic relationships between alleles were depicted with haplotype networks. A Bayesian clustering method (STRUCTURE) was applied to identify the main gene pools. We found an average of 18.4 alleles per locus. Native Mediterranean and African olives only share one allele, which testifies for ancient admixture on the Red Sea hills. The presence of divergent alleles in the Mediterranean olive, as well as the identification of two main genetic clusters, suggests a complex origin with two highly differentiated gene pools from the eastern and western Mediterranean that recently admixed. In the invasive range, relatively high nucleotide diversity is observed as a consequence of the introduction of alleles from two subspecies. Our data confirm that four invasive individuals are early-generation hybrids. Finally, the utility of single-copy gene sequences in olive population genomic and phylogenetic studies is briefly discussed.

  15. Patterns of Genome-Wide Nucleotide Diversity in the Gynodioecious Plant Thymus vulgaris Are Compatible with Recent Sweeps of Cytoplasmic Genes.

    Science.gov (United States)

    Mollion, Maeva; Ehlers, Bodil K; Figuet, Emeric; Santoni, Sylvain; Lenormand, Thomas; Maurice, Sandrine; Galtier, Nicolas; Bataillon, Thomas

    2018-01-01

    Gynodioecy is a sexual dimorphism where females coexist with hermaphrodite individuals. In most cases, this dimorphism involves the interaction of cytoplasmic male sterility (CMS) genes and nuclear restorer genes. Two scenarios can account for how these interactions maintain gynodioecy. Either CMS genes recurrently enter populations at low frequency via mutation or migration and go to fixation unimpeded (successive sweeps), or CMS genes maintain polymorphism over evolutionary time through interactions with a nuclear restorer allele (balanced polymorphism). To distinguish between these scenarios, we used transcriptome sequencing in gynodioecious Thymus vulgaris and surveyed genome-wide diversity in 18 naturally occurring individuals sampled from populations at a local geographic scale. We contrast the amount and patterns of nucleotide diversity in the nuclear and cytoplasmic genome, and find ample diversity at the nuclear level (π = 0.019 at synonymous sites) but reduced genetic diversity and an excess of rare polymorphisms in the cytoplasmic genome relative to the nuclear genome. Our finding is incompatible with the maintenance of gynodioecy via scenarios invoking long-term balancing selection, and instead suggests the recent fixation of CMS lineages in the populations studied. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  16. Bacterial diversity of biofilm samples from deep mines in South ...

    African Journals Online (AJOL)

    JTEkanem

    microbial diversity of mines in South Africa, biofilm samples were collected from Goldfield and diamond ... understand microbial biosynthetic processes and enhance remediation of contaminated environments3. The microbial diversity in these extreme environments has been the key to the ..... Biodiversity of acidophilic.

  17. Genetic diversity and population structure analysis of spinach by single-nucleotide polymorphisms identified through genotyping-by-sequencing.

    Directory of Open Access Journals (Sweden)

    Ainong Shi

    Full Text Available Spinach (Spinacia oleracea L., 2n = 2x = 12 is an economically important vegetable crop worldwide and one of the healthiest vegetables due to its high concentrations of nutrients and minerals. The objective of this research was to conduct genetic diversity and population structure analysis of a collection of world-wide spinach genotypes using single nucleotide polymorphisms (SNPs markers. Genotyping by sequencing (GBS was used to discover SNPs in spinach genotypes. Three sets of spinach genotypes were used: 1 268 USDA GRIN spinach germplasm accessions originally collected from 30 countries; 2 45 commercial spinach F1 hybrids from three countries; and 3 30 US Arkansas spinach cultivars/breeding lines. The results from this study indicated that there was genetic diversity among the 343 spinach genotypes tested. Furthermore, the genetic background in improved commercial F1 hybrids and in Arkansas cultivars/lines had a different structured populations from the USDA germplasm. In addition, the genetic diversity and population structures were associated with geographic origin and germplasm from the US Arkansas breeding program had a unique genetic background. These data could provide genetic diversity information and the molecular markers for selecting parents in spinach breeding programs.

  18. DivStat: a user-friendly tool for single nucleotide polymorphism analysis of genomic diversity.

    Directory of Open Access Journals (Sweden)

    Inês Soares

    Full Text Available Recent developments have led to an enormous increase of publicly available large genomic data, including complete genomes. The 1000 Genomes Project was a major contributor, releasing the results of sequencing a large number of individual genomes, and allowing for a myriad of large scale studies on human genetic variation. However, the tools currently available are insufficient when the goal concerns some analyses of data sets encompassing more than hundreds of base pairs and when considering haplotype sequences of single nucleotide polymorphisms (SNPs. Here, we present a new and potent tool to deal with large data sets allowing the computation of a variety of summary statistics of population genetic data, increasing the speed of data analysis.

  19. Nucleotide diversity in the mitochondrial and nuclear compartments of Chlamydomonas reinhardtii: investigating the origins of genome architecture

    Directory of Open Access Journals (Sweden)

    Lee Robert W

    2008-05-01

    Full Text Available Abstract Background The magnitude of intronic and intergenic DNA can vary substantially both within and among evolutionary lineages; however, the forces responsible for this disparity in genome compactness are conjectural. One explanation, termed the mutational-burden hypothesis, posits that genome compactness is primarily driven by two nonadaptive processes: mutation and random genetic drift – the effects of which can be discerned by measuring the nucleotide diversity at silent sites (πsilent, defined as noncoding sites and the synonymous sites of protein-coding regions. The mutational-burden hypothesis holds that πsilent is negatively correlated to genome compactness. We used the model organism Chlamydomonas reinhardtii, which has a streamlined, coding-dense mitochondrial genome and an noncompact, intron-rich nuclear genome, to investigate the mutational-burden hypothesis. For measuring πsilent we sequenced the complete mitochondrial genome and portions of 7 nuclear genes from 7 geographical isolates of C. reinhardtii. Results We found significantly more nucleotide diversity in the nuclear compartment of C. reinhardtii than in the mitochondrial compartment: net values of πsilent for the nuclear and mitochondrial genomes were 32 × 10-3 and 8.5 × 10-3, respectively; and when insertions and deletions (indels are factored in, these values become 49 × 10-3 for the nuclear DNA and 11 × 10-3 for the mitochondrial DNA (mtDNA. Furthermore, our investigations of C. reinhardtii revealed 4 previously undiscovered mitochondrial introns, one of which contains a fragment of the large-subunit (LSU rRNA gene and another of which is found in a region of the LSU-rRNA gene not previously reported (for any taxon to contain introns. Conclusion At first glance our results are in opposition to the mutational-burden hypothesis: πsilent was approximately 4 times greater in the nuclear compartment of C. reinhardtii relative to the mitochondrial compartment

  20. Empirical Comparison of Simple Sequence Repeats and Single Nucleotide Polymorphisms in Assessment of Maize Diversity and Relatedness

    Science.gov (United States)

    Hamblin, Martha T.; Warburton, Marilyn L.; Buckler, Edward S.

    2007-01-01

    While Simple Sequence Repeats (SSRs) are extremely useful genetic markers, recent advances in technology have produced a shift toward use of single nucleotide polymorphisms (SNPs). The different mutational properties of these two classes of markers result in differences in heterozygosities and allele frequencies that may have implications for their use in assessing relatedness and evaluation of genetic diversity. We compared analyses based on 89 SSRs (primarily dinucleotide repeats) to analyses based on 847 SNPs in individuals from the same 259 inbred maize lines, which had been chosen to represent the diversity available among current and historic lines used in breeding. The SSRs performed better at clustering germplasm into populations than did a set of 847 SNPs or 554 SNP haplotypes, and SSRs provided more resolution in measuring genetic distance based on allele-sharing. Except for closely related pairs of individuals, measures of distance based on SSRs were only weakly correlated with measures of distance based on SNPs. Our results suggest that 1) large numbers of SNP loci will be required to replace highly polymorphic SSRs in studies of diversity and relatedness and 2) relatedness among highly-diverged maize lines is difficult to measure accurately regardless of the marker system. PMID:18159250

  1. Signatures of Reproductive Isolation in Patterns of Single Nucleotide Diversity Across Inbred Strains of Mice

    Science.gov (United States)

    Payseur, Bret A.; Hoekstra, Hopi E.

    2005-01-01

    Reproductive isolation is often caused by the disruption of genic interactions that evolve in geographically separate populations. Identifying the genomic regions and genes involved in these interactions, known as “Dobzhansky-Muller incompatibilities,” can be challenging but is facilitated by the wealth of genetic markers now available in model systems. In recent years, the complete genome sequence and thousands of single nucleotide polymorphisms (SNPs) from laboratory mice, which are largely genetic hybrids between Mus musculus and M. domesticus, have become available. Here, we use these resources to locate genomic regions that may underlie reproductive isolation between these two species. Using genotypes from 332 SNPs that differ between wild-derived strains of M. musculus and M. domesticus, we identified several physically unlinked SNP pairs that show exceptional gametic disequilibrium across the lab strains. Conspecific alleles were associated in a disproportionate number of these cases, consistent with the action of natural selection against hybrid gene combinations. As predicted by the Dobzhansky-Muller model, this bias was differentially attributable to locus pairs for which one hybrid genotype was missing. We assembled a list of potential Dobzhansky-Muller incompatibilities from locus pairs that showed extreme associations (only three gametic types) among conspecific alleles. Two SNPs in this list map near known hybrid sterility loci on chromosome 17 and the X chromosome, allowing us to nominate partners for disrupted interactions involving these genomic regions for the first time. Together, these results indicate that patterns produced by speciation between M. musculus and M. domesticus are visible in the genomes of lab strains of mice, underscoring the potential of these genetic model organisms for addressing general questions in evolutionary biology. PMID:16143616

  2. Grinding up Wheat: a Massive Loss of Nucleotide Diversity Since Domestication

    DEFF Research Database (Denmark)

    Haudry, Anabelle; Cenci, Alberto; Ravel, Catherine

    2007-01-01

    individuals representing 4 taxa corresponding to representative steps in the recent evolution of wheat (wild, domesticated, cultivated durum, and bread wheats) to unravel the evolutionary history of cultivated wheats and to quantify its impact on genetic diversity. Sequence relationships are consistent......, the average intensity of domestication bottleneck was estimated at about 3-giving a population size for the domesticated form about one third that of wild dicoccoides. The most severe bottleneck, with an intensity of about 6, occurred in the evolution of durum wheat. We investigated whether some of the genes...... reveal selection on the linked locus Gsp1A, which may affect grain softness-an important trait for end-use quality in wheat....

  3. Quantitative extraction of nucleotides from frozen muscle samples of Atlantic salmon ( Salmo salar ) and rainbow trout ( Oncorhynchus mykiss ) : Effects of time taken to sample and extraction method

    DEFF Research Database (Denmark)

    Thomas, P.M.; Bremner, Allan; Pankhurst, N.W.

    2000-01-01

    Muscle excised from the dorsal flank of Atlantic salmon and rainbow trout at death and up to 120 min postmortem (P.M.) was frozen in liquid N-2 and stored at -80C. Following acid extraction, on ice (method I), or dry ice (method 2) samples were analyzed for cyclic nucleotides to determine...... the effect of time to sample, and extraction method. There was no pattern of change in nucleotide profile in either species up to 10 min P.M. At 120 min P.M., Atlantic salmon muscle extracted by method 2 had a higher IMP concentration than at any other time but there was no difference in adenylates. Ignoring.......8 to -5C) prior to enzyme inactivation....

  4. Sensitivity of functional diversity metrics to sampling intensity

    NARCIS (Netherlands)

    van der Plas, Fons; van Klink, Roel; Manning, Pete; Olff, Han; Fischer, Andmarkus

    1. Functional diversity (FD) metrics are increasingly used in ecological research, particularly in the studies of community assembly and ecosystem functioning. However, studies using the FD metrics vary greatly in the intensity by which ecological communities were sampled and it is largely unknown

  5. Frequency of single nucleotide polymorphisms of some immune response genes in a population sample from São Paulo, Brazil

    Directory of Open Access Journals (Sweden)

    Léa Campos de Oliveira

    2011-09-01

    Full Text Available Objective: To present the frequency of single nucleotide polymorphismsof a few immune response genes in a population sample from SãoPaulo City (SP, Brazil. Methods: Data on allele frequencies ofknown polymorphisms of innate and acquired immunity genes werepresented, the majority with proven impact on gene function. Datawere gathered from a sample of healthy individuals, non-HLA identicalsiblings of bone marrow transplant recipients from the Hospital dasClínicas da Faculdade de Medicina da Universidade de São Paulo,obtained between 1998 and 2005. The number of samples variedfor each single nucleotide polymorphism analyzed by polymerasechain reaction followed by restriction enzyme cleavage. Results:Allele and genotype distribution of 41 different gene polymorphisms,mostly cytokines, but also including other immune response genes,were presented. Conclusion: We believe that the data presentedhere can be of great value for case-control studies, to define whichpolymorphisms are present in biologically relevant frequencies and toassess targets for therapeutic intervention in polygenic diseases witha component of immune and inflammatory responses.

  6. Nucleotide variation in genes invloved in wood formation in two pine species

    Science.gov (United States)

    David Pot; Lisa McMillan; Craig Echt; Gregoire Le Provost; Pauline Garnier-Gere; Sheree Cato; Christophe Plomion

    2005-01-01

    Nucleotide diversity in eight genes related to wood formation was investigated in two pine species, Pinus pinaster and P. radiata. The nucleotide diversity patterns observed and their properties were compared between the two species according to the specific characteristics of the samples analysed. A lower diversity was observed in P. radiata...

  7. [Actinobacterial diversity of marine sediment samples from Chile].

    Science.gov (United States)

    Jiang, Hong; Lin, Ru; Chen, Lujie; Lin, Hao; Nie, Yilei; Lian, Yunyang

    2010-07-01

    The aim of this study was to investigate actinobacterial diversity in Chilean marine sediments. Actinobacterial diversity in these sediments was investigated by selective isolation method, culture-independent method and phylogenetic analysis based on 16S rRNA gene sequences. Six selective media were used to isolate actinomycetes from sediment samples. The primers for the class Actinobacteria were used for Actinobacterial 16S rRNA gene amplification and then a clone library was constructed for the sediment sample btt. Twenty-two strains with different culture characteristics and 59 clones from sample btt were selected for 16S rRNA gene sequences analysis. To determine requirement for seawater each strain was grown on oatmeal agar prepared with deionized water and with seawater, respectively. Strains were screened for antibiotic activity against bacteria and fungi. In total 328 actinomycetes were obtained. Twenty-two strains which were selected belonged to Streptomyces, Micromonospora, Polymorphospora, Aeromicrobium and Brachybacterium. Fifty-nine clones (40 OTUs) were sequenced, and 60% OTUs belonged to Actinobacteridae, Acidimicrobidae and Rubrobacteridae. The other 40% OTUs, which formed several distinct clades in phylogenetic tree among phylum Actinobacteria may represent new taxonomical groups. 50% of the 47 sea water dependant strains and nineteen strains out of the above 22 strains exhibited antimicrobial activity. There was abundant actinobacterial diversity in the marine sediments of Chile, and the result implied that there were large numbers of unknown actinobacterial groups in the sediments. Actinomycetes from Chilean marine sediments had the potential of producing bioactive secondary metabolites.

  8. It's in the Sample: The Effects of Sample Size and Sample Diversity on the Breadth of Inductive Generalization

    Science.gov (United States)

    Lawson, Chris A.; Fisher, Anna V.

    2011-01-01

    Developmental studies have provided mixed evidence with regard to the question of whether children consider sample size and sample diversity in their inductive generalizations. Results from four experiments with 105 undergraduates, 105 school-age children (M = 7.2 years), and 105 preschoolers (M = 4.9 years) showed that preschoolers made a higher…

  9. New insights on the speciation history and nucleotide diversity of three boreal spruce species and a Tertiary relict.

    Science.gov (United States)

    Chen, J; Källman, T; Gyllenstrand, N; Lascoux, M

    2010-01-01

    In all, 10 nuclear loci were re-sequenced in four spruce species. Three of the species are boreal species with very large natural ranges: Picea mariana and P. glauca are North American, and P. abies, is Eurasian. The fourth species, P. breweriana, is a Tertiary relict from Northern California, with a very small natural range. Although the boreal species population sizes have fluctuated through the Ice Ages, P. breweriana is believed to have had a rather stable population size through the Quaternary. Indeed, the average Tajima's D was close to zero in this species and negative in the three boreal ones. Reflecting differences in current population sizes, nucleotide diversity was an order of magnitude lower in P. breweriana than in the boreal species. This is in contrast to the similar and high levels of heterozygosity observed in previous studies at allozyme loci across species. As the species have very different histories and effective population sizes, selection at allozyme loci rather than demography appears to be a better explanation for this discrepancy. Parameters of Isolation-with-Migration (IM) models were also estimated for pairs of species. Shared polymorphisms were extensive and fixed polymorphisms few. Divergence times were much shorter than those previously reported. There was also evidence of historical gene flow between P. abies and P. glauca. The latter was more closely related to P. abies than to its sympatric relative P. mariana. This last result suggests that North American and Eurasian species might have been geographically much closer in the recent past than they are today.

  10. How hot are drosophila hotspots? examining recombination rate variation and associations with nucleotide diversity, divergence, and maternal age in Drosophila pseudoobscura.

    Directory of Open Access Journals (Sweden)

    Brenda Manzano-Winkler

    Full Text Available Fine scale meiotic recombination maps have uncovered a large amount of variation in crossover rate across the genomes of many species, and such variation in mammalian and yeast genomes is concentrated to <5kb regions of highly elevated recombination rates (10-100x the background rate called "hotspots." Drosophila exhibit substantial recombination rate heterogeneity across their genome, but evidence for these highly-localized hotspots is lacking. We assayed recombination across a 40Kb region of Drosophila pseudoobscura chromosome 2, with one 20kb interval assayed every 5Kb and the adjacent 20kb interval bisected into 10kb pieces. We found that recombination events across the 40kb stretch were relatively evenly distributed across each of the 5kb and 10kb intervals, rather than concentrated in a single 5kb region. This, in combination with other recent work, indicates that the recombination landscape of Drosophila may differ from the punctate recombination pattern observed in many mammals and yeast. Additionally, we found no correlation of average pairwise nucleotide diversity and divergence with recombination rate across the 20kb intervals, nor any effect of maternal age in weeks on recombination rate in our sample.

  11. Single-nucleotide polymorphism markers from de-novo assembly of the pomegranate transcriptome reveal germplasm genetic diversity.

    Science.gov (United States)

    Ophir, Ron; Sherman, Amir; Rubinstein, Mor; Eshed, Ravit; Sharabi Schwager, Michal; Harel-Beja, Rotem; Bar-Ya'akov, Irit; Holland, Doron

    2014-01-01

    Pomegranate is a valuable crop that is grown commercially in many parts of the world. Wild species have been reported from India, Turkmenistan and Socotra. Pomegranate fruit has a variety of health-beneficial qualities. However, despite this crop's importance, only moderate effort has been invested in studying its biochemical or physiological properties or in establishing genomic and genetic infrastructures. In this study, we reconstructed a transcriptome from two phenotypically different accessions using 454-GS-FLX Titanium technology. These data were used to explore the functional annotation of 45,187 fully annotated contigs. We further compiled a genetic-variation resource of 7,155 simple-sequence repeats (SSRs) and 6,500 single-nucleotide polymorphisms (SNPs). A subset of 480 SNPs was sampled to investigate the genetic structure of the broad pomegranate germplasm collection at the Agricultural Research Organization (ARO), which includes accessions from different geographical areas worldwide. This subset of SNPs was found to be polymorphic, with 10.7% loci with minor allele frequencies of (MAFpomegranate collection into two major groups of accessions: one from India, China and Iran, composed of mainly unknown country origin and which was more of an admixture than the other major group, composed of accessions mainly from the Mediterranean basin, Central Asia and California. This study establishes a high-throughput transcriptome and genetic-marker infrastructure. Moreover, it sheds new light on the genetic interrelations between pomegranate species worldwide and more accurately defines their genetic nature.

  12. Genotyping of human parvovirus B19 in clinical samples from Brazil and Paraguay using heteroduplex mobility assay, single-stranded conformation polymorphism and nucleotide sequencing

    Directory of Open Access Journals (Sweden)

    Marcos César Lima de Mendonça

    2011-06-01

    Full Text Available Heteroduplex mobility assay, single-stranded conformation polymorphism and nucleotide sequencing were utilised to genotype human parvovirus B19 samples from Brazil and Paraguay. Ninety-seven serum samples were collected from individuals presenting with abortion or erythema infectiosum, arthropathies, severe anaemia and transient aplastic crisis; two additional skin samples were collected by biopsy. After the procedure, all clinical samples were classified as genotype 1.

  13. Securing maximum diversity of Non Pollen Palynomorphs in palynological samples

    DEFF Research Database (Denmark)

    Enevold, Renée; Odgaard, Bent Vad

    2015-01-01

    Palynology is no longer synonymous with analysis of pollen with the addition of a few fern spores. A wide range of Non Pollen Palynomorphs are now described and are potential palaeoenvironmental proxies in the palynological surveys. The contribution of NPP’s has proven important to the interpreta......Palynology is no longer synonymous with analysis of pollen with the addition of a few fern spores. A wide range of Non Pollen Palynomorphs are now described and are potential palaeoenvironmental proxies in the palynological surveys. The contribution of NPP’s has proven important.......g. Schulz & Shumilovskikh 2013). Increasingly it has become customary for palynologists to quantify at least some of the NPP’s appearing on the pollen slides (e.g. Strother et al. 2015, Odgaard 1994). Are these samples representative of the initial NPP assemblages? The usual sample preparation method...... for pollen analysis is based on acetylization (Erdtman 1969) and HF-treatment which are of variable destructiveness to the NPP’s. Some NPP’s might completely vanish and the prepared sample might hold less NPP diversity than the initial NPP assemblage. Consequently, it may be advisable to consider...

  14. Integrative analysis of single nucleotide polymorphisms and gene expression efficiently distinguishes samples from closely related ethnic populations

    Directory of Open Access Journals (Sweden)

    Yang Hsin-Chou

    2012-07-01

    Full Text Available Abstract Background Ancestry informative markers (AIMs are a type of genetic marker that is informative for tracing the ancestral ethnicity of individuals. Application of AIMs has gained substantial attention in population genetics, forensic sciences, and medical genetics. Single nucleotide polymorphisms (SNPs, the materials of AIMs, are useful for classifying individuals from distinct continental origins but cannot discriminate individuals with subtle genetic differences from closely related ancestral lineages. Proof-of-principle studies have shown that gene expression (GE also is a heritable human variation that exhibits differential intensity distributions among ethnic groups. GE supplies ethnic information supplemental to SNPs; this motivated us to integrate SNP and GE markers to construct AIM panels with a reduced number of required markers and provide high accuracy in ancestry inference. Few studies in the literature have considered GE in this aspect, and none have integrated SNP and GE markers to aid classification of samples from closely related ethnic populations. Results We integrated a forward variable selection procedure into flexible discriminant analysis to identify key SNP and/or GE markers with the highest cross-validation prediction accuracy. By analyzing genome-wide SNP and/or GE markers in 210 independent samples from four ethnic groups in the HapMap II Project, we found that average testing accuracies for a majority of classification analyses were quite high, except for SNP-only analyses that were performed to discern study samples containing individuals from two close Asian populations. The average testing accuracies ranged from 0.53 to 0.79 for SNP-only analyses and increased to around 0.90 when GE markers were integrated together with SNP markers for the classification of samples from closely related Asian populations. Compared to GE-only analyses, integrative analyses of SNP and GE markers showed comparable testing

  15. Heteropolymeric triplex-based genomic assay to detect pathogens or single-nucleotide polymorphisms in human genomic samples.

    Directory of Open Access Journals (Sweden)

    Jasmine I Daksis

    Full Text Available Human genomic samples are complex and are considered difficult to assay directly without denaturation or PCR amplification. We report the use of a base-specific heteropolymeric triplex, formed by native duplex genomic target and an oligonucleotide third strand probe, to assay for low copy pathogen genomes present in a sample also containing human genomic duplex DNA, or to assay human genomic duplex DNA for Single Nucleotide Polymorphisms (SNP, without PCR amplification. Wild-type and mutant probes are used to identify triplexes containing FVL G1691A, MTHFR C677T and CFTR mutations. The specific triplex structure forms rapidly at room temperature in solution and may be detected without a separation step. YOYO-1, a fluorescent bis-intercalator, promotes and signals the formation of the specific triplex. Genomic duplexes may be assayed homogeneously with single base pair resolution. The specific triple-stranded structures of the assay may approximate homologous recombination intermediates, which various models suggest may form in either the major or minor groove of the duplex. The bases of the stable duplex target are rendered specifically reactive to the bases of the probe because of the activity of intercalated YOYO-1, which is known to decondense duplex locally 1.3 fold. This may approximate the local decondensation effected by recombination proteins such as RecA in vivo. Our assay, while involving triplex formation, is sui generis, as it is not homopurine sequence-dependent, as are "canonical triplexes". Rather, the base pair-specific heteropolymeric triplex of the assay is conformation-dependent. The highly sensitive diagnostic assay we present allows for the direct detection of base sequence in genomic duplex samples, including those containing human genomic duplex DNA, thereby bypassing the inherent problems and cost associated with conventional PCR based diagnostic assays.

  16. Comparison of single nucleotide polymorphisms and simple sequence repeats in genotype identification and diversity assessment of cacao germplasm

    Science.gov (United States)

    Accurate identification of individual genotypes in an efficient manner is especially important for cacao (Theobroma cacao L.) germplasm conservation and breeding. The development of single nucleotide polymorphism (SNP) markers in cacao offers the opportunity to use a high throughput genotyping syste...

  17. Assessing genetic diversity of wild and hatchery samples of the Chinese sucker (Myxocyprinus asiaticus) by the mitochondrial DNA control region.

    Science.gov (United States)

    Wu, Jiayun; Wu, Bo; Hou, Feixia; Chen, Yongbai; Li, Chong; Song, Zhaobin

    2016-01-01

    To restore the natural populations of Chinese sucker (Myxocyprinus asiaticus), a hatchery release program has been underway for nearly 10 years. Using DNA sequences of the mitochondrial control region, we assessed the genetic diversity and genetic structure among samples collected from three sites of the wild population as well as from three hatcheries. The haplotype diversity of the wild samples (h = 0.899-0.975) was significantly higher than that of the hatchery ones (h = 0.296-0.666), but the nucleotide diversity was almost identical between them (π = 0.0170-0.0280). Relatively high gene flow was detected between the hatchery and wild samples. Analysis of effective population size indicated that M. asiaticus living in the Yangtze River has been expanding following a bottleneck in the recent past. Our results suggest the hatchery release programs for M. asiaticus have not reduced the genetic diversity, but have influenced the genetic structure of the species in the upper Yangtze River.

  18. Assessing Racial Microaggression Distress in a Diverse Sample.

    Science.gov (United States)

    Torres-Harding, Susan; Turner, Tasha

    2015-12-01

    Racial microaggressions are everyday subtle or ambiguous racially related insults, slights, mistreatment, or invalidations. Racial microaggressions are a type of perceived racism that may negatively impact the health and well-being of people of color in the United States. This study examined the reliability and validity of the Racial Microaggression Scale distress subscales, which measure the perceived stressfulness of six types of microaggression experiences in a racially and ethnically diverse sample. These subscales exhibited acceptable to good internal consistency. The distress subscales also evidenced good convergent validity; the distress subscales were positively correlated with additional measures of stressfulness due to experiencing microaggressions or everyday discrimination. When controlling for the frequency of one's exposure to microaggression incidents, some racial/ethnic group differences were found. Asian Americans reported comparatively lower distress and Latinos reporting comparatively higher distress in response to Foreigner, Low-Achieving, Invisibility, and Environmental microaggressions. African Americans reported higher distress than the other groups in response to Environmental microaggressions. Results suggest that the Racial Microaggressions Scale distress subscales may aid health professionals in assessing the distress elicited by different types of microaggressions. In turn, this may facilitate diagnosis and treatment planning in order to provide multiculturally competent care for African American, Latino, and Asian American clients. © The Author(s) 2014.

  19. Identification of single nucleotide polymorphisms (SNPs) and other sequence changes and estimation of nucleotide diversity in coding and flanking regions of the NMDAR1 receptor gene in schizophrenic patients.

    Science.gov (United States)

    Rice, S R; Niu, N; Berman, D B; Heston, L L; Sobell, J L

    2001-05-01

    Glutamatergic dysregulation has been hypothesized to play a role in schizophrenia. The N-methyl-D-aspartate (NMDA) type of glutamate receptor especially is of interest because, in addition to binding sites for glutamate and glycine, a necessary co-agonist, this receptor also contains noncompetitive binding sites for the psychotomimetics phencyclidine (PCP), MK-801, and ketamine. PCP-induced psychosis has been a useful disease model in that both the positive as well as the negative symptomatologies seen in schizophrenia are observed. Recently, a mouse deficient in expression of the NR1 subunit gene (NMDAR1) of the heteromeric receptor has been developed and shown to display aberrant behaviors, with reduced social and sexual interactions as well as increased stereotypic motor activity. In an extensive examination of the NMDAR1 gene in our laboratory in approximately 100 chronic schizophrenic patients, 28 unique sequence changes were identified, including eight single nucleotide polymorphisms (SNPs) in the 5' untranslated region (5'UTR), six SNPs in coding regions (cSNPs), eleven intronic SNPs, two intronic deletions of 7 and 30 bp, and an intronic microinsertion/deletion. With the exception of one previously reported cSNP, all of the identified changes were novel. The frequency of polymorphisms differed significantly by ethnicity and several appeared to be in linkage disequilibrium. None of the changes appeared likely to be of functional significance, thus suggesting that changes in the genomic NMDAR1 are unlikely to contribute to the etiology of schizophrenia. Estimates of nucleotide diversity are comparable to those observed in studies of other genes.

  20. Renin gene haplotype diversity and linkage disequilibrium in two Mexican and one German population samples.

    Science.gov (United States)

    Valdez-Velazquez, Laura L; Mendoza-Carrera, Francisco; Perez-Parra, Sandra A; Rodarte-Hurtado, Katia; Sandoval-Ramirez, Lucila; Montoya-Fuentes, Héctor; Quintero-Ramos, Antonio; Delgado-Enciso, Ivan; Montes-Galindo, Daniel A; Gomez-Sandoval, Zeferino; Olivares, Norma; Rivas, Fernando

    2011-09-01

    Renin is the main rate-limiting enzyme in the renin-angiotensin-aldosterone system. Its gene, REN, is a candidate crucial factor in essential hypertension and cardiovascular disease. The aim of this study was to evaluate allele and haplotype distributions of REN polymorphisms, and to estimate normalised linkage disequilibrium (D') in Mexican and German populations. Four groups were studied for the REN single nucleotide polymorphisms (SNPs) 1205C>T, 1303G>A, and 10607G>A, in population samples of Mexican Mestizo (n = 86), Mexican Huichol (n = 49), German (n = 39), and individuals with hypertension diagnosis (n = 66). Polymorphisms were detected by PCR-RFLP. Genotype, allele and haplotype frequencies were estimated. SNP 1205C>T and 10607G>A allele and genotype distribution showed inter-group differences. The 1205T and 10607A allele showed a significance difference in hypertensive population. Haplotype analysis also showed some inter-group differences, especially in 1205C-1303G-10607G, 1205C-1303G-10607A and 1205T-1303G-10607G haplotypes. The segregation analysis disclosed complete linkage disequilibrium between 1205 and 1303 loci. These results provide an example of genetic diversity in related populations and illustrate the convenience of increasing the number of loci in associative studies between diseases and candidate genes.

  1. Nucleotide diversity of the ZmPox3 maize peroxidase gene: Relationships between a MITE insertion in exon 2 and variation in forage maize digestibility

    Directory of Open Access Journals (Sweden)

    Rigau Joan

    2004-07-01

    Full Text Available Abstract Background Polymorphisms were investigated within the ZmPox3 maize peroxidase gene, possibly involved in lignin biosynthesis because of its colocalization with a cluster of QTL related to lignin content and cell wall digestibility. The purpose of this study was to identify, on the basis of 37 maize lines chosen for their varying degrees of cell wall digestibility and representative of temperate regions germplasm, ZmPox3 haplotypes or individual polymorphisms possibly associated with digestibility. Results Numerous haplotypes with high diversity were identified. Frequency of nucleotide changes was high with on average one SNP every 57 bp. Nucleotide diversity was not equally distributed among site categories: the estimated π was on average eight times higher for silent sites than for non-synonymous sites. Numerous sites were in linkage disequilibrium that decayed with increasing physical distance. A zmPox3 mutant allele, carrying an insertion of a transposable element in the second exon, was found in lines derived from the early flint inbred line, F7. This element possesses many structural features of miniature inverted-repeat transposable elements (MITE. The mutant allele encodes a truncated protein lacking important functional sites. An ANOVA performed with a subset of 31 maize lines indicated that the transposable element was significantly associated with cell wall digestibility. This association was confirmed using an additional set of 25 flint lines related to F7. Moreover, RT-PCR experiments revealed a decreased amount of corresponding mRNA in plants with the MITE insertion. Conclusion These results showed that ZmPox3 could possibly be involved in monolignol polymerisation, and that a deficiency in ZmPox3 peroxidase activity seemingly has a negative effect on cell wall digestibility. Also, genetic diversity analyses of ZmPox3 indicated that this peroxidase could be a relevant target for grass digestibility improvement using

  2. Nucleotide Metabolism

    DEFF Research Database (Denmark)

    Martinussen, Jan; Willemoës, M.; Kilstrup, Mogens

    2011-01-01

    Metabolic pathways are connected through their utilization of nucleotides as supplier of energy, allosteric effectors, and their role in activation of intermediates. Therefore, any attempt to exploit a given living organism in a biotechnological process will have an impact on nucleotide metabolism....... The aim of this article is to provide knowledge of nucleotide metabolism and its regulation to facilitate interpretation of data arising from genetics, proteomics, and transcriptomics in connection with biotechnological processes and beyond....

  3. Development of single nucleotide polymorphism (SNP) markers from the mango (Mangiferaindica) transcriptome for mapping and estimation of genetic diversity

    Science.gov (United States)

    The development of resources for genomic studies in Mangifera indica (mango) will allow marker-assisted selection and identification of genetically diverse germplasm, greatly aiding mango breeding programs. We report here a first step in developing such resources, our identification of thousands una...

  4. Genetic diversity and population structure analysis of spinach by single-nucleotide polymorphisms identified through genotyping-by-sequencing

    Science.gov (United States)

    Spinach (Spinacia oleracea L., 2n=2x=12) is an economically important vegetable crop worldwide and one of the healthiest vegetables due to its high concentrations of nutrients and mineral compounds. The objective of this research is to conduct genetic diversity and population structure analysis of w...

  5. DEFLATE Compression Algorithm Corrects for Overestimation of Phylogenetic Diversity by Grantham Approach to Single-Nucleotide Polymorphism Classification

    Directory of Open Access Journals (Sweden)

    Arran Schlosberg

    2014-05-01

    Full Text Available Improvements in speed and cost of genome sequencing are resulting in increasing numbers of novel non-synonymous single nucleotide polymorphisms (nsSNPs in genes known to be associated with disease. The large number of nsSNPs makes laboratory-based classification infeasible and familial co-segregation with disease is not always possible. In-silico methods for classification or triage are thus utilised. A popular tool based on multiple-species sequence alignments (MSAs and work by Grantham, Align-GVGD, has been shown to underestimate deleterious effects, particularly as sequence numbers increase. We utilised the DEFLATE compression algorithm to account for expected variation across a number of species. With the adjusted Grantham measure we derived a means of quantitatively clustering known neutral and deleterious nsSNPs from the same gene; this was then used to assign novel variants to the most appropriate cluster as a means of binary classification. Scaling of clusters allows for inter-gene comparison of variants through a single pathogenicity score. The approach improves upon the classification accuracy of Align-GVGD while correcting for sensitivity to large MSAs. Open-source code and a web server are made available at https://github.com/aschlosberg/CompressGV.

  6. Deciphering the fine nucleotide diversity of full HLA class I and class II genes in a well-documented population from sub-Saharan Africa.

    Science.gov (United States)

    Goeury, T; Creary, L E; Brunet, L; Galan, M; Pasquier, M; Kervaire, B; Langaney, A; Tiercy, J-M; Fernández-Viña, M A; Nunes, J M; Sanchez-Mazas, A

    2018-01-01

    With the aim to understand how next-generation sequencing (NGS) improves both our assessment of genetic variation within populations and our knowledge on HLA molecular evolution, we sequenced and analysed 8 HLA loci in a well-documented population from sub-Saharan Africa (Mandenka). The results of full-gene NGS-MiSeq sequencing compared with those obtained by traditional typing techniques or limited sequencing strategies showed that segregating sites located outside exon 2 are crucial to describe not only class I but also class II population diversity. A comprehensive analysis of exons 2, 3, 4 and 5 nucleotide diversity at the 8 HLA loci revealed remarkable differences among these gene regions, notably a greater variation concentrated in the antigen recognition sites of class I exons 3 and some class II exons 2, likely associated with their peptide-presentation function, a lower diversity of HLA-C exon 3, possibly related to its role as a KIR ligand, and a peculiar molecular diversity of HLA-A exon 2, revealing demographic signals. Based on full-length HLA sequences, we also propose that the most frequent DRB1 allele in the studied population, DRB1*13:04, emerged from an allelic conversion involving 3 potential alleles as donors and DRB1*11:02:01 as recipient. Finally, our analysis revealed a high occurrence of the DRB1*13:04-DQA1*05:05:01-DQB1*03:19 haplotype, possibly resulting from a selective sweep due to protection to Onchorcerca volvulus, a prevalent pathogen in West Africa. This study unveils highly relevant information on the molecular evolution of HLA genes in relation to their immune function, calling for similar analyses in other populations living in contrasting environments. © 2017 The Authors HLA: Immune Response Genetics Published by John Wiley & Sons Ltd.

  7. Deciphering the fine nucleotide diversity of full HLA class I and class II genes in a well‐documented population from sub‐Saharan Africa

    Science.gov (United States)

    Creary, L. E.; Brunet, L.; Galan, M.; Pasquier, M.; Kervaire, B.; Langaney, A.; Tiercy, J.‐M.; Fernández‐Viña, M. A.; Nunes, J. M.

    2017-01-01

    With the aim to understand how next‐generation sequencing (NGS) improves both our assessment of genetic variation within populations and our knowledge on HLA molecular evolution, we sequenced and analysed 8 HLA loci in a well‐documented population from sub‐Saharan Africa (Mandenka). The results of full‐gene NGS‐MiSeq sequencing compared with those obtained by traditional typing techniques or limited sequencing strategies showed that segregating sites located outside exon 2 are crucial to describe not only class I but also class II population diversity. A comprehensive analysis of exons 2, 3, 4 and 5 nucleotide diversity at the 8 HLA loci revealed remarkable differences among these gene regions, notably a greater variation concentrated in the antigen recognition sites of class I exons 3 and some class II exons 2, likely associated with their peptide‐presentation function, a lower diversity of HLA‐C exon 3, possibly related to its role as a KIR ligand, and a peculiar molecular diversity of HLA‐A exon 2, revealing demographic signals. Based on full‐length HLA sequences, we also propose that the most frequent DRB1 allele in the studied population, DRB1*13:04, emerged from an allelic conversion involving 3 potential alleles as donors and DRB1*11:02:01 as recipient. Finally, our analysis revealed a high occurrence of the DRB1*13:04‐DQA1*05:05:01‐DQB1*03:19 haplotype, possibly resulting from a selective sweep due to protection to Onchorcerca volvulus, a prevalent pathogen in West Africa. This study unveils highly relevant information on the molecular evolution of HLA genes in relation to their immune function, calling for similar analyses in other populations living in contrasting environments. PMID:29160618

  8. Ad-Hoc vs. Standardized and Optimized Arthropod Diversity Sampling

    Directory of Open Access Journals (Sweden)

    Pedro Cardoso

    2009-09-01

    Full Text Available The use of standardized and optimized protocols has been recently advocated for different arthropod taxa instead of ad-hoc sampling or sampling with protocols defined on a case-by-case basis. We present a comparison of both sampling approaches applied for spiders in a natural area of Portugal. Tests were made to their efficiency, over-collection of common species, singletons proportions, species abundance distributions, average specimen size, average taxonomic distinctness and behavior of richness estimators. The standardized protocol revealed three main advantages: (1 higher efficiency; (2 more reliable estimations of true richness; and (3 meaningful comparisons between undersampled areas.

  9. Social Dating Goals in Female College Students: Failure to Replicate in a Diverse Sample

    Science.gov (United States)

    Killeya-Jones, Ley A.

    2004-01-01

    This article reports a failure to replicate aspects of the Social Dating Goals Scale (SDGS; Sanderson & Cantor, 1995) with an ethnically diverse group of female college students. The SDGS was developed and validated with predominantly White samples. In the present study, a diverse sample of 82 Asian, Black, Hispanic and White female college…

  10. Genetic diversity of the obligate intracellular bacterium Chlamydophila pneumoniae by genome-wide analysis of single nucleotide polymorphisms: evidence for highly clonal population structure

    Directory of Open Access Journals (Sweden)

    Solbach Werner

    2007-10-01

    Full Text Available Abstract Background Chlamydophila pneumoniae is an obligate intracellular bacterium that replicates in a biphasic life cycle within eukaryotic host cells. Four published genomes revealed an identity of > 99 %. This remarkable finding raised questions about the existence of distinguishable genotypes in correlation with geographical and anatomical origin. Results We studied the genetic diversity of C. pneumoniae by analysing synonymous single nucleotide polymorphisms (sSNPs that are under reduced selection pressure. We conducted an in silico analysis of the four sequenced genomes, chose 232 representative sSNPs and analysed the loci in 38 C. pneumoniae isolates. We identified 15 different genotypes that were separated in four major clusters. Clusters were not associated with anatomical or geographical origin. However, animal lineages are basal on the C. pneumomiae phylogeny, suggesting a recent transmission to humans through successive bottlenecks some 150,000 years ago. A lack of detectable variation in 17 isolates emphasizes the extraordinary genetic conservation of this species and the high clonality of the population. Moreover, the largest cluster, which encompasses 80% of all analysed strains, is an extremely young clade, that went through an important population expansion some 3,300 years ago. Conclusion sSNPs have proven useful as a sensitive marker to gain new insights into genetic diversity, population structure and evolutionary history of C. pneumoniae.

  11. Genetic diversity and relatedness of sweet cherry (Prunus avium L. cultivars based on single nucleotide polymorphic (SNP markers

    Directory of Open Access Journals (Sweden)

    Angel eFernandez i Marti

    2012-06-01

    Full Text Available Most previous studies on genetic fingerprinting and cultivar relatedness in sweet cherry were based on isoenzyme, RAPD and SSR markers. This study was carried out to assess the utility of SNP markers generated from 3’UTRs for genetic fingerprinting in sweet cherry. A total of 114 sweet cherry germplasm representing advanced selections, commercial cultivars and old cultivars imported from different parts of the world were screened with 7 SSR markers developed from other Prunus species and with 40 SNPs obtained from 3’UTR sequences of Rainier and Bing sweet cherry cultivars. Both types of marker study had 99 accessions in common. The SSR data was used to validate the SNP results. Results showed that the average number of alleles per locus, mean observed heterozygosity, expected heterozygosity and polymorphic information content (PIC values were higher in SSRs than in SNPs although both set of markers were similar in their grouping of the sweet cherry accessions as shown in the dendrogram. SNPs were able to distinguish sport mutants from their wild type germplasm. For example, ‘Stella’ was separated from ‘Compact Stella’. This demonstrates the greater power of SNPs for discriminating mutants from their original parents than SSRs. In addition, SNP markers confirmed parentage and also determined relationships of the accessions in a manner consistent with their pedigree relationships. We would recommend the use of 3’ UTR SNPs for genetic fingerprinting, parentage verification, gene mapping and study of genetic diversity in sweet cherry.

  12. Microbial diversity in fecal samples depends on DNA extraction method

    DEFF Research Database (Denmark)

    Mirsepasi, Hengameh; Persson, Søren; Struve, Carsten

    2014-01-01

    BACKGROUND: There are challenges, when extracting bacterial DNA from specimens for molecular diagnostics, since fecal samples also contain DNA from human cells and many different substances derived from food, cell residues and medication that can inhibit downstream PCR. The purpose of the study w...

  13. Molecular characterization of diverse CIMMYT maize inbred lines from eastern and southern Africa using single nucleotide polymorphic markers.

    Science.gov (United States)

    Semagn, Kassa; Magorokosho, Cosmos; Vivek, Bindiganavile S; Makumbi, Dan; Beyene, Yoseph; Mugo, Stephen; Prasanna, B M; Warburton, Marilyn L

    2012-03-25

    Knowledge of germplasm diversity and relationships among elite breeding materials is fundamentally important in crop improvement. We genotyped 450 maize inbred lines developed and/or widely used by CIMMYT breeding programs in both Kenya and Zimbabwe using 1065 SNP markers to (i) investigate population structure and patterns of relationship of the germplasm for better exploitation in breeding programs; (ii) assess the usefulness of SNPs for identifying heterotic groups commonly used by CIMMYT breeding programs; and (iii) identify a subset of highly informative SNP markers for routine and low cost genotyping of CIMMYT germplasm in the region using uniplex assays. Genetic distance for about 94% of the pairs of lines fell between 0.300 and 0.400. Eighty four percent of the pairs of lines also showed relative kinship values ≤ 0.500. Model-based population structure analysis, principal component analysis, neighbor-joining cluster analysis and discriminant analysis revealed the presence of 3 major groups and generally agree with pedigree information. The SNP markers did not show clear separation of heterotic groups A and B that were established based on combining ability tests through diallel and line x tester analyses. Our results demonstrated large differences among the SNP markers in terms of reproducibility, ease of scoring, polymorphism, minor allele frequency and polymorphic information content. About 40% of the SNPs in the multiplexed chip-based GoldenGate assays were found to be uninformative in this study and we recommend 644 of the 1065 for low to medium density genotyping in tropical maize germplasm using uniplex assays. There were high genetic distance and low kinship coefficients among most pairs of lines, clearly indicating the uniqueness of the majority of the inbred lines in these maize breeding programs. The results from this study will be useful to breeders in selecting best parental combinations for new breeding crosses, mapping population development

  14. Molecular characterization of diverse CIMMYT maize inbred lines from eastern and southern Africa using single nucleotide polymorphic markers

    Directory of Open Access Journals (Sweden)

    Semagn Kassa

    2012-03-01

    Full Text Available Abstract Background Knowledge of germplasm diversity and relationships among elite breeding materials is fundamentally important in crop improvement. We genotyped 450 maize inbred lines developed and/or widely used by CIMMYT breeding programs in both Kenya and Zimbabwe using 1065 SNP markers to (i investigate population structure and patterns of relationship of the germplasm for better exploitation in breeding programs; (ii assess the usefulness of SNPs for identifying heterotic groups commonly used by CIMMYT breeding programs; and (iii identify a subset of highly informative SNP markers for routine and low cost genotyping of CIMMYT germplasm in the region using uniplex assays. Results Genetic distance for about 94% of the pairs of lines fell between 0.300 and 0.400. Eighty four percent of the pairs of lines also showed relative kinship values ≤ 0.500. Model-based population structure analysis, principal component analysis, neighbor-joining cluster analysis and discriminant analysis revealed the presence of 3 major groups and generally agree with pedigree information. The SNP markers did not show clear separation of heterotic groups A and B that were established based on combining ability tests through diallel and line x tester analyses. Our results demonstrated large differences among the SNP markers in terms of reproducibility, ease of scoring, polymorphism, minor allele frequency and polymorphic information content. About 40% of the SNPs in the multiplexed chip-based GoldenGate assays were found to be uninformative in this study and we recommend 644 of the 1065 for low to medium density genotyping in tropical maize germplasm using uniplex assays. Conclusions There were high genetic distance and low kinship coefficients among most pairs of lines, clearly indicating the uniqueness of the majority of the inbred lines in these maize breeding programs. The results from this study will be useful to breeders in selecting best parental combinations

  15. Multi Class Active Learning by Uncertainty Sampling with Diversity Maximization

    Science.gov (United States)

    2014-11-13

    where d is the dimension of the sample. To better utilize the distribution of the pool data and the seed set, we propose to evaluate the uncertainty...represented by 1,000 dimension BoW STIP feature (Laptev et al. 2008). KTH action dataset contains six types of human actions (walking, jogging, running...soccer juggling, swinging, ten- nis swinging, trampoline jumping, volleyball spiking, and walking with a dog (Liu et al. 2009). Four videos in

  16. Species-genetic diversity correlations in habitat fragmentation can be biased by small sample sizes.

    Science.gov (United States)

    Nazareno, Alison G; Jump, Alistair S

    2012-06-01

    Predicted parallel impacts of habitat fragmentation on genes and species lie at the core of conservation biology, yet tests of this rule are rare. In a recent article in Ecology Letters, Struebig et al. (2011) report that declining genetic diversity accompanies declining species diversity in tropical forest fragments. However, this study estimates diversity in many populations through extrapolation from very small sample sizes. Using the data of this recent work, we show that results estimated from the smallest sample sizes drive the species-genetic diversity correlation (SGDC), owing to a false-positive association between habitat fragmentation and loss of genetic diversity. Small sample sizes are a persistent problem in habitat fragmentation studies, the results of which often do not fit simple theoretical models. It is essential, therefore, that data assessing the proposed SGDC are sufficient in order that conclusions be robust.

  17. A Comparison of Two Sampling Strategies to Assess Discomycete Diversity in Wet Tropical Forests

    Science.gov (United States)

    SHARON A. CANTRELL

    2004-01-01

    Most of the fungal diversity studies that have used a systematic collecting scheme have not included the discomycetes, so optimal sampling methods are not available for this group. In this study, I tested two sampling methods at each sites in the Caribbean National Forest, Puerto Rico and Ebano Verde Reserve, Dominican Republic. For a plot-based sampling method, 10 ×...

  18. Unbiased Estimation of Gene Diversity in Samples Containing Related Individuals: Exact Variance and Arbitrary Ploidy

    OpenAIRE

    DeGiorgio, Michael; Jankovic, Ivana; Rosenberg, Noah A.

    2010-01-01

    Gene diversity, a commonly used measure of genetic variation, evaluates the proportion of heterozygous individuals expected at a locus in a population, under the assumption of Hardy–Weinberg equilibrium. When using the standard estimator of gene diversity, the inclusion of related or inbred individuals in a sample produces a downward bias. Here, we extend a recently developed estimator shown to be unbiased in a diploid autosomal sample that includes known related or inbred individuals to the ...

  19. Sampling and Selection Factors that Enhance the Diversity of Microbial Collections: Application to Biopesticide Development

    Directory of Open Access Journals (Sweden)

    Jun-Kyung Park

    2013-06-01

    Full Text Available Diverse bacteria are known to colonize plants. However, only a small fraction of that diversity has been evaluated for their biopesticide potential. To date, the criteria for sampling and selection in such bioprospecting endeavors have not been systematically evaluated in terms of the relative amount of diversity they provide for analysis. The present study aimed to enhance the success of bio-prospecting efforts by increasing the diversity while removing the genotypic redundancy often present in large collections of bacteria. We developed a multivariate sampling and marker-based selection strategy that significantly increase the diversity of bacteria recovered from plants. In doing so, we quantified the effects of varying sampling intensity, media composition, incubation conditions, plant species, and soil source on the diversity of recovered isolates. Subsequent sequencing and high-throughput phenotypic analyses of a small fraction of the collected isolates revealed that this approach led to the recovery of over a dozen rare and, to date, poorly characterized genera of plant-associated bacteria with significant biopesticide activities. Overall, the sampling and selection approach described led to an approximately 5-fold improvement in efficiency and the recovery of several novel strains of bacteria with significant biopesticide potential.

  20. Who Are We Studying? Sample Diversity in Teaching of Psychology Research

    Science.gov (United States)

    Richmond, Aaron S.; Broussard, Kristin A.; Sterns, Jillian L.; Sanders, Kristina K.; Shardy, Justin C.

    2015-01-01

    The purpose of the current study was to examine the sample diversity of empirical articles published in four premier teaching of psychology journals from 2008 to 2013. We investigated which demographic information was commonly reported and if samples were ethnically representative and whether gender was representative compared to National…

  1. Sampling plant diversity and rarity at landscape scales: importance of sampling time in species detectability.

    Science.gov (United States)

    Zhang, Jian; Nielsen, Scott E; Grainger, Tess N; Kohler, Monica; Chipchar, Tim; Farr, Daniel R

    2014-01-01

    Documenting and estimating species richness at regional or landscape scales has been a major emphasis for conservation efforts, as well as for the development and testing of evolutionary and ecological theory. Rarely, however, are sampling efforts assessed on how they affect detection and estimates of species richness and rarity. In this study, vascular plant richness was sampled in 356 quarter hectare time-unlimited survey plots in the boreal region of northeast Alberta. These surveys consisted of 15,856 observations of 499 vascular plant species (97 considered to be regionally rare) collected by 12 observers over a 2 year period. Average survey time for each quarter-hectare plot was 82 minutes, ranging from 20 to 194 minutes, with a positive relationship between total survey time and total plant richness. When survey time was limited to a 20-minute search, as in other Alberta biodiversity methods, 61 species were missed. Extending the survey time to 60 minutes, reduced the number of missed species to 20, while a 90-minute cut-off time resulted in the loss of 8 species. When surveys were separated by habitat type, 60 minutes of search effort sampled nearly 90% of total observed richness for all habitats. Relative to rare species, time-unlimited surveys had ∼ 65% higher rare plant detections post-20 minutes than during the first 20 minutes of the survey. Although exhaustive sampling was attempted, observer bias was noted among observers when a subsample of plots was re-surveyed by different observers. Our findings suggest that sampling time, combined with sample size and observer effects, should be considered in landscape-scale plant biodiversity surveys.

  2. Nucleotide sequences from the genomes of diverse cowpea accessions for discovery of genetic variation as part of the Feed the Future Innovation Lab for Climate Resilient Cowpea

    Data.gov (United States)

    US Agency for International Development — Nucleotide sequences were generated from 37 cowpea (Vigna unguiculata L. Walp.) accessions relevant to Africa, China and the USA to discover at type of genetic...

  3. Bee (Hymenoptera: Apoidea) Diversity and Sampling Methodology in a Midwestern USA Deciduous Forest.

    Science.gov (United States)

    McCravy, Kenneth W; Ruholl, Jared D

    2017-08-04

    Forests provide potentially important bee habitat, but little research has been done on forest bee diversity and the relative effectiveness of bee sampling methods in this environment. Bee diversity and sampling methodology were studied in an Illinois, USA upland oak-hickory forest using elevated and ground-level pan traps, malaise traps, and vane traps. 854 bees and 55 bee species were collected. Elevated pan traps collected the greatest number of bees (473), but ground-level pan traps collected greater species diversity (based on Simpson's diversity index) than did elevated pan traps. Elevated and ground-level pan traps collected the greatest bee species richness, with 43 and 39 species, respectively. An estimated sample size increase of over 18-fold would be required to approach minimum asymptotic richness using ground-level pan traps. Among pan trap colors/elevations, elevated yellow pan traps collected the greatest number of bees (266) but the lowest diversity. Malaise traps were relatively ineffective, collecting only 17 bees. Vane traps collected relatively low species richness (14 species), and Chao1 and abundance coverage estimators suggested that minimum asymptotic species richness was approached for that method. Bee species composition differed significantly between elevated pan traps, ground-level pan traps, and vane traps. Indicator species were significantly associated with each of these trap types, as well as with particular pan trap colors/elevations. These results indicate that Midwestern deciduous forests provide important bee habitat, and that the performance of common bee sampling methods varies substantially in this environment.

  4. Molecular diversity and distribution of marine fungi across 130 European environmental samples.

    Science.gov (United States)

    Richards, Thomas A; Leonard, Guy; Mahé, Frédéric; Del Campo, Javier; Romac, Sarah; Jones, Meredith D M; Maguire, Finlay; Dunthorn, Micah; De Vargas, Colomban; Massana, Ramon; Chambouvet, Aurélie

    2015-11-22

    Environmental DNA and culture-based analyses have suggested that fungi are present in low diversity and in low abundance in many marine environments, especially in the upper water column. Here, we use a dual approach involving high-throughput diversity tag sequencing from both DNA and RNA templates and fluorescent cell counts to evaluate the diversity and relative abundance of fungi across marine samples taken from six European near-shore sites. We removed very rare fungal operational taxonomic units (OTUs) selecting only OTUs recovered from multiple samples for a detailed analysis. This approach identified a set of 71 fungal 'OTU clusters' that account for 66% of all the sequences assigned to the Fungi. Phylogenetic analyses demonstrated that this diversity includes a significant number of chytrid-like lineages that had not been previously described, indicating that the marine environment encompasses a number of zoosporic fungi that are new to taxonomic inventories. Using the sequence datasets, we identified cases where fungal OTUs were sampled across multiple geographical sites and between different sampling depths. This was especially clear in one relatively abundant and diverse phylogroup tentatively named Novel Chytrid-Like-Clade 1 (NCLC1). For comparison, a subset of the water column samples was also investigated using fluorescent microscopy to examine the abundance of eukaryotes with chitin cell walls. Comparisons of relative abundance of RNA-derived fungal tag sequences and chitin cell-wall counts demonstrate that fungi constitute a low fraction of the eukaryotic community in these water column samples. Taken together, these results demonstrate the phylogenetic position and environmental distribution of 71 lineages, improving our understanding of the diversity and abundance of fungi in marine environments. © 2015 The Authors.

  5. A new enrichment method for isolation of Bacillus thuringiensis from diverse sample types.

    Science.gov (United States)

    Patel, Ketan D; Bhanshali, Forum C; Chaudhary, Avani V; Ingle, Sanjay S

    2013-05-01

    New or more efficient methodologies having different principles are needed, as one method could not be suitable for isolation of organisms from samples of diverse types and from various environments. In present investigation, growth kinetics study revealed a higher germination rate, a higher growth rate, and maximum sporulation of Bacillus thuringiensis (Bt) compared to other Bacillus species. Considering these facts, a simple and efficient enrichment method was devised which allowed propagation of spores and vegetative cells of Bt and thereby increased Bt cell population proportionately. The new enrichment method yielded Bt from 44 out of 58 samples. Contrarily, Bt was isolated only from 16 and 18 samples by sodium acetate selection and dry heat pretreatment methods, respectively. Moreover, the percentages of Bt colonies isolated by the enrichment method were higher comparatively. Vegetative whole cell protein profile analysis indicated isolation of diverse population of Bt from various samples. Bt strains isolated by the enrichment method represented novel serovars and possibly new cry2 gene.

  6. Maintaining and Enhancing Diversity of Sampled Protein Conformations in Robotics-Inspired Methods.

    Science.gov (United States)

    Abella, Jayvee R; Moll, Mark; Kavraki, Lydia E

    2017-10-16

    The ability to efficiently sample structurally diverse protein conformations allows one to gain a high-level view of a protein's energy landscape. Algorithms from robot motion planning have been used for conformational sampling, and several of these algorithms promote diversity by keeping track of "coverage" in conformational space based on the local sampling density. However, large proteins present special challenges. In particular, larger systems require running many concurrent instances of these algorithms, but these algorithms can quickly become memory intensive because they typically keep previously sampled conformations in memory to maintain coverage estimates. In addition, robotics-inspired algorithms depend on defining useful perturbation strategies for exploring the conformational space, which is a difficult task for large proteins because such systems are typically more constrained and exhibit complex motions. In this article, we introduce two methodologies for maintaining and enhancing diversity in robotics-inspired conformational sampling. The first method addresses algorithms based on coverage estimates and leverages the use of a low-dimensional projection to define a global coverage grid that maintains coverage across concurrent runs of sampling. The second method is an automatic definition of a perturbation strategy through readily available flexibility information derived from B-factors, secondary structure, and rigidity analysis. Our results show a significant increase in the diversity of the conformations sampled for proteins consisting of up to 500 residues when applied to a specific robotics-inspired algorithm for conformational sampling. The methodologies presented in this article may be vital components for the scalability of robotics-inspired approaches.

  7. Impact of diversity of colonizing strains on strategies for sampling Escherichia coli from fecal specimens.

    Science.gov (United States)

    Lautenbach, Ebbing; Bilker, Warren B; Tolomeo, Pam; Maslow, Joel N

    2008-09-01

    Of 49 subjects, 21 were colonized with more than one strain of Escherichia coli and 12 subjects had at least one strain present in fewer than 20% of colonies. The ability to accurately characterize E. coli strain diversity is directly related to the number of colonies sampled and the underlying prevalence of the strain.

  8. Depressive Symptoms and Mental Health Treatment in an Ethnoracially Diverse College Student Sample

    Science.gov (United States)

    Herman, Steve; Archambeau, Olga G.; Deliramich, Aimee N.; Kim, Bryan S. K.; Chiu, Pearl H.; Frueh, B. Christopher

    2011-01-01

    Objectives: To study (a) the prevalence of depressive symptoms and (b) the utilization of mental health treatment in an ethnoracially diverse sample consisting primarily of Asian Americans, European Americans, Native Hawaiians, and Pacific Islanders. Participants: Five hundred eighty-nine college students. Method: A questionnaire packet that…

  9. Children's Use of Sample Size and Diversity Information within Basic-Level Categories.

    Science.gov (United States)

    Gutheil, Grant; Gelman, Susan A.

    1997-01-01

    Three studies examined the ability of 8- and 9-year-olds and young adults to use sample monotonicity and diversity information according to the similarity-coverage model of category-based induction. Found that children's difficulty with this information was independent of category level, and may be based on preferences for other strategies…

  10. Patterns of oribatid mite species diversity: testing the effects of elevation, area and sampling effort.

    Science.gov (United States)

    Mumladze, Levan; Murvanidze, Maka; Maraun, Mark

    2017-07-01

    Elevational gradients in species diversity and species area relationships are two well established patterns that are not mutually exclusive in space and time. Elevation and area are both considered as good proxies to detect and characterize the patterns of species diversity distribution. However, such studies are hampered by the incomplete biodiversity data available for ecologists, which may affect the pattern perceptions. Using the large dataset of oribatid mite communities sampled in Georgia, we tested the effects of altitude and area on species distribution using various approaches, while explicitly considering the biases from sampling effort. Our results showed that elevation and area are strongly correlated (with increasing absolute elevation, land area decreases) and both have strong linear effects on species diversity distribution when studied separately. Approaches based on multiple regression and direct removal of co-varied factors, indicated that the effect of area can actually override the effect of elevation in describing the oribatid species diversity distribution along with elevation. On the other hand, the bias of sampling proved significant in perception of elevational species richness pattern with less effect on elevational species area relationship. We suggest that the sampling alone may be responsible for patterns observed and thus should be considered in ecological studies when eligible.

  11. The Modified Checklist for Autism in Toddlers: Reliability in a Diverse Rural American Sample

    Science.gov (United States)

    Scarpa, Angela; Reyes, Nuri M.; Patriquin, Michelle A.; Lorenzi, Jill; Hassenfeldt, Tyler A.; Desai, Varsha J.; Kerkering, Kathryn W.

    2013-01-01

    This study investigated the psychometric properties of the modified checklist for autism in toddlers (M-CHAT) in a diverse rural American low-socioeconomic status (SES) sample. Four hundred and forty-seven English (n = 335) and Spanish (n = 112) speaking caregivers completed the M-CHAT during their toddler's 18- or 24-month well visit in a…

  12. Student-teacher relationships and achievement goal orientations : Examining student perceptions in an ethnically diverse sample

    NARCIS (Netherlands)

    Thijs, J.T.; Fleischmann, F.

    2015-01-01

    Among an ethnically diverse sample of 803 preadolescent students (ages 9-13 years), the present study examined the associations between students’ perceptions of the student-teacher relationship and their achievement goal orientations. Multilevel analyses showed that students who perceived more

  13. A simple method for estimating genetic diversity in large populations from finite sample sizes

    Directory of Open Access Journals (Sweden)

    Rajora Om P

    2009-12-01

    Full Text Available Abstract Background Sample size is one of the critical factors affecting the accuracy of the estimation of population genetic diversity parameters. Small sample sizes often lead to significant errors in determining the allelic richness, which is one of the most important and commonly used estimators of genetic diversity in populations. Correct estimation of allelic richness in natural populations is challenging since they often do not conform to model assumptions. Here, we introduce a simple and robust approach to estimate the genetic diversity in large natural populations based on the empirical data for finite sample sizes. Results We developed a non-linear regression model to infer genetic diversity estimates in large natural populations from finite sample sizes. The allelic richness values predicted by our model were in good agreement with those observed in the simulated data sets and the true allelic richness observed in the source populations. The model has been validated using simulated population genetic data sets with different evolutionary scenarios implied in the simulated populations, as well as large microsatellite and allozyme experimental data sets for four conifer species with contrasting patterns of inherent genetic diversity and mating systems. Our model was a better predictor for allelic richness in natural populations than the widely-used Ewens sampling formula, coalescent approach, and rarefaction algorithm. Conclusions Our regression model was capable of accurately estimating allelic richness in natural populations regardless of the species and marker system. This regression modeling approach is free from assumptions and can be widely used for population genetic and conservation applications.

  14. Fungi in the sea fan Gorgonia ventalina: diversity and sampling strategies

    Science.gov (United States)

    Toledo-Hernández, C.; Bones-González, A.; Ortiz-Vázquez, O. E.; Sabat, A. M.; Bayman, P.

    2007-09-01

    Fungal communities from gorgonians have been poorly documented and most studies of these communities have lacked defined sampling strategies. The objectives of this study were: (1) to estimate fungal diversity in Gorgonia ventalina; (2) to compare two sampling and tissue processing strategies: tissue fragments of different sizes vs. homogenized tissue. A total of seven genera and fourteen species of fungi were isolated on culture medium and identified by sequencing the nrITS. All but one species were new reports. In both treatments Aspergillus and Penicillium were the most common genera isolated. Most species isolated from fragments were not observed from homogenized tissue and vice versa. Reducing the size fragment increased significantly the number of species isolated per fragment. To better estimate fungal diversity in sea fans a strategy is proposed that combines sampling of small tissue fragments with homogenized tissue, since each technique yielded fungal species not detected by the other.

  15. Preparation method matters: Aiming at higher NPP diversity and representativeness in sediment samples

    DEFF Research Database (Denmark)

    Enevold, Renée; Odgaard, Bent Vad

    2016-01-01

    of palynology in archaeological and forensic sciences. NPPs in anthropogenic soils and archaeological samples may be numerous in types as well as in abundance. However, preparing these soil samples with methods based on acid digestion potentially biases NPP assemblages because of differential damage or even...... dissolution of microfossils. In spite of this potential bias standard preparation procedures for pollen analysis have, in most cases without modification, generally been applied to palynological samples used for NPP analysis. We review briefly the advantages of high diversity NPP-analysis and preparation...

  16. Targeted genomic enrichment and sequencing of CyHV-3 from carp tissues confirms low nucleotide diversity and mixed genotype infections

    Directory of Open Access Journals (Sweden)

    Saliha Hammoumi

    2016-09-01

    Full Text Available Koi herpesvirus disease (KHVD is an emerging disease that causes mass mortality in koi and common carp, Cyprinus carpio L. Its causative agent is Cyprinid herpesvirus 3 (CyHV-3, also known as koi herpesvirus (KHV. Although data on the pathogenesis of this deadly virus is relatively abundant in the literature, still little is known about its genomic diversity and about the molecular mechanisms that lead to such a high virulence. In this context, we developed a new strategy for sequencing full-length CyHV-3 genomes directly from infected fish tissues. Total genomic DNA extracted from carp gill tissue was specifically enriched with CyHV-3 sequences through hybridization to a set of nearly 2 million overlapping probes designed to cover the entire genome length, using KHV-J sequence (GenBank accession number AP008984 as reference. Applied to 7 CyHV-3 specimens from Poland and Indonesia, this targeted genomic enrichment enabled recovery of the full genomes with >99.9% reference coverage. The enrichment rate was directly correlated to the estimated number of viral copies contained in the DNA extracts used for library preparation, which varied between ∼5000 and ∼2×107. The average sequencing depth was >200 for all samples, thus allowing the search for variants with high confidence. Sequence analyses highlighted a significant proportion of intra-specimen sequence heterogeneity, suggesting the presence of mixed infections in all investigated fish. They also showed that inter-specimen genetic diversity at the genome scale was very low (>99.95% of sequence identity. By enabling full genome comparisons directly from infected fish tissues, this new method will be valuable to trace outbreaks rapidly and at a reasonable cost, and in turn to understand the transmission routes of CyHV-3.

  17. The diversion of stimulant medications among a convenience sample of college students with current prescriptions.

    Science.gov (United States)

    Gallucci, Andrew R; Martin, Ryan J; Usdan, Stuart L

    2015-03-01

    Diversion is defined as the unlawful channeling of regulated pharmaceuticals from legal sources to the illicit marketplace. Persons with legal prescriptions often give away or sell their medications to others. The misuse of prescription stimulant medications continues to be a problem on college campuses and a need to understand how students are obtaining stimulant medications exists. The object of the study was to identify the prevalence, correlates, and motivations associated with diversion of prescription stimulants among current prescription holders. A large sample of undergraduates (n = 1,022) between the ages of 18 and 24 enrolled at a large public university in the southeastern United States completed an in class questionnaire. Among those respondents, we identified 151 current stimulant prescription holders and analyzed the prevalence, motivations, and correlates associated with lifetime and current diversion. Overall, 58.9% of current prescription holders had given away or sold their stimulant medication during their lifetime. Those with a history of nonmedical use of prescription stimulants were almost 5 times more likely to divert their medication during their lifetime. The majority of those engaging in lifetime and current diversion medication did so infrequently. The most common motivations reported for both lifetime and current diversion were "to make extra money" and to "help during a time of high academic stress." Students who reported a history of prescription misuse were also more likely to engage in current diversion. Diversion-related behaviors should be explored further and programs aimed at the reducing these behaviors should be considered. (c) 2015 APA, all rights reserved).

  18. Woody species diversity in forest plantations in a mountainous region of Beijing, China: effects of sampling scale and species selection.

    Directory of Open Access Journals (Sweden)

    Yuxin Zhang

    Full Text Available The role of forest plantations in biodiversity conservation has gained more attention in recent years. However, most work on evaluating the diversity of forest plantations focuses only on one spatial scale; thus, we examined the effects of sampling scale on diversity in forest plantations. We designed a hierarchical sampling strategy to collect data on woody species diversity in planted pine (Pinus tabuliformis Carr., planted larch (Larix principis-rupprechtii Mayr., and natural secondary deciduous broadleaf forests in a mountainous region of Beijing, China. Additive diversity partition analysis showed that, compared to natural forests, the planted pine forests had a different woody species diversity partitioning pattern at multi-scales (except the Simpson diversity in the regeneration layer, while the larch plantations did not show multi-scale diversity partitioning patterns that were obviously different from those in the natural secondary broadleaf forest. Compare to the natural secondary broadleaf forests, the effects of planted pine forests on woody species diversity are dependent on the sampling scale and layers selected for analysis. Diversity in the planted larch forest, however, was not significantly different from that in the natural forest for all diversity components at all sampling levels. Our work demonstrated that the species selected for afforestation and the sampling scales selected for data analysis alter the conclusions on the levels of diversity supported by plantations. We suggest that a wide range of scales should be considered in the evaluation of the role of forest plantations on biodiversity conservation.

  19. Molecular diversity sample generation on the basis of quantum-mechanical computations and principal component analysis.

    Science.gov (United States)

    Gutierrez-De-Teran, H; Lozano, J J; Segarra, V; Sanz, F

    2002-02-01

    The present study introduces a new strategy of selection of a maximum diversity sample of n compounds from N available in a molecular database. This strategy can be useful in pharmacological screening, combinatorial chemistry or parallel synthesis planning. It consists of first describing the compounds by means of parameters derived from quantum mechanical computations (water solvation deltaG, benzene solvation deltaG, octanol solvation deltaG, dipolar moment), as well as standard molecular parameters such as solvent-accessible surface area and molecular weight. Solvation parameters are used because of the importance of this phenomenon in the pharmacological behaviour. Redundant information in the description of the compounds is eliminated by using principal components (PC) instead of the original descriptors. Based on the similarity between the N compounds in the PC space, they are classified into n groups by k-means cluster analysis. The compounds that are nearest to the centroid of each cluster constituted the maximum diversity sample. When practical difficulties exist for the use of one of the proposed compounds, another also close to the cluster centroid can substitute for it. This strategy has been tested in the selection of a sample of 50 amines from the 923 available in the Aldrich catalogue. The results have been contrasted with those obtained from an optimal, distance-based experimental design, resulting in an 86% of agreement between both approaches. An R(2)-like diversity coefficient has been used to assess the quality of the proposed solutions.

  20. Evaluation of bacterial diversity recovered from petroleum samples using different physical matrices

    Directory of Open Access Journals (Sweden)

    Bruna Martins Dellagnezze

    Full Text Available ABSTRACT Unraveling the microbial diversity and its complexity in petroleum reservoir environments has been a challenge throughout the years. Despite the techniques developed in order to improve methodologies involving DNA extraction from crude oil, microbial enrichments using different culture conditions can be applied as a way to increase the recovery of DNA from environments with low cellular density for further microbiological analyses. This work aimed at the evaluation of different matrices (arenite, shale and polyurethane foam as support materials for microbial growth and biofilm formation in enrichments using a biodegraded petroleum sample as inoculum in sulfate reducing condition. Subsequent microbial diversity characterization was carried out using Scanning Electronic Microscopy (SEM, Denaturing Gradient Gel Electrophoresis (DGGE and 16S rRNA gene libraries in order to compare the microbial biomass yield, DNA recovery efficiency and diversity among the enrichments. The DNA from microbial communities in petroleum enrichments was purified according to a protocol established in this work and used for 16S rRNA amplification with bacterial generic primers. The PCR products were cloned, and positive clones were screened by Amplified Ribosomal DNA Restriction Analysis (ARDRA. Sequencing and phylogenetic analyses revealed that the bacterial community was mostly represented by members of the genera Petrotoga, Bacillus, Pseudomonas, Geobacillus and Rahnella. The use of different support materials in the enrichments yielded an increase in microbial biomass and biofilm formation, indicating that these materials may be employed for efficient biomass recovery from petroleum reservoir samples. Nonetheless, the most diverse microbiota were recovered from the biodegraded petroleum sample using polyurethane foam cubes as support material.

  1. Genetic diversity of Cryptosporidium identified in clinical samples from cities in Brazil and Argentina

    Directory of Open Access Journals (Sweden)

    Regina Helena Saramago Peralta

    2016-01-01

    Full Text Available The identification and characterisation of Cryptosporidiumgenotypes and subtypes are fundamental to the study of cryptosporidiosis epidemiology, aiding in prevention and control strategies. The objective was to determine the genetic diversity ofCryptosporidium in samples obtained from hospitals of Rio de Janeiro, Brazil, and Buenos Aires, Argentina. Samples were analysed by microscopy and TaqMan polymerase chain reaction (PCR assays forCryptosporidium detection, genotyped by nested-PCR-restriction fragment length polymorphism (RFLP analysis of the 18S rRNA gene and subtyped by DNA sequencing of the gp60 gene. Among the 89 samples from Rio de Janeiro, Cryptosporidium spp were detected in 26 by microscopy/TaqMan PCR. In samples from Buenos Aires,Cryptosporidium was diagnosed in 15 patients of the 132 studied. The TaqMan PCR and the nested-PCR-RFLP detected Cryptosporidium parvum, Cryptosporidium hominis, and co-infections of both species. In Brazilian samples, the subtypes IbA10G2 and IIcA5G3 were observed. The subtypes found in Argentinean samples were IbA10G2, IaA10G1R4, IaA11G1R4, and IeA11G3T3, and mixed subtypes of Ia and IIa families were detected in the co-infections. C. hominis was the species more frequently detected, and subtype family Ib was reported in both countries. Subtype diversity was higher in Buenos Aires than in Rio de Janeiro and two new subtypes were described for the first time.

  2. Patterns of Nucleotide Diversity at the Regions Encompassing the Drosophila Insulin-Like Peptide (dilp) Genes: Demography vs. Positive Selection in Drosophila melanogaster

    Science.gov (United States)

    Guirao-Rico, Sara; Aguadé, Montserrat

    2013-01-01

    In Drosophila, the insulin-signaling pathway controls some life history traits, such as fertility and lifespan, and it is considered to be the main metabolic pathway involved in establishing adult body size. Several observations concerning variation in body size in the Drosophila genus are suggestive of its adaptive character. Genes encoding proteins in this pathway are, therefore, good candidates to have experienced adaptive changes and to reveal the footprint of positive selection. The Drosophila insulin-like peptides (DILPs) are the ligands that trigger the insulin-signaling cascade. In Drosophila melanogaster, there are several peptides that are structurally similar to the single mammalian insulin peptide. The footprint of recent adaptive changes on nucleotide variation can be unveiled through the analysis of polymorphism and divergence. With this aim, we have surveyed nucleotide sequence variation at the dilp1-7 genes in a natural population of D. melanogaster. The comparison of polymorphism in D. melanogaster and divergence from D. simulans at different functional classes of the dilp genes provided no evidence of adaptive protein evolution after the split of the D. melanogaster and D. simulans lineages. However, our survey of polymorphism at the dilp gene regions of D. melanogaster has provided some evidence for the action of positive selection at or near these genes. The regions encompassing the dilp1-4 genes and the dilp6 gene stand out as likely affected by recent adaptive events. PMID:23308258

  3. Microbial diversity within Juan de Fuca ridge basement fluids sampled from oceanic borehole observatories

    Science.gov (United States)

    Jungbluth, S.; Bowers, R.; Lin, H.; Hsieh, C.; Cowen, J. P.; Rappé, M.

    2012-12-01

    Three generations of sampling and instrumentation platforms known as Circulation Obviation Retrofit Kit (CORK) observatories affixed to Ocean Drilling Program (ODP) and Integrated Ocean Drilling Program (IODP) boreholes are providing unrivaled access to fluids originating from 1.2-3.5 million-years (Myr) old basaltic crust of the eastern flank of the Juan de Fuca ridge. Borehole fluid samples obtained via a custom seafloor fluid pumping and sampling system coupled to CORK continuous fluid delivery lines are yielding critical insights into the biogeochemistry and nature of microbial life inhabiting the sediment-covered basement environment. Direct microscopic enumeration revealed microbial cell abundances that are 2-41% of overlying bottom seawater. Snapshots of basement fluid microbial diversity and community structure have been obtained through small subunit ribosomal RNA (SSU rRNA) gene cloning and sequencing from five boreholes that access a range of basement ages and temperatures at the sediment-basement interface. SSU rRNA gene clones were derived from four different CORK installations (1026B, 1301A, 1362A, and 1362B) accessing relatively warmer (65°C) and older (3.5 Myr) ridge flank, and one location (1025C) accessing relatively cooler (39°C) and younger (1.2 Myr) ridge flank, revealing that warmer basement fluids had higher microbial diversity. A sampling time-series collected from borehole 1301A has revealed a microbial community that is temporally variable, with the dominant lineages changing between years. Each of the five boreholes sampled contained a unique microbial assemblage, however, common members are found from both cultivated and uncultivated lineages within the archaeal and bacterial domains, including meso- and thermophilic microbial lineages involved with sulfur cycling (e.g Thiomicrospira, Sulfurimonas, Desulfocapsa, Desulfobulbus). In addition, borehole fluid environmental gene clones were also closely related to uncultivated lineages

  4. The Impact of Attachment Style on Sexual Satisfaction and Sexual Desire in a Sexually Diverse Sample.

    Science.gov (United States)

    Mark, Kristen P; Patrick, Laura M; Murray, Sarah H

    2017-11-22

    Research has indicated that adult romantic attachment is influential and important to sexual and relationship satisfaction. Sexual desire, although not a direct focus of attachment literature, is highly related to sexual and relationship satisfaction, suggesting it may also be impacted by attachment style in romantic couples. However, the research conducted on sexual desire, sexual satisfaction, and attachment has been largely heterocentric, making it difficult to determine whether the findings documented in the literature thus far are relevant in a sexually diverse group of individuals. The current study aimed to better understand the way that attachment style may impact sexual desire, sexual satisfaction, and relationship satisfaction in a sample of sexually diverse men and women. In total, 955 individuals (63.4% cis-gender women, 30.7% cis-gender men, 6.0% genderqueer; 54.8% straight, 20.4% bisexual, 18.4% gay) participated in a web-based study examining relationship dynamics. In three multivariate regression models indicated that attachment style significantly predicted relationship satisfaction (29% of variance accounted for), sexual satisfaction (19% of variance accounted for), and sexual desire (4% of variance accounted for). Attachment style appears to be a more important contributing factor to satisfaction than desire amongst diverse sexual orientations. Clinical implications and future directions are discussed.

  5. NUCLEOTIDES IN INFANT FEEDING

    Directory of Open Access Journals (Sweden)

    L.G. Mamonova

    2007-01-01

    Full Text Available The article reviews the application of nucleotides-metabolites, playing a key role in many biological processes, for the infant feeding. The researcher provides the date on the nucleotides in the women's milk according to the lactation stages. She also analyzes the foreign experience in feeding newborns with nucleotides-containing milk formulas. The article gives a comparison of nucleotides in the adapted formulas represented in the domestic market of the given products.Key words: children, feeding, nucleotides.

  6. Metagenomic analysis of viral diversity in respiratory samples from patients with respiratory tract infections in Kuwait.

    Science.gov (United States)

    Madi, Nada; Al-Nakib, Widad; Mustafa, Abu Salim; Habibi, Nazima

    2018-03-01

    A metagenomic approach based on target independent next-generation sequencing has become a known method for the detection of both known and novel viruses in clinical samples. This study aimed to use the metagenomic sequencing approach to characterize the viral diversity in respiratory samples from patients with respiratory tract infections. We have investigated 86 respiratory samples received from various hospitals in Kuwait between 2015 and 2016 for the diagnosis of respiratory tract infections. A metagenomic approach using the next-generation sequencer to characterize viruses was used. According to the metagenomic analysis, an average of 145, 019 reads were identified, and 2% of these reads were of viral origin. Also, metagenomic analysis of the viral sequences revealed many known respiratory viruses, which were detected in 30.2% of the clinical samples. Also, sequences of non-respiratory viruses were detected in 14% of the clinical samples, while sequences of non-human viruses were detected in 55.8% of the clinical samples. The average genome coverage of the viruses was 12% with the highest genome coverage of 99.2% for respiratory syncytial virus, and the lowest was 1% for torque teno midi virus 2. Our results showed 47.7% agreement between multiplex Real-Time PCR and metagenomics sequencing in the detection of respiratory viruses in the clinical samples. Though there are some difficulties in using this method to clinical samples such as specimen quality, these observations are indicative of the promising utility of the metagenomic sequencing approach for the identification of respiratory viruses in patients with respiratory tract infections. © 2017 Wiley Periodicals, Inc.

  7. Validation of the Sexual Orientation Microaggression Inventory in Two Diverse Samples of LGBTQ Youth.

    Science.gov (United States)

    Swann, Gregory; Minshew, Reese; Newcomb, Michael E; Mustanski, Brian

    2016-08-01

    Critical race theory asserts that microaggressions, or low-level, covert acts of aggression, are commonplace in the lives of people of color. These theorists also assert a taxonomy of microaggressions, which includes "microassaults," "microinsults," and "microinvalidations". The theory of microaggressions has been adopted by researchers of LGBTQ communities. This study investigated the three-factor taxonomy as it relates to a diverse sample of LGBTQ youth using the newly developed Sexual Orientation Microaggression Inventory (SOMI). Exploratory factor analysis was used to determine the number of factors that exist in SOMI in a sample of 206 LGBTQ-identifying youth. Follow up confirmatory factor analyses were conducted in order to compare single-factor, unrestricted four-factor, second-order, and bi-factor models in a separate sample of 363 young men who have sex with men. The best fitting model was used to predict victimization, depressive symptoms, and depression diagnosis in order to test validity. The best fitting model was a bi-factor model utilizing 19 of the original 26 items with a general factor and four specific factors representing anti-gay attitudes ("microinsults"), denial of homosexuality, heterosexism ("microinvalidations"), and societal disapproval ("microassaults"). Reliability analyses found that the majority of reliable variance was accounted for by the general factor. The general factor was a significant predictor of victimization and depressive symptoms, as well as unrelated to social desirability, suggesting convergent, criterion-related, and discriminant validity. SOMI emerged as a scale with evidence of validity for assessing exposure to microaggressions in a diverse sample of LGBTQ youth.

  8. Molecular investigation of the distribution, abundance and diversity of the genus Pseudoalteromonas in marine samples.

    Science.gov (United States)

    Skovhus, Torben L; Holmström, Carola; Kjelleberg, Staffan; Dahllöf, Ingela

    2007-08-01

    The genus Pseudoalteromonas has attracted interest because it has frequently been found in association with eukaryotic hosts, and because many Pseudoalteromonas species produce biologically active compounds. One distinct group of Pseudoalteromonas species is the antifouling subgroup containing Pseudoalteromonas tunicata and Ps. ulvae, which both produce extracellular compounds that inhibit growth and colonization by different marine organisms. PCR primers targeting the 16S rRNA gene of the genus Pseudoalteromonas and the antifouling subgroup were developed and applied in this study. Real-time quantitative PCR (qPCR) was applied to determine the relative bacterial abundance of the genus and the antifouling subgroup, and denaturing gradient gel electrophoresis (DGGE) was applied to study the diversity of the genus in 11 different types of marine samples from Danish coastal waters. The detection of Ps. tunicata that contain the antifouling subgroup was achieved through specific PCR amplification of the antibacterial protein gene (alpP). The Pseudoalteromonas species accounted for 1.6% of the total bacterial abundance across all samples. The Pseudoalteromonas diversity on the three unfouled marine organisms Ciona intestinalis, Ulva lactuca and Ulvaria fusca was found to be low, and Ps. tunicata was only detected on these three hosts, which all contain accessible cellulose polymers in their cell walls.

  9. Genetic diversity and parentage in farmer varieties of cacao (Theobroma cacao L.) from Honduras and Nicaragua as revealed by Single Nucleotide Polymorphism (SNP) markers

    Science.gov (United States)

    Cacao (Theobroma cacao L.) is the main source for chocolate with an annual production of four million tons worldwide. This Neotropical tree crop was domesticated in Mesoamerica as far back as 3,000 years ago. Knowledge of genetic diversity and population structure in farmer varieties of cacao in the...

  10. Genetic Characterization of Cylindrospermopsis raciborskii (Cyanobacteria) Isolates from Diverse Geographic Origins Based on nifH and cpcBA-IGS Nucleotide Sequence Analysis

    OpenAIRE

    Dyble, Julianne; Paerl, Hans W.; Neilan, Brett A.

    2002-01-01

    Isolates of the toxic, N2-fixing species Cylindrospermopsis raciborskii from various geographic locations were analyzed with respect to their genetic diversity based on the nifH and cpcBA-IGS genes. Gene sequences clustered according to their geographic origin, with the nifH sequences separating into European, Australian, and American groups and the cpcBA-IGS sequences separating into American and European or Australian groups. PCR primers for both genes were designed to exclusively amplify D...

  11. Exploring Body Image, Contraceptive Use, and Sexual Health Outcomes Among an Ethnically Diverse Sample of Women.

    Science.gov (United States)

    Ramseyer Winter, Virginia; Ruhr, Lindsay; Pevehouse, Danielle; Pilgrim, Sarah

    2018-01-05

    This cross-sectional study examined the links between body appreciation, contraceptive use, and sexual health outcomes. Body appreciation has been shown to influence contraceptive use in homogenous samples of women. However, a common problem in body image literature is a lack of racial and ethnic diversity with regard to sample; this study was able to take steps toward overcoming that limitation. A sample of 499 women aged 18-56 (M = 26.24; SD = 6.15) was recruited via Reddit.com-White (29.3%, n = 120), Asian (19%, n = 78), Black (17.3%, n = 73), multiracial (13.9%, n = 57), and Latina (13.9%, n = 57). Covariates included race/ethnicity, body size as measured by body mass index, relationship status, age, sexual orientation, and education level. Results indicated that higher levels of body appreciation were related to a higher likelihood of using non-barrier contraception. Regarding the covariates, race, relationship status, age, and education were related to non-barrier contraceptive use and age was related to dual contraceptive use. Further exploration is needed to determine how body appreciation may affect contraceptive use and sexual health outcomes and how these differ by race/ethnicity.

  12. Forgiveness, depression, and suicidal behavior among a diverse sample of college students.

    Science.gov (United States)

    Hirsch, Jameson K; Webb, Jon R; Jeglic, Elizabeth L

    2011-09-01

    Depression and suicide are significant public health concerns for college-age young adults. Meaning-based characteristics, such as forgiveness, a voluntary coping process involving offering, feeling, or seeking a change from negative to positive cognitions, behaviors, and affect toward a transgressor, may buffer such poor mental health outcomes. Utilizing mediation analyses, we examined cross-sectional associations between forgiveness, depression, and suicidal behavior in a diverse student sample reporting mild to severe depressive symptoms. The effect of self-forgiveness on suicidal behavior was fully mediated by depression; self-forgiveness was associated with depression and, in turn, with suicidal behavior. Forgiveness of others was directly associated with suicidal behavior. Prospective research is needed, yet self and other-forgiveness may be appropriate targets for promotion in suicide prevention efforts. © 2011 Wiley Periodicals, Inc.

  13. Diversity of microorganisms isolated from the soil sample surround Chroogomphus rutilus in the Beijing region

    DEFF Research Database (Denmark)

    Wang, P; Liu, Y; Yin, Y

    2011-01-01

    to isolate and classify beneficial microorganisms that could affect its growth, which could be used in future research on artificial cultivation. In total, 342 isolates were isolated from soil samples collected around a C. rutilus colony in the Beijing region. Of these, 22 bacterial and 14 fungal isolates......Artificially cultivating Chroogomphus rutilus is too inefficient to be commercially feasible. Furthermore, isolating C. rutilus mycelia in the wild is difficult. Thus, it is important to de-termine the natural habitat of its fruiting body. This study focused on the ecology of the C. rutilus habitat....... Using internal transcribed spacer (ITS) sequence analysis, fungal isolates were divided into four monophyletic clusters: Penicillium, Trichoderma, Mortierella, and Bionectria. Moreover, the phylogenetic diversity of these isolates was analysed. The results indicated that numerous microorganisms were...

  14. Single-Nucleotide Polymorphisms Reveal Spatial Diversity Among Clones of Yersinia pestis During Plague Outbreaks in Colorado and the Western United States.

    Science.gov (United States)

    Lowell, Jennifer L; Antolin, Michael F; Andersen, Gary L; Hu, Ping; Stokowski, Renee P; Gage, Kenneth L

    2015-05-01

    In western North America, plague epizootics caused by Yersinia pestis appear to sweep across landscapes, primarily infecting and killing rodents, especially ground squirrels and prairie dogs. During these epizootics, the risk of Y. pestis transmission to humans is highest. While empirical models that include climatic conditions and densities of rodent hosts and fleas can predict when epizootics are triggered, bacterial transmission patterns across landscapes, and the scale at which Y. pestis is maintained in nature during inter-epizootic periods, are poorly defined. Elucidating the spatial extent of Y. pestis clones during epizootics can determine whether bacteria are propagated across landscapes or arise independently from local inter-epizootic maintenance reservoirs. We used DNA microarray technology to identify single-nucleotide polymorphisms (SNPs) in 34 Y. pestis isolates collected in the western United States from 1980 to 2006, 21 of which were collected during plague epizootics in Colorado. Phylogenetic comparisons were used to elucidate the hypothesized spread of Y. pestis between the mountainous Front Range and the eastern plains of northern Colorado during epizootics. Isolates collected from across the western United States were included for regional comparisons. By identifying SNPs that mark individual clones, our results strongly suggest that Y. pestis is maintained locally and that widespread epizootic activity is caused by multiple clones arising independently at small geographic scales. This is in contrast to propagation of individual clones being transported widely across landscapes. Regionally, our data are consistent with the notion that Y. pestis diversifies at relatively local scales following long-range translocation events. We recommend that surveillance and prediction by public health and wildlife management professionals focus more on models of local or regional weather patterns and ecological factors that may increase risk of widespread

  15. Type II Supernova Spectral Diversity. I. Observations, Sample Characterization, and Spectral Line Evolution

    Science.gov (United States)

    Gutiérrez, Claudia P.; Anderson, Joseph P.; Hamuy, Mario; Morrell, Nidia; González-Gaitan, Santiago; Stritzinger, Maximilian D.; Phillips, Mark M.; Galbany, Lluis; Folatelli, Gastón; Dessart, Luc; Contreras, Carlos; Della Valle, Massimo; Freedman, Wendy L.; Hsiao, Eric Y.; Krisciunas, Kevin; Madore, Barry F.; Maza, José; Suntzeff, Nicholas B.; Prieto, Jose Luis; González, Luis; Cappellaro, Enrico; Navarrete, Mauricio; Pizzella, Alessandro; Ruiz, Maria T.; Smith, R. Chris; Turatto, Massimo

    2017-11-01

    We present 888 visual-wavelength spectra of 122 nearby type II supernovae (SNe II) obtained between 1986 and 2009, and ranging between 3 and 363 days post-explosion. In this first paper, we outline our observations and data reduction techniques, together with a characterization based on the spectral diversity of SNe II. A statistical analysis of the spectral matching technique is discussed as an alternative to nondetection constraints for estimating SN explosion epochs. The time evolution of spectral lines is presented and analyzed in terms of how this differs for SNe of different photometric, spectral, and environmental properties: velocities, pseudo-equivalent widths, decline rates, magnitudes, time durations, and environment metallicity. Our sample displays a large range in ejecta expansion velocities, from ˜9600 to ˜1500 km s-1 at 50 days post-explosion with a median {{{H}}}α value of 7300 km s-1. This is most likely explained through differing explosion energies. Significant diversity is also observed in the absolute strength of spectral lines, characterized through their pseudo-equivalent widths. This implies significant diversity in both temperature evolution (linked to progenitor radius) and progenitor metallicity between different SNe II. Around 60% of our sample shows an extra absorption component on the blue side of the {{{H}}}α P-Cygni profile (“Cachito” feature) between 7 and 120 days since explosion. Studying the nature of Cachito, we conclude that these features at early times (before ˜35 days) are associated with Si II λ 6355, while past the middle of the plateau phase they are related to high velocity (HV) features of hydrogen lines. This paper includes data gathered with the 6.5 m Magellan Telescopes located at Las Campanas Observatory, Chile; and the Gemini Observatory, Cerro Pachon, Chile (Gemini Program GS-2008B-Q-56). Based on observations collected at the European Organisation for Astronomical Research in the Southern Hemisphere

  16. Genetic characterization of Cylindrospermopsis raciborskii (cyanobacteria) isolates from diverse geographic origins based on nifH and cpcBA-IGS nucleotide sequence analysis.

    Science.gov (United States)

    Dyble, Julianne; Paerl, Hans W; Neilan, Brett A

    2002-05-01

    Isolates of the toxic, N(2)-fixing species Cylindrospermopsis raciborskii from various geographic locations were analyzed with respect to their genetic diversity based on the nifH and cpcBA-IGS genes. Gene sequences clustered according to their geographic origin, with the nifH sequences separating into European, Australian, and American groups and the cpcBA-IGS sequences separating into American and European or Australian groups. PCR primers for both genes were designed to exclusively amplify DNA from Cylindrospermopsis species, and an additional primer set for cpcBA-IGS was designed to specifically amplify the American C. raciborskii strains.

  17. Epidemiology of mixed martial arts and youth violence in an ethnically diverse sample.

    Science.gov (United States)

    Hishinuma, Earl S; Umemoto, Karen N; Nguyen, Toan Gia; Chang, Janice Y; Bautista, Randy Paul M

    2012-01-01

    Mixed martial arts' (MMAs) growing international popularity has rekindled the discussion on the advantages (e.g., exercise) and disadvantages (e.g., possible injury) of contact sports. This study was the first of its kind to examine the psychosocial aspects of MMA and youth violence using an epidemiologic approach with an Asian American and Pacific Islander (AAPI) adolescent sample (N = 881). The results were consistent with the increased popularity of MMA with 52% (adolescent males = 73%, adolescent females = 39%) enjoying watching MMA and 24% (adolescent males = 39%, adolescent females = 13%) practicing professional fight moves with friends. Although statistically significant ethnic differences were found for the two MMA items on a bivariate level, these findings were not statistically significant when considering other variables in the model. The bivariate results revealed a cluster of risk-protective factors. Regarding the multiple regression findings, although enjoying watching MMA remained associated with positive attitudes toward violence and practicing fight moves remained associated with negative out-group orientation, the MMA items were not associated with unique variances of youth violence perpetration and victimization. Implications included the need for further research that includes other diverse samples, more comprehensive and objective MMA and violence measures, and observational and intervention longitudinal studies.

  18. Bacterial Composition and Diversity in Breast Milk Samples from Mothers Living in Taiwan and Mainland China

    Directory of Open Access Journals (Sweden)

    Shiao-Wen Li

    2017-05-01

    Full Text Available Human breast milk is widely recognized as the best source of nutrients for healthy growth and development of infants; it contains a diverse microbiota. Here, we characterized the diversity of the microbiota in the breast milk of East Asian women and assessed whether delivery mode influenced the microbiota in the milk of healthy breast-feeding mothers. We profiled the microbiota in breast milk samples collected from 133 healthy mothers in Taiwan and in six regions of mainland China (Central, East, North, Northeast, South, and Southwest China by using 16S rRNA pyrosequencing. Lactation stage (months postpartum when the milk sample was collected and maternal body mass index did not influence the breast milk microbiota. Bacterial composition at the family level differed significantly among samples from the seven geographical regions. The five most predominant bacterial families were Streptococcaceae (mean relative abundance: 24.4%, Pseudomonadaceae (14.0%, Staphylococcaceae (12.2%, Lactobacillaceae (6.2%, and Oxalobacteraceae (4.8%. The microbial profiles were classified into three clusters, driven by Staphylococcaceae (abundance in Cluster 1: 42.1%, Streptococcaceae (Cluster 2: 48.5%, or Pseudomonadaceae (Cluster 3: 26.5%. Microbial network analysis at the genus level revealed that the abundances of the Gram-positive Staphylococcus, Streptococcus, and Rothia were negatively correlated with those of the Gram-negative Acinetobacter, Bacteroides, Halomonas, Herbaspirillum, and Pseudomonas. Milk from mothers who had undergone Caesarian section (C-section group had a significantly higher abundance of Lactobacillus (P < 0.05 and a higher number of unique unclassified operational taxonomic units (OTUs (P < 0.001 than that from mothers who had undergone vaginal delivery (vaginal group. These findings revealed that (i geographic differences in the microbial profiles were found in breast milk from mothers living in Taiwan and mainland China, (ii the

  19. How taxonomic diversity, community structure, and sample size determine the reliability of higher taxon surrogates.

    Science.gov (United States)

    Neeson, Thomas M; Van Rijn, Itai; Mandelik, Yael

    2013-07-01

    Ecologists and paleontologists often rely on higher taxon surrogates instead of complete inventories of biological diversity. Despite their intrinsic appeal, the performance of these surrogates has been markedly inconsistent across empirical studies, to the extent that there is no consensus on appropriate taxonomic resolution (i.e., whether genus- or family-level categories are more appropriate) or their overall usefulness. A framework linking the reliability of higher taxon surrogates to biogeographic setting would allow for the interpretation of previously published work and provide some needed guidance regarding the actual application of these surrogates in biodiversity assessments, conservation planning, and the interpretation of the fossil record. We developed a mathematical model to show how taxonomic diversity, community structure, and sampling effort together affect three measures of higher taxon performance: the correlation between species and higher taxon richness, the relative shapes and asymptotes of species and higher taxon accumulation curves, and the efficiency of higher taxa in a complementarity-based reserve-selection algorithm. In our model, higher taxon surrogates performed well in communities in which a few common species were most abundant, and less well in communities with many equally abundant species. Furthermore, higher taxon surrogates performed well when there was a small mean and variance in the number of species per higher taxa. We also show that empirically measured species-higher-taxon correlations can be partly spurious (i.e., a mathematical artifact), except when the species accumulation curve has reached an asymptote. This particular result is of considerable practical interest given the widespread use of rapid survey methods in biodiversity assessment and the application of higher taxon methods to taxa in which species accumulation curves rarely reach an asymptote, e.g., insects.

  20. Energy drink use, problem drinking and drinking motives in a diverse sample of Alaskan college students.

    Science.gov (United States)

    Skewes, Monica C; Decou, Christopher R; Gonzalez, Vivian M

    2013-01-01

    Recent research has identified the use of caffeinated energy drinks as a common, potentially risky behavior among college students that is linked to alcohol misuse and consequences. Research also suggests that energy drink consumption is related to other risky behaviors such as tobacco use, marijuana use and risky sexual activity. This research sought to examine the associations between frequency of energy drink consumption and problematic alcohol use, alcohol-related consequences, symptoms of alcohol dependence and drinking motives in an ethnically diverse sample of college students in Alaska. We also sought to examine whether ethnic group moderated these associations in the present sample of White, Alaska Native/American Indian and other ethnic minority college students. A paper-and-pencil self-report questionnaire was completed by a sample of 298 college students. Analysis of covariance (ANCOVA) was used to examine the effects of energy drink use, ethnic group and energy drink by ethnic group interactions on alcohol outcomes after controlling for variance attributed to gender, age and frequency of binge drinking. Greater energy drink consumption was significantly associated with greater hazardous drinking, alcohol consequences, alcohol dependence symptoms, drinking for enhancement motives and drinking to cope. There were no main effects of ethnic group, and there were no significant energy drink by ethnic group interactions. These findings replicate those of other studies examining the associations between energy drink use and alcohol problems, but contrary to previous research we did not find ethnic minority status to be protective. It is possible that energy drink consumption may serve as a marker for other health risk behaviors among students of various ethnic groups.

  1. Energy drink use, problem drinking and drinking motives in a diverse sample of Alaskan college students

    Directory of Open Access Journals (Sweden)

    Monica C. Skewes

    2013-08-01

    Full Text Available Background. Recent research has identified the use of caffeinated energy drinks as a common, potentially risky behaviour among college students that is linked to alcohol misuse and consequences. Research also suggests that energy drink consumption is related to other risky behaviours such as tobacco use, marijuana use and risky sexual activity. Objective. This research sought to examine the associations between frequency of energy drink consumption and problematic alcohol use, alcohol-related consequences, symptoms of alcohol dependence and drinking motives in an ethnically diverse sample of college students in Alaska. We also sought to examine whether ethnic group moderated these associations in the present sample of White, Alaska Native/American Indian and other ethnic minority college students. Design. A paper-and-pencil self-report questionnaire was completed by a sample of 298 college students. Analysis of covariance (ANCOVA was used to examine the effects of energy drink use, ethnic group and energy drink by ethnic group interactions on alcohol outcomes after controlling for variance attributed to gender, age and frequency of binge drinking. Results. Greater energy drink consumption was significantly associated with greater hazardous drinking, alcohol consequences, alcohol dependence symptoms, drinking for enhancement motives and drinking to cope. There were no main effects of ethnic group, and there were no significant energy drink by ethnic group interactions. Conclusion. These findings replicate those of other studies examining the associations between energy drink use and alcohol problems, but contrary to previous research we did not find ethnic minority status to be protective. It is possible that energy drink consumption may serve as a marker for other health risk behaviours among students of various ethnic groups.

  2. Detection of a diverse marine fish fauna using environmental DNA from seawater samples.

    Science.gov (United States)

    Thomsen, Philip Francis; Kielgast, Jos; Iversen, Lars Lønsmann; Møller, Peter Rask; Rasmussen, Morten; Willerslev, Eske

    2012-01-01

    Marine ecosystems worldwide are under threat with many fish species and populations suffering from human over-exploitation. This is greatly impacting global biodiversity, economy and human health. Intriguingly, marine fish are largely surveyed using selective and invasive methods, which are mostly limited to commercial species, and restricted to particular areas with favourable conditions. Furthermore, misidentification of species represents a major problem. Here, we investigate the potential of using metabarcoding of environmental DNA (eDNA) obtained directly from seawater samples to account for marine fish biodiversity. This eDNA approach has recently been used successfully in freshwater environments, but never in marine settings. We isolate eDNA from ½-litre seawater samples collected in a temperate marine ecosystem in Denmark. Using next-generation DNA sequencing of PCR amplicons, we obtain eDNA from 15 different fish species, including both important consumption species, as well as species rarely or never recorded by conventional monitoring. We also detect eDNA from a rare vagrant species in the area; European pilchard (Sardina pilchardus). Additionally, we detect four bird species. Records in national databases confirmed the occurrence of all detected species. To investigate the efficiency of the eDNA approach, we compared its performance with 9 methods conventionally used in marine fish surveys. Promisingly, eDNA covered the fish diversity better than or equal to any of the applied conventional methods. Our study demonstrates that even small samples of seawater contain eDNA from a wide range of local fish species. Finally, in order to examine the potential dispersal of eDNA in oceans, we performed an experiment addressing eDNA degradation in seawater, which shows that even small (100-bp) eDNA fragments degrades beyond detectability within days. Although further studies are needed to validate the eDNA approach in varying environmental conditions, our

  3. Frequency, Antimicrobial Resistance and Genetic Diversity of Klebsiella pneumoniae in Food Samples.

    Directory of Open Access Journals (Sweden)

    Yumei Guo

    Full Text Available This study aimed to assess the frequency of Klebsiella pneumoniae in food samples and to detect antibiotic resistance phenotypes, antimicrobial resistance genes and the molecular subtypes of the recovered isolates. A total of 998 food samples were collected, and 99 (9.9% K. pneumoniae strains were isolated; the frequencies were 8.2% (4/49 in fresh raw seafood, 13.8% (26/188 in fresh raw chicken, 11.4% (34/297 in frozen raw food and 7.5% (35/464 in cooked food samples. Antimicrobial resistance was observed against 16 antimicrobials. The highest resistance rate was observed for ampicillin (92.3%, followed by tetracycline (31.3%, trimethoprim-sulfamethoxazole (18.2%, and chloramphenicol (10.1%. Two K. pneumoniae strains were identified as extended-spectrum β-lactamase (ESBL-one strain had three beta-lactamases genes (blaSHV, blaCTX-M-1, and blaCTX-M-10 and one had only the blaSHV gene. Nineteen multidrug-resistant (MDR strains were detected; the percentage of MDR strains in fresh raw chicken samples was significantly higher than in other sample types (P<0.05. Six of the 18 trimethoprim-sulfamethoxazole-resistant strains carried the folate pathway inhibitor gene (dhfr. Four isolates were screened by PCR for quinolone resistance genes; aac(6'-Ib-cr, qnrB, qnrA and qnrS were detected. In addition, gyrA gene mutations such as T247A (Ser83Ile, C248T (Ser83Phe, and A260C (Asp87Ala and a parC C240T (Ser80Ile mutation were identified. Five isolates were screened for aminoglycosides resistance genes; aacA4, aacC2, and aadA1 were detected. Pulsed-field gel electrophoresis-based subtyping identified 91 different patterns. Our results indicate that food, especially fresh raw chicken, is a reservoir of antimicrobial-resistant K. pneumoniae, and the potential health risks posed by such strains should not be underestimated. Our results demonstrated high prevalence, antibiotic resistance rate and genetic diversity of K. pneumoniae in food in China. Improved

  4. Comparative Sequence and Structure Analysis Reveals the Conservation and Diversity of Nucleotide Positions and Their Associated Tertiary Interactions in the Riboswitches

    Science.gov (United States)

    Appasamy, Sri D.; Ramlan, Effirul Ikhwan; Firdaus-Raih, Mohd

    2013-01-01

    The tertiary motifs in complex RNA molecules play vital roles to either stabilize the formation of RNA 3D structure or to provide important biological functionality to the molecule. In order to better understand the roles of these tertiary motifs in riboswitches, we examined 11 representative riboswitch PDB structures for potential agreement of both motif occurrences and conservations. A total of 61 unique tertiary interactions were found in the reference structures. In addition to the expected common A-minor motifs and base-triples mainly involved in linking distant regions the riboswitch structures three highly conserved variants of A-minor interactions called G-minors were found in the SAM-I and FMN riboswitches where they appear to be involved in the recognition of the respective ligand’s functional groups. From our structural survey as well as corresponding structure and sequence alignments, the agreement between motif occurrences and conservations are very prominent across the representative riboswitches. Our analysis provide evidence that some of these tertiary interactions are essential components to form the structure where their sequence positions are conserved despite a high degree of diversity in other parts of the respective riboswitches sequences. This is indicative of a vital role for these tertiary interactions in determining the specific biological function of riboswitch. PMID:24040136

  5. Structure and function of nucleotide sugar transporters: Current progress

    NARCIS (Netherlands)

    Hadley, B.; Maggioni, A.; Ashikov, A.M.; Day, C.J.; Haselhorst, T.; Tiralongo, J.

    2014-01-01

    The proteomes of eukaryotes, bacteria and archaea are highly diverse due, in part, to the complex post-translational modification of protein glycosylation. The diversity of glycosylation in eukaryotes is reliant on nucleotide sugar transporters to translocate specific nucleotide sugars that are

  6. Island-wide diversity in single nucleotide polymorphisms of the Plasmodium vivax dihydrofolate reductase and dihydropteroate synthetase genes in Sri Lanka

    DEFF Research Database (Denmark)

    Schousboe, Mette L; Rajakaruna, Rupika S; Salanti, Ali

    2007-01-01

    into the level of drug pressure caused by SP use and presumably other antifolate drugs. In Sri Lanka, chloroquine (CQ) with primaquine (PQ) and SP with PQ is used as first and second line treatment, respectively, against uncomplicated Plasmodium falciparum and/or P. vivax infections. CQ/PQ is still efficacious...... against P. vivax infections, thus SP is rarely used and it is assumed that the prevalence of SNPs related to P. vivax SP resistance is low. However, this has not been assessed in Sri Lanka as in most other parts of Asia. This study describes the prevalence and distribution of SNPs related to P. vivax SP...... resistance across Sri Lanka. SUBJECTS AND METHODS: P. vivax-positive samples were collected from subjects presenting at government health facilities across nine of the major malaria endemic districts on the island. The samples were analysed for SNPs/haplotypes at codon 57, 58, 61 and 117 of the Pvdhfr gene...

  7. HapMap-based study of human soluble glutathione S-transferase enzymes: the role of natural selection in shaping the single nucleotide polymorphism diversity of xenobiotic-metabolizing genes.

    Science.gov (United States)

    Polimanti, Renato; Piacentini, Sara; Fuciarelli, Maria

    2011-10-01

    Glutathione S-transferase enzymes (GSTs; EC: 2.5.1.18) constitute the principal phase II superfamily, which plays a key role in cellular detoxification. GST genes are organized in chromosomal clusters; most of these genes are polymorphic, mainly due to single nucleotide substitutions. Different studies proved significant interethnic differences in GST allelic frequencies but, at present, the role of natural selection in human genetic variability of GSTs is poorly understood. The aim of this study is to investigate the role of natural selection in shaping single nucleotide polymorphism (SNP) diversity of soluble GST genes. Using the HapMap database, we analyzed the population differences in the soluble GST genes using the phasing data from unrelated individuals shared among 11 populations in the International HapMap project. A Fst-based selection test was applied to HapMap data to detect soluble GST loci under selection. Comparisons between GST gene polymorphisms among HapMap populations highlight that ethnicity is an influencing factor of GST genetic variability. By applying a genome scan based on F-statistics, we identified nine SNPs that present F-coefficients significantly more different than those expected under neutrality (rs2239892, rs3814309, rs7483, rs1571858, rs929166, rs11807, rs4715344, rs4715354, and rs3734431). Our study confirms that GST gene variation reflects human demographic history, but it also demonstrates that natural selection could shape the genetic profile of some GST SNPs. Moreover, the identification of human genome regions and targets of natural selection may have detected candidate genes for complex diseases. In analyzing the literature, we provide complex disease hypothesis (male infertility, embryotoxicity) for the identified GST SNPs.

  8. Randomized Controlled Trial of Attention Bias Modification in a Racially Diverse, Socially Anxious, Alcohol Dependent Sample

    Science.gov (United States)

    Clerkin, Elise M.; Magee, Joshua C.; Wells, Tony T.; Beard, Courtney; Barnett, Nancy P.

    2016-01-01

    Objective Attention biases may be an important treatment target for both alcohol dependence and social anxiety. This is the first ABM trial to investigate two (vs. one) targets of attention bias within a sample with co-occurring symptoms of social anxiety and alcohol dependence. Additionally, we used trial-level bias scores (TL-BS) to capture the phenomena of attention bias in a more ecologically valid, dynamic way compared to traditional attention bias scores. Method Adult participants (N=86; 41% Female; 52% African American; 40% White) with elevated social anxiety symptoms and alcohol dependence were randomly assigned to an 8-session training condition in this 2 (Social Anxiety ABM vs. Social Anxiety Control) by 2 (Alcohol ABM vs. Alcohol Control) design. Symptoms of social anxiety, alcohol dependence, and attention bias were assessed across time. Results Multilevel models estimated the trajectories for each measure within individuals, and tested whether these trajectories differed according to the randomized training conditions. Across time, there were significant or trending decreases in all attention TL-BS parameters (but not traditional attention bias scores) and most symptom measures. However, there were not significant differences in the trajectories of change between any ABM and control conditions for any symptom measures. Conclusions These findings add to previous evidence questioning the robustness of ABM and point to the need to extend the effects of ABM to samples that are racially diverse and/or have co-occurring psychopathology. The results also illustrate the potential importance of calculating trial-level attention bias scores rather than only including traditional bias scores. PMID:27591918

  9. Perceptions of care coordination in a population-based sample of diverse breast cancer patients.

    Science.gov (United States)

    Hawley, Sarah T; Janz, Nancy K; Lillie, Sarah E; Friese, Christopher R; Griggs, Jennifer J; Graff, John J; Hamilton, Ann S; Jain, Sarika; Katz, Steven J

    2010-12-01

    To identify factors associated with perceptions of care coordination in a diverse sample of breast cancer patients. Breast cancer patients reported to the metropolitan SEER registries of Detroit or Los Angeles from 6/05 to 2/07 were surveyed after diagnosis (N=2268, RR=72.4%). Outcomes were two dichotomous measures reflecting patient appraisal of care coordination during their treatment experience. Primary independent variables were race/ethnicity (white, African American, Latina-high acculturated, Latina-low acculturated) and health literacy (low, moderate, high). Logistic regression was used to evaluate factors associated with both measures of care coordination. 2148 subjects were included in the analytic dataset. 16.4% of women perceived low care coordination and 12.5% reported low satisfaction. Race/ethnicity was not significantly associated with care coordination. Women with low subjective health literacy were 3-4 times as likely as those with high health literacy to perceive low care coordination and low satisfaction with care coordination (OR=3.88; 95% CI: 2.78-5.41; OR=3.19 95% CI: 2.25-4.52, respectively). Many breast cancer patients positively appraised their care coordination, but patients with low health literacy perceived low care coordination. Providers should be aware of the health literacy deficits that may contribute to their patients' attitudes towards their breast cancer care coordination. Published by Elsevier Ireland Ltd.

  10. Diversity of microorganisms isolated from the soil sample surround Chroogomphus rutilus in the Beijing region.

    Science.gov (United States)

    Wang, Peng; Liu, Yu; Yin, Yonggang; Jin, Haojie; Wang, Shouxian; Xu, Feng; Zhao, Shuang; Geng, Xiaoli

    2011-03-02

    Artificially cultivating Chroogomphus rutilus is too inefficient to be commercially feasible. Furthermore, isolating C. rutilus mycelia in the wild is difficult. Thus, it is important to determine the natural habitat of its fruiting body. This study focused on the ecology of the C. rutilus habitat to isolate and classify beneficial microorganisms that could affect its growth, which could be used in future research on artificial cultivation. In total, 342 isolates were isolated from soil samples collected around a C. rutilus colony in the Beijing region. Of these, 22 bacterial and 14 fungal isolates were selected for sequencing and phylogenetic analysis, based on their growth characteristics and colony morphology. Using 16S rRNA gene sequence analysis, the bacterial isolates were divided into two monophyletic clusters which had significant hits to the genera Bacillus and Pseudomonas, respectively. Using internal transcribed spacer (ITS) sequence analysis, fungal isolates were divided into four monophyletic clusters: Penicillium, Trichoderma, Mortierella, and Bionectria. Moreover, the phylogenetic diversity of these isolates was analysed. The results indicated that numerous microorganisms were present in C. rutilus habitat. This was the first reported examination of the microbiological ecology of C. rutilus.

  11. Precuneus proportions and cortical folding: A morphometric evaluation on a racially diverse human sample.

    Science.gov (United States)

    Bruner, Emiliano; Pereira-Pedro, Ana Sofia; Chen, Xu; Rilling, James K

    2017-05-01

    Recent analyses have suggested that the size and proportions of the precuneus are remarkably variable among adult humans, representing a major source of geometrical difference in midsagittal brain morphology. The same area also represents the main midsagittal brain difference between humans and chimpanzees, being more expanded in our species. Enlargement of the upper parietal surface is a specific feature of Homo sapiens, when compared with other fossil hominids, suggesting the involvement of these cortical areas in recent modern human evolution. Here, we provide a survey on midsagittal brain morphology by investigating whether precuneus size represents the largest component of variance within a larger and racially diverse sample of 265 adult humans. Additionally, we investigate the relationship between precuneus shape variation and folding patterns. Precuneus proportions are confirmed to be a major source of human brain variation even when racial variability is considered. Larger precuneus size is associated with additional precuneal gyri, generally in its anterior district. Spatial variation is most pronounced in the dorsal areas, with no apparent differences between hemispheres, between sexes, or among different racial groups. These dorsal areas integrate somatic and visual information together with the lateral elements of the parietal cortex, representing a crucial node for self-centered mental imagery. The histological basis and functional significance of this intra-specific variation in the upper precuneus remains to be evaluated. Copyright © 2017 Elsevier GmbH. All rights reserved.

  12. Prevalence and genetic diversity of Aichi virus strains in stool samples from community and hospitalized patients.

    Science.gov (United States)

    Ambert-Balay, K; Lorrot, M; Bon, F; Giraudon, H; Kaplon, J; Wolfer, M; Lebon, P; Gendrel, D; Pothier, P

    2008-04-01

    Aichi virus has been proposed as a causative agent of gastroenteritis. A total of 457 stool specimens from children hospitalized with acute diarrhea and 566 stool specimens from adults and children involved in 110 gastroenteritis outbreaks were screened for the presence of Aichi virus by reverse transcription-PCR (RT-PCR) amplification of the genomic region of the 3C and 3D (3CD) nonstructural proteins. Our results show a low incidence of Aichi virus in pediatric samples and the existence of mixed infections with other microbiological agents in some cases. From the outbreak survey, it appears that the presence of Aichi virus is an indicator of mixed infections causing gastroenteritis outbreaks and that it could be involved in half of the oyster-associated outbreaks. A second RT-PCR was developed to amplify a part of the VP1 gene. The phylogenetic analysis showed a good correlation between the two classifications based on 3CD and VP1 gene sequences and revealed the prevalence of genotype A in France. It also allowed us to partially describe an Aichi virus strain that could represent a new genotype, thus suggesting the existence of a certain diversity.

  13. Optimal protein extraction methods from diverse sample types for protein profiling by using Two-Dimensional Electrophoresis (2DE).

    Science.gov (United States)

    Tan, A A; Azman, S N; Abdul Rani, N R; Kua, B C; Sasidharan, S; Kiew, L V; Othman, N; Noordin, R; Chen, Y

    2011-12-01

    There is a great diversity of protein samples types and origins, therefore the optimal procedure for each sample type must be determined empirically. In order to obtain a reproducible and complete sample presentation which view as many proteins as possible on the desired 2DE gel, it is critical to perform additional sample preparation steps to improve the quality of the final results, yet without selectively losing the proteins. To address this, we developed a general method that is suitable for diverse sample types based on phenolchloroform extraction method (represented by TRI reagent). This method was found to yield good results when used to analyze human breast cancer cell line (MCF-7), Vibrio cholerae, Cryptocaryon irritans cyst and liver abscess fat tissue. These types represent cell line, bacteria, parasite cyst and pus respectively. For each type of samples, several attempts were made to methodically compare protein isolation methods using TRI-reagent Kit, EasyBlue Kit, PRO-PREP™ Protein Extraction Solution and lysis buffer. The most useful protocol allows the extraction and separation of a wide diversity of protein samples that is reproducible among repeated experiments. Our results demonstrated that the modified TRI-reagent Kit had the highest protein yield as well as the greatest number of total proteins spots count for all type of samples. Distinctive differences in spot patterns were also observed in the 2DE gel of different extraction methods used for each type of sample.

  14. Genetic diversity and structure found in samples of Eritrean bread wheat

    DEFF Research Database (Denmark)

    Desta, Zeratsion Abera; Orabi, Jihad; Jahoor, Ahmed

    2014-01-01

    Genetic diversity and structure plays a key role in the selection of parents for crosses in plant breeding programmes. The aim of the present study was to analyse the genetic diversity and structure of Eritrean bread wheat accessions. We analysed 284 wheat accessions from Eritrea using 30 simple...... major groups. This is the first report of the genetic diversity and structure of Eritrean bread wheat....

  15. Detection of a diverse marine fish fauna using environmental DNA from seawater samples.

    Directory of Open Access Journals (Sweden)

    Philip Francis Thomsen

    Full Text Available Marine ecosystems worldwide are under threat with many fish species and populations suffering from human over-exploitation. This is greatly impacting global biodiversity, economy and human health. Intriguingly, marine fish are largely surveyed using selective and invasive methods, which are mostly limited to commercial species, and restricted to particular areas with favourable conditions. Furthermore, misidentification of species represents a major problem. Here, we investigate the potential of using metabarcoding of environmental DNA (eDNA obtained directly from seawater samples to account for marine fish biodiversity. This eDNA approach has recently been used successfully in freshwater environments, but never in marine settings. We isolate eDNA from ½-litre seawater samples collected in a temperate marine ecosystem in Denmark. Using next-generation DNA sequencing of PCR amplicons, we obtain eDNA from 15 different fish species, including both important consumption species, as well as species rarely or never recorded by conventional monitoring. We also detect eDNA from a rare vagrant species in the area; European pilchard (Sardina pilchardus. Additionally, we detect four bird species. Records in national databases confirmed the occurrence of all detected species. To investigate the efficiency of the eDNA approach, we compared its performance with 9 methods conventionally used in marine fish surveys. Promisingly, eDNA covered the fish diversity better than or equal to any of the applied conventional methods. Our study demonstrates that even small samples of seawater contain eDNA from a wide range of local fish species. Finally, in order to examine the potential dispersal of eDNA in oceans, we performed an experiment addressing eDNA degradation in seawater, which shows that even small (100-bp eDNA fragments degrades beyond detectability within days. Although further studies are needed to validate the eDNA approach in varying environmental

  16. Quantitative measurement of odor detection thresholds using an air dilution olfactometer, and association with genetic variants in a sample of diverse ancestry

    Directory of Open Access Journals (Sweden)

    Gillian R. Cook

    2014-11-01

    Full Text Available Genetic association studies require a quantitative and reliable method for odor threshold assessment in order to examine the contribution of genetic variants to complex olfactory phenotypes. Our main goal was to assess the feasibility of a portable Scentroid air dilution olfactometer for use in such studies. Using the Scentroid SM110C and the SK5 n-butanol Sensitivity Kit (IDES Canada Inc., n-butanol odor thresholds were determined for 182 individuals of diverse ancestry (mean age: 20.4 ± 2.5 years; n = 128 female; n = 54 male. Threshold scores from repeat participants were used to calculate a test–retest reliability coefficient, which was statistically significant (r = 0.754, p < 0.001, n = 29, indicating that the Scentroid provides reliable estimates of odor thresholds. In addition, we performed a preliminary genetic analysis evaluating the potential association of n-butanol odor thresholds to six single-nucleotide polymorphisms (SNPs putatively involved in general olfactory sensitivity (GOS. The results of multiple linear regression analysis revealed no significant association between the SNPs tested and threshold scores. However, our sample size was relatively small, and our study was only powered to identify genetic markers with strong effects on olfactory sensitivity. Overall, we find that the Scentroid provides reliable quantitative measures of odor detection threshold and is well suited for genetic studies of olfactory sensitivity.

  17. How does host ecology influence sampling effort in parasite diversity estimates? A case study using Neotropical freshwater fishes.

    Science.gov (United States)

    Yamada, Fábio Hideki; Takemoto, Ricardo Massato

    2017-06-01

    Accurately estimating biodiversity is fundamental to ecological understanding and prediction. Helminthes are often neglected in biodiversity estimates and when included are often underestimated. Here we examine how sampling effort affects estimates of parasite diversity in an assemblage of freshwater fish from a floodplain in Brazil. We also examine how ecological and behavioral factors influence the sampling effort necessary to accurately estimate the parasite diversity associated with a fish species. We use our dataset to suggest that host species with wide geographic distribution (i.e., long migrations), gregarious behavior (i.e., shoal), larger body size, higher population density, wide diet breadth (i.e., omnivorous), and autochthonous origin, increase the effort necessary to estimate the total diversity of parasites. However, estimating this parasitic fauna has several restrictions and limitations, due to the highly complex of the floodplain ecosystems, with non-linear and non-random responses.

  18. The effects of forest conversion to oil palm on ground-foraging ant communities depend on beta diversity and sampling grain.

    Science.gov (United States)

    Wang, Wendy Y; Foster, William A

    2015-08-01

    Beta diversity - the variation in species composition among spatially discrete communities - and sampling grain - the size of samples being compared - may alter our perspectives of diversity within and between landscapes before and after agricultural conversion. Such assumptions are usually based on point comparisons, which do not accurately capture actual differences in total diversity. Beta diversity is often not rigorously examined. We investigated the beta diversity of ground-foraging ant communities in fragmented oil palm and forest landscapes in Sabah, Malaysia, using diversity metrics transformed from Hill number equivalents to remove dependences on alpha diversity. We compared the beta diversities of oil palm and forest, across three hierarchically nested sampling grains. We found that oil palm and forest communities had a greater percentage of total shared species when larger samples were compared. Across all grains and disregarding relative abundances, there was higher beta diversity of all species among forest communities. However, there were higher beta diversities of common and very abundant (dominant) species in oil palm as compared to forests. Differences in beta diversities between oil palm and forest were greatest at the largest sampling grain. Larger sampling grains in oil palm may generate bigger species pools, increasing the probability of shared species with forest samples. Greater beta diversity of all species in forest may be attributed to rare species. Oil palm communities may be more heterogeneous in common and dominant species because of variable community assembly events. Rare and also common species are better captured at larger grains, boosting differences in beta diversity between larger samples of forest and oil palm communities. Although agricultural landscapes support a lower total diversity than natural forests, diversity especially of abundant species is still important for maintaining ecosystem stability. Diversity in

  19. Demonstration/Validation of Incremental Sampling at Two Diverse Military Ranges and Development of an Incremental Sampling Tool

    Science.gov (United States)

    2010-06-01

    characterize ten decision units $62,725 $39,500 $18,900 E2S2 - June 20102 2 –40National Defense Center for Energy and Environment Validation of EVC Soil...Stick • EVC Soil Stick used in Fort Lewis to collect eight replicate samples (0-2.5 cm depth) of 100 increments each • Same decision unit as...Energy and Environment Fort Lewis Live-Fire Laboratory Replicates NG Results Using EVC Tool (mg/kg) Sample Type Replicates Mean Std Dev % RSD 1 2 3

  20. The Effects of Dating Violence, Substance Use and Risky Sexual Behavior among a Diverse Sample of Illinois Youth

    Science.gov (United States)

    Alleyne, Binta; Coleman-Cowger, Victoria H.; Crown, Laurel; Gibbons, Maya A.; Vines, Linda N.

    2011-01-01

    This study examines the relationship between dating violence, forced sexual intercourse (FSI), and four measures of sexual risk taking (i.e., age at first sex, number of recent (within the last three months) sex partners, alcohol/drug use at last sex, and condom use at last sex) among a sample of 1124 ethnically diverse sexually active adolescents…

  1. Understanding Differences in College Persistence: A Longitudinal Examination of Financial Circumstances, Family Obligations, and Discrimination in an Ethnically Diverse Sample

    Science.gov (United States)

    Witkow, Melissa R.; Huynh, Virginia; Fuligni, Andrew J.

    2015-01-01

    Ethnic and generational differences in motivation and achievement have been well-established. However, minimal research has examined the role of social factors on educational outcomes among individuals from diverse backgrounds. With a longitudinal sample of 408 Latino, Asian, and European-American students, we examine family, discrimination, and…

  2. "Do You Trust Him?" Children's Trust Beliefs and Developmental Trajectories of Aggressive Behavior in an Ethnically Diverse Sample

    Science.gov (United States)

    Malti, Tina; Averdijk, Margit; Ribeaud, Denis; Rotenberg, Ken J.; Eisner, Manuel P.

    2013-01-01

    This study investigated the role of trust beliefs (i.e., trustworthiness, trustfulness) on aggression trajectories in a four-wave longitudinal study using an ethnically diverse sample of 8- to 11-year-old children (N = 1,028), as well as the risk profiles of low trust beliefs and low socioeconomic status on aggression trajectories. At Time 1 to…

  3. Impact of habitat diversity on the sampling effort required for the assessment of river fish communities and IBI

    NARCIS (Netherlands)

    Van Liefferinge, C.; Simoens, I.; Vogt, C.; Cox, T.J.S.; Breine, J.; Ercken, D.; Goethals, P.; Belpaire, C.; Meire, P.

    2010-01-01

    The spatial variation in the fish communities of four small Belgian rivers with variable habitat diversity was investigated by electric fishing to define the minimum sampling distance required for optimal fish stock assessment and determination of the Index of Biotic Integrity. This study shows that

  4. Feeding Practices and Styles Used by a Diverse Sample of Low-Income Parents of Preschool-age Children

    Science.gov (United States)

    Ventura, Alison K.; Gromis, Judy C.; Lohse, Barbara

    2010-01-01

    Objective: To describe the feeding practices and styles used by a diverse sample of low-income parents of preschool-age children. Design: Thirty- to 60-minute meetings involving a semistructured interview and 2 questionnaires administered by the interviewer. Setting: Low-income communities in Philadelphia, PA. Participants: Thirty-two parents of…

  5. Propionibacterium acnes: disease-causing agent or common contaminant? Detection in diverse patient samples by next generation sequencing

    DEFF Research Database (Denmark)

    Mollerup, Sarah; Friis-Nielsen, Jens; Vinner, Lasse

    2016-01-01

    Propionibacterium acnes is the most abundant bacterium on human skin, particularly in sebaceous areas. P. acnes is suggested to be an opportunistic pathogen involved in the development of diverse medical conditions, but is also a proven contaminant of human samples and surgical wounds. Its...... significance as a pathogen is consequently a matter of debate.In the present study we investigated the presence of P. acnes DNA in 250 next generation sequencing datasets generated from 180 samples of 20 different sample types, mostly of cancerous origin. The samples were either subjected to microbial...... enrichment, involving nuclease treatment to reduce the amount of host nucleic acids, or shotgun-sequenced.We detected high proportions of P. acnes in enriched samples, particularly skin derived and other tissue samples, with levels being higher in enriched compared to shotgun-sequenced samples. P. acnes...

  6. Propionibacterium acnes: disease-causing agent or common contaminant? Detection in diverse patient samples by next generation sequencing

    DEFF Research Database (Denmark)

    Mollerup, Sarah; Friis-Nielsen, Jens; Vinner, Lasse

    2016-01-01

    Propionibacterium acnes is the most abundant bacterium on human skin, particularly in sebaceous areas. P. acnes is suggested to be an opportunistic pathogen involved in the development of diverse medical conditions, but is also a proven contaminant of human samples and surgical wounds. Its...... significance as a pathogen is consequently a matter of debate.In the present study we investigated the presence of P. acnes DNA in 250 next generation sequencing datasets generated from 180 samples of 20 different sample types, mostly of cancerous origin. The samples were either subjected to microbial...... reads were detected in most samples analysed, though the proportions in most shotgun-sequenced samples were low.Our results show that P. acnes can be detected in practically all sample types when employing molecular methods such as next generation sequencing. The possibility of contamination from...

  7. Reductions in genetic diversity of Schistosoma mansoni populations under chemotherapeutic pressure: the effect of sampling approach and parasite population definition.

    Science.gov (United States)

    French, Michael D; Churcher, Thomas S; Basáñez, María-Gloria; Norton, Alice J; Lwambo, Nicholas J S; Webster, Joanne P

    2013-11-01

    Detecting potential changes in genetic diversity in schistosome populations following chemotherapy with praziquantel (PZQ) is crucial if we are to fully understand the impact of such chemotherapy with respect to the potential emergence of resistance and/or other evolutionary outcomes of interventions. Doing so by implementing effective, and cost-efficient sampling protocols will help to optimise time and financial resources, particularly relevant to a disease such as schistosomiasis currently reliant on a single available drug. Here we explore the effect on measures of parasite genetic diversity of applying various field sampling approaches, both in terms of the number of (human) hosts sampled and the number of transmission stages (miracidia) sampled per host for a Schistosoma mansoni population in Tanzania pre- and post-treatment with PZQ. In addition, we explore population structuring within and between hosts by comparing the estimates of genetic diversity obtained assuming a 'component population' approach with those using an 'infrapopulation' approach. We found that increasing the number of hosts sampled, rather than the number of miracidia per host, gives more robust estimates of genetic diversity. We also found statistically significant population structuring (using Wright's F-statistics) and significant differences in the measures of genetic diversity depending on the parasite population definition. The relative advantages, disadvantages and, hence, subsequent reliability of these metrics for parasites with complex life-cycles are discussed, both for the specific epidemiological and ecological scenario under study here and for their future application to other areas and schistosome species. Copyright © 2012 Elsevier B.V. All rights reserved.

  8. Fungi associated with chimney and sulfide samples from a South Mid-Atlantic Ridge hydrothermal site: Distribution, diversity and abundance

    Science.gov (United States)

    Xu, Wei; Guo, Shuangshuang; Pang, Ka-Lai; Luo, Zhu-Hua

    2017-05-01

    Deep-sea hydrothermal vent ecosystems are known to support remarkably diverse microbial communities, ranging from chemoautotrophic prokaryotes to heterotrophic prokaryotes and microeukaryotes. While fungi have generally been identified as an important component of various microbial communities in the environment, little is known about the species richness and abundance of such microorganisms in deep-sea hydrothermal vent ecosystems. In this study, a combined culture-dependent and culture-independent sequence-based approach was used to investigate fungal distribution and diversity at a deep-sea hydrothermal vent site located at the Mid-Atlantic Ridge of the South Atlantic Ocean. Sequence analyses showed that the fungal community was dominated by members of the Ascomycota and the Basidiomycota. Several new phylotypes (28 of 65 total fungal OTUs and 2 of 19 culturable fungal phylotypes) were identified, contributing to the literally unknown diversity of fungi in this understudied habitat. The fungal community structures in the chimney samples were distinct from those in three sulfide samples. The qPCR results revealed that fungal LSU rRNA gene copy numbers ranged from 5.88×105 to 6.77×106 copies/gram rock (wet weight), and the Ascomycota was significantly more abundant 2-3 orders) than the Basidiomycota. Our findings provide new insights into the diversity and abundance of fungi in deep-sea hydrothermal vent ecosystems, which increases our knowledge and understanding of the fungal diversity in deep-sea environments.

  9. Feasibility of recruiting a diverse sample of men who have sex with men: observation from Nanjing, China.

    Directory of Open Access Journals (Sweden)

    Weiming Tang

    Full Text Available Respondent-driven-sampling (RDS has well been recognized as a method for sampling from most hard-to-reach populations like commercial sex workers, drug users and men who have sex with men. However the feasibility of this sampling strategy in terms of recruiting a diverse spectrum of these hidden populations has not been understood well yet in developing countries.In a cross sectional study in Nanjing city of Jiangsu province of China, 430 MSM were recruited including 9 seeds in 14 weeks of study period using RDS. Information regarding socio-demographic characteristics and sexual risk behavior were collected and testing was done for HIV and syphilis. Duration, completion, participant characteristics and the equilibrium of key factors were used for assessing feasibility of RDS. Homophily of key variables, socio-demographic distribution and social network size were used as the indicators of diversity.In the study sample, adjusted HIV and syphilis prevalence were 6.6% and 14.6% respectively. Majority (96.3% of the participants were recruited by members of their own social network. Although there was a tendency for recruitment within the same self-identified group (homosexuals recruited 60.0% homosexuals, considerable cross-group recruitment (bisexuals recruited 52.3% homosexuals was also seen. Homophily of the self-identified sexual orientations was 0.111 for homosexuals. Upon completion of the recruitment process, participant characteristics and the equilibrium of key factors indicated that RDS was feasible for sampling MSM in Nanjing. Participants recruited by RDS were found to be diverse after assessing the homophily of key variables in successive waves of recruitment, the proportion of characteristics after reaching equilibrium and the social network size. The observed design effects were nearly the same or even better than the theoretical design effect of 2.RDS was found to be an efficient and feasible sampling method for recruiting a diverse

  10. Diversity of spore-forming bacteria in cattle manure, slaughterhouse waste and samples from biogas plants

    National Research Council Canada - National Science Library

    Bagge, E; Persson, M; Johansson, K-E

    2010-01-01

    .... In this study, the effect of the biogas process on Bacillus spp. and Clostridium spp. was investigated. We analysed 97 faecal samples, 20 slaughterhouse waste samples and 60 samples collected at different stages in the biogas process...

  11. Multiple health behaviors in an ethnically diverse sample of adults with risk factors for cardiovascular disease.

    Science.gov (United States)

    Heinrich, Katie M; Maddock, Jay

    2011-01-01

    Health behaviors of adults living with cardiovascular disease (CVD) risk factors affect additional risk, where lifestyle behavioral choices become even more important in controlling disease and preventing additional negative health outcomes. In addition, both lifestyle behaviors and CVD risk factor prevalence can vary by ethnicity. We compared multiple health behaviors of adults with diabetes, hypertension, high cholesterol, and obesity to the behaviors of adults without those conditions in a diverse ethnic sample to determine if significant differences existed between groups. Data were obtained from 30-minute random-digit-dial telephone surveys in 2007 (n = 3607). All data were self-reports. Healthy behaviors included meeting recommendations for intake of fruits and vegetables; consuming low or very low amounts of dietary fat; eating breakfast six or seven days per week; having a healthy diet; and meeting recommendations for walking, moderate, and vigorous physical activity. Unhealthy behaviors included frequent consumption of soda and fast food, smoking, binge drinking, and high stress. More than 6% of respondents had diabetes, 15.9% had hypertension, 16.4% had high cholesterol, and 18.5% were obese. Significantly fewer healthy and more unhealthy behaviors were reported for those who had CVD risk factors than were reported by those who did not have such conditions. Ethnic differences in CVD risk factor prevalence and health behaviors existed as well (p eating a healthy diet (odds ratio [OR] = 1.82) was a significant predictor for diabetes; not eating a healthy diet (OR = 1.52) and not doing vigorous physical activity (OR = 1.79) were significant predictors for hypertension; consumption of high amounts of dietary fat (OR = 1.70) and of fast food (OR = 1.51) were significant predictors for high cholesterol levels; and not eating a healthy diet (OR = 1.52), high consumption of dietary fat (OR = 2.20), not eating breakfast (OR = 1.33) and not performing vigorous

  12. Nucleotide diversity and phylogenetic relationships among ...

    Indian Academy of Sciences (India)

    RESEARCH ARTICLE Volume 96 Issue 1 March 2017 pp 135-145 ... Present study revealed that psbA–trnH region are useful in addressing questions of phylogenetic relationships among the Gladiolus cultivars, as these intergenic spacers are more variable and have more phylogenetically informative sites than the ...

  13. Nucleotide diversity and phylogenetic relationships among ...

    Indian Academy of Sciences (India)

    NIRAJ SINGH

    the region of tropical Africa, Madagascar, Arabian Peninsula, the Mediterranean basin, Europe and Asia, including Iran and Afghanistan (Goldblatt and Manning 1998; Goldblatt et al. 2001). The basic chromosome number is x = 15, rang- ing from diploid (2n = 30) to hypododecaploid (2n = 180),. (Bamford 1935; Ohri and ...

  14. Use of respondent driven sampling (RDS generates a very diverse sample of men who have sex with men (MSM in Buenos Aires, Argentina.

    Directory of Open Access Journals (Sweden)

    Alex Carballo-Diéguez

    Full Text Available Prior research focusing on men who have sex with men (MSM conducted in Buenos Aires, Argentina, used convenience samples that included mainly gay identified men. To increase MSM sample representativeness, we used Respondent Driven Sampling (RDS for the first time in Argentina. Using RDS, under certain specified conditions, the observed estimates for the percentage of the population with a specific trait are asymptotically unbiased. We describe, the diversity of the recruited sample, from the point of view of sexual orientation, and contrast the different subgroups in terms of their HIV sexual risk behavior.500 MSM were recruited using RDS. Behavioral data were collected through face-to-face interviews and Web-based CASI.In contrast with prior studies, RDS generated a very diverse sample of MSM from a sexual identity perspective. Only 24.5% of participants identified as gay; 36.2% identified as bisexual, 21.9% as heterosexual, and 17.4% were grouped as "other." Gay and non-gay identified MSM differed significantly in their sexual behavior, the former having higher numbers of partners, more frequent sexual contacts and less frequency of condom use. One third of the men (gay, 3%; bisexual, 34%, heterosexual, 51%; other, 49% reported having had sex with men, women and transvestites in the two months prior to the interview. This population requires further study and, potentially, HIV prevention strategies tailored to such diversity of partnerships. Our results highlight the potential effectiveness of using RDS to reach non-gay identified MSM. They also present lessons learned in the implementation of RDS to recruit MSM concerning both the importance and limitations of formative work, the need to tailor incentives to circumstances of the less affluent potential participants, the need to prevent masking, and the challenge of assessing network size.

  15. Microbial diversity in firework chemical exposed soil and water samples collected in Virudhunagar district, Tamil Nadu, India

    OpenAIRE

    Dhasarathan, P.; Theriappan, P.; Ashokraja, C.

    2009-01-01

    Microbial diversity of soil and water samples collected from pyrochemicals exposed areas of Virdhunagar district (Tamil Nadu, India) was studied. Soil and water samples from cultivable area, waste land and city area of the same region were also studied for a comparative acount. There is a remarkable reduction in total heterotrophic bacterial population (THB) in pyrochemicals exposed soil and water samples (42 × 104 CFU/g and 5.6 × 104 CFU/ml respectively), compared to the THB of cultivable ar...

  16. Diversity of non-acarine arachnids of the Ophathe Game Reserve, South Africa: Testing a rapid sampling protocol

    Directory of Open Access Journals (Sweden)

    Charles R. Haddad

    2015-03-01

    Full Text Available As part of the second phase of the South African National Survey of Arachnida (SANSA, field surveys were conducted in many degree-square grids throughout the country using a standardised rapid sampling protocol. This study reports on the arachnid diversity of the Ophathe Game Reserve (OGR in northern KwaZulu-Natal, as found during a preliminary survey in June 2007 (mid winter and a SANSA field survey in October 2008 (mid spring in four representative habitats. The SANSA survey included seven sampling methods: pitfalls, beating, sweep-netting, litter sifting, hand collecting, night collecting and Winkler traps. A total of 282 species in six arachnid orders were collected during the two surveys, of which spiders were the most species-rich order (268 species in 47 families. The SANSA survey yielded 966 adult arachnids, representing six orders and 197 species, with a further 67 species represented only by immatures. Although adult arachnid abundance (n differed considerably between the four habitats (range: 156–321, adult species richness (Sobs was less variable (range: 65–85. These survey results are comparable with several longer-term surveys in the Savanna biome, and indicate that the SANSA sampling protocol can yield an impressive diversity of arachnids during a relatively short period of sampling, with a high level of coverage (> 0.8 for sites and most sampling methods and moderate levels of sample completion for adults (> 0.55 for all sites, despite logistical and temporal challenges. Additional repetitions of the SANSA sampling protocol in other seasons will likely increase biodiversity knowledge of arachnids in OGR considerably.Conservation implications: The implementation of rapid sampling protocols in an atlas project is essential to generate a large volume of species-level data. The SANSA protocol is an efficient means for rapidly generating arachnid data, and in future will allow for an assessment of diversity patterns in degree

  17. [Verification and Validation on Single Nucleotide Polymorphism Analysis of Alcohol Metabolism-Related Genes ADH1B and ALDH2, Using Dried-Saliva Samples].

    Science.gov (United States)

    Murata, Shigenori; Hayashida, Mariko; Ishiguro-Tanaka, Yuko; Imazeki, Hiromi; Hayashi, Emiko; Yokoyama, Akira; Kinoshita, Kenji

    2015-11-01

    We have developed a new method for unprocessed biological specimens as templates directly into the TaqMan assay. Saliva was needed to be put on a water-soluble paper and dried, because foreign substances, such as a filter paper, hinder fluorescence detection through the assay. Genotyping of alcohol metabolism-related genes ADH1B (rs1229984) and ALDH2 (rs671) polymorphisms was, subsequently, performed by TaqMan PCR assay using dried saliva in the present investigation. The optimized technique was tested on 114 samples of alcoholic patients. The PCR-RFLP methods with purified DNA from blood samples were employed for validation of the assay. Upon validation, complete concordance was observed between the two independent results. These results highlight the ability of TaqMan PCR assays using dried saliva on water-soluble paper in genotyping of ADH1B and ALDH2 genes. Our results showed a rapid, simple, reliable, and cost-effective method for SNP genotyping of mutations in ADH1B and ALDH2 genes. This will be very useful for large-scale association studies in various fields. [Original].

  18. Genetic diversity of lake whitefish in lakes Michigan and Huron: sampling, standardization, and research priorities

    Science.gov (United States)

    Stott, Wendylee; VanDeHey, Justin A.; Sloss, Brian L.

    2010-01-01

    We combined data from two laboratories to increase the spatial extent of a genetic data set for lake whitefish Coregonus clupeaformis from lakes Huron and Michigan and saw that genetic diversity was greatest between lakes, but that there was also structuring within lakes. Low diversity among stocks may be a reflection of relatively recent colonization of the Great Lakes, but other factors such as recent population fluctuation and localized stresses such as lamprey predation or heavy exploitation may also have a homogenizing effect. Our data suggested that there is asymmetrical movement of lake whitefish between Lake Huron and Lake Michigan; more genotypes associated with Lake Michigan were observed in Lake Huron. Adding additional collections to the calibrated set will allow further examination of diversity in other Great Lakes, answer questions regarding movement among lakes, and estimate contributions of stocks to commercial yields. As the picture of genetic diversity and population structure of lake whitefish in the Great Lakes region emerges, we need to develop methods to combine data types to help identify important areas for biodiversity and thus conservation. Adding genetic data to existing models will increase the precision of predictions of the impacts of new stresses and changes in existing pressures on an ecologically and commercially important species.

  19. Molecular method to assess the diversity of Burkholderia species in environmental samples

    NARCIS (Netherlands)

    Salles, J.F.; De Souza, F.A.; Van Elsas, J.D.

    2002-01-01

    In spite of the importance of many members of the genus Burkholderia in the soil microbial community, no direct method to assess the diversity of this genus has been developed so far. The aim of this work was the development of soil DNA-based PCR-denaturing gradient get electrophoresis (DGGE), a

  20. Molecular method to assess the diversity of Burkholderia species in environmental samples

    NARCIS (Netherlands)

    Salles, J.; Souza, de F.A.; Elsas, van J.D.

    2002-01-01

    In spite of the importance of many members of the genus Burkholderia in the soil microbial community, no direct method to assess the diversity of this genus has been developed so far. The aim of this work was the development of soil DNA-based PCR-denaturing gradient gel electrophoresis (DGGE), a

  1. Sampling and estimation procedures for the vegetation diversity and structure indicator

    Science.gov (United States)

    Bethany K. Schulz; William A. Bechtold; Stanley J. Zarnoch

    2009-01-01

    The Vegetation Diversity and Structure Indicator (VEG) is an extensive inventory of vascular plants in the forests of the United States. The VEG indicator provides baseline data to assess trends in forest vascular plant species richness and composition, and the relative abundance and spatial distribution of those species, including invasive and introduced species. The...

  2. Nucleotide excision repair and human syndromes

    NARCIS (Netherlands)

    J. de Boer (Jan); J.H.J. Hoeijmakers (Jan)

    2000-01-01

    textabstractDNA damage is implicated in cancer and aging, and several DNA repair mechanisms exist that safeguard the genome from these deleterious consequences. Nucleotide excision repair (NER) removes a wide diversity of lesions, the main of which include UV-induced lesions, bulky chemical adducts

  3. Main: Nucleotide Analysis [KOME

    Lifescience Database Archive (English)

    Full Text Available -acting regulatory DNA elements Database kome_place_search_result.zip kome_place_search_result ... ...Nucleotide Analysis PLACE search result Result of signal search against PLACE : cis

  4. Main: Nucleotide Analysis [KOME

    Lifescience Database Archive (English)

    Full Text Available Nucleotide Analysis Japonica genome blast search result Result of blastn search against japon...ica genome sequence kome_japonica_genome_blast_search_result.zip kome_japonica_genome_blast_search_result ...

  5. Design and synthesis of ATP-based nucleotide analogues and profiling of nucleotide-binding proteins

    NARCIS (Netherlands)

    Wolters, Justina. C.; Roelfes, Gerard; Poolman, Bert

    Two nucleotide-based probes were designed and synthesized in order to enrich samples for specific classes of proteins by affinity-based protein profiling. We focused on the profiling of adenine nucleotide-binding proteins. Two properties were considered in the design of the probes: the bait needs to

  6. Evolving nucleotide binding surfaces

    Science.gov (United States)

    Kieber-Emmons, T.; Rein, R.

    1981-01-01

    An analysis is presented of the stability and nature of binding of a nucleotide to several known dehydrogenases. The employed approach includes calculation of hydrophobic stabilization of the binding motif and its intermolecular interaction with the ligand. The evolutionary changes of the binding motif are studied by calculating the Euclidean deviation of the respective dehydrogenases. Attention is given to the possible structural elements involved in the origin of nucleotide recognition by non-coded primordial polypeptides.

  7. Diversity of sainfoin (Onobrychis Mill. collection samples according to the spectra of storage proteins

    Directory of Open Access Journals (Sweden)

    Bulatova Kulpash

    2015-01-01

    Full Text Available Sainfoin (Onobrychis Mill. is a valuable forage plant of the legume family (Fabaceae. In Kazakhstan the sainfoin introduced as field fodder in the 50s of the XX century and because of its biological features widely spread as a promising crop for forage resources increasing. The electrophoresis of seed storage proteins of Onobrychis viciifolia, Onobrychis arenaria and Onobrychis transcaucasica species was carried out. Considerable diversity of the number, mobility and intensity of components was determined.

  8. Parent Rated Symptoms of Inattention in Childhood Predict High School Academic Achievement Across Two Culturally and Diagnostically Diverse Samples

    Directory of Open Access Journals (Sweden)

    Astri J. Lundervold

    2017-08-01

    Full Text Available Objective: To investigate parent reports of childhood symptoms of inattention as a predictor of adolescent academic achievement, taking into account the impact of the child’s intellectual functioning, in two diagnostically and culturally diverse samples.Method: Samples: (a an all-female sample in the U.S. predominated by youth with ADHD (Berkeley Girls with ADHD Longitudinal Study [BGALS], N = 202, and (b a mixed-sex sample recruited from a Norwegian population-based sample (the Bergen Child Study [BCS], N = 93. Inattention and intellectual function were assessed via the same measures in the two samples; academic achievement scores during and beyond high school and demographic covariates were country-specific.Results: Childhood inattention predicted subsequent academic achievement in both samples, with a somewhat stronger effect in the BGALS sample, which included a large subgroup of children with ADHD. Intellectual function was another strong predictor, but the effect of early inattention remained statistically significant in both samples when intellectual function was covaried.Conclusion: The effect of early indicators of inattention on future academic success was robust across the two samples. These results support the use of remediation procedures broadly applied. Future longitudinal multicenter studies with pre-planned common inclusion criteria should be performed to increase our understanding of the importance of inattention in primary school children for concurrent and prospective functioning.

  9. Diversity of nuclear short tandem repeat loci in representative sample of North-eastern Bosnian and Herzegovina population

    Directory of Open Access Journals (Sweden)

    Hadžiavdić Vesna

    2012-01-01

    Full Text Available Diversity of nuclear microsatellite markers were analyzed in a reference sample of the population of northeast Bosnia and Herzegovina. 437 samples taken from unrelated individuals were processed and three samples of paternity proof were shown. Detection effectiveness profile of the research, points to a valid choice of method of extraction, amplification and genotyping short tandem repeat (STR loci with PowerPlextm16 kit. Genetic analysis of allelic variants of the 15 STR loci PowerPlextm16 kit detected 17 samples determined as rare allelic variants or microvariants. Samples were divided into 15 different allelic variants at 7 different loci, and are: in locus D7S820, D16S539, D3S1358, D18S51, PENTA D, PENTA E and in locus vWA. Genetic analysis of mutations in cases of paternity determined three examples of single-step mutations in the loci FGA, Penta D and D3S1358. Genetic analysis of observed STR loci detected three allelic variant of genotype combination 7/10/11.3 in locus D7S820 Type II. Population genetic analysis of STR loci in a representative sample of the population of northeast Bosnia and Herzegovina included the application of the assessment tests of within-population genetic diversity and interpopulation diversity, as well as genetic differentiation between populations: North-eastern Bosnia and Herzegovina (BH and BH general reference, then the Croatian population, Macedonian, Serbian and Slovenian. Based on the result analysis of specific forensic parameters, it can be assumed that the most informative marker is PENTA E for population genetic analysis and forensic testing in the population of northeast Bosnia and Herzegovina. Research results fit regional STR database of this part of Europe.

  10. Deep COI sequencing of standardized benthic samples unveils overlooked diversity of Jordanian coral reefs in the northern Red Sea.

    Science.gov (United States)

    Al-Rshaidat, Mamoon M D; Snider, Allison; Rosebraugh, Sydney; Devine, Amanda M; Devine, Thomas D; Plaisance, Laetitia; Knowlton, Nancy; Leray, Matthieu

    2016-09-01

    High-throughput sequencing (HTS) of DNA barcodes (metabarcoding), particularly when combined with standardized sampling protocols, is one of the most promising approaches for censusing overlooked cryptic invertebrate communities. We present biodiversity estimates based on sequencing of the cytochrome c oxidase subunit 1 (COI) gene for coral reefs of the Gulf of Aqaba, a semi-enclosed system in the northern Red Sea. Samples were obtained from standardized sampling devices (Autonomous Reef Monitoring Structures (ARMS)) deployed for 18 months. DNA barcoding of non-sessile specimens >2 mm revealed 83 OTUs in six phyla, of which only 25% matched a reference sequence in public databases. Metabarcoding of the 2 mm - 500 μm and sessile bulk fractions revealed 1197 OTUs in 15 animal phyla, of which only 4.9% matched reference barcodes. These results highlight the scarcity of COI data for cryptobenthic organisms of the Red Sea. Compared with data obtained using similar methods, our results suggest that Gulf of Aqaba reefs are less diverse than two Pacific coral reefs but much more diverse than an Atlantic oyster reef at a similar latitude. The standardized approaches used here show promise for establishing baseline data on biodiversity, monitoring the impacts of environmental change, and quantifying patterns of diversity at regional and global scales.

  11. Are affluent youth truly “at risk”? Vulnerability and resilience across three diverse samples

    OpenAIRE

    Luthar, Suniya S.; BARKIN, SAMUEL H.

    2012-01-01

    Building upon prior findings of elevated problems among East Coast suburban youth through the 11th grade, this study establishes disproportionately high incidence of maladjustment across three disparate samples: East Coast Suburban youth at the end of their senior year in high school, and 11th and 12th graders in (a) a Northwest suburb and (b) an East Coast city. Both East Coast samples showed pronounced elevations in substance use, whereas the Northwest suburban sample showed marked vulnerab...

  12. Dietary Behaviors of a Racially and Ethnically Diverse Sample of Overweight and Obese Californians

    Science.gov (United States)

    Sorkin, Dara H.; Billimek, John

    2012-01-01

    Objectives: To examine racial/ethnic differences in the dietary behaviors of overweight or obese adults using the 2007 California Health Interview Survey. Method: Data were obtained from the 2007 California Health Interview Survey, a population-based sample of noninstitutionalized adults in California. The sample included 26,721 adults aged 18…

  13. Abundance, distribution and diversity of gelatinous predators along the northern Mid-Atlantic Ridge: A comparison of different sampling methodologies.

    Science.gov (United States)

    Hosia, Aino; Falkenhaug, Tone; Baxter, Emily J; Pagès, Francesc

    2017-01-01

    The diversity and distribution of gelatinous zooplankton were investigated along the northern Mid-Atlantic Ridge (MAR) from June to August 2004.Here, we present results from macrozooplankton trawl sampling, as well as comparisons made between five different methodologies that were employed during the MAR-ECO survey. In total, 16 species of hydromedusae, 31 species of siphonophores and four species of scyphozoans were identified to species level from macrozooplankton trawl samples. Additional taxa were identified to higher taxonomic levels and a single ctenophore genus was observed. Samples were collected at 17 stations along the MAR between the Azores and Iceland. A divergence in the species assemblages was observed at the southern limit of the Subpolar Frontal Zone. The catch composition of gelatinous zooplankton is compared between different sampling methodologies including: a macrozooplankton trawl; a Multinet; a ringnet attached to bottom trawl; and optical platforms (Underwater Video Profiler (UVP) & Remotely Operated Vehicle (ROV)). Different sampling methodologies are shown to exhibit selectivity towards different groups of gelatinous zooplankton. Only ~21% of taxa caught during the survey were caught by both the macrozooplankton trawl and the Multinet when deployed at the same station. The estimates of gelatinous zooplankton abundance calculated using these two gear types also varied widely (1.4 ± 0.9 individuals 1000 m-3 estimated by the macrozooplankton trawl vs. 468.3 ± 315.4 individuals 1000 m-3 estimated by the Multinet (mean ± s.d.) when used at the same stations (n = 6). While it appears that traditional net sampling can generate useful data on pelagic cnidarians, comparisons with results from the optical platforms suggest that ctenophore diversity and abundance are consistently underestimated, particularly when net sampling is conducted in combination with formalin fixation. The results emphasise the importance of considering sampling methodology

  14. Abundance, distribution and diversity of gelatinous predators along the northern Mid-Atlantic Ridge: A comparison of different sampling methodologies.

    Directory of Open Access Journals (Sweden)

    Aino Hosia

    Full Text Available The diversity and distribution of gelatinous zooplankton were investigated along the northern Mid-Atlantic Ridge (MAR from June to August 2004.Here, we present results from macrozooplankton trawl sampling, as well as comparisons made between five different methodologies that were employed during the MAR-ECO survey. In total, 16 species of hydromedusae, 31 species of siphonophores and four species of scyphozoans were identified to species level from macrozooplankton trawl samples. Additional taxa were identified to higher taxonomic levels and a single ctenophore genus was observed. Samples were collected at 17 stations along the MAR between the Azores and Iceland. A divergence in the species assemblages was observed at the southern limit of the Subpolar Frontal Zone. The catch composition of gelatinous zooplankton is compared between different sampling methodologies including: a macrozooplankton trawl; a Multinet; a ringnet attached to bottom trawl; and optical platforms (Underwater Video Profiler (UVP & Remotely Operated Vehicle (ROV. Different sampling methodologies are shown to exhibit selectivity towards different groups of gelatinous zooplankton. Only ~21% of taxa caught during the survey were caught by both the macrozooplankton trawl and the Multinet when deployed at the same station. The estimates of gelatinous zooplankton abundance calculated using these two gear types also varied widely (1.4 ± 0.9 individuals 1000 m-3 estimated by the macrozooplankton trawl vs. 468.3 ± 315.4 individuals 1000 m-3 estimated by the Multinet (mean ± s.d. when used at the same stations (n = 6. While it appears that traditional net sampling can generate useful data on pelagic cnidarians, comparisons with results from the optical platforms suggest that ctenophore diversity and abundance are consistently underestimated, particularly when net sampling is conducted in combination with formalin fixation. The results emphasise the importance of considering

  15. Culture-dependent and culture-independent diversity surveys target different bacteria: a case study in a freshwater sample.

    Science.gov (United States)

    Vaz-Moreira, Ivone; Egas, Conceição; Nunes, Olga C; Manaia, Célia M

    2011-08-01

    Compared with culture-independent approaches, traditionally used culture-dependent methods have a limited capacity to characterize water microbiota. Nevertheless, for almost a century the latter have been optimized to detect and quantify relevant bacteria. A pertinent question is if culture-independent diversity surveys give merely an extended perspective of the bacterial diversity or if, even with a higher coverage, focus on a different set of organisms. We compared the diversity and phylogeny of bacteria in a freshwater sample recovered by currently used culture-dependent and culture-independent methods (DGGE and 454 pyrosequencing). The culture-dependent diversity survey presented lower coverage than the other methods. However, it allowed bacterial identifications to the species level, in contrast with the other procedures that rarely produced identifications below the order. Although the predominant bacterial phyla detected by both approaches were the same (Proteobacteria, Actinobacteria, Bacteroidetes), sequence similarity analysis showed that, in general, different operational taxonomical units were targeted by each method. The observation that culture-dependent and independent approaches target different organisms has implications for the use of the latter for studies in which taxonomic identification has a predictive value. In comparison to DGGE, 454 pyrosequencing method had a higher capacity to explore the bacterial richness and to detect cultured organisms, being also less laborious.

  16. Y-STR diversity and ethnic admixture in White and Mulatto Brazilian population samples

    Directory of Open Access Journals (Sweden)

    Luzitano Brandão Ferreira

    2006-01-01

    Full Text Available We investigated 50 Mulatto and 120 White Brazilians for the Y-chromosome short tandem repeat (Y-STR markers (DYS19, DYS390, DYS391, DYS392 and DYS393 and found 79 different haplotypes in the White and 35 in the Mulatto sample. Admixture estimates based on allele frequencies showed that the admixture of the white sample was 89% European, 6% African and 5% Amerindian while the Mulatto sample was 93% European and 7% African. Results were consistent with historical records of the directional mating between European males and Amerindian or African females.

  17. Effects of Fertilization and Sampling Time on Composition and Diversity of Entire and Active Bacterial Communities in German Grassland Soils

    Science.gov (United States)

    Herzog, Sarah; Wemheuer, Franziska; Wemheuer, Bernd; Daniel, Rolf

    2015-01-01

    Soil bacteria are major players in driving and regulating ecosystem processes. Thus, the identification of factors shaping the diversity and structure of these communities is crucial for understanding bacterial-mediated processes such as nutrient transformation and cycling. As most studies only target the entire soil bacterial community, the response of active community members to environmental changes is still poorly understood. The objective of this study was to investigate the effect of fertilizer application and sampling time on structure and diversity of potentially active (RNA-based) and the entire (DNA-based) bacterial communities in German grassland soils. Analysis of more than 2.3 million 16S rRNA transcripts and gene sequences derived from amplicon-based sequencing of 16S rRNA genes revealed that fertilizer application and sampling time significantly altered the diversity and composition of entire and active bacterial communities. Although the composition of both the entire and the active bacterial community was correlated with environmental factors such as pH or C/N ratio, the active community showed a higher sensitivity to environmental changes than the entire community. In addition, functional analyses were performed based on predictions derived from 16S rRNA data. Genes encoding the uptake of nitrate/nitrite, nitrification, and denitrification were significantly more abundant in fertilized plots compared to non-fertilized plots. Hence, this study provided novel insights into changes in dynamics and functions of soil bacterial communities as response to season and fertilizer application. PMID:26694644

  18. Diversity of Microbial Carbohydrate-Active enZYmes (CAZYmes) Associated with Freshwater and Soil Samples from Caatinga Biome.

    Science.gov (United States)

    Andrade, Ana Camila; Fróes, Adriana; Lopes, Fabyano Álvares Cardoso; Thompson, Fabiano L; Krüger, Ricardo Henrique; Dinsdale, Elizabeth; Bruce, Thiago

    2017-07-01

    Semi-arid and arid areas occupy about 33% of terrestrial ecosystems. However, little information is available about microbial diversity in the semi-arid Caatinga, which represents a unique biome that extends to about 11% of the Brazilian territory and is home to extraordinary diversity and high endemism level of species. In this study, we characterized the diversity of microbial genes associated with biomass conversion (carbohydrate-active enzymes, or so-called CAZYmes) in soil and freshwater of the Caatinga. Our results showed distinct CAZYme profiles in the soil and freshwater samples. Glycoside hydrolases and glycosyltransferases were the most abundant CAZYme families, with glycoside hydrolases more dominant in soil (∼44%) and glycosyltransferases more abundant in freshwater (∼50%). The abundances of individual glycoside hydrolase, glycosyltransferase, and carbohydrate-binding module subfamilies varied widely between soil and water samples. A predominance of glycoside hydrolases was observed in soil, and a higher contribution of enzymes involved in carbohydrate biosynthesis was observed in freshwater. The main taxa associated with the CAZYme sequences were Planctomycetia (relative abundance in soil, 29%) and Alphaproteobacteria (relative abundance in freshwater, 27%). Approximately 5-7% of CAZYme sequences showed low similarity with sequences deposited in non-redundant databases, suggesting putative homologues. Our findings represent a first attempt to describe specific microbial CAZYme profiles for environmental samples. Characterizing these enzyme groups associated with the conversion of carbohydrates in nature will improve our understanding of the significant roles of enzymes in the carbon cycle. We identified a CAZYme signature that can be used to discriminate between soil and freshwater samples, and this signature may be related to the microbial species adapted to the habitat. The data show the potential ecological roles of the CAZYme repertoire and

  19. Molecular diversity of methanogens in fecal samples from Bactrian camels (Camelus bactrianus) at two zoos.

    Science.gov (United States)

    Turnbull, Kathryn L; Smith, Rachel P; St-Pierre, Benoit; Wright, André-Denis G

    2012-08-01

    Animals are dependent on mutualistic microbial communities that reside in their gastrointestinal track for essential physiological functions such as nutrition and pathogen resistance. The composition of microbial communities in an animal is influenced by various factors, including species, diet and geographical location. In this preliminary study, the population structure of fecal methanogens in Bactrian camels (Camelus bactrianus) from two zoos was studied using separate 16S rRNA gene libraries for each zoo. While methanogen sequences belonging to the genus Methanobrevibacter were dominant in both libraries, they showed significant differences in diversity (p=0.05) and structure (pZoo library and seven OTUs were unique to the Potter Park Zoo library. These preliminary results highlight how methanogen population structures can vary greatly between animals of the same species maintained in captivity at different locations. Copyright © 2011 Elsevier Ltd. All rights reserved.

  20. Liquid chromatography/time-of-flight mass spectrometry for the analysis of plant samples: a method for simultaneous screening of common cofactors or nucleotides and application to an engineered plant line.

    Science.gov (United States)

    Guérard, Florence; Pétriacq, Pierre; Gakière, Bertrand; Tcherkez, Guillaume

    2011-10-01

    Intense efforts are currently devoted to improve plant metabolomic analyses so as to describe more accurately the whole picture of metabolic pathways. Analyses based on liquid chromatography/time-of-flight mass spectrometry (LC-TOF) are now widely distributed among plant science laboratories. However, the use of reliable, sensitive LC-TOF methods to identify and quantify micromolar or inframicromolar key metabolites is often impeded by the sensitivity of the technique to sample preparation or chromatographic conditions. Typically, the sample matrix has a substantial influence on ionization efficiency and therefore, on the detectability of such compounds. Here, we describe a new method to analyze simultaneously 23 nucleotides and cofactors from plant extracts, taking advantage of solid-phase extraction (SPE) prior to injection. The influence of common m/z fragments in several metabolites and adducts is considered. We applied this method to characterise metabolic intermediates of NAD biosynthesis in Arabidopsis thaliana, using a wild-type and an engineered transgenic plant line that produces bacterial quinolinate phosphoribosyl transferase (nadc). We show that sample pre-purification with SPE is strictly required not only for compound quantification and identification but also to allow ionization of matrix-sensitive compounds (e.g. nicotinamide) or alleviate fragmentation of others (e.g. NAD). When exogenous substrate quinolinate was infiltrated into Arabidopsis leaves to increase the natural content in downstream metabolites, a clear correlation between intermediates of NAD biosynthesis was seen, showing the accuracy of our method for quantification in biological samples. Nadc plants only showed very modest changes in NAD-related metabolites and furthermore, they were associated with slightly lower photosynthetic performance and ATP production. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

  1. Genotyping of Leptospira directly in urine samples of cattle demonstrates a diversity of species and strains in Brazil.

    Science.gov (United States)

    Hamond, C; Pestana, C P; Medeiros, M A; Lilenbaum, W

    2016-01-01

    The aim of this study was to identify Leptospira in urine samples of cattle by direct sequencing of the secY gene. The validity of this approach was assessed using ten Leptospira strains obtained from cattle in Brazil and 77 DNA samples previously extracted from cattle urine, that were positive by PCR for the genus-specific lipL32 gene of Leptospira. Direct sequencing identified 24 (31·1%) interpretable secY sequences and these were identical to those obtained from direct DNA sequencing of the urine samples from which they were recovered. Phylogenetic analyses identified four species: L. interrogans, L. borgpetersenii, L. noguchii, and L. santarosai with the most prevalent genotypes being associated with L. borgpetersenii. While direct sequencing cannot, as yet, replace culturing of leptospires, it is a valid additional tool for epidemiological studies. An unexpected finding from this study was the genetic diversity of Leptospira infecting Brazilian cattle.

  2. A Note on Two-Sample Tests for Comparing Intra-Individual Genetic Sequence Diversity between Populations

    Science.gov (United States)

    Giorgi, E. E.; Bhattacharya, T.

    2013-01-01

    Summary present four U-statistic based tests to compare genetic diversity between different samples. The proposed tests improved upon previously used methods by accounting for the correlations in the data. We find, however, that the same correlations introduce an unacceptable bias in the sample estimators used for the variance and covariance of the inter-sequence genetic distances for modest sample sizes. Here, we compute unbiased estimators for these and test the resulting improvement using simulated data. We also show that, contrary to the claims in Gilbert et al., it is not always possible to apply the Welch–Satterthwaite approximate t-test, and we provide explicit formulas for the degrees of freedom to be used when, on the other hand, such approximation is indeed possible. PMID:23004569

  3. The Chemical Diversity of Lantana camara: Analyses of Essential Oil Samples from Cuba, Nepal, and Yemen.

    Science.gov (United States)

    Satyal, Prabodh; Crouch, Rebecca A; Monzote, Lianet; Cos, Paul; Awadh Ali, Nasser A; Alhaj, Mehdi A; Setzer, William N

    2016-03-01

    The aerial parts of Lantana camara L. were collected from three different geographical locations: Artemisa (Cuba), Biratnagar (Nepal), and Sana'a (Yemen). The essential oils were obtained by hydrodistillation and analyzed by gas chromatography/mass spectrometry. A cluster analysis of 39 L. camara essential oil compositions revealed eight major chemotypes: β-caryophyllene, germacrene D, ar-curcumene/zingiberene, γ-curcumen-15-al/epi-β-bisabolol, (E)-nerolidol, davanone, eugenol/alloaromadendrene, and carvone. The sample from Cuba falls into the group dominated by (E)-nerolidol, the sample from Nepal is a davanone chemotype, and the sample from Yemen belongs to the β-caryophyllene chemotype. The chemical composition of L. camara oil plays a role in the biological activity; the β-caryophyllene and (E)-nerolidol chemotypes showed antimicrobial and cytotoxic activities. © 2016 Verlag Helvetica Chimica Acta AG, Zürich.

  4. Advancing Research on Racial–Ethnic Health Disparities: Improving Measurement Equivalence in Studies with Diverse Samples

    Science.gov (United States)

    Landrine, Hope; Corral, Irma

    2014-01-01

    To conduct meaningful, epidemiologic research on racial–ethnic health disparities, racial–ethnic samples must be rendered equivalent on other social status and contextual variables via statistical controls of those extraneous factors. The racial–ethnic groups must also be equally familiar with and have similar responses to the methods and measures used to collect health data, must have equal opportunity to participate in the research, and must be equally representative of their respective populations. In the absence of such measurement equivalence, studies of racial–ethnic health disparities are confounded by a plethora of unmeasured, uncontrolled correlates of race–ethnicity. Those correlates render the samples, methods, and measures incomparable across racial–ethnic groups, and diminish the ability to attribute health differences discovered to race–ethnicity vs. to its correlates. This paper reviews the non-equivalent yet normative samples, methodologies and measures used in epidemiologic studies of racial–ethnic health disparities, and provides concrete suggestions for improving sample, method, and scalar measurement equivalence. PMID:25566524

  5. Depression and Racial/Ethnic Variations within a Diverse Nontraditional College Sample

    Science.gov (United States)

    Hudson, Richard; Towey, James; Shinar, Ori

    2008-01-01

    The study's objective was to ascertain whether rates of depression were significantly higher for Dominican, Puerto Rican, South and Central American and Jamaican/Haitian students than for African American and White students. The sample consisted of 987 predominantly nontraditional college students. The depression rate for Dominican students was…

  6. Are affluent youth truly “at risk”? Vulnerability and resilience across three diverse samples

    Science.gov (United States)

    LUTHAR, SUNIYA S.; BARKIN, SAMUEL H.

    2015-01-01

    Building upon prior findings of elevated problems among East Coast suburban youth through the 11th grade, this study establishes disproportionately high incidence of maladjustment across three disparate samples: East Coast Suburban youth at the end of their senior year in high school, and 11th and 12th graders in (a) a Northwest suburb and (b) an East Coast city. Both East Coast samples showed pronounced elevations in substance use, whereas the Northwest suburban sample showed marked vulnerability in serious internalizing and externalizing symptoms. Across all samples, parents’ low perceived containment for substance use (lax repercussions on discovering use) was a major vulnerability factor, followed by parents’ knowledge of their teens’ activities. Overall, adolescents’ symptom levels were more strongly related to their relationships with mothers than with fathers. An exception was boys’ apparent vulnerability to fathers’, but not mothers’, perceived depressive symptoms. As with affluent eighth graders, we found that “overscheduling” in extracurriculars is not a critical vulnerability factor among these high school students. Finally, youth reports suggested that most affluent parents do not indiscriminately bail their children out of all problem situations (although a small subset, apparently, do). Results are discussed along with the implications for practice and for future research. PMID:22559123

  7. Diversity of Microorganisms Isolated from the Soil Sample surround Chroogomphus rutilus in the Beijing Region

    OpenAIRE

    Wang, Peng; Liu, Yu; Yin, Yonggang; Jin, Haojie; Wang, Shouxian; Xu, Feng; Zhao, Shuang; Geng, Xiaoli

    2011-01-01

    Artificially cultivating Chroogomphus rutilus is too inefficient to be commercially feasible. Furthermore, isolating C. rutilus mycelia in the wild is difficult. Thus, it is important to determine the natural habitat of its fruiting body. This study focused on the ecology of the C. rutilus habitat to isolate and classify beneficial microorganisms that could affect its growth, which could be used in future research on artificial cultivation. In total, 342 isolates were isolated from soil sampl...

  8. Prevalence, Distribution, and Diversity of Salmonella spp. in Meat Samples Collected from Italian Slaughterhouses.

    Science.gov (United States)

    Carraturo, Federica; Gargiulo, Giuseppe; Giorgio, Antonella; Aliberti, Francesco; Guida, Marco

    2016-10-01

    Recently worldwide food safety authorities indicated the rise of foodborne outbreaks linked to Salmonella: this highlighted the need to intensify monitoring and apply more targeted controls to help manage the spread of the disease. The aim of this study was to assess the prevalence and distribution of Salmonella serotypes in 7 slaughterhouses, located in different areas of Naples province (Regione Campania, Italy). Meat samples collected from the slaughterhouses were submitted for standardized microbiological analysis in 2015. Results of routine testing for Salmonella spp. were analyzed and then compared to biochemical and molecular evaluations. Salmonella spp. were detected in 12% of 320 samples examined (39/320) and the isolation rates ranged from 87% (32 samples) for raw poultry meat to 13% (7 samples) for pork meat. Biochemical serotyping showed that approximately 50% of the isolates belonged to Salmonella enterica serotype Choleraesuis. Rapid detection methods, such as molecular analysis (polymerase chain reaction and gel electrophoresis), able to confirm food matrices contamination, represent a valid support to the fast identification of Salmonella species. A further aspect of the study consisted, indeed, on analyzing isolated strains through molecular evaluations. By amplifying bacterial DNA-using invA primers, selective for Salmonella-it was possible, in less than 3 h, to classify the isolates as Salmonella spp., confirming the results of microbiological outcomes. Results of distribution analysis, supported by rapid molecular approaches, showed the difficulty of reducing Salmonella risk on food chain. This emphasized the importance of periodic surveillance to prevent outbreaks. © 2016 Institute of Food Technologists®.

  9. Zooplankton diversity analysis through single-gene sequencing of a community sample

    Directory of Open Access Journals (Sweden)

    Nishida Mutsumi

    2009-09-01

    Full Text Available Abstract Background Oceans cover more than 70% of the earth's surface and are critical for the homeostasis of the environment. Among the components of the ocean ecosystem, zooplankton play vital roles in energy and matter transfer through the system. Despite their importance, understanding of zooplankton biodiversity is limited because of their fragile nature, small body size, and the large number of species from various taxonomic phyla. Here we present the results of single-gene zooplankton community analysis using a method that determines a large number of mitochondrial COI gene sequences from a bulk zooplankton sample. This approach will enable us to estimate the species richness of almost the entire zooplankton community. Results A sample was collected from a depth of 721 m to the surface in the western equatorial Pacific off Pohnpei Island, Micronesia, with a plankton net equipped with a 2-m2 mouth opening. A total of 1,336 mitochondrial COI gene sequences were determined from the cDNA library made from the sample. From the determined sequences, the occurrence of 189 species of zooplankton was estimated. BLASTN search results showed high degrees of similarity (>98% between the query and database for 10 species, including holozooplankton and merozooplankton. Conclusion In conjunction with the Census of Marine Zooplankton and Barcode of Life projects, single-gene zooplankton community analysis will be a powerful tool for estimating the species richness of zooplankton communities.

  10. Diverse protocols for correlative super-resolution fluorescence imaging and electron microscopy of chemically fixed samples

    Science.gov (United States)

    Kopek, Benjamin G.; Paez-Segala, Maria G.; Shtengel, Gleb; Sochacki, Kem A.; Sun, Mei G.; Wang, Yalin; Xu, C. Shan; van Engelenburg, Schuyler B.; Taraska, Justin W.; Looger, Loren L.; Hess, Harald F.

    2017-01-01

    Our groups have recently developed related approaches for sample preparation for super-resolution imaging within endogenous cellular environments using correlative light and electron microscopy (CLEM). Four distinct techniques for preparing and acquiring super-resolution CLEM datasets on aldehyde-fixed specimens are provided, including Tokuyasu cryosectioning, whole-cell mount, cell unroofing and platinum replication, and resin embedding and sectioning. Choice of the best protocol for a given application depends on a number of criteria that are discussed in detail. Tokuyasu cryosectioning is relatively rapid but is limited to small, delicate specimens. Whole-cell mount has the simplest sample preparation but is restricted to surface structures. Cell unroofing and platinum replica creates high-contrast, 3-dimensional images of the cytoplasmic surface of the plasma membrane, but is more challenging than whole-cell mount. Resin embedding permits serial sectioning of large samples, but is limited to osmium-resistant probes, and is technically difficult. Expected results from these protocols include super-resolution localization (~10–50 nm) of fluorescent targets within the context of electron microscopy ultrastructure, which can help address cell biological questions. These protocols can be completed in 2–7 days, are compatible with a number of super-resolution imaging protocols, and are broadly applicable across biology. PMID:28384138

  11. Diversity of reductive dehalogenase genes from environmental samples and enrichment cultures identified with degenerate primer PCR screens.

    Directory of Open Access Journals (Sweden)

    Laura Audrey Hug

    2013-11-01

    Full Text Available Reductive dehalogenases are the critical enzymes for anaerobic organohalide respiration, a microbial metabolic process that has been harnessed for bioremediation efforts to resolve chlorinated solvent contamination in groundwater and is implicated in the global halogen cycle. Reductive dehalogenase sequence diversity is informative for the dechlorination potential of the site or enrichment culture. A suite of degenerate PCR primers targeting a comprehensive curated set of reductive dehalogenase genes was designed and applied to twelve DNA samples extracted from contaminated and pristine sites, as well as six enrichment cultures capable of reducing chlorinated compounds to non-toxic end-products. The amplified gene products from four environmental sites and two enrichment cultures were sequenced using Illumina HiSeq, and the reductive dehalogenase complement of each sample determined. The results indicate that the diversity of the reductive dehalogenase gene family is much deeper than is currently accounted for: one-third of the translated proteins have less than 70% pairwise amino acid identity to database sequences. Approximately 60% of the sequenced reductive dehalogenase genes were broadly distributed, being identified in four or more samples, and often in previously sequenced genomes as well. In contrast, 17% of the sequenced reductive dehalogenases were unique, present in only a single sample and bearing less than 90% pairwise amino acid identity to any previously identified proteins. Many of the broadly distributed reductive dehalogenases are uncharacterized in terms of their substrate specificity, making these intriguing targets for further biochemical experimentation. Finally, comparison of samples from a contaminated site and an enrichment culture derived from the same site eight years prior allowed examination of the effect of the enrichment process.

  12. Social Communication Coaching Smartglasses: Well Tolerated in a Diverse Sample of Children and Adults With Autism.

    Science.gov (United States)

    Keshav, Neha U; Salisbury, Joseph P; Vahabzadeh, Arshya; Sahin, Ned T

    2017-09-21

    Augmented reality (AR) smartglasses are an emerging technology that is under investigation as a social communication aid for children and adults with autism spectrum disorder (ASD) and as a research tool to aid with digital phenotyping. Tolerability of this wearable technology in people with ASD is an important area for research, especially as these individuals may experience sensory, cognitive, and attentional challenges. The aim of this study was to assess the tolerability and usability of a novel smartglasses system that has been designed as a social communication aid for children and adults with autism (the Brain Power Autism System [BPAS]). BPAS runs on Google Glass Explorer Edition and other smartglasses, uses both AR and affective artificial intelligence, and helps users learn key social and emotional skills. A total of 21 children and adults with ASD across a spectrum of severity used BPAS for a coaching session. The user's tolerability to the smartglasses, user being able to wear the smartglasses for 1 minute (initial tolerability threshold), and user being able to wear the smartglasses for the entire duration of the coaching session (whole session tolerability threshold) were determined through caregiver report. Of 21 users, 19 (91%) demonstrated tolerability on all 3 measures. Caregivers reported 21 out of 21 users (100%) as tolerating the experience, while study staff found only 19 out of 21 users managed to demonstrate initial tolerability (91%). Of the 19 users who demonstrated initial tolerability, all 19 (100%) were able to use the smartglasses for the entire session (whole session tolerability threshold). Caregivers reported that 19 out of 21 users (91%) successfully used BPAS, and users surpassed caregiver expectations in 15 of 21 cases (71%). Users who could communicate reported BPAS as being comfortable (94%). This preliminary report suggests that BPAS is well tolerated and usable to a diverse age- and severity-range of people with ASD. This is

  13. Detection of a diverse marine fish fauna using environmental DNA from seawater samples

    DEFF Research Database (Denmark)

    Thomsen, Philip Francis; Kielgast, Jos; Iversen, Lars Lønsmann

    2012-01-01

    eDNA from 15 different fish species, including both important consumption species, as well as species rarely or never recorded by conventional monitoring. We also detect eDNA from a rare vagrant species in the area; European pilchard (Sardina pilchardus). Additionally, we detect four bird species......Marine ecosystems worldwide are under threat with many fish species and populations suffering from human over-exploitation. This is greatly impacting global biodiversity, economy and human health. Intriguingly, marine fish are largely surveyed using selective and invasive methods, which are mostly...... for marine fish biodiversity. This eDNA approach has recently been used successfully in freshwater environments, but never in marine settings. We isolate eDNA from 1/2-litre seawater samples collected in a temperate marine ecosystem in Denmark. Using next-generation DNA sequencing of PCR amplicons, we obtain...

  14. Realistic weight perception and body size assessment in a racially diverse community sample of dieters.

    Science.gov (United States)

    Cachelin, F M; Striegel-Moore, R H; Elder, K A

    1998-01-01

    Recently, a shift in obesity treatment away from emphasizing ideal weight loss goals to establishing realistic weight loss goals has been proposed; yet, what constitutes "realistic" weight loss for different populations is not clear. This study examined notions of realistic shape and weight as well as body size assessment in a large community-based sample of African-American, Asian, Hispanic, and white men and women. Participants were 1893 survey respondents who were all dieters and primarily overweight. Groups were compared on various variables of body image assessment using silhouette ratings. No significant race differences were found in silhouette ratings, nor in perceptions of realistic shape or reasonable weight loss. Realistic shape and weight ratings by both women and men were smaller than current shape and weight but larger than ideal shape and weight ratings. Compared with male dieters, female dieters considered greater weight loss to be realistic. Implications of the findings for the treatment of obesity are discussed.

  15. The relationships among coping styles and fatigue in an ethnically diverse sample.

    Science.gov (United States)

    Njoku, Mary Gloria C; Jason, Leonard A; Torres-Harding, Susan R

    2005-11-01

    The present study focused on coping strategies among African Americans, Latinos, and European Americans with chronic fatigue syndrome (CFS) and idiopathic chronic fatigue (ICF). The coping strategies examined were measured by using the COPE Scales, which assess Seeking Emotional Social Support, Positive Reinterpretation and Growth, Acceptance, Denial, Turning to Religion, Behavioral Disengagement, and Focusing on and Venting Emotions. In addition, the four coping strategies specifically designed for people with CFS, including maintaining activity, accommodating to the illness, focusing on symptoms, and information-seeking, were used in this study. It was hypothesized that African Americans and Latinos in comparison to European Americans would be more likely to use religious coping, behavioral disengagement, and denial. As predicted, African Americans were significantly more likely to turn to religion than European Americans, and Latinos and African Americans used denial significantly more often than European Americans. An additional finding was that focusing on symptoms was associated with greater fatigue and more physical disability among African Americans. Within the Latino sample, acceptance was related to greater fatigue and less physical disability, and greater optimism predicted less mental disability. Among European American participants, maintaining activity was related to less mental disability, whereas accommodating to the illness predicted more physical disability. These results indicate that coping varies among various ethnic groups with CFS and ICF; however, denial is consistently related to less adaptive outcomes. Therefore, healthcare professionals should find ways to reduce patient use of denial and promote alternative strategies for managing life events.

  16. The geographic diversity of nontuberculous mycobacteria isolated from pulmonary samples: an NTM-NET collaborative study.

    Science.gov (United States)

    Hoefsloot, Wouter; van Ingen, Jakko; Andrejak, Claire; Angeby, Kristian; Bauriaud, Rosine; Bemer, Pascale; Beylis, Natalie; Boeree, Martin J; Cacho, Juana; Chihota, Violet; Chimara, Erica; Churchyard, Gavin; Cias, Raquel; Daza, Rosa; Daley, Charles L; Dekhuijzen, P N Richard; Domingo, Diego; Drobniewski, Francis; Esteban, Jaime; Fauville-Dufaux, Maryse; Folkvardsen, Dorte Bek; Gibbons, Noel; Gómez-Mampaso, Enrique; Gonzalez, Rosa; Hoffmann, Harald; Hsueh, Po-Ren; Indra, Alexander; Jagielski, Tomasz; Jamieson, Frances; Jankovic, Mateja; Jong, Eefje; Keane, Joseph; Koh, Wo-Jung; Lange, Berit; Leao, Sylvia; Macedo, Rita; Mannsåker, Turid; Marras, Theodore K; Maugein, Jeannette; Milburn, Heather J; Mlinkó, Tamas; Morcillo, Nora; Morimoto, Kozo; Papaventsis, Dimitrios; Palenque, Elia; Paez-Peña, Mar; Piersimoni, Claudio; Polanová, Monika; Rastogi, Nalin; Richter, Elvira; Ruiz-Serrano, Maria Jesus; Silva, Anabela; da Silva, M Pedro; Simsek, Hulya; van Soolingen, Dick; Szabó, Nora; Thomson, Rachel; Tórtola Fernandez, Teresa; Tortoli, Enrico; Totten, Sarah E; Tyrrell, Greg; Vasankari, Tuula; Villar, Miguel; Walkiewicz, Renata; Winthrop, Kevin L; Wagner, Dirk

    2013-12-01

    A significant knowledge gap exists concerning the geographical distribution of nontuberculous mycobacteria (NTM) isolation worldwide. To provide a snapshot of NTM species distribution, global partners in the NTM-Network European Trials Group (NET) framework (www.ntm-net.org), a branch of the Tuberculosis Network European Trials Group (TB-NET), provided identification results of the total number of patients in 2008 in whom NTM were isolated from pulmonary samples. From these data, we visualised the relative distribution of the different NTM found per continent and per country. We received species identification data for 20 182 patients, from 62 laboratories in 30 countries across six continents. 91 different NTM species were isolated. Mycobacterium avium complex (MAC) bacteria predominated in most countries, followed by M. gordonae and M. xenopi. Important differences in geographical distribution of MAC species as well as M. xenopi, M. kansasii and rapid-growing mycobacteria were observed. This snapshot demonstrates that the species distribution among NTM isolates from pulmonary specimens in the year 2008 differed by continent and differed by country within these continents. These differences in species distribution may partly determine the frequency and manifestations of pulmonary NTM disease in each geographical location.

  17. Identification of fluency and word-finding difficulty in samples of children with diverse language backgrounds.

    Science.gov (United States)

    Howell, Peter; Tang, Kevin; Tuomainen, Outi; Chan, Sin Kan; Beltran, Kirsten; Mirawdeli, Avin; Harris, John

    2017-09-01

    Stuttering and word-finding difficulty (WFD) are two types of communication difficulty that occur frequently in children who learn English as an additional language (EAL), as well as those who only speak English. The two disorders require different, specific forms of intervention. Prior research has described the symptoms of each type of difficulty. This paper describes the development of a non-word repetition test (UNWR), applicable across languages, that was validated by comparing groups of children identified by their speech and language symptoms as having either stuttering or WFD. To evaluate whether non-word repetition scores using the UNWR test distinguished between children who stutter and those who have a WFD, irrespective of the children's first language. UNWR was administered to ninety-six 4-5-year-old children attending UK schools (20.83% of whom had EAL). The children's speech samples in English were assessed for symptoms of stuttering and WFD. UNWR scores were calculated. Regression models were fitted to establish whether language group (English only/EAL) and symptoms of (1) stuttering and (2) WFD predicted UNWR scores. Stuttering symptoms predicted UNWR, whereas WFD did not. These two findings suggest that UNWR scores dissociate stuttering from WFD. There were no differences between monolingual English-speakers and children who had EAL. UNWR scores distinguish between stuttering and WFD irrespective of language(s) spoken, allowing future evaluation of a range of languages in clinics or schools. © 2016 Royal College of Speech and Language Therapists.

  18. Self-esteem, diet self-efficacy, body mass index, and eating disorders: modeling effects in an ethnically diverse sample.

    Science.gov (United States)

    Saunders, Jessica F; Frazier, Leslie D; Nichols-Lopez, Kristin A

    2016-09-01

    Disordered eating patterns, particularly binge eating, are prevalent in Hispanic samples, yet the biopsychosocial risk factors remain understudied in minority populations. The relationship between diet self-efficacy and bulimic symptoms has been established in non-Hispanic white samples but not yet in Hispanics. This study sought to identify the direct role of diet self-efficacy on eating disorder risk and symptomology in a multicultural Hispanic sample, and to investigate the potential indirect relations among diet self-efficacy, self-esteem, body mass index (BMI), and eating disorder risk and symptomology in Hispanics and non-Hispanic whites. The present study surveyed 1339 college students from diverse ethnic backgrounds. Participants completed four standardized scales to assess acculturation, diet self-efficacy, global self-esteem, and eating disorder symptomology and risk. Self-reported height and weight were used for BMI calculations, and the data were analyzed in a robust maximum-likelihood structural equation modeling (SEM) framework. The findings highlighted diet self-efficacy as a predictor of eating disorder risk and symptomology. Diet self-efficacy partially explained the covariation between self-esteem and eating disorder risk and symptomology, and between BMI and eating disorder risk and symptomology for the entire sample. Diet self-efficacy emerged as an important construct to consider in developing eating disorder prevention and treatment models.

  19. Bacterial diversity of autotrophic enriched cultures from remote, glacial Antarctic, Alpine and Andean aerosol, snow and soil samples

    Science.gov (United States)

    González-Toril, E.; Amils, R.; Delmas, R. J.; Petit, J.-R.; Komárek, J.; Elster, J.

    2009-01-01

    Four different communities and one culture of autotrophic microbial assemblages were obtained by incubation of samples collected from high elevation snow in the Alps (Mt. Blanc area) and the Andes (Nevado Illimani summit, Bolivia), from Antarctic aerosol (French station Dumont d'Urville) and a maritime Antarctic soil (King George Island, South Shetlands, Uruguay Station Artigas), in a minimal mineral (oligotrophic) media. Molecular analysis of more than 200 16S rRNA gene sequences showed that all cultured cells belong to the Bacteria domain. Phylogenetic comparison with the currently available rDNA database allowed sequences belonging to Proteobacteria Alpha-, Beta- and Gamma-proteobacteria), Actinobacteria and Bacteroidetes phyla to be identified. The Andes snow culture was the richest in bacterial diversity (eight microorganisms identified) and the marine Antarctic soil the poorest (only one). Snow samples from Col du Midi (Alps) and the Andes shared the highest number of identified microorganisms (Agrobacterium, Limnobacter, Aquiflexus and two uncultured Alphaproteobacteria clones). These two sampling sites also shared four sequences with the Antarctic aerosol sample (Limnobacter, Pseudonocardia and an uncultured Alphaproteobacteriaclone). The only microorganism identified in the Antarctica soil (Brevundimonas sp.) was also detected in the Antarctic aerosol. Most of the identified microorganisms had been detected previously in cold environments, marine sediments soils and rocks. Air current dispersal is the best model to explain the presence of very specific microorganisms, like those identified in this work, in environments very distant and very different from each other.

  20. Genetic diversity of Lombok chickens based on D-loop mitochondrial DNA sequences

    Directory of Open Access Journals (Sweden)

    M. Syamsul Arifin Zein

    2008-12-01

    Full Text Available Mitochondrial DNA (mtDNA displacement (D-loop sequences were used to study the genetic diversity and relationship of Lombok chickens. A total of 45 individuals were sampled. The D-loop segment was PCR amplified and subsequently sequenced. The sequences of the 785 nucleotides were used for analysis. Twelve haplotypes were identified from 25 polymorphic sites with polymorphism between nucleotides 200 and 400 contributing to 80% of the variation. Fu’s Fs value was - 8.768 (all samples, P = 0, indicating high genetic diversity and population expansion, a conclusion supported by a neighbor– joining analysis of the haplotypes. Nucleotides diversity of the Lombok chicken were 0.00221 and haplotype diversity were 0.654 + 0.08. The dominant haplotype found among the Lombok chickens was haplotype B (62% and genetic distances value ranged from 0.001 to 0.017.

  1. Sampling

    CERN Document Server

    Thompson, Steven K

    2012-01-01

    Praise for the Second Edition "This book has never had a competitor. It is the only book that takes a broad approach to sampling . . . any good personal statistics library should include a copy of this book." —Technometrics "Well-written . . . an excellent book on an important subject. Highly recommended." —Choice "An ideal reference for scientific researchers and other professionals who use sampling." —Zentralblatt Math Features new developments in the field combined with all aspects of obtaining, interpreting, and using sample data Sampling provides an up-to-date treat

  2. Dispersal and neutral sampling mediate contingent effects of disturbance on plant beta-diversity: a meta-analysis.

    Science.gov (United States)

    Catano, Christopher P; Dickson, Timothy L; Myers, Jonathan A

    2017-03-01

    A major challenge in ecology, conservation and global-change biology is to understand why biodiversity responds differently to similar environmental changes. Contingent biodiversity responses may depend on how disturbance and dispersal interact to alter variation in community composition (β-diversity) and assembly mechanisms. However, quantitative syntheses of these patterns and processes across studies are lacking. Using null-models and meta-analyses of 22 factorial experiments in herbaceous plant communities across Europe and North America, we show that disturbance diversifies communities when dispersal is limited, but homogenises communities when combined with increased immigration from the species pool. In contrast to the hypothesis that disturbance and dispersal mediate the strength of niche assembly, both processes altered β-diversity through neutral-sampling effects on numbers of individuals and species in communities. Our synthesis suggests that stochastic effects of disturbance and dispersal on community assembly play an important, but underappreciated, role in mediating biotic homogenisation and biodiversity responses to environmental change. © 2017 John Wiley & Sons Ltd/CNRS.

  3. Feeding practices and styles used by a diverse sample of low-income parents of preschool-age children.

    Science.gov (United States)

    Ventura, Alison K; Gromis, Judy C; Lohse, Barbara

    2010-01-01

    To describe the feeding practices and styles used by a diverse sample of low-income parents of preschool-age children. Thirty- to 60-minute meetings involving a semistructured interview and 2 questionnaires administered by the interviewer. Low-income communities in Philadelphia, PA. Thirty-two parents of 2- to 6-year-old children. The feeding practices and styles of low-income parents of preschoolers. Qualitative interviews analyzed iteratively following a thematic approach; quantitative data analyzed using nonparametric and chi-square tests. Qualitative analyses revealed parents used a myriad of feeding practices to accomplish child-feeding goals. Racial/ethnic differences were seen; East Asian parents used more child-focused decision-making processes, whereas black parents used more parent-focused decision-making processes. Quantitative analyses substantiated racial/ethnic differences; black parents placed significantly higher demands on children for the amounts (H = 5.89, 2 df, P = .05; Kruskal-Wallis) and types (H = 8.39, 2 df, P = .01; Kruskal-Wallis) of food eaten compared to parents of other races/ethnicities. In contrast, significantly higher proportions of East Asian parents were classified as having an indulgent feeding style compared to black parents and parents of other races/ethnicities (chi(2)[4, n = 32] = 9.29, P < .05). Findings provide support for tailoring nutrition education programs to meet the diverse needs of this target audience. Copyright 2010 Society for Nutrition Education. Published by Elsevier Inc. All rights reserved.

  4. Diversity of bacteria producing pigmented colonies in aerosol, snow and soil samples from remote glacial areas (Antarctica, Alps and Andes)

    Science.gov (United States)

    González-Toril, E.; Amils, R.; Delmas, R. J.; Petit, J.-R.; Komárek, J.; Elster, J.

    2008-04-01

    Four different communities and one culture of pigmented microbial assemblages were obtained by incubation in mineral medium of samples collected from high elevation snow in the Alps (Mt. Blanc area) and the Andes (Nevado Illimani summit, Bolivia), from Antarctic aerosol (French station Dumont d'Urville) and a maritime Antarctic soil (King George Island, South Shetlands, Uruguay Station Artigas). Molecular analysis of more than 200 16S rRNA gene sequences showed that all cultured cells belong to the Bacteria domain. The phylogenetic comparison with the currently available rDNA database allowed the identification of sequences belonging to Proteobacteria (Alpha-, Beta- and Gamma-proteobacteria), Actinobacteria and Bacteroidetes phyla. The Andes snow culture was the richest in bacterial diversity (eight microorganisms identified) and the maritime Antarctic soil the poorest (only one). Snow samples from Col du midi (Alps) and the Andes shared the highest number of identified microorganisms (Agrobacterium, Limnobacter, Aquiflexus and two uncultured Alphaproteobacteria clones). These two sampling sites also shared four sequences with the Antarctic aerosol sample (Limnobacter, Pseudonocardia and an uncultured Alphaproteobacteria clone). The only microorganism identified in the maritime Antarctica soil (Brevundimonas sp.) was also detected in the Antarctic aerosol. The two snow samples from the Alps only shared one common microorganism. Most of the identified microorganisms have been detected previously in cold environments (Dietzia kujamenisi, Pseudonocardia Antarctica, Hydrogenophaga palleronii and Brebundimonas sp.), marine sediments (Aquiflexus balticus, Pseudomonas pseudoalkaligenes, Pseudomonas sp. and one uncultured Alphaproteobacteria), and soils and rocks (Pseudonocardia sp., Agrobactrium sp., Limnobacter sp. and two uncultured Alphaproteobacetria clones). Air current dispersal is the best model to explain the presence of very specific microorganisms, like those

  5. Nucleotide polymorphism and within-gene recombination in Daphnia magna and D. pulex, two cyclical parthenogens.

    Science.gov (United States)

    Haag, Christoph R; McTaggart, Seanna J; Didier, Anaïs; Little, Tom J; Charlesworth, Deborah

    2009-05-01

    Theory predicts that partially asexual organisms may make the "best of both worlds": for the most part, they avoid the costs of sexual reproduction, while still benefiting from an enhanced efficiency of selection compared to obligately asexual organisms. There is, however, little empirical data on partially asexual organisms to test this prediction. Here we examine patterns of nucleotide diversity at eight nuclear loci in continentwide samples of two species of cyclically parthenogenetic Daphnia to assess the effect of partial asexual reproduction on effective population size and amount of recombination. Both species have high nucleotide diversities and show abundant evidence for recombination, yielding large estimates of effective population sizes (300,000-600,000). This suggests that selection will act efficiently even on mutations with small selection coefficients. Divergence between the two species is less than one-tenth of previous estimates, which were derived using a mitochondrial molecular clock. As the two species investigated are among the most distantly related species of the genus, this suggests that the genus Daphnia may be considerably younger than previously thought. Daphnia has recently received increased attention because it is being developed as a model organism for ecological and evolutionary genomics. Our results confirm the attractiveness of Daphnia as a model organism, because the high nucleotide diversity and low linkage disequilibrium suggest that fine-scale mapping of genes affecting phenotypes through association studies should be feasible.

  6. Longitudinal Prediction of Suicide Attempts for a Diverse Adolescent Sample of Native Hawaiians, Pacific Peoples, and Asian Americans.

    Science.gov (United States)

    Hishinuma, Earl S; Smith, Myra D; McCarthy, Kayne; Lee, Mark; Goebert, Deborah A; Sugimoto-Matsuda, Jeanelle J; Andrade, Naleen N; Philip, Jacques B; Chung-Do, Jane J; Hamamoto, Reid S; Andrade, Joy K L

    2017-01-10

    The objective of this study was to determine the longitudinal predictors of past-6-month suicide attempts for a diverse adolescent sample of Native Hawaiians, Pacific peoples, and Asian Americans. The study used longitudinal data from the Hawaiian High Schools Health Survey (N = 2,083, 9th to 11th graders, 1992-1993 and 1993-1994 school years). A stepwise multiple logistic regression was conducted. The final model consisted of three statistically significant predictors: (1) Time 1 suicide attempt, odds ratio = 30.6; (2) state anxiety, odds ratio = 4.9; and (3) parent expectations, odds ratio = 1.9. Past suicide attempt was by far the strongest predictor of future suicide attempts. Implications are discussed, including the need for screening of prior suicide attempts and focused interventions after suicide attempts.

  7. DArT, SNP, and SSR analyses of genetic diversity in Lolium perenne L. using bulk sampling.

    Science.gov (United States)

    Liu, Siyang; Feuerstein, Ulf; Luesink, Wilbert; Schulze, Sabine; Asp, Torben; Studer, Bruno; Becker, Heiko C; Dehmer, Klaus J

    2018-01-22

    Lolium perenne L. is the most important forage grass species in temperate regions. It is also considered as a sustainable source of biomass for energy production. However, improvement in biomass yield has been limited by comparison with other major crops. More efficient utilisation of genetic resources and improved breeding schemes are required to advance L. perenne breeding. In an attempt to elucidate the extent of genetic diversity in L. perenne, 1384 DArT, 182 SNP and 48 SSR markers were applied to 297 accessions (Set I) contributed by three German breeding companies and the IPK Genebank. Due to the heterogeneous nature of Lolium accessions, bulk samples were used. Apart from germplasm set I, additional set II and set III was used to determine the reproducibility of marker system and judge the feasibility of bulk strategy in this study. By assessing different bulk sizes, 24 individuals per sample were shown to be a representative number of plants to discriminate different accessions. Among the 297 accessions, all marker types revealed a high polymorphism rate; 1.99, 2.00 and 8.19 alleles, were obtained per locus on average using DArTs, SNPs and SSRs, respectively. The Jaccard distance for DArT markers ranged from 0.00 to 0.73, the Modified Roger's distance (MRD) for SNP markers ranged from 0.03 to 0.52, and for SSR markers from 0.26 to 0.76. Gene diversity for dominant DArT and co-dominant SNP and SSR markers was found to be 0.26, 0.32 and 0.45, respectively. DArT markers showed the highest consistency and reproducibility. The resulting data were evaluated using a number of different classification methods, but none of the methods showed a clear differentiation into distinct genetic pools. With regard to hybrid breeding, this will possibly impede substantial progress towards increased biomass yields of L. perenne by utilising heterosis.

  8. Single Nucleotide Polymorphism

    DEFF Research Database (Denmark)

    Børsting, Claus; Pereira, Vania; Andersen, Jeppe Dyrberg

    2014-01-01

    Single nucleotide polymorphisms (SNPs) are the most frequent DNA sequence variations in the genome. They have been studied extensively in the last decade with various purposes in mind. In this chapter, we will discuss the advantages and disadvantages of using SNPs for human identification...... technologies (also called next generation sequencing or NGS) have the potential to completely transform forensic genetic investigations as we know them today. Here, we will make a short introduction to NGS and explain how NGS may combine analysis of the traditional forensic genetic markers with analysis...

  9. Ultradeep 16S rRNA sequencing analysis of geographically similar but diverse unexplored marine samples reveal varied bacterial community composition.

    Directory of Open Access Journals (Sweden)

    Chairmandurai Aravindraja

    Full Text Available BACKGROUND: Bacterial community composition in the marine environment differs from one geographical location to another. Reports that delineate the bacterial diversity of different marine samples from geographically similar location are limited. The present study aims to understand whether the bacterial community compositions from different marine samples harbour similar bacterial diversity since these are geographically related to each other. METHODS AND PRINCIPAL FINDINGS: In the present study, 16S rRNA deep sequencing analysis targeting V3 region was performed using Illumina bar coded sequencing. A total of 22.44 million paired end reads were obtained from the metagenomic DNA of Marine sediment, Rhizosphere sediment, Seawater and the epibacterial DNA of Seaweed and Seagrass. Diversity index analysis revealed that Marine sediment has the highest bacterial diversity and the least bacterial diversity was observed in Rhizosphere sediment. Proteobacteria, Actinobacteria and Bacteroidetes were the dominant taxa present in all the marine samples. Nearly 62-71% of rare species were identified in all the samples and most of these rare species were unique to a particular sample. Further taxonomic assignment at the phylum and genus level revealed that the bacterial community compositions differ among the samples. CONCLUSION: This is the first report that supports the fact that, bacterial community composition is specific for specific samples irrespective of its similar geographical location. Existence of specific bacterial community for each sample may drive overall difference in bacterial structural composition of each sample. Further studies like whole metagenomic sequencing will throw more insights to the key stone players and its interconnecting metabolic pathways. In addition, this is one of the very few reports that depicts the unexplored bacterial diversity of marine samples (Marine sediment, Rhizosphere sediment, Seawater and the host associated

  10. Ultradeep 16S rRNA sequencing analysis of geographically similar but diverse unexplored marine samples reveal varied bacterial community composition.

    Science.gov (United States)

    Aravindraja, Chairmandurai; Viszwapriya, Dharmaprakash; Karutha Pandian, Shunmugiah

    2013-01-01

    Bacterial community composition in the marine environment differs from one geographical location to another. Reports that delineate the bacterial diversity of different marine samples from geographically similar location are limited. The present study aims to understand whether the bacterial community compositions from different marine samples harbour similar bacterial diversity since these are geographically related to each other. In the present study, 16S rRNA deep sequencing analysis targeting V3 region was performed using Illumina bar coded sequencing. A total of 22.44 million paired end reads were obtained from the metagenomic DNA of Marine sediment, Rhizosphere sediment, Seawater and the epibacterial DNA of Seaweed and Seagrass. Diversity index analysis revealed that Marine sediment has the highest bacterial diversity and the least bacterial diversity was observed in Rhizosphere sediment. Proteobacteria, Actinobacteria and Bacteroidetes were the dominant taxa present in all the marine samples. Nearly 62-71% of rare species were identified in all the samples and most of these rare species were unique to a particular sample. Further taxonomic assignment at the phylum and genus level revealed that the bacterial community compositions differ among the samples. This is the first report that supports the fact that, bacterial community composition is specific for specific samples irrespective of its similar geographical location. Existence of specific bacterial community for each sample may drive overall difference in bacterial structural composition of each sample. Further studies like whole metagenomic sequencing will throw more insights to the key stone players and its interconnecting metabolic pathways. In addition, this is one of the very few reports that depicts the unexplored bacterial diversity of marine samples (Marine sediment, Rhizosphere sediment, Seawater) and the host associated marine samples (Seaweed and Seagrass) at higher depths from

  11. Palindromic nucleotide analysis in human T cell receptor rearrangements.

    Directory of Open Access Journals (Sweden)

    Santosh K Srivastava

    Full Text Available Diversity of T cell receptor (TCR genes is primarily generated by nucleotide insertions upon rearrangement from their germ line-encoded V, D and J segments. Nucleotide insertions at V-D and D-J junctions are random, but some small subsets of these insertions are exceptional, in that one to three base pairs inversely repeat the sequence of the germline DNA. These short complementary palindromic sequences are called P nucleotides. We apply the ImmunoSeq deep-sequencing assay to the third complementarity determining region (CDR3 of the β chain of T cell receptors, and use the resulting data to study P nucleotides in the repertoire of naïve and memory CD8(+ and CD4(+ T cells. We estimate P nucleotide distributions in a cross section of healthy adults and different T cell subtypes. We show that P nucleotide frequency in all T cell subtypes ranges from 1% to 2%, and that the distribution is highly biased with respect to the coding end of the gene segment. Classification of observed palindromic sequences into P nucleotides using a maximum conditional probability model shows that single base P nucleotides are very rare in VDJ recombination; P nucleotides are primarily two bases long. To explore the role of P nucleotides in thymic selection, we compare P nucleotides in productive and non-productive sequences of CD8(+ naïve T cells. The naïve CD8(+ T cell clones with P nucleotides are more highly expanded.

  12. Bacterial diversity of autotrophic enriched cultures from remote, glacial Antarctic, Alpine and Andean aerosol, snow and soil samples

    Directory of Open Access Journals (Sweden)

    E. González-Toril

    2009-01-01

    Full Text Available Four different communities and one culture of autotrophic microbial assemblages were obtained by incubation of samples collected from high elevation snow in the Alps (Mt. Blanc area and the Andes (Nevado Illimani summit, Bolivia, from Antarctic aerosol (French station Dumont d'Urville and a maritime Antarctic soil (King George Island, South Shetlands, Uruguay Station Artigas, in a minimal mineral (oligotrophic media. Molecular analysis of more than 200 16S rRNA gene sequences showed that all cultured cells belong to the Bacteria domain. Phylogenetic comparison with the currently available rDNA database allowed sequences belonging to Proteobacteria Alpha-, Beta- and Gamma-proteobacteria, Actinobacteria and Bacteroidetes phyla to be identified. The Andes snow culture was the richest in bacterial diversity (eight microorganisms identified and the marine Antarctic soil the poorest (only one. Snow samples from Col du Midi (Alps and the Andes shared the highest number of identified microorganisms (Agrobacterium, Limnobacter, Aquiflexus and two uncultured Alphaproteobacteria clones. These two sampling sites also shared four sequences with the Antarctic aerosol sample (Limnobacter, Pseudonocardia and an uncultured Alphaproteobacteriaclone. The only microorganism identified in the Antarctica soil (Brevundimonas sp. was also detected in the Antarctic aerosol. Most of the identified microorganisms had been detected previously in cold environments, marine sediments soils and rocks. Air current dispersal is the best model to explain the presence of very specific microorganisms, like those identified in this work, in environments very distant and very different from each other.

  13. Sexual identity development and self-esteem as predictors of body image in a racially diverse sample of gay men.

    Science.gov (United States)

    Udall-Weiner, Dana

    2009-01-01

    The current study examined the relationship between sexual identity development and body image, as well as the potential mediating effect of self-esteem, in a community sample of gay men. A diverse group of participants (N = 172), recruited through listservs and flyers, completed an online survey. Regression analyses were conducted to assess the relationships between identity development and self-esteem, identity development and body image, self-esteem and body image, and the mediating role of self-esteem. As predicted, significant relationships were identified between each pair of variables, and self-esteem was found to be a mediator when the sample was considered as a whole. When participants of color were compared to those who were White, however, between-group differences emerged; identity stage did not predict self-esteem or body image for participants of color, nor did the mediated relationship exist. Self-esteem did predict body image in both groups. The sociocultural context of these findings is considered.

  14. Diversity in the stellar velocity dispersion profiles of a large sample of Brightest Cluster Galaxies z ≤ 0.3

    Science.gov (United States)

    Loubser, S. I.; Hoekstra, H.; Babul, A.; O'Sullivan, E.

    2018-02-01

    We analyse spatially-resolved deep optical spectroscopy of Brightest Cluster Galaxies (BCGs) located in 32 massive clusters with redshifts of 0.05 ≤z ≤ 0.30, to investigate their velocity dispersion profiles. We compare these measurements to those of other massive early-type galaxies, as well as central group galaxies, where relevant. This unique, large sample extends to the most extreme of massive galaxies, spanning MK between -25.7 to -27.8 mag, and host cluster halo mass M500 up to 1.7 × 1015 M⊙. To compare the kinematic properties between brightest group and cluster members, we analyse similar spatially-resolved long-slit spectroscopy for 23 nearby Brightest Group Galaxies (BGGs) from the Complete Local-Volume Groups Sample (CLoGS). We find a surprisingly large variety in velocity dispersion slopes for BCGs, with a significantly larger fraction of positive slopes, unique compared to other (non-central) early-type galaxies as well as the majority of the brightest members of the groups. We find that the velocity dispersion slopes of the BCGs and BGGs correlate with the luminosity of the galaxies, and we quantify this correlation. It is not clear whether the full diversity in velocity dispersion slopes that we see is reproduced in simulations.

  15. A high diversity of Eurasian lineage low pathogenicity avian influenza A viruses circulate among wild birds sampled in Egypt.

    Directory of Open Access Journals (Sweden)

    Nancy A Gerloff

    Full Text Available Surveillance for influenza A viruses in wild birds has increased substantially as part of efforts to control the global movement of highly pathogenic avian influenza A (H5N1 virus. Studies conducted in Egypt from 2003 to 2007 to monitor birds for H5N1 identified multiple subtypes of low pathogenicity avian influenza A viruses isolated primarily from migratory waterfowl collected in the Nile Delta. Phylogenetic analysis of 28 viral genomes was performed to estimate their nearest ancestors and identify possible reassortants. Migratory flyway patterns were included in the analysis to assess gene flow between overlapping flyways. Overall, the viruses were most closely related to Eurasian, African and/or Central Asian lineage low pathogenicity viruses and belonged to 15 different subtypes. A subset of the internal genes seemed to originate from specific flyways (Black Sea-Mediterranean, East African-West Asian. The remaining genes were derived from a mixture of viruses broadly distributed across as many as 4 different flyways suggesting the importance of the Nile Delta for virus dispersal. Molecular clock date estimates suggested that the time to the nearest common ancestor of all viruses analyzed ranged from 5 to 10 years, indicating frequent genetic exchange with viruses sampled elsewhere. The intersection of multiple migratory bird flyways and the resulting diversity of influenza virus gene lineages in the Nile Delta create conditions favoring reassortment, as evident from the gene constellations identified by this study. In conclusion, we present for the first time a comprehensive phylogenetic analysis of full genome sequences from low pathogenic avian influenza viruses circulating in Egypt, underscoring the significance of the region for viral reassortment and the potential emergence of novel avian influenza A viruses, as well as representing a highly diverse influenza A virus gene pool that merits continued monitoring.

  16. Risk of radiation-induced subcutaneous fibrosis in relation to single nucleotide polymorphisms in TGFB1, SOD2, XRCC1, XRCC3, APEX and ATM - a study based on DNA from formalin fixed paraffin embedded tissue samples

    DEFF Research Database (Denmark)

    Andreassen, Christian Nicolaj; Alsner, Jan; Overgaard, Marie

    2006-01-01

    Purpose: In two previously published studies, associations with risk of radiation-induced subcutaneous fibrosis were found for single nucleotide polymorphisms (SNP) in TGFB1 (transforming growth factor beta 1 gene), XRCC1 (X-ray repair cross-complementing 1 gene), XRCC3 (X-ray repair cross-comple...

  17. Bacterial Diversity in Oral Samples of Children in Niger with Acute Noma, Acute Necrotizing Gingivitis, and Healthy Controls

    Science.gov (United States)

    Stadelmann, Benoît; Baratti-Mayer, Denise; Gizard, Yann; Mombelli, Andrea; Pittet, Didier; Schrenzel, Jacques

    2012-01-01

    Background Noma is a gangrenous disease that leads to severe disfigurement of the face with high morbidity and mortality, but its etiology remains unknown. Young children in developing countries are almost exclusively affected. The purpose of the study was to record and compare bacterial diversity in oral samples from children with or without acute noma or acute necrotizing gingivitis from a defined geographical region in Niger by culture-independent molecular methods. Methods and Principal Findings Gingival samples from 23 healthy children, nine children with acute necrotizing gingivitis, and 23 children with acute noma (both healthy and diseased oral sites) were amplified using “universal” PCR primers for the 16 S rRNA gene and pooled according to category (noma, healthy, or acute necrotizing gingivitis), gender, and site status (diseased or control site). Seven libraries were generated. A total of 1237 partial 16 S rRNA sequences representing 339 bacterial species or phylotypes at a 98–99% identity level were obtained. Analysis of bacterial composition and frequency showed that diseased (noma or acute necrotizing gingivitis) and healthy site bacterial communities are composed of similar bacteria, but differ in the prevalence of a limited group of phylotypes. Large increases in counts of Prevotella intermedia and members of the Peptostreptococcus genus are associated with disease. In contrast, no clear-cut differences were found between noma and non-noma libraries. Conclusions Similarities between acute necrotizing gingivitis and noma samples support the hypothesis that the disease could evolve from acute necrotizing gingivitis in certain children for reasons still to be elucidated. This study revealed oral microbiological patterns associated with noma and acute necrotizing gingivitis, but no evidence was found for a specific infection-triggering agent. PMID:22413030

  18. Bacterial diversity in oral samples of children in niger with acute noma, acute necrotizing gingivitis, and healthy controls.

    Directory of Open Access Journals (Sweden)

    Ignacio Bolivar

    Full Text Available Noma is a gangrenous disease that leads to severe disfigurement of the face with high morbidity and mortality, but its etiology remains unknown. Young children in developing countries are almost exclusively affected. The purpose of the study was to record and compare bacterial diversity in oral samples from children with or without acute noma or acute necrotizing gingivitis from a defined geographical region in Niger by culture-independent molecular methods.Gingival samples from 23 healthy children, nine children with acute necrotizing gingivitis, and 23 children with acute noma (both healthy and diseased oral sites were amplified using "universal" PCR primers for the 16 S rRNA gene and pooled according to category (noma, healthy, or acute necrotizing gingivitis, gender, and site status (diseased or control site. Seven libraries were generated. A total of 1237 partial 16 S rRNA sequences representing 339 bacterial species or phylotypes at a 98-99% identity level were obtained. Analysis of bacterial composition and frequency showed that diseased (noma or acute necrotizing gingivitis and healthy site bacterial communities are composed of similar bacteria, but differ in the prevalence of a limited group of phylotypes. Large increases in counts of Prevotella intermedia and members of the Peptostreptococcus genus are associated with disease. In contrast, no clear-cut differences were found between noma and non-noma libraries.Similarities between acute necrotizing gingivitis and noma samples support the hypothesis that the disease could evolve from acute necrotizing gingivitis in certain children for reasons still to be elucidated. This study revealed oral microbiological patterns associated with noma and acute necrotizing gingivitis, but no evidence was found for a specific infection-triggering agent.

  19. Bacterial diversity in oral samples of children in niger with acute noma, acute necrotizing gingivitis, and healthy controls.

    Science.gov (United States)

    Bolivar, Ignacio; Whiteson, Katrine; Stadelmann, Benoît; Baratti-Mayer, Denise; Gizard, Yann; Mombelli, Andrea; Pittet, Didier; Schrenzel, Jacques

    2012-01-01

    Noma is a gangrenous disease that leads to severe disfigurement of the face with high morbidity and mortality, but its etiology remains unknown. Young children in developing countries are almost exclusively affected. The purpose of the study was to record and compare bacterial diversity in oral samples from children with or without acute noma or acute necrotizing gingivitis from a defined geographical region in Niger by culture-independent molecular methods. Gingival samples from 23 healthy children, nine children with acute necrotizing gingivitis, and 23 children with acute noma (both healthy and diseased oral sites) were amplified using "universal" PCR primers for the 16 S rRNA gene and pooled according to category (noma, healthy, or acute necrotizing gingivitis), gender, and site status (diseased or control site). Seven libraries were generated. A total of 1237 partial 16 S rRNA sequences representing 339 bacterial species or phylotypes at a 98-99% identity level were obtained. Analysis of bacterial composition and frequency showed that diseased (noma or acute necrotizing gingivitis) and healthy site bacterial communities are composed of similar bacteria, but differ in the prevalence of a limited group of phylotypes. Large increases in counts of Prevotella intermedia and members of the Peptostreptococcus genus are associated with disease. In contrast, no clear-cut differences were found between noma and non-noma libraries. Similarities between acute necrotizing gingivitis and noma samples support the hypothesis that the disease could evolve from acute necrotizing gingivitis in certain children for reasons still to be elucidated. This study revealed oral microbiological patterns associated with noma and acute necrotizing gingivitis, but no evidence was found for a specific infection-triggering agent.

  20. Genomic lineages of Rhizobium etli revealed by the extent of nucleotide polymorphisms and low recombination

    Directory of Open Access Journals (Sweden)

    González Víctor

    2011-10-01

    Full Text Available Abstract Background Most of the DNA variations found in bacterial species are in the form of single nucleotide polymorphisms (SNPs, but there is some debate regarding how much of this variation comes from mutation versus recombination. The nitrogen-fixing symbiotic bacteria Rhizobium etli is highly variable in both genomic structure and gene content. However, no previous report has provided a detailed genomic analysis of this variation at nucleotide level or the role of recombination in generating diversity in this bacterium. Here, we compared draft genomic sequences versus complete genomic sequences to obtain reliable measures of genetic diversity and then estimated the role of recombination in the generation of genomic diversity among Rhizobium etli. Results We identified high levels of DNA polymorphism in R. etli, and found that there was an average divergence of 4% to 6% among the tested strain pairs. DNA recombination events were estimated to affect 3% to 10% of the genomic sample analyzed. In most instances, the nucleotide diversity (π was greater in DNA segments with recombinant events than in non-recombinant segments. However, this degree of recombination was not sufficiently large to disrupt the congruence of the phylogenetic trees, and further evaluation of recombination in strains quartets indicated that the recombination levels in this species are proportionally low. Conclusion Our data suggest that R. etli is a species composed of separated lineages with low homologous recombination among the strains. Horizontal gene transfer, particularly via the symbiotic plasmid characteristic of this species, seems to play an important role in diversity but the lineages maintain their evolutionary cohesiveness.

  1. An analysis of Apollo lunar soil samples 12070,889, 12030,187 and 12070,891: basaltic diversity at the Apollo 12 landing site and implications for classification of small-sized lunar samples.

    OpenAIRE

    Alexander, Louise; Snape, J. F.; Joy, K.H.; Downes, Hilary; Crawford, Ian

    2016-01-01

    Lunar mare basalts provide insights into the compositional diversity of the Moon's interior. Basalt fragments from the lunar regolith can potentially sample lava flows from regions of the Moon not previously visited, thus, increasing our understanding of lunar geological evolution. As part of a study of basaltic diversity at the Apollo 12 landing site, detailed petrological and geochemical data are provided here for 13 basaltic chips. In addition to bulk chemistry, we have analyzed the major,...

  2. Everyday Discrimination and Metabolic Syndrome Incidence in a Racially/Ethnically Diverse Sample: Study of Women's Health Across the Nation.

    Science.gov (United States)

    Beatty Moody, Danielle L; Chang, Yuefang; Brown, Charlotte; Bromberger, Joyce T; Matthews, Karen A

    2018-01-01

    Everyday discrimination may contribute to incident metabolic syndrome (MetS) in the United States and related racial/ethnic differences in MetS. The study investigated whether everyday discrimination predicted MetS in a diverse sample. A longitudinal, cohort study of 2132 women (mean [standard deviation] = 45.8 [2.7] years) who self-reported as black (n = 523), white (n = 1065), Chinese (n = 194), Japanese (n = 227), or Hispanic (n = 123) at baseline drawn from seven cities across the United States was conducted. MetS was defined in accordance with the National Cholesterol Education Program Adult Treatment Panel III criteria. The Everyday Discrimination scale was used to assess exposure to and level of everyday discrimination. Everyday discrimination exposure at baseline predicted a 33% greater incidence of MetS during the 13.89-year (standard deviation = 3.83, hazard ratio (HR) = 1.33, 95% confidence interval [CI] = 1.11-1.64, p = .001) follow-up in the full sample and was most pronounced in black, Hispanic, and Japanese women. Each 1-point increase in the continuous everyday discrimination score (HR = 1.03, 95% CI =1.01-1.05, p = .001) predicted a 3% greater incidence of MetS and, specifically, blood pressure (HR = 1.01, 95% CI = 1.00-1.03, p = .04), waist circumference (HR = 1.05, 95% CI =1.03-1.06, p level (HR = 1.02, 95% CI =1.00-1.04, p = .01). These associations were independent of risk factors including physical activity, socioeconomic status, smoking, and alcohol consumption. Everyday discrimination contributes to poorer metabolic health in midlife women in the United States. These findings have clinical implications for the development of MetS and, ultimately, cardiovascular disease and diabetes, and intervention strategies to reduce these outcomes.

  3. Disparities in reported reasons for not initiating or stopping antiretroviral treatment among a diverse sample of persons living with HIV.

    Science.gov (United States)

    Johnson, Mallory O; Chesney, Margaret A; Neilands, Torsten B; Dilworth, Samantha E; Remien, Robert H; Weinhardt, Lance S; Wong, F Lennie; Morin, Stephen F

    2009-02-01

    Disparities in the use of antiretroviral therapy (ART) for HIV disease have been documented across race, gender, and substance use groups. The current analysis compares self-reported reasons for never taking or stopping ART among a diverse sample of men and women living with HIV. Cross-sectional interview. HIV + (N = 3,818) adults, 968 of whom reported discontinuing or never using ART. Computerized self-administered and interviewer-administered self-reported demographic and treatment variables, including gender, race, ethnicity, CD4 count, detectable viral load, and reported reasons for not taking antiretroviral therapy. Despite equivalent use of ART in the current sample, African-American respondents were 1.7 times more likely to report wanting to hide their HIV status and 1.7 times more likely to report a change in doctors/clinics as reasons for stopping ART (p = .049, and p = .042) and had odds 4.5 times those of non-African Americans of reporting waiting for viral marker counts to worsen (p = tendency (OR = 0.4) for women to endorse concerns of keeping their HIV status hidden as a reason for stopping ART compared to men (p = .003). Although those with an IDU history were less likely to be on ART, no differences in reasons for stopping or never initiating ART were found between those with and without an IDU history. A desire to conceal HIV status as well as a change in doctors/clinics as reasons for discontinuing ART were considerably more common among African Americans, suggesting that perceived HIV/AIDS stigma is an obstacle to maintenance of treatment. Findings also indicate differences in reasons for stopping ART by gender and a perceived desire to wait for counts to worsen as a reason for not taking ART by African Americans, regardless of detectable viral load, CD4 count, age, education, employment, sexual orientation, and site.

  4. Body Dissatisfaction in a Diverse Sample of Young Men Who Have Sex With Men: The P18 Cohort Study.

    Science.gov (United States)

    Siconolfi, Daniel E; Kapadia, Farzana; Moeller, Robert W; Eddy, Jessica A; Kupprat, Sandra A; Kingdon, Molly J; Halkitis, Perry N

    2016-07-01

    Young men who have sex with men (YMSM) may be at greater risk for body dissatisfaction, compared to their heterosexual peers. However, differences within YMSM populations are understudied, precluding the identification of YMSM who are at greatest risk. This study examined body dissatisfaction in a racially/ethnically diverse sample of YMSM ages 18-19 in New York City. Using cross-sectional data from the baseline visit of a longitudinal cohort study of YMSM (N = 591), body dissatisfaction was assessed using the Male Body Attitudes Scale. Three outcomes were modeled using linear regression: (1) overall body dissatisfaction, (2) muscularity dissatisfaction, and (3) body fat dissatisfaction. Covariates in the models included race/ethnicity, sexual orientation, BMI, gay community affiliation, and internalized homonegativity. White YMSM experienced greater body dissatisfaction across the three models. Internalized homonegativity was a statistically significant predictor of dissatisfaction across the three models, though its association with body dissatisfaction was relatively small. The findings point to future avenues of research, particularly qualitative research to explore demographic and cultural nuances in body attitudes among YMSM.

  5. Socioenvironmental, Personal, and Behavioral Correlates of Severe Obesity among an Ethnically/Racially Diverse Sample of US Adolescents.

    Science.gov (United States)

    Bauer, Katherine W; Marcus, Marsha D; Larson, Nicole; Neumark-Sztainer, Dianne

    2017-06-26

    Severe obesity among adolescents, also known as class 2 and 3 obesity, is increasing in prevalence, yet, little is known about adolescents with severe obesity. The objective of this study was to identify the socioenvironmental, personal, and behavioral correlates of severe obesity among an ethnically/racially diverse sample of US adolescents. A cross-sectional analysis of data from participants in the EAT 2010 study (n = 2706) was conducted. Adolescents completed in-class surveys, and height and weight were measured. Severe obesity was defined as a BMI ≥120% of the 95th percentile or ≥35 kg/m(2); class 1 obesity as a BMI ≥95th percentile but below severe obesity cut points, overweight as a BMI 5th percentile. General linear models were used to identify differences between adolescents by weight status, adjusted for covariates. Nine percent of adolescents had severe obesity. Compared with peers of other weight statuses, a greater proportion of adolescents with severe obesity reported parental encouragement to diet and peer weight teasing. Adolescents with severe obesity also reported lower self-esteem and body satisfaction. Binge eating was three times as prevalent among adolescents with severe obesity compared with peers of normal weight and twice as prevalent as among peers with class 1 obesity. Adolescents with severe obesity report several unique socioenvironmental, personal, and behavioral concerns that may diminish quality of life and may predict increased weight gain over time.

  6. Predictors of maternal child-feeding practices in an ethnically diverse sample and the relationship to child obesity.

    Science.gov (United States)

    Cachelin, Fary M; Thompson, Doug

    2013-08-01

    To investigate the relationship between maternal child-feeding practices and child adiposity in an ethnically diverse sample by examining three categories of relationships: 1) mothers' weight status; 2) mothers' investment in eating-related issues; and 3) mothers' concerns about child's weight. It was predicted that these variables would be related to mothers' use of restriction, monitoring, and pressure in child feeding, influencing child adiposity. A total of 563 mothers (306 Hispanic, 76 Asian, 36 Black, and 145 White) with children aged 2-11 years completed the Child Feeding Questionnaire and Eating Attitudes Test. Analyses used structural equation modeling. Ethnic differences in the resulting models emerged. Mothers' weight status negatively predicted maternal control over child's eating; heavier mothers reported less control over child's eating. Greater concern about child's weight was associated with more maternal control of child's eating for all groups. Maternal control over child's eating was predictive of child's body mass index only in the White group. Although maternal investment in eating-related issues did predict maternal control over child's eating for White mothers, this relationship did not exist for Hispanics. Different maternal factors influence mothers' control over their child's eating in Hispanic and White groups. In ethnic minorities, maternal control over child's eating may not influence child adiposity. Copyright © 2013 The Obesity Society.

  7. The arabidopsis cyclic nucleotide interactome

    KAUST Repository

    Donaldson, Lara Elizabeth

    2016-05-11

    Background Cyclic nucleotides have been shown to play important signaling roles in many physiological processes in plants including photosynthesis and defence. Despite this, little is known about cyclic nucleotide-dependent signaling mechanisms in plants since the downstream target proteins remain unknown. This is largely due to the fact that bioinformatics searches fail to identify plant homologs of protein kinases and phosphodiesterases that are the main targets of cyclic nucleotides in animals. Methods An affinity purification technique was used to identify cyclic nucleotide binding proteins in Arabidopsis thaliana. The identified proteins were subjected to a computational analysis that included a sequence, transcriptional co-expression and functional annotation analysis in order to assess their potential role in plant cyclic nucleotide signaling. Results A total of twelve cyclic nucleotide binding proteins were identified experimentally including key enzymes in the Calvin cycle and photorespiration pathway. Importantly, eight of the twelve proteins were shown to contain putative cyclic nucleotide binding domains. Moreover, the identified proteins are post-translationally modified by nitric oxide, transcriptionally co-expressed and annotated to function in hydrogen peroxide signaling and the defence response. The activity of one of these proteins, GLYGOLATE OXIDASE 1, a photorespiratory enzyme that produces hydrogen peroxide in response to Pseudomonas, was shown to be repressed by a combination of cGMP and nitric oxide treatment. Conclusions We propose that the identified proteins function together as points of cross-talk between cyclic nucleotide, nitric oxide and reactive oxygen species signaling during the defence response.

  8. Synthetic Nucleotides as Probes of DNA Polymerase Specificity

    Directory of Open Access Journals (Sweden)

    Jason M. Walsh

    2012-01-01

    Full Text Available The genetic code is continuously expanding with new nucleobases designed to suit specific research needs. These synthetic nucleotides are used to study DNA polymerase dynamics and specificity and may even inhibit DNA polymerase activity. The availability of an increasing chemical diversity of nucleotides allows questions of utilization by different DNA polymerases to be addressed. Much of the work in this area deals with the A family DNA polymerases, for example, Escherichia coli DNA polymerase I, which are DNA polymerases involved in replication and whose fidelity is relatively high, but more recent work includes other families of polymerases, including the Y family, whose members are known to be error prone. This paper focuses on the ability of DNA polymerases to utilize nonnatural nucleotides in DNA templates or as the incoming nucleoside triphosphates. Beyond the utility of nonnatural nucleotides as probes of DNA polymerase specificity, such entities can also provide insight into the functions of DNA polymerases when encountering DNA that is damaged by natural agents. Thus, synthetic nucleotides provide insight into how polymerases deal with nonnatural nucleotides as well as into the mutagenic potential of nonnatural nucleotides.

  9. Assessing the sampling effort required to estimate a species diversity in the groundfish assemblages of the North Sea

    NARCIS (Netherlands)

    Greenstreet, S.P.R.; Piet, G.J.

    2008-01-01

    Conserving and restoring biodiversity are key objectives for an ecosystem approach to management in the North Sea, but ecological quality objectives for the groundfish community instead concentrate on restoring size structure. Species richness and diversity estimates are strongly influenced by

  10. Mind-Mindedness as a Multidimensional Construct: Appropriate and Nonattuned Mind-Related Comments Independently Predict Infant-Mother Attachment in a Socially Diverse Sample

    Science.gov (United States)

    Meins, Elizabeth; Fernyhough, Charles; de Rosnay, Marc; Arnott, Bronia; Leekam, Susan R.; Turner, Michelle

    2012-01-01

    In a socially diverse sample of 206 infant-mother pairs, we investigated predictors of infants' attachment security at 15 months, with a particular emphasis on mothers' tendency to comment appropriately or in a non-attuned manner on their 8-month-olds' internal states (so-called mind-mindedness). Multinomial logistic regression analyses showed…

  11. Standardized subsets of the HGDP-CEPH Human Genome Diversity Cell Line Panel, accounting for atypical and duplicated samples and pairs of close relatives.

    Science.gov (United States)

    Rosenberg, Noah A

    2006-11-01

    The HGDP-CEPH Human Genome Diversity Cell Line Panel is a widely-used resource for studies of human genetic variation. Here, pairs of close relatives that have been included in the panel are identified. Together with information on atypical and duplicated samples, the inferred relative pairs suggest standardized subsets of the panel for use in future population-genetic studies.

  12. Prevalence and Serogroup Diversity of Salmonella for Broiler Neck Skin, Whole Carcass Rinse, and Whole Carcass Enrichment Sampling Methodologies following Air or Immersion Chilling.

    Science.gov (United States)

    Bourassa, D V; Holmes, J M; Cason, J A; Cox, N A; Rigsby, L L; Buhr, R J

    2015-11-01

    The purpose of this study was to evaluate neck skin (NS), whole carcass rinse (WCR), and whole carcass enrichment (WCE) sampling procedures for Salmonella isolation and serogroup identification from the same broiler chicken carcass treated with air or immersion chilling. Commercially processed and eviscerated broiler carcasses were collected from a commercial processing plant, individually bagged, and transported to the pilot processing plant. In experiment 1, carcasses were air chilled to 4°C. In experiment 2, carcasses were immersion chilled with or without chlorine. After air chilling, Salmonella was detected on 78% of NS and 89% of WCE samples. Only one Salmonella serogroup was detected from each of 13 Salmonella-positive NS samples, and two serogroups were detected on 1 Salmonella-positive NS sample. Only one Salmonella serogroup was detected from each of 13 Salmonella-positive WCE samples, and two serogroups were detected from 3 Salmonella-positive WCE samples. After immersion chilling without chlorine, Salmonella was detected on 38% of NS, 45% of WCR, and 100% of WCE samples. Without chlorine, the 15 Salmonella-positive NS samples included 14 samples with one serogroup and 1 sample with two serogroups. Only one Salmonella serogroup was detected from WCR samples after immersion chilling. Of 40 Salmonella-positive WCE samples, 23 had a one, 14 had two, and 3 had three Salmonella serogroups. After immersion chilling with chlorine, Salmonella was detected on 35% of NS, 0% of WCR, and 90% of WCE samples. With chlorine, the 14 Salmonella-positive NS samples included 11 samples with one serogroup and 3 samples with two serogroups. No Salmonella serogroups were detected from WCR samples after immersion chilling with 20 mg/liter free chlorine. The 36 Salmonella-positive WCE samples included 21 samples with one serogroup and 15 samples with two serogroups. NS and WCE sampling methodologies yielded similar prevalence and serogroup diversity after air chilling. However

  13. Single nucleotide polymorphism genotyping and its application on ...

    African Journals Online (AJOL)

    The nucleotide diversity across a genome is the source of most phenotypic variation. Such DNA polymorphism is the basis for the development of molecular markers, an indispensable tool in genetic mapping studies. In general, the high resolution fine mapping of genes is often limited by lack of sufficient number of ...

  14. Spatial patterns of distribution, abundance, and species diversity of small odontocetes estimated using density surface modeling with line transect sampling

    Science.gov (United States)

    Kanaji, Yu; Okazaki, Makoto; Miyashita, Tomio

    2017-06-01

    Spatial patterns of distribution, abundance, and species diversity of small odontocetes including species in the Delphinidae and Phocoenidae families were investigated using long-term dedicated sighting survey data collected between 1983 and 2006 in the North Pacific. Species diversity indices were calculated from abundance estimated using density surface modeling of line-transect data. The estimated abundance ranged from 19,521 individuals in killer whale to 1,886,022 in pantropical spotted dolphin. The predicted density maps showed that the habitats of small odontocetes corresponded well with distinct oceanic domains. Species richness was estimated to be highest between 30 and 40°N where warm- and cold-water currents converge. Simpson's Diversity Index showed latitudinal diversity gradients of decreasing species numbers toward the poles. Higher diversity was also estimated in the coastal areas and the zonal areas around 35-42°N. Coastal-offshore gradients and latitudinal gradients are known for many taxa. The zonal areas around 35°N and 40°N coincide with the Kuroshio Current and its extension and the subarctic boundary, respectively. These results suggest that the species diversity of small odontocetes primarily follows general patterns of latitudinal and longitudinal gradients, while the confluence of faunas originating in distinct water masses increases species diversify in frontal waters around 30-40°N. Population densities tended to be higher for the species inhabiting higher latitudes, but were highest for intermediate latitudes at approximately 35-40°N. According to latitudinal gradients in water temperature and biological productivity, the costs for thermoregulation will decrease in warmer low latitudes, while feeding efficiency will increase in colder high latitudes. These trade-offs could optimize population density in intermediate latitudes.

  15. Assessment of contemporary genetic diversity and inter-taxa/inter-region exchange of avian paramyxovirus serotype 1 in wild birds sampled in North America.

    Science.gov (United States)

    Ramey, Andrew M; Goraichuk, Iryna V; Hicks, Joseph T; Dimitrov, Kiril M; Poulson, Rebecca L; Stallknecht, David E; Bahl, Justin; Afonso, Claudio L

    2017-03-03

    Avian paramyxovirus serotype 1 (APMV-1) viruses are globally distributed, infect wild, peridomestic, and domestic birds, and sometimes lead to outbreaks of disease. Thus, the maintenance, evolution, and spread of APMV-1 viruses are relevant to avian health. In this study we sequenced the fusion gene from 58 APMV-1 isolates recovered from thirteen species of wild birds sampled throughout the USA during 2007-2014. We analyzed sequence information with previously reported data in order to assess contemporary genetic diversity and inter-taxa/inter-region exchange of APMV-1 in wild birds sampled in North America. Our results suggest that wild birds maintain previously undescribed genetic diversity of APMV-1; however, such diversity is unlikely to be pathogenic to domestic poultry. Phylogenetic analyses revealed that APMV-1 diversity detected in wild birds of North America has been found in birds belonging to numerous taxonomic host orders and within hosts inhabiting multiple geographic regions suggesting some level of viral exchange. However, our results also provide statistical support for associations between phylogenetic tree topology and host taxonomic order/region of sample origin which supports restricted exchange among taxa and geographical regions of North America for some APMV-1 sub-genotypes. We identify previously unrecognized genetic diversity of APMV-1 in wild birds in North America which is likely a function of continued viral evolution in reservoir hosts. We did not, however, find support for the emergence or maintenance of APMV-1 strains predicted to be pathogenic to poultry in wild birds of North America outside of the order Suliformes (i.e., cormorants). Furthermore, genetic evidence suggests that ecological drivers or other mechanisms may restrict viral exchange among taxa and regions of North America. Additional and more systematic sampling for APMV-1 in North America would likely provide further inference on viral dynamics for this infectious agent

  16. Assessment of contemporary genetic diversity and inter-taxa/inter-region exchange of avian paramyxovirus serotype 1 in wild birds sampled in North America

    Science.gov (United States)

    Ramey, Andy M.; Goraichuk, Iryna V.; Hicks, Joseph T.; Dimitrov, Kiril M.; Poulson, Rebecca L.; Stallknecht, David E.; Bahl, Justin; Afonso, Claudio L.

    2017-01-01

    BackgroundAvian paramyxovirus serotype 1 (APMV-1) viruses are globally distributed, infect wild, peridomestic, and domestic birds, and sometimes lead to outbreaks of disease. Thus, the maintenance, evolution, and spread of APMV-1 viruses are relevant to avian health.MethodsIn this study we sequenced the fusion gene from 58 APMV-1 isolates recovered from thirteen species of wild birds sampled throughout the USA during 2007–2014. We analyzed sequence information with previously reported data in order to assess contemporary genetic diversity and inter-taxa/inter-region exchange of APMV-1 in wild birds sampled in North America.ResultsOur results suggest that wild birds maintain previously undescribed genetic diversity of APMV-1; however, such diversity is unlikely to be pathogenic to domestic poultry. Phylogenetic analyses revealed that APMV-1 diversity detected in wild birds of North America has been found in birds belonging to numerous taxonomic host orders and within hosts inhabiting multiple geographic regions suggesting some level of viral exchange. However, our results also provide statistical support for associations between phylogenetic tree topology and host taxonomic order/region of sample origin which supports restricted exchange among taxa and geographical regions of North America for some APMV-1 sub-genotypes.ConclusionsWe identify previously unrecognized genetic diversity of APMV-1 in wild birds in North America which is likely a function of continued viral evolution in reservoir hosts. We did not, however, find support for the emergence or maintenance of APMV-1 strains predicted to be pathogenic to poultry in wild birds of North America outside of the order Suliformes (i.e., cormorants). Furthermore, genetic evidence suggests that ecological drivers or other mechanisms may restrict viral exchange among taxa and regions of North America. Additional and more systematic sampling for APMV-1 in North America would likely provide further inference on viral

  17. Clonal diversity of extended-spectrum beta-lactamase producing Escherichia coli isolates in fecal samples of wild animals.

    Science.gov (United States)

    Cristóvão, Filipe; Alonso, Carla Andrea; Igrejas, Gilberto; Sousa, Margarida; Silva, Vanessa; Pereira, José Eduardo; Lozano, Carmen; Cortés-Cortés, Gerardo; Torres, Carmen; Poeta, Patrícia

    2017-03-01

    The clonal diversity of extended-spectrum-β-lactamase (ESBL)-producing Escherichia coli isolates from nine different species of wild animals from distinct regions of Portugal and Spain and their content in replicon plasmids were analyzed. Among the initial 53 ESBL-producing E. coli isolates that were studied (from previous studies), 28 were selected, corresponding to different animal origins with distinct ESBL types and pulsed-field gel electrophoresis (PFGE) patterns. These 28 isolates produced different ESBLs ascribed to the following families: CTX-M, SHV and TEM. The isolates were classified into three phylogenetic groups: B1 (n = 11), A (n = 10) and D (n = 7). The seven E. coli of phylogroup D were then typed by multilocus sequence typing and ascribed to four distinct sequence types: ST117, ST115, ST2001 and ST69. The clonal diversity and relationship between isolates was studied by PFGE. Lastly, the plasmids were analyzed according to their incompatibility group using the PCR-based-replicon-typing scheme. A great diversity of replicon types was identified, with up to five per isolate. Most of the CTX-M-1 and SHV-12 producing E. coli isolates carried IncI1 or IncN replicons. The diversity of ESBL-producing E. coli isolates in wild animals, which can be disseminated in the environment, emphasizes the environmental and health problems that we face nowadays. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  18. Derivation of two well-behaved theoretical contagion indices and their sampling properties and application for assessing forest landscape diversity

    Science.gov (United States)

    Bernard R. Parresol

    2011-01-01

    Studies of spatial patterns of landscapes are useful to quantify human impact, predict wildlife effects, or describe variability of landscape features. A common approach to identify and quantify landscape structure is with a landscape scale model known as a contagion index. A contagion index quantifies two distinct components of landscape diversity: composition and...

  19. Stress, Mental Health, and Substance Abuse Problems in a Sample of Diversion Program Youths: An Exploratory Latent Class Analysis

    Science.gov (United States)

    Dembo, Richard; Briones, Rhissa; Gulledge, Laura; Karas, Lora; Winters, Ken C.; Belenko, Steven; Greenbaum, Paul E.

    2012-01-01

    Reflective of interest in mental health and substance abuse issues among youths involved with the justice system, we performed a latent class analysis on baseline information collected on 100 youths involved in two diversion programs. Results identified two groups of youths: Group 1: a majority of the youths, who had high levels of delinquency,…

  20. Single Nucleotide Polymorphisms and Linkage Disequilibrium in Sunflower

    Science.gov (United States)

    Kolkman, Judith M.; Berry, Simon T.; Leon, Alberto J.; Slabaugh, Mary B.; Tang, Shunxue; Gao, Wenxiang; Shintani, David K.; Burke, John M.; Knapp, Steven J.

    2007-01-01

    Genetic diversity in modern sunflower (Helianthus annuus L.) cultivars (elite oilseed inbred lines) has been shaped by domestication and breeding bottlenecks and wild and exotic allele introgression−the former narrowing and the latter broadening genetic diversity. To assess single nucleotide polymorphism (SNP) frequencies, nucleotide diversity, and linkage disequilibrium (LD) in modern cultivars, alleles were resequenced from 81 genic loci distributed throughout the sunflower genome. DNA polymorphisms were abundant; 1078 SNPs (1/45.7 bp) and 178 insertions-deletions (INDELs) (1/277.0 bp) were identified in 49.4 kbp of DNA/genotype. SNPs were twofold more frequent in noncoding (1/32.1 bp) than coding (1/62.8 bp) sequences. Nucleotide diversity was only slightly lower in inbred lines (θ = 0.0094) than wild populations (θ = 0.0128). Mean haplotype diversity was 0.74. When extraploted across the genome (∼3500 Mbp), sunflower was predicted to harbor at least 76.4 million common SNPs among modern cultivar alleles. LD decayed more slowly in inbred lines than wild populations (mean LD declined to 0.32 by 5.5 kbp in the former, the maximum physical distance surveyed), a difference attributed to domestication and breeding bottlenecks. SNP frequencies and LD decay are sufficient in modern sunflower cultivars for very high-density genetic mapping and high-resolution association mapping. PMID:17660563

  1. The EMBL Nucleotide Sequence Database.

    Science.gov (United States)

    Kanz, Carola; Aldebert, Philippe; Althorpe, Nicola; Baker, Wendy; Baldwin, Alastair; Bates, Kirsty; Browne, Paul; van den Broek, Alexandra; Castro, Matias; Cochrane, Guy; Duggan, Karyn; Eberhardt, Ruth; Faruque, Nadeem; Gamble, John; Diez, Federico Garcia; Harte, Nicola; Kulikova, Tamara; Lin, Quan; Lombard, Vincent; Lopez, Rodrigo; Mancuso, Renato; McHale, Michelle; Nardone, Francesco; Silventoinen, Ville; Sobhany, Siamak; Stoehr, Peter; Tuli, Mary Ann; Tzouvara, Katerina; Vaughan, Robert; Wu, Dan; Zhu, Weimin; Apweiler, Rolf

    2005-01-01

    The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl), maintained at the European Bioinformatics Institute (EBI) near Cambridge, UK, is a comprehensive collection of nucleotide sequences and annotation from available public sources. The database is part of an international collaboration with DDBJ (Japan) and GenBank (USA). Data are exchanged daily between the collaborating institutes to achieve swift synchrony. Webin is the preferred tool for individual submissions of nucleotide sequences, including Third Party Annotation (TPA) and alignments. Automated procedures are provided for submissions from large-scale sequencing projects and data from the European Patent Office. New and updated data records are distributed daily and the whole EMBL Nucleotide Sequence Database is released four times a year. Access to the sequence data is provided via ftp and several WWW interfaces. With the web-based Sequence Retrieval System (SRS) it is also possible to link nucleotide data to other specialist molecular biology databases maintained at the EBI. Other tools are available for sequence similarity searching (e.g. FASTA and BLAST). Changes over the past year include the removal of the sequence length limit, the launch of the EMBLCDSs dataset, extension of the Sequence Version Archive functionality and the revision of quality rules for TPA data.

  2. Increased Sampling Reveals Novel Lineages of Entamoeba: Consequences of Genetic Diversity and Host Specificity for Taxonomy and Molecular Detection

    OpenAIRE

    Stensvold, CR; LEBBAD, M.; Victory, EL; Verweij, JJ; Tannich, E.; Alfellani, M; Legarraga, P; Clark, CG

    2011-01-01

    To expand the representation for phylogenetic analysis, ten additional complete Entamoeba small-subunit rRNA gene sequences were obtained from humans, non-human primates, cattle and a tortoise. For some novel sequences no corresponding morphological data were available, and we suggest that these organisms should be referred to as ribosomal lineages (RL) rather than being assigned species names at present. To investigate genetic diversity and host specificity of selected Entamoeba species, a t...

  3. Microbial diversity in fecal samples depends on DNA extraction method: easyMag DNA extraction compared to QIAamp DNA stool mini kit extraction

    OpenAIRE

    Mirsepasi, Hengameh; Persson,Søren; Struve, Carsten; Andersen, Lee O B; Petersen, Andreas M.; Krogfelt, Karen A.

    2014-01-01

    Background There are challenges, when extracting bacterial DNA from specimens for molecular diagnostics, since fecal samples also contain DNA from human cells and many different substances derived from food, cell residues and medication that can inhibit downstream PCR. The purpose of the study was to evaluate two different DNA extraction methods in order to choose the most efficient method for studying intestinal bacterial diversity using Denaturing Gradient Gel Electrophoresis (DGGE). Findin...

  4. Multilocus analysis of nucleotide variation and speciation in three closely related Populus (Salicaceae) species.

    Science.gov (United States)

    Du, Shuhui; Wang, Zhaoshan; Ingvarsson, Pär K; Wang, Dongsheng; Wang, Junhui; Wu, Zhiqiang; Tembrock, Luke R; Zhang, Jianguo

    2015-10-01

    Historical tectonism and climate oscillations can isolate and contract the geographical distributions of many plant species, and they are even known to trigger species divergence and ultimately speciation. Here, we estimated the nucleotide variation and speciation in three closely related Populus species, Populus tremuloides, P. tremula and P. davidiana, distributed in North America and Eurasia. We analysed the sequence variation in six single-copy nuclear loci and three chloroplast (cpDNA) fragments in 497 individuals sampled from 33 populations of these three species across their geographic distributions. These three Populus species harboured relatively high levels of nucleotide diversity and showed high levels of nucleotide differentiation. Phylogenetic analysis revealed that P. tremuloides diverged earlier than the other two species. The cpDNA haplotype network result clearly illustrated the dispersal route from North America to eastern Asia and then into Europe. Molecular dating results confirmed that the divergence of these three species coincided with the sundering of the Bering land bridge in the late Miocene and a rapid uplift of the Qinghai-Tibetan Plateau around the Miocene/Pliocene boundary. Vicariance-driven successful allopatric speciation resulting from historical tectonism and climate oscillations most likely played roles in the formation of the disjunct distributions and divergence of these three Populus species. © 2015 John Wiley & Sons Ltd.

  5. Effects of Sample Size and Full Sibs on Genetic Diversity Characterization: A Case Study of Three Syntopic Iberian Pond-Breeding Amphibians.

    Science.gov (United States)

    Sánchez-Montes, Gregorio; Ariño, Arturo H; Vizmanos, José L; Wang, Jinliang; Martínez-Solano, Íñigo

    2017-07-01

    Accurate characterization of genetic diversity is essential for understanding population demography, predicting future trends and implementing efficient conservation policies. For that purpose, molecular markers are routinely developed for nonmodel species, but key questions regarding sampling design, such as calculation of minimum sample sizes or the effect of relatives in the sample, are often neglected. We used accumulation curves and sibship analyses to explore how these 2 factors affect marker performance in the characterization of genetic diversity. We illustrate this approach with the analysis of an empirical dataset including newly optimized microsatellite sets for 3 Iberian amphibian species: Hyla molleri, Epidalea calamita, and Pelophylax perezi. We studied 17-21 populations per species (total n = 547, 652, and 516 individuals, respectively), including a reference locality in which the effect of sample size was explored using larger samples (77-96 individuals). As expected, FIS and tests for Hardy-Weinberg equilibrium and linkage disequilibrium were affected by the presence of full sibs, and most initially inferred disequilibria were no longer statistically significant when full siblings were removed from the sample. We estimated that to obtain reliable estimates, the minimum sample size (potentially including full sibs) was close to 20 for expected heterozygosity, and between 50 and 80 for allelic richness. Our pilot study based on a reference population provided a rigorous assessment of marker properties and the effects of sample size and presence of full sibs in the sample. These examples illustrate the advantages of this approach to produce robust and reliable results for downstream analyses. © The American Genetic Association 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  6. Genetic Diversity of Campylobacter jejuni and Campylobacter coli Isolates from Conventional Broiler Flocks and the Impacts of Sampling Strategy and Laboratory Method.

    Science.gov (United States)

    Vidal, A B; Colles, F M; Rodgers, J D; McCarthy, N D; Davies, R H; Maiden, M C J; Clifton-Hadley, F A

    2016-04-01

    The genetic diversity of Campylobacter jejuni and Campylobacter coliisolates from commercial broiler farms was examined by multilocus sequence typing (MLST), with an assessment of the impact of the sample type and laboratory method on the genotypes of Campylobacter isolated. A total of 645C. jejuniand 106C. coli isolates were obtained from 32 flocks and 17 farms, with 47 sequence types (STs) identified. The Campylobacter jejuniisolates obtained by different sampling approaches and laboratory methods were very similar, with the same STs identified at similar frequencies, and had no major effect on the genetic profile of Campylobacter population in broiler flocks at the farm level. ForC. coli, the results were more equivocal. While some STs were widely distributed within and among farms and flocks, analysis of molecular variance (AMOVA) revealed a high degree of genetic diversity among farms forC. jejuni, where farm effects accounted for 70.5% of variance, and among flocks from the same farm (9.9% of variance for C. jejuni and 64.1% forC. coli). These results show the complexity of the population structure of Campylobacterin broiler production and that commercial broiler farms provide an ecological niche for a wide diversity of genotypes. The genetic diversity of C. jejuni isolates among broiler farms should be taken into account when designing studies to understand Campylobacter populations in broiler production and the impact of interventions. We provide evidence that supports synthesis of studies on C. jejuni populations even when laboratory and sampling methods are not identical. Copyright © 2016 Vidal et al.

  7. Genetic Diversity of Campylobacter jejuni and Campylobacter coli Isolates from Conventional Broiler Flocks and the Impacts of Sampling Strategy and Laboratory Method

    Science.gov (United States)

    Colles, F. M.; Rodgers, J. D.; McCarthy, N. D.; Davies, R. H.; Maiden, M. C. J.; Clifton-Hadley, F. A.

    2016-01-01

    The genetic diversity of Campylobacter jejuni and Campylobacter coli isolates from commercial broiler farms was examined by multilocus sequence typing (MLST), with an assessment of the impact of the sample type and laboratory method on the genotypes of Campylobacter isolated. A total of 645 C. jejuni and 106 C. coli isolates were obtained from 32 flocks and 17 farms, with 47 sequence types (STs) identified. The Campylobacter jejuni isolates obtained by different sampling approaches and laboratory methods were very similar, with the same STs identified at similar frequencies, and had no major effect on the genetic profile of Campylobacter population in broiler flocks at the farm level. For C. coli, the results were more equivocal. While some STs were widely distributed within and among farms and flocks, analysis of molecular variance (AMOVA) revealed a high degree of genetic diversity among farms for C. jejuni, where farm effects accounted for 70.5% of variance, and among flocks from the same farm (9.9% of variance for C. jejuni and 64.1% for C. coli). These results show the complexity of the population structure of Campylobacter in broiler production and that commercial broiler farms provide an ecological niche for a wide diversity of genotypes. The genetic diversity of C. jejuni isolates among broiler farms should be taken into account when designing studies to understand Campylobacter populations in broiler production and the impact of interventions. We provide evidence that supports synthesis of studies on C. jejuni populations even when laboratory and sampling methods are not identical. PMID:26873321

  8. Increased sampling reveals novel lineages of Entamoeba: consequences of genetic diversity and host specificity for taxonomy and molecular detection.

    Science.gov (United States)

    Stensvold, C Rune; Lebbad, Marianne; Victory, Emma L; Verweij, Jaco J; Tannich, Egbert; Alfellani, Mohammed; Legarraga, Paulette; Clark, C Graham

    2011-07-01

    To expand the representation for phylogenetic analysis, ten additional complete Entamoeba small-subunit rRNA gene sequences were obtained from humans, non-human primates, cattle and a tortoise. For some novel sequences no corresponding morphological data were available, and we suggest that these organisms should be referred to as ribosomal lineages (RL) rather than being assigned species names at present. To investigate genetic diversity and host specificity of selected Entamoeba species, a total of 91 new partial small subunit rRNA gene sequences were obtained, including 49 from Entamoeba coli, 18 from Entamoeba polecki, and 17 from Entamoeba hartmanni. We propose a new nomenclature for significant variants within established Entamoeba species. Based on current data we propose that the uninucleated-cyst-producing Entamoeba infecting humans is called Entamoeba polecki and divided into four subtypes (ST1-ST4) and that Entamoeba coli is divided into two subtypes (ST1-ST2). New hosts for several species were detected and, while host specificity and genetic diversity of several species remain to be clarified, it is clear that previous reliance on cultivated material has given us a misleading and incomplete picture of variation within the genus Entamoeba. Copyright © 2010 Elsevier GmbH. All rights reserved.

  9. Free amino acids and 5'-nucleotides in Finnish forest mushrooms.

    Science.gov (United States)

    Manninen, Hanna; Rotola-Pukkila, Minna; Aisala, Heikki; Hopia, Anu; Laaksonen, Timo

    2018-05-01

    Edible mushrooms are valued because of their umami taste and good nutritional values. Free amino acids, 5'-nucleotides and nucleosides were analyzed from four Nordic forest mushroom species (Lactarius camphoratus, Boletus edulis, Cantharellus cibarius, Craterellus tubaeformis) using high precision liquid chromatography analysis. To our knowledge, these taste components were studied for the first time from Craterellus tubaeformis and Lactarius camphoratus. The focus was on the umami amino acids and 5'-nucleotides. The free amino acid and 5'-nucleotide/nucleoside contents of studied species differed from each other. In all studied samples, umami amino acids were among five major free amino acids. The highest concentration of umami amino acids was on L. camphoratus whereas B. edulis had the highest content of sweet amino acids and C. cibarius had the highest content of bitter amino acids. The content of umami enhancing 5'-nucleotides were low in all studied species. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Sequencing, analyzing, and modeling small samples from large T cell repertoires

    NARCIS (Netherlands)

    Gerritsen, Bram

    2018-01-01

    Characterizing T cell repertoires is challenging, because repertoires are much larger (i.e. more diverse) than the samples that are sequenced. Additionally, TCRs may differ from each other by as little as a single nucleotide, making it difficult to distinguish erroneous sequences from genuine TCRs.

  11. Nucleotide excision repair in yeast

    NARCIS (Netherlands)

    Eijk, Patrick van

    2012-01-01

    Nucleotide Excision Repair (NER) is a conserved DNA repair pathway capable of removing a broad spectrum of DNA damage. In human cells a defect in NER leads to the disorder Xeroderma pigmentosum (XP). The yeast Saccharomyces cerevisiae is an excellent model organism to study the mechanism of NER. The

  12. Sampling a biodiversity hotspot: the orchid-bee fauna (Hymenoptera: Apidae) of Tarapoto, northeastern Peru, the richest and most diverse site of the Neotropics.

    Science.gov (United States)

    Nemésio, A; Rasmussen, C

    2014-08-01

    The orchid-bee fauna of the region of Tarapoto, northeastern Peru, was surveyed using seventeen different scents as baits to attract orchid-bee males. Six hundred and fifty-nine males belonging to 41 species were actively collected with insect nets during 120 hours in late July and early August, 2012. Euglossa dressleri Moure, 1968, Euglossa laurensi Bembé, 2008, and Euglossa maculilabris Moure, 1968, three species belonging to the Euglossa cybelia species-group, are here reported for Peru for the first time. Previous sporadic and unpublished samplings in the area recorded eleven additional species. With 53 species, the region of Tarapoto can be considered the richest single site in the Neotropics for orchid bees. Diversity, estimated with the Shannon-Wiener diversity index (H' = 3.02), was also the highest ever recorded for orchid bees.

  13. Sampling a biodiversity hotspot: the orchid-bee fauna (Hymenoptera: Apidae of Tarapoto, northeastern Peru, the richest and most diverse site of the Neotropics

    Directory of Open Access Journals (Sweden)

    A Nemésio

    Full Text Available The orchid-bee fauna of the region of Tarapoto, northeastern Peru, was surveyed using seventeen different scents as baits to attract orchid-bee males. Six hundred and fifty-nine males belonging to 41 species were actively collected with insect nets during 120 hours in late July and early August, 2012. Euglossa dressleriMoure, 1968, Euglossa laurensiBembé, 2008, and Euglossa maculilabrisMoure, 1968, three species belonging to the Euglossa cybelia species-group, are here reported for Peru for the first time. Previous sporadic and unpublished samplings in the area recorded eleven additional species. With 53 species, the region of Tarapoto can be considered the richest single site in the Neotropics for orchid bees. Diversity, estimated with the Shannon-Wiener diversity index (H′ = 3.02, was also the highest ever recorded for orchid bees.

  14. Single Nucleotide Polymorphisms in Common Bean: Their Discovery and Genotyping Using a Multiplex Detection System

    Directory of Open Access Journals (Sweden)

    E. Gaitán-Solís

    2008-11-01

    Full Text Available Single nucleotide polymorphism (SNP markers are by far the most common form of DNA polymorphism in a genome. The objectives of this study were to discover SNPs in common bean ( L. by comparing sequences from coding and noncoding regions obtained from the GenBank and genomic DNA and to compare sequencing results with those obtained using single base extension (SBE assays on the Luminex-100 system for use in high-throughput germplasm evaluation. We assessed the frequency of SNPs in 47 fragments of common bean DNA, using SBE as the evaluation methodology. We conducted a sequence analysis of 10 genotypes of cultivated and wild beans belonging to the Mesoamerican and Andean genetic pools of . For the 10 genotypes evaluated, a total of 20,964 bp of sequence were analyzed in each genotype and compared, resulting in the discovery of 239 SNPs and 133 InDels, giving an average SNP frequency of one per 88 bp and an InDel frequency of one per 157 bp. This is the equivalent of a nucleotide diversity (θ of 6.27 × 10. Comparisons with the SNP genotypes previously obtained by direct sequencing showed that the SBE assays on the Luminex-100 were accurate, with 2.5% being miscalled and 1% showing no signal. These results indicate that the Luminex-100 provides a high-throughput system that can be used to analyze SNPs in large samples of genotypes both for purposes of assessing diversity and also for mapping studies.

  15. Assessment of minimum sample sizes required to adequately represent diversity reveals inadequacies in datasets of domestic dog mitochondrial DNA.

    Science.gov (United States)

    Webb, Kristen; Allard, Marc

    2010-02-01

    Evolutionary and forensic studies commonly choose the mitochondrial control region as the locus for which to evaluate the domestic dog. However, the number of dogs that need to be sampled in order to represent the control region variation present in the worldwide population is yet to be determined. Following the methods of Pereira et al. (2004), we have demonstrated the importance of surveying the complete control region rather than only the popular left domain. We have also evaluated sample saturation in terms of the haplotype number and the number of polymorphisms within the control region. Of the most commonly cited evolutionary research, only a single study has adequately surveyed the domestic dog population, while all forensic studies have failed to meet the minimum values. We recommend that future studies consider dataset size when designing experiments and ideally sample both domains of the control region in an appropriate number of domestic dogs.

  16. C15271. The Chemical Diversity of Lantana camara: Analyses of Essential Oil Samples from Cuba, Nepal, and Yemen.

    Science.gov (United States)

    Satyal, Prabodh; Crouch, Rebecca A; Monzote, Lianet; Cos, Paul; Awadh Ali, Nasser A; Alhaj, Mehdi A; Setzer, William N

    2016-02-10

    The aerial parts of Lantana camara L. were collected from three different geographical locations: Artemisa (Cuba), Biratnagar (Nepal), and Sana'a (Yemen). The essential oils were obtained by hydrodistillation and analyzed by gas chromatography - mass spectrometry. A cluster analysis of 39 L. camara essential oil compositions revealed eight major chemotypes: β-caryophyllene, germacrene D, ar-curcumene/zingiberene, γ-curcumen-15-al/epi-β-bisabolol, (E)-nerolidol, davanone, eugenol/alloaromadendrene, and carvone. The sample from Cuba falls into the group dominated by (E)-nerolidol, the sample from Nepal is a davanone chemotype, and the sample from Yemen belongs to the β-caryophyllene chemotype. The chemical composition of L. camara oil plays a role in the biological activity; the β-caryophyllene and (E)-nerolidol chemotypes showed antimicrobial and cytotoxic activities. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  17. Phosphate-Modified Nucleotides for Monitoring Enzyme Activity.

    Science.gov (United States)

    Ermert, Susanne; Marx, Andreas; Hacker, Stephan M

    2017-04-01

    Nucleotides modified at the terminal phosphate position have been proven to be interesting entities to study the activity of a variety of different protein classes. In this chapter, we present various types of modifications that were attached as reporter molecules to the phosphate chain of nucleotides and briefly describe the chemical reactions that are frequently used to synthesize them. Furthermore, we discuss a variety of applications of these molecules. Kinase activity, for instance, was studied by transfer of a phosphate modified with a reporter group to the target proteins. This allows not only studying the activity of kinases, but also identifying their target proteins. Moreover, kinases can also be directly labeled with a reporter at a conserved lysine using acyl-phosphate probes. Another important application for phosphate-modified nucleotides is the study of RNA and DNA polymerases. In this context, single-molecule sequencing is made possible using detection in zero-mode waveguides, nanopores or by a Förster resonance energy transfer (FRET)-based mechanism between the polymerase and a fluorophore-labeled nucleotide. Additionally, fluorogenic nucleotides that utilize an intramolecular interaction between a fluorophore and the nucleobase or an intramolecular FRET effect have been successfully developed to study a variety of different enzymes. Finally, also some novel techniques applying electron paramagnetic resonance (EPR)-based detection of nucleotide cleavage or the detection of the cleavage of fluorophosphates are discussed. Taken together, nucleotides modified at the terminal phosphate position have been applied to study the activity of a large diversity of proteins and are valuable tools to enhance the knowledge of biological systems.

  18. Insertions/deletions-associated nucleotide polymorphism in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Changjiang Guo

    2016-11-01

    Full Text Available Although high levels of within-species variation are commonly observed, a general mechanism for the origin of such variation is still lacking. Insertions and deletions (indels are a widespread feature of genomes and we hypothesize that there might be an association between indels and patterns of nucleotide polymorphism. Here, we investigate flanking sequences around 18 indels (>100bp among a large number of accessions of the plant, Arabidopsis thaliana. We found two distinct haplotypes, i.e. a nucleotide dimorphism, present around each of these indels and dimorphic haplotypes always corresponded to the indel-present/-absent patterns. In addition, the peaks of nucleotide diversity between the two divergent alleles were closely associated with these indels. Thus, there exists a close association between indels and dimorphisms. Further analysis suggests that indel-associated substitutions could be an important component of genetic variation shaping nucleotide polymorphism in Arabidopsis. Finally, we suggest a mechanism by which indels might generate these highly divergent haplotypes. This study provides evidence that nucleotide dimorphisms, which are frequently regarded as evidence of frequency-dependent selection, could be explained simply by structural variation in the genome.

  19. Bacterial contamination of whole-blood-derived platelets: the introduction of sample diversion and prestorage pooling with culture testing in the American Red Cross.

    Science.gov (United States)

    Benjamin, Richard J; Kline, Linda; Dy, Beth A; Kennedy, Jean; Pisciotto, Patricia; Sapatnekar, Suneeti; Mercado, Rachel; Eder, Anne F

    2008-11-01

    Bacterial sepsis following whole blood-derived platelet (WBP) transfusion has remained a substantial patient risk, primarily due to a lack of practical and effective means to limit or detect bacterial contamination. We describe the risk of reported septic reactions to WBPs and the introduction of prestorage-pooled whole blood-derived platelets (PSPs) collected using initial sample diversion and cultured for bacterial contamination. Product qualification and quality control (QC) testing with the Acrodose PL system (Pall Medical) were evaluated in four regional blood centers. Bacterial contamination risk was assessed by review of reported septic transfusion reactions to WBPs and by aerobic QC culture of leukoreduced PSPs utilizing automated microbial detection system cultures (BacT/ALERT 3D, bioMérieux). Before implementing PSPs (January 2003-December 2006), we distributed 2,535,043 WBP units and received 20 reports of septic reactions including 2 fatalities (7.9 per million [1:126,752] reactions and 0.79 per million [1:1,267,522] fatalities). In October 2006, PSPs were effectively implemented with a product qualification success rate of 99.6 percent and a mean yield of 4.0 x 10(11) platelets (PLTs) per pool. Whole blood collection sets with sample diversion technology were introduced during the operational trial and decreased the rate of confirmed-positive bacterial culture of PSPs from 2111 (1:474) to 965 (1:1036) per million (odds ratio, 0.46; 95% confidence interval, 0.22-0.95). No septic reactions to PSPs were reported (25,936 PSP units distributed). Sample diversion and bacterial culture are effective methods to reduce bacterial risk with WBP transfusion. Bacterial contamination of PSPs was assessed at 5.8-fold our current rate for apheresis PLTs utilizing comparable culture protocols.

  20. Sexual diversity in the United States: Results from a nationally representative probability sample of adult women and men.

    Science.gov (United States)

    Herbenick, Debby; Bowling, Jessamyn; Fu, Tsung-Chieh Jane; Dodge, Brian; Guerra-Reyes, Lucia; Sanders, Stephanie

    2017-01-01

    In 2015, we conducted a cross-sectional, Internet-based, U.S. nationally representative probability survey of 2,021 adults (975 men, 1,046 women) focused on a broad range of sexual behaviors. Individuals invited to participate were from the GfK KnowledgePanel®. The survey was titled the 2015 Sexual Exploration in America Study and survey completion took about 12 to 15 minutes. The survey was confidential and the researchers never had access to respondents' identifiers. Respondents reported on demographic items, lifetime and recent sexual behaviors, and the appeal of 50+ sexual behaviors. Most (>80%) reported lifetime masturbation, vaginal sex, and oral sex. Lifetime anal sex was reported by 43% of men (insertive) and 37% of women (receptive). Common lifetime sexual behaviors included wearing sexy lingerie/underwear (75% women, 26% men), sending/receiving digital nude/semi-nude photos (54% women, 65% men), reading erotic stories (57% of participants), public sex (≥43%), role-playing (≥22%), tying/being tied up (≥20%), spanking (≥30%), and watching sexually explicit videos/DVDs (60% women, 82% men). Having engaged in threesomes (10% women, 18% men) and playful whipping (≥13%) were less common. Lifetime group sex, sex parties, taking a sexuality class/workshop, and going to BDSM parties were uncommon (each diverse adult sexual behaviors than has previously been captured in U.S. nationally representative probability surveys. Implications for sexuality educators, clinicians, and individuals in the general population are discussed.

  1. Understanding and supporting women with polycystic ovary syndrome: a qualitative study in an ethnically diverse UK sample.

    Science.gov (United States)

    Hadjiconstantinou, Michelle; Mani, Hamidreza; Patel, Naina; Levy, Miles; Davies, Melanie; Khunti, Kamlesh; Stone, Margaret

    2017-07-01

    Polycystic ovary syndrome (PCOS) is a lifelong condition. Its symptoms have been linked with psychological consequences, but less attention has been given to the daily implications of living with PCOS. We aimed to explore women's experiences living with PCOS, and the potential acceptability of group education sessions for this target group. Women with PCOS were recruited from an ethnically diverse UK community. Twelve semi-structured interviews were conducted. Analysis was underpinned by the constant comparative approach and involved the identification and exploration of key themes. Participants reported a range of symptoms linked with PCOS, including problems relating to menstruation and weight difficulties. Hirsutism was reported as the most distressing symptom. Emergent themes included perceptions about symptoms and delays in receiving a diagnosis; psychological distress; practical implications of living with the condition; coping with PCOS and perceived support needs. Some findings were specific to cultural backgrounds. Participants were supportive of the idea of group education for women with PCOS and suggested a need to provide education within the community and health care providers. Women with PCOS experience high psychological distress and difficulties with coping with their condition. Suggested strategies to reduce the negative psychological impact include education at various levels. © 2017 The authors.

  2. Parental Expectations and Investments: Links to children's academic performance in an ethnically diverse low-income sample

    OpenAIRE

    Byrne, Cristal Lynn

    2013-01-01

    The aim of this short-term longitudinal study was to provide empirical support for the role that parental investments in children's education play in mediating the association between parental expectations and child academic outcomes. Participants were a hetergeneous sample of 426 low-income urban youth, ages 6 through 16 at the first time point of the current study. Results from regression analyses indicated that parental expectations at Time 1 predicted children's academic achievement outco...

  3. Psychometric properties of the intuitive eating scale-2 (IES-2) in a culturally diverse Hispanic American sample.

    Science.gov (United States)

    Saunders, Jessica F; Nichols-Lopez, Kristin A; Frazier, Leslie D

    2017-11-14

    Intuitive eating is an adaptive eating tendency consistently associated with positive physical and mental health outcomes, including lower risk for obesity and eating disorders (EDs). Obesity rates are disproportionately high in Hispanic American populations, yet the properties of intuitive eating remain to be examined in such samples. The current study examined the psychometric properties of the Intuitive Eating Scale-2 (IES-2) in a Hispanic American sample of adult college students (N=482), and related IES-2 scores to levels of disordered eating, body mass index (BMI), fruit and vegetable consumption, and body shape satisfaction. The final confirmatory factor analysis supported a three factor, 11 item measure with the subscales of Eating for Physical Rather Than Emotional Reasons, Reliance on Hunger and Satiety Cues, and Body Food Choice Congruence. The Unconditional Permission to Eat subscale could not be replicated in the current sample. As predicted, scores on the revised measure differed by BMI category and body shape satisfaction, and correlated with disordered eating tendencies and fruit and vegetable consumption. The current findings demonstrate that the modified IES-2 is better tailored to assess the cultural nuances influencing intuitive eating and can advance understanding how intuitive eating is understood and practiced in Hispanic Americans, compared to the original measure. Copyright © 2017. Published by Elsevier Ltd.

  4. The relationship between family-based adverse childhood experiences and substance use behaviors among a diverse sample of college students.

    Science.gov (United States)

    Forster, Myriam; Grigsby, Timothy J; Rogers, Christopher J; Benjamin, Stephanie M

    2018-01-01

    Research suggests that college students are an especially vulnerable subset of the population for substance use and misuse. However, despite evidence of the high prevalence of adverse childhood experiences (ACE) among students and the link between family-based ACE and substance use among older adults, this relationship remains understudied in college populations. Moreover, whether ACE represents a shared risk across substance use behaviors and ethnic groups is unknown. Data are student responses (n=2953) on the 2015 American College Health Association's National College Health Assessment II (ACHA-NCHA II) administered at one of the largest, most diverse public universities in California. Multivariable logistic and negative binomial regression models tested the association between individual and accumulated ACE and past 30-day alcohol, tobacco, marijuana, and illicit drug use, past 12-month prescription medication misuse and polysubstance use. Between 50% and 75% of students involved in substance use were ACE exposed. There was a significant dose-response relationship between ACE and substance use and polysubstance use. Although accumulated ACE increased risk for substance use, there was considerable ethnic variability in these associations. The graded effects of ACE for substance use underscore the link between family-based stressors and these behaviors in emergent adult college students. Our findings make a compelling case for investing in health initiatives that prioritize ACE screening and access to trauma-informed care in campus communities. Continued research with college populations is needed to replicate findings and clarify the role of ethnicity and culture in trauma response and help seeking behaviors. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Sexual diversity in the United States: Results from a nationally representative probability sample of adult women and men.

    Directory of Open Access Journals (Sweden)

    Debby Herbenick

    Full Text Available In 2015, we conducted a cross-sectional, Internet-based, U.S. nationally representative probability survey of 2,021 adults (975 men, 1,046 women focused on a broad range of sexual behaviors. Individuals invited to participate were from the GfK KnowledgePanel®. The survey was titled the 2015 Sexual Exploration in America Study and survey completion took about 12 to 15 minutes. The survey was confidential and the researchers never had access to respondents' identifiers. Respondents reported on demographic items, lifetime and recent sexual behaviors, and the appeal of 50+ sexual behaviors. Most (>80% reported lifetime masturbation, vaginal sex, and oral sex. Lifetime anal sex was reported by 43% of men (insertive and 37% of women (receptive. Common lifetime sexual behaviors included wearing sexy lingerie/underwear (75% women, 26% men, sending/receiving digital nude/semi-nude photos (54% women, 65% men, reading erotic stories (57% of participants, public sex (≥43%, role-playing (≥22%, tying/being tied up (≥20%, spanking (≥30%, and watching sexually explicit videos/DVDs (60% women, 82% men. Having engaged in threesomes (10% women, 18% men and playful whipping (≥13% were less common. Lifetime group sex, sex parties, taking a sexuality class/workshop, and going to BDSM parties were uncommon (each <8%. More Americans identified behaviors as "appealing" than had engaged in them. Romantic/affectionate behaviors were among those most commonly identified as appealing for both men and women. The appeal of particular behaviors was associated with greater odds that the individual had ever engaged in the behavior. This study contributes to our understanding of more diverse adult sexual behaviors than has previously been captured in U.S. nationally representative probability surveys. Implications for sexuality educators, clinicians, and individuals in the general population are discussed.

  6. Candida species diversity and antifungal susceptibility patterns in oral samples of HIV/AIDS patients in Baja California, Mexico.

    Science.gov (United States)

    Clark-Ordóñez, Isadora; Callejas-Negrete, Olga A; Aréchiga-Carvajal, Elva T; Mouriño-Pérez, Rosa R

    2017-04-01

    Candidiasis is the most common opportunistic fungal infection in HIV patients. The aims of this study were to identify the prevalence of carriers of Candida, Candida species diversity, and in vitro susceptibility to antifungal drugs. In 297 HIV/AIDS patients in Baja California, Mexico, Candida strains were identified by molecular methods (PCR-RFLP) from isolates of oral rinses of patients in Tijuana, Mexicali, and Ensenada. 56.3% of patients were colonized or infected with Candida. In Tijuana, there was a significantly higher percentage of carriers (75.5%). Out of the 181 strains that were isolated, 71.8% were Candida albicans and 28.2% were non-albicans species. The most common non-albicans species was Candida tropicalis (12.2%), followed by Candida glabrata (8.3%), Candida parapsilosis (2.2%), Candida krusei (1.7%), and Candida guilliermondii (1.1%). Candida dubliniensis was not isolated. Two associated species were found in 11 patients. In Mexicali and Ensenada, there was a lower proportion of Candida carriers compared to other regions in Mexico and worldwide, however, in Tijuana, a border town with many peculiarities, a higher carrier rate was found. In this population, only a high viral load was associated with oral Candida carriers. Other factors such as gender, use of antiretroviral therapy, CD4+ T-lymphocyte levels, time since diagnosis, and alcohol/ tobacco consumption, were not associated with Candida carriers. © The Author 2016. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  7. Executive functioning in a racially diverse sample of children who are overweight and at risk for eating disorders.

    Science.gov (United States)

    Goldschmidt, Andrea B; O'Brien, Setareh; Lavender, Jason M; Pearson, Carolyn M; Le Grange, Daniel; Hunter, Scott J

    2017-03-18

    Difficulties with executive functioning may underlie both overweight and loss of control (LOC) eating behavior across the age spectrum, but there is a relative paucity of research in children with both conditions. This study aimed to characterize general executive functioning among children with overweight and LOC eating as compared to their overweight and normal-weight peers. Participants were 75 racially diverse children (58.7% female; 81.3% African-American), aged 9-12y (M age = 10.5 ± 1.1), of whom 26 were overweight/obese and endorsed LOC eating (OW-LOC), 34 were overweight controls (OW-CON), and 15 were normal-weight controls (NW-CON). All children completed interview-based measures of eating pathology, and behavioral measures of executive functioning. Parents reported on behavioral facets of children's executive functioning. Groups were compared across parent-report measures and behavioral tasks using analyses of covariance (ANCOVAs) and multivariate analyses of covariance (MANCOVAs) which adjusted for general intellectual functioning. Significant group differences were revealed on a behavioral measure of planning, the Tower of London task [F (5,65) = 3.52; p = 0.007], and a behavioral measure of working memory, the List Sorting task [F (2,71) = 6.45; p = 0.003]. Post-hoc tests revealed that OW-LOC and OW-CON performed worse than NW-CON on the Tower of London, with relative decrements in accuracy rather than performance time. Further, OW-LOC performed worse than both OW-CON and NW-CON on the List Sorting task. Overweight with or without concomitant LOC eating in children may characterize a unique pattern of executive dysfunction. Interventions for eating- and weight-related problems in youth should address underlying deficits in planning and working memory. Copyright © 2017. Published by Elsevier Ltd.

  8. Sexual diversity in the United States: Results from a nationally representative probability sample of adult women and men

    Science.gov (United States)

    Herbenick, Debby; Bowling, Jessamyn; Fu, Tsung-Chieh (Jane); Guerra-Reyes, Lucia; Sanders, Stephanie

    2017-01-01

    In 2015, we conducted a cross-sectional, Internet-based, U.S. nationally representative probability survey of 2,021 adults (975 men, 1,046 women) focused on a broad range of sexual behaviors. Individuals invited to participate were from the GfK KnowledgePanel®. The survey was titled the 2015 Sexual Exploration in America Study and survey completion took about 12 to 15 minutes. The survey was confidential and the researchers never had access to respondents’ identifiers. Respondents reported on demographic items, lifetime and recent sexual behaviors, and the appeal of 50+ sexual behaviors. Most (>80%) reported lifetime masturbation, vaginal sex, and oral sex. Lifetime anal sex was reported by 43% of men (insertive) and 37% of women (receptive). Common lifetime sexual behaviors included wearing sexy lingerie/underwear (75% women, 26% men), sending/receiving digital nude/semi-nude photos (54% women, 65% men), reading erotic stories (57% of participants), public sex (≥43%), role-playing (≥22%), tying/being tied up (≥20%), spanking (≥30%), and watching sexually explicit videos/DVDs (60% women, 82% men). Having engaged in threesomes (10% women, 18% men) and playful whipping (≥13%) were less common. Lifetime group sex, sex parties, taking a sexuality class/workshop, and going to BDSM parties were uncommon (each <8%). More Americans identified behaviors as “appealing” than had engaged in them. Romantic/affectionate behaviors were among those most commonly identified as appealing for both men and women. The appeal of particular behaviors was associated with greater odds that the individual had ever engaged in the behavior. This study contributes to our understanding of more diverse adult sexual behaviors than has previously been captured in U.S. nationally representative probability surveys. Implications for sexuality educators, clinicians, and individuals in the general population are discussed. PMID:28727762

  9. Necessary relations for nucleotide frequencies.

    Science.gov (United States)

    Sinclair, Robert

    2015-06-07

    Genome composition analysis of di-, tri- and tetra-nucleotide frequencies is known to be evolutionarily informative, and useful in metagenomic studies, where binning of raw sequence data is often an important first step. Patterns appearing in genome composition analysis may be due to evolutionary processes or purely mathematical relations. For example, the total number of dinucleotides in a sequence is equal to the sum of the individual totals of the sixteen types of dinucleotide, and this is entirely independent of any assumptions made regarding mutation or selection, or indeed any physical or chemical process. Before any statistical analysis can be attempted, a knowledge of all necessary mathematical relations is required. I show that 25% of di-, tri- and tetra-nucleotide frequencies can be written as simple sums and differences of the remainder. The vast majority of organisms have circular genomes, for which these relations are exact and necessary. In the case of linear molecules, the absolute error is very nearly zero, and does not grow with contiguous sequence length. As a result of the new, necessary relations presented here, the foundations of the statistical analysis of di-, tri- and tetra-nucleotide frequencies, and k-mer analysis in general, need to be revisited. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. The intersection of interpersonal and self-directed violence among general adult, college student and sexually diverse samples.

    Science.gov (United States)

    Cramer, Robert J; Desmarais, Sarah L; Johnson, Kiersten L; Gemberling, Tess M; Nobles, Matt R; Holley, Sarah R; Wright, Susan; Van Dorn, Richard

    2017-02-01

    Suicide and interpersonal violence (i.e. victimization and perpetration) represent pressing public health problems, and yet remain mostly addressed as separate topics. To identify the (1) frequency and overlap of suicide and interpersonal violence and (2) characteristics differentiating subgroups of violence-related experiences. A health survey was completed by 2,175 respondents comprised of three groups: college students ( n = 702), adult members of a sexuality special interest organization ( n = 816) and a community adult sample ( n = 657). Latent class analysis was used to identify subgroups characterized by violence experiences; logistic regression was used to identify respondent characteristics differentiating subgroups. Overall rates of violence perpetration were low; perpetration, victimization and self-directed violence all varied by sample. Adults with alternative sexual interests reported high rates of victimization and self-directed violence. Analyses indicated two subgroups: (1) victimization + self-directed violence and (2) self-directed violence only. The victimization + self-directed violence subgroup was characterized by older, White, female and sexual orientation minority persons. The self-directed violence subgroup was characterized by younger, non-White, male and straight counterparts engaging with more sexual partners and more frequent drug use. Findings support the Centers for Disease Control and Prevention (CDC) definition of suicide as self-directed violence. Suicide intervention and prevention should further account for the role of violent victimization by focusing on the joint conceptualization of self-directed and interpersonal violence. Additional prevention implications are discussed.

  11. The impact of conduct disorder and stimulant medication on later substance use in an ethnically diverse sample of individuals with attention-deficit/hyperactivity disorder in childhood.

    Science.gov (United States)

    Harty, Seth C; Ivanov, Iliyan; Newcorn, Jeffrey H; Halperin, Jeffrey M

    2011-08-01

    To examine late adolescent substance use outcomes in relation to childhood conduct disorder (CD) and psychostimulant treatment in urban youth found to have attention-deficit/hyperactivity disorder (ADHD) in childhood. Ninety-seven adolescents, evaluated during childhood, were seen for follow-up on average 9.30 (SD = 1.65) years later along with a well-matched never-ADHD control group. Stimulant treatment history was coded: Never (n = 28), up to 1 year (n = 19), 1 to 5 years (n = 28), and greater than 5 years (n = 22). Substance use at outcome was coded dimensionally for severity (frequency × intensity) and categorically for substance use disorders (SUDs). Individuals with ADHD+CD in childhood had significantly higher rates of SUD and substance use severity than those with childhood ADHD and controls. The ADHD and control groups did not differ significantly. Among those with childhood ADHD, there were no significant differences in SUD status or substance use severity as a function of medication history. Within an ethnically diverse urban sample, the increased rate of substance use associated with ADHD was fully accounted for by the presence of CD. These results extend previous findings indicating little impact of psychostimulant treatment on later substance use to an ethnically diverse urban sample and to individuals who received treatment for up to 12 years.

  12. High acceptability of rapid HIV self-testing among a diverse sample of MSM from Buenos Aires, Argentina.

    Directory of Open Access Journals (Sweden)

    Maria A Pando

    Full Text Available The objective of this study was to explore the acceptability of rapid HIV self-testing (RHST among men who have sex with men (MSM.During 2006-2009, a sample of 500 MSM was recruited through Respondent Driven Sampling for an HIV prevalence/incidence study. Attitude toward RHST was explored among HIV negative MSM. Data were weighted prior to analyses.Participants reported they were likely to buy RHST (74%, test themselves more frequently than they currently do (77%, and that the procedure would simplify testing (70%. Furthermore, 71% reported they would probably use it alone, 66% would use it with a steady partner, and 56% with a friend/partner. While a majority acknowledged that RHST use would deprive them of receiving counseling (61%, 74% declared they would go for help if they tested positive; 57% would use an RHST in order to avoid condoms. Probability of use surpassed 70% among gay and non-gay identified MSM as well as those with and without a previous HIV test. Those likely to buy RHST were older (p = 0.025 and more likely to identify as gay (p = 0.036. A total of 17% said they would think about killing themselves and 9% would attempt suicide if they tested positive. These MSM were more likely to be younger (p<0.001, with lower mood level (p<0.001 and greater feelings of loneliness (p = 0.026.The high acceptability of RHST found among MSM should encourage the authorities to consider the possibility of offering it for self-testing, as it can improve early diagnosis and prevention of future transmissions. However, further research is needed to understand how to best disseminate RHST among MSM who wish to use it and to offer support and linkage to care for those who test HIV-positive.

  13. Diversity and evolutionary relationship of nucleotide binding site ...

    Indian Academy of Sciences (India)

    PRAKASH KUMAR

    Five distinct clusters of RGAs (22 sequences) with the characteristic NBS representing a highly ..... sweet potato RGA sequences were grouped into five clusters or families (A–E), all of which were highly ... to families of closely related RGA sequences. The numbers on the branches indicate bootstrap values (1000 iterations).

  14. Mitochondrial DNA analysis reveals a low nucleotide diversity of ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-06-17

    Jun 17, 2009 ... breeds of pigs in South west China: An approach from mitochondrial. DNA polymorphism. Biochem. Genet. 31: 51-60. Liu YQ, Lu C, Qin L, Xiang ZH (2006). Genetic relationships of. Antheraea pernyi cultivars based on RAPD markers. Scientia. Agricultura Sinica, 39: 2608-2614. Nei M, Kumar S (2000).

  15. Mitochondrial DNA analysis reveals a low nucleotide diversity of ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-06-17

    Jun 17, 2009 ... Biotechnology, Shenyang Agricultural University. DNA isolation, polymerase chain reaction and DNA sequencing. Total genomic DNA was extracted from partial abdomen of pupa according to the method previously published (Zhao et al., 2000). The COI gene was PCR amplified (polymerase chain ...

  16. [Identification of single nucleotide polymorphisms in centenarians].

    Science.gov (United States)

    Gambini, Juan; Gimeno-Mallench, Lucía; Inglés, Marta; Olaso, Gloria; Abdelaziz, Kheira Mohamed; Avellana, Juan Antonio; Belenguer, Ángel; Cruz, Raquel; Mas-Bargues, Cristina; Borras, Consuelo; Viña, José

    2016-01-01

    Longevity is determined by genetic and external factors, such as nutritional, environmental, social, etc. Nevertheless, when living conditions are optimal, longevity is determined by genetic variations between individuals. In a same population, with relative genotypic homogeneity, subtle changes in the DNA sequence affecting a single nucleotide can be observed. These changes, called single nucleotide polymorphisms (SNP) are present in 1-5% of the population. A total of 92 subjects were recruited, including 28 centenarians and 64 controls, in order to find SNP that maybe implicated in the extreme longevity, as in the centenarians. Blood samples were collected to isolate and amplify the DNA in order to perform the analysis of SPN by Axiom™ Genotyping of Affymetrix technology. Statistical analyses were performed using the Plink program and libraries SNPassoc and skatMeta. Our results show 12 mutations with a p<.001, where 5 of these (DACH1, LOC91948, BTB16, NFIL3 y HDAC4) have regulatory functions of the expressions of others genes. Therefore, these results suggest that the genetic variation between centenarians and controls occurs in five genes that are involved in the regulation of gene expression to adapt to environmental changes better than controls. Copyright © 2015 SEGG. Published by Elsevier Espana. All rights reserved.

  17. Interrelationships between LGBT-based victimization, suicide, and substance use problems in a diverse sample of sexual and gender minorities.

    Science.gov (United States)

    Mereish, Ethan H; O'Cleirigh, Conall; Bradford, Judith B

    2014-01-01

    Research has documented significant relationships between sexual and gender minority stress and higher rates of suicidality (i.e. suicidal ideation and attempts) and substance use problems. We examined the potential mediating role of substance use problems on the relationship between sexual and gender minority stress (i.e. victimization based on lesbian, gay, bisexual, or transgender identity [LGBT]) and suicidality. A nonprobability sample of LGBT patients from a community health center (N = 1457) ranged in age from 19-70 years. Participants reported history of lifetime suicidal ideation and attempts, substance use problems, as well as experiences of LGBT-based verbal and physical attacks. Substance use problems were a significant partial mediator between LGBT-based victimization and suicidal ideation and between LGBT-based victimization and suicide attempts for sexual and gender minorities. Nuanced gender differences revealed that substance use problems did not significantly mediate the relationship between victimization and suicide attempts for sexual minority men. Substance use problems may be one insidious pathway that partially mediates the risk effects of sexual and gender minority stress on suicidality. Substances might be a temporary and deleterious coping resource in response to LGBT-based victimization, which have serious effects on suicidal ideation and behaviors.

  18. Valuing health in a racially and ethnically diverse community sample: an analysis using the valuation metrics of money and time

    Science.gov (United States)

    Horvitz-Lennon, Marcela; Chen, Chih-nan; Laderman, Mara; Alegría, Margarita

    2013-01-01

    Purpose Limited research in health valuation analyzes samples with high proportions of racial/ethnic minorities within the United States. The primary objective was to explore patterns of health valuation across race/ethnicity using the Collaborative Psychiatric Epidemiology Surveys. A secondary objective was to analyze whether mental health disorder and immigrant status were associated with these estimates. Methods Health valuation questions using different metrics (time and money) were analyzed. Ordered logit models stratified across poor and moderate health tested differences by race/ethnicity, with mental health disorder and immigrant status as covariates. Results Asians in moderate health and Latinos were willing to pay more for health than non-Latino whites. Asians in moderate health were willing to trade more time for health. Latinos in poor health were less willing to trade time and gave disproportionate zero-trade responses. Lifetime history of anxiety disorder was positively associated with both metrics. Immigrant status confounded money valuation for Asians in moderate health, and time valuation for Latinos in poor health. Conclusions Health valuation estimates vary across race/ethnicity depending upon the metric. Time valuation scenarios appear less feasible for Latinos in poor health. More research is necessary to understand these differences and the role of immigrant status in health valuation. PMID:20680690

  19. Analysis of ASPM in an ethnically diverse cohort of 400 patient samples: perspectives of the molecular diagnostic laboratory.

    Science.gov (United States)

    Tan, C A; del Gaudio, D; Dempsey, M A; Arndt, K; Botes, S; Reeder, A; Das, S

    2014-04-01

    Primary Autosomal Recessive Microcephaly (MCPH) is characterized by congenital microcephaly usually without additional clinical findings. The most common gene implicated in MCPH is ASPM and a large percentage of mutations described have been homozygous and in consanguineous families primarily of East Asian and Middle Eastern origin. ASPM sequencing was performed on 400 patients between the years 2009 and 2012. Seventy of the patient samples were also analyzed for copy number changes in the ASPM gene. Forty protein truncating mutations, including 29 novel mutations, were identified in 39 patients with MCPH. Approximately one third of patients were compound heterozygotes, indicative of non-consanguinity in these patients. In addition, 46 non-synonymous variants were identified and interpreted as variants of uncertain significance. No deletion/duplication in ASPM was identified in the patients analyzed. A wide ethnic distribution was observed, including the first reported patients with ASPM-related MCPH of Hispanic descent. Clinical information was collected for 26 of the ASPM-positive patients and 41 of the ASPM-negative patients. As more individuals are identified with MCPH, we anticipate that we will continue to identify ASPM mutation-positive patients from all ethnic origins supporting the occurrence of this genetic condition beyond that of consanguineous families of certain ethnic populations. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  20. Microbial diversity in fecal samples depends on DNA extraction method: easyMag DNA extraction compared to QIAamp DNA stool mini kit extraction.

    Science.gov (United States)

    Mirsepasi, Hengameh; Persson, Søren; Struve, Carsten; Andersen, Lee O B; Petersen, Andreas M; Krogfelt, Karen A

    2014-01-21

    There are challenges, when extracting bacterial DNA from specimens for molecular diagnostics, since fecal samples also contain DNA from human cells and many different substances derived from food, cell residues and medication that can inhibit downstream PCR. The purpose of the study was to evaluate two different DNA extraction methods in order to choose the most efficient method for studying intestinal bacterial diversity using Denaturing Gradient Gel Electrophoresis (DGGE). In this study, a semi-automatic DNA extraction system (easyMag®, BioMérieux, Marcy I'Etoile, France) and a manual one (QIAamp DNA Stool Mini Kit, Qiagen, Hilden, Germany) were tested on stool samples collected from 3 patients with Inflammatory Bowel disease (IBD) and 5 healthy individuals. DNA extracts obtained by the QIAamp DNA Stool Mini Kit yield a higher amount of DNA compared to DNA extracts obtained by easyMag® from the same fecal samples. Furthermore, DNA extracts obtained using easyMag® seemed to contain inhibitory compounds, since in order to perform a successful PCR-analysis, the sample should be diluted at least 10 times. DGGE performed on PCR from DNA extracted by QIAamp DNA Stool Mini Kit DNA was very successful. QIAamp DNA Stool Mini Kit DNA extracts are optimal for DGGE runs and this extraction method yields a higher amount of DNA compared to easyMag®.

  1. A descriptive study of beverage consumption among an ethnically diverse sample of public school students in Texas.

    Science.gov (United States)

    Evans, Alexandra E; Springer, Andrew E; Evans, Martin H; Ranjit, Nalini; Hoelscher, Deanna M

    2010-08-01

    The purpose of this study was to examine prevalence rates of 5 types of beverage consumption by sociodemographic factors among 4th-, 8th-, and 11th-grade public school students in Texas. This study is based on secondary analyses of cross-sectional data from the 2004-2005 School Physical Activity and Nutrition study, a comprehensive surveillance study of energy balance-related behaviors and behavioral antecedents in a state-representative sample of 4th-, 8th-, and 11th-grade public school students in Texas (N = 23,190). Previous-day beverage consumption prevalence estimates were calculated for 5 types of beverages (i.e., fruit-flavored drinks, regular sodas, diet sodas, milk, and 100% fruit juice) by grade level, gender, ethnicity, school-level socioeconomic status, and metropolitan status. Logistic regression estimates of consumption prevalence were obtained for important sociodemographic indicators, including sex, grade, and ethnicity. Adjusted Wald tests were used to derive significance tests for sex differences in consumption, as sex emerged as a key determinant of consumption prevalence and varied systematically by type of beverage. The most commonly consumed beverage by all participants was milk. However, more than 50% of students also reported regular soda and fruit-flavored drink consumption during the previous day. Milk and fruit juice consumption showed a steady decline with grade level, while consumption of regular soda increased with grade level. By 11th grade, the prevalence of any beverage consumption, including milk and juice, was significantly greater among boys. Ethnic differences in sugar-sweetened beverage consumption were most prevalent in 8th and 11th grades, with the highest estimated prevalence of sugar-sweetened beverages (i.e., fruit-flavored drink and regular soda) consumption among African Americans. Differences in beverage consumption by school-level socioeconomic status and metropolitan status were small. These findings indicate that a

  2. Nucleotide variation at the dopa decarboxylase (Ddc) gene in ...

    Indian Academy of Sciences (India)

    We studied nucleotide sequence variation at the gene coding for dopa decarboxylase (Ddc) in seven populations of Drosophila melanogaster. Strength and pattern of linkage disequilibrium are somewhat distinct in the extensively sampled Spanish and Raleigh populations. In the Spanish population, a few sites are in ...

  3. Nucleotide variation at the methionine synthase locus in an ...

    African Journals Online (AJOL)

    Nucleotide variation at the methionine synthase (MetE) locus within and among populations of an endangered forest tree Fokienia hodginsii in Vietnam was investigated in the present study. A total of 12 populations were sampled across Vietnam. The length of the sequenced locus varied from 1567 to 1559 bp. A total of 42 ...

  4. Selective inferior petrosal sinus sampling without venous outflow diversion in the detection of a pituitary adenoma in Cushing's syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Andereggen, Lukas [Bern University Hospital, University Institute of Diagnostic and Interventional Neuroradiology, Bern (Switzerland); Bern University Hospital, Department of Neurosurgery, Bern (Switzerland); Schroth, Gerhard; Gralla, Jan; Ozdoba, Christoph [Bern University Hospital, University Institute of Diagnostic and Interventional Neuroradiology, Bern (Switzerland); Seiler, Rolf; Mariani, Luigi; Beck, Juergen; Widmer, Hans-Rudolf; Andres, Robert H. [Bern University Hospital, Department of Neurosurgery, Bern (Switzerland); Christ, Emanuel [Bern University Hospital, Division of Endocrinology, Diabetology and Clinical Nutrition, Bern (Switzerland)

    2012-05-15

    Conventional MRI may still be an inaccurate method for the non-invasive detection of a microadenoma in adrenocorticotropin (ACTH)-dependent Cushing's syndrome (CS). Bilateral inferior petrosal sinus sampling (BIPSS) with ovine corticotropin-releasing hormone (oCRH) stimulation is an invasive, but accurate, intervention in the diagnostic armamentarium surrounding CS. Until now, there is a continuous controversial debate regarding lateralization data in detecting a microadenoma. Using BIPSS, we evaluated whether a highly selective placement of microcatheters without diversion of venous outflow might improve detection of pituitary microadenoma. We performed BIPSS in 23 patients that met clinical and biochemical criteria of CS and with equivocal MRI findings. For BIPSS, the femoral veins were catheterized bilaterally with a 6-F catheter and the inferior petrosal sinus bilaterally with a 2.7-F microcatheter. A third catheter was placed in the right femoral vein. Blood samples were collected from each catheter to determine ACTH blood concentration before and after oCRH stimulation. In 21 patients, a central-to-peripheral ACTH gradient was found and the affected side determined. In 18 of 20 patients where transsphenoidal partial hypophysectomy was performed based on BIPSS findings, microadenoma was histologically confirmed. BIPSS had a sensitivity of 94% and a specificity of 67% after oCRH stimulation in detecting a microadenoma. Correct localization of the adenoma was achieved in all Cushing's disease patients. BIPSS remains the gold standard in the detection of a microadenoma in CS. Our findings show that the selective placement of microcatheters without venous outflow diversion might further enhance better recognition to localize the pituitary tumor. (orig.)

  5. Complete nucleotide sequence and genome organization of a novel allexivirus from alfalfa (Medicago sativa)

    Science.gov (United States)

    A new species of the family Alphaflexiviridae provisionally named Alfalfa virus S (AVS) was diagnosed in alfalfa samples originating from Sudan. A complete nucleotide sequence of the viral genome consisting of 8,349 nucleotides excluding the 3’ poly(A) tail was determined by Illumina NGS technology ...

  6. Species diversity and persistence in restored and remnant tallgrass prairies of North America: a function of species' life history, habitat type, or sampling bias?

    Science.gov (United States)

    Summerville, Keith S

    2008-05-01

    1. The re-assembly of native animal communities in restored landscapes is a relatively unexplored phenomenon for many taxa. Specifically, ecologists lack the ability to generalize about how species traits, habitat size, habitat type (here, remnant prairie vs. restored grassland), and temporal variation interact to affect species diversity or species' persistence probabilities. 2. To investigate these relationships, moth communities from 10 prairie remnants and restorations were sampled over a 3-year interval and a combination of NMDS ordination, logistic regression, and repeated measures anova were used to test hypotheses regarding how life history variables and habitat characteristics determine the degree to which restored habitats develop a moth fauna similar to remnants. 3. Within sampling years, restored tallgrass prairies that were >or= 7 years old possessed lepidopteran species assemblages that were generally similar to those in prairie remnants. Community similarity, however, was driven by common moth species likely to also occur in the surrounding agricultural habitat. Species persistence was significantly influenced by a series of trait combinations identified using principal components analysis. Temporal variation independent of habitat type or patch size was the most significant determination of variation in species composition among sites. 4. These results suggest that lepidopteran persistence in restored landscapes is at least partially determined by species' life history attributes. The correlation between sampling year and species richness suggests that both weather effects on species voltinism and interannual differences in sampling bias may make it difficult for land managers to detect changes in species abundance following disturbance or habitat management. 5. Species may not necessarily possess specific life history traits that reduce extinction risk or enhance recolonization probabilities in the highly modified agricultural landscape of the

  7. Modified RNA-seq method for microbial community and diversity analysis using rRNA in different types of environmental samples

    Science.gov (United States)

    Yan, Yong-Wei; Zou, Bin; Zhu, Ting; Hozzein, Wael N.

    2017-01-01

    RNA-seq-based SSU (small subunit) rRNA (ribosomal RNA) analysis has provided a better understanding of potentially active microbial community within environments. However, for RNA-seq library construction, high quantities of purified RNA are typically required. We propose a modified RNA-seq method for SSU rRNA-based microbial community analysis that depends on the direct ligation of a 5’ adaptor to RNA before reverse-transcription. The method requires only a low-input quantity of RNA (10–100 ng) and does not require a DNA removal step. The method was initially tested on three mock communities synthesized with enriched SSU rRNA of archaeal, bacterial and fungal isolates at different ratios, and was subsequently used for environmental samples of high or low biomass. For high-biomass salt-marsh sediments, enriched SSU rRNA and total nucleic acid-derived RNA-seq datasets revealed highly consistent community compositions for all of the SSU rRNA sequences, and as much as 46.4%-59.5% of 16S rRNA sequences were suitable for OTU (operational taxonomic unit)-based community and diversity analyses with complete coverage of V1-V2 regions. OTU-based community structures for the two datasets were also highly consistent with those determined by all of the 16S rRNA reads. For low-biomass samples, total nucleic acid-derived RNA-seq datasets were analyzed, and highly active bacterial taxa were also identified by the OTU-based method, notably including members of the previously underestimated genus Nitrospira and phylum Acidobacteria in tap water, members of the phylum Actinobacteria on a shower curtain, and members of the phylum Cyanobacteria on leaf surfaces. More than half of the bacterial 16S rRNA sequences covered the complete region of primer 8F, and non-coverage rates as high as 38.7% were obtained for phylum-unclassified sequences, providing many opportunities to identify novel bacterial taxa. This modified RNA-seq method will provide a better snapshot of diverse

  8. Characterization of nucleotide misincorporation patterns in the iceman's mitochondrial DNA.

    Directory of Open Access Journals (Sweden)

    Cristina Olivieri

    Full Text Available BACKGROUND: The degradation of DNA represents one of the main issues in the genetic analysis of archeological specimens. In the recent years, a particular kind of post-mortem DNA modification giving rise to nucleotide misincorporation ("miscoding lesions" has been the object of extensive investigations. METHODOLOGY/PRINCIPAL FINDINGS: To improve our knowledge regarding the nature and incidence of ancient DNA nucleotide misincorporations, we have utilized 6,859 (629,975 bp mitochondrial (mt DNA sequences obtained from the 5,350-5,100-years-old, freeze-desiccated human mummy popularly known as the Tyrolean Iceman or Otzi. To generate the sequences, we have applied a mixed PCR/pyrosequencing procedure allowing one to obtain a particularly high sequence coverage. As a control, we have produced further 8,982 (805,155 bp mtDNA sequences from a contemporary specimen using the same system and starting from the same template copy number of the ancient sample. From the analysis of the nucleotide misincorporation rate in ancient, modern, and putative contaminant sequences, we observed that the rate of misincorporation is significantly lower in modern and putative contaminant sequence datasets than in ancient sequences. In contrast, type 2 transitions represent the vast majority (85% of the observed nucleotide misincorporations in ancient sequences. CONCLUSIONS/SIGNIFICANCE: This study provides a further contribution to the knowledge of nucleotide misincorporation patterns in DNA sequences obtained from freeze-preserved archeological specimens. In the Iceman system, ancient sequences can be clearly distinguished from contaminants on the basis of nucleotide misincorporation rates. This observation confirms a previous identification of the ancient mummy sequences made on a purely phylogenetical basis. The present investigation provides further indication that the majority of ancient DNA damage is reflected by type 2 (cytosine

  9. Identities among actin-encoding cDNAs of the Nile tilapia (Oreochromis niloticus and other eukaryote species revealed by nucleotide and amino acid sequence analyses

    Directory of Open Access Journals (Sweden)

    Andréia B. Poletto

    2008-01-01

    Full Text Available Actin-encoding cDNAs of Nile tilapia (Oreochromis niloticus were isolated by RT-PCR using total RNA samples of different tissues and further characterized by nucleotide sequencing and in silico amino acid (aa sequence analysis. Comparisons among the actin gene sequences of O. niloticus and those of other species evidenced that the isolated genes present a high similarity to other fish and other vertebrate actin genes. The highest nucleotide resemblance was observed between O. niloticus and O. mossambicus a-actin and b-actin genes. Analysis of the predicted aa sequences revealed two distinct types of cytoplasmic actins, one cardiac muscle actin type and one skeletal muscle actin type that were expressed in different tissues of Nile tilapia. The evolutionary relationships between the Nile tilapia actin genes and diverse other organisms is discussed.

  10. Nucleotide Selectivity in Abiotic RNA Polymerization Reactions

    Science.gov (United States)

    Coari, Kristin M.; Martin, Rebecca C.; Jain, Kopal; McGown, Linda B.

    2017-09-01

    In order to establish an RNA world on early Earth, the nucleotides must form polymers through chemical rather than biochemical reactions. The polymerization products must be long enough to perform catalytic functions, including self-replication, and to preserve genetic information. These functions depend not only on the length of the polymers, but also on their sequences. To date, studies of abiotic RNA polymerization generally have focused on routes to polymerization of a single nucleotide and lengths of the homopolymer products. Less work has been done the selectivity of the reaction toward incorporation of some nucleotides over others in nucleotide mixtures. Such information is an essential step toward understanding the chemical evolution of RNA. To address this question, in the present work RNA polymerization reactions were performed in the presence of montmorillonite clay catalyst. The nucleotides included the monophosphates of adenosine, cytosine, guanosine, uridine and inosine. Experiments included reactions of mixtures of an imidazole-activated nucleotide (ImpX) with one or more unactivated nucleotides (XMP), of two or more ImpX, and of XMP that were activated in situ in the polymerization reaction itself. The reaction products were analyzed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to identify the lengths and nucleotide compositions of the polymerization products. The results show that the extent of polymerization, the degree of heteropolymerization vs. homopolymerization, and the composition of the polymeric products all vary among the different nucleotides and depend upon which nucleotides and how many different nucleotides are present in the mixture.

  11. Associations of hair cortisol concentration with self-reported measures of stress and mental health-related factors in a pooled database of diverse community samples.

    Science.gov (United States)

    Wells, Samantha; Tremblay, Paul F; Flynn, Andrea; Russell, Evan; Kennedy, James; Rehm, Jürgen; Van Uum, Stan; Koren, Gideon; Graham, Kathryn

    2014-07-01

    A pooled database from diverse community samples was used to examine the associations of hair cortisol concentration (HCC) with self-reported stress and stress-linked mental health measures, including depression, anxiety, alcohol and drug use, disability and experiences with aggression. As part of innovative research using a mobile laboratory to study community mental health, data were pooled from five sub-studies: a random sample of the general population (n = 70), people who had received treatment for a mental health and/or substance use problem (n = 78), family members of people treated for mental health and/or substance use problems (n = 49), community volunteers who sometimes felt sad or blue or thought they drank too much (n = 83) and young adults in intimate partner relationships (n = 44). All participants completed a computerized questionnaire including standard measures of perceived stress, chronic stress, depression, anxiety, hazardous drinking, tobacco use, prescription drug use, illicit drug use, disability and intimate partner aggression. HCC was significantly associated with use of antidepressants, hazardous drinking, smoking and disability after adjusting for sub-study and potential confounders (sex, body-mass index, use of glucocorticoids and hair dyed). In addition, preliminary analyses suggest a significant curvilinear relationship between HCC and perceived stress; specifically, HCC increased with higher perceived stress but decreased at the highest level of stress. Overall, HCC was associated with mental health-related variables mainly reflecting substance use or experiencing a disability. The relationship between HCC and self-reported stress is unclear and needs further research.

  12. Effects of education and word reading on cognitive scores in a community-based sample of Spanish elders with diverse socioeconomic status.

    Science.gov (United States)

    Contador, Israel; Bermejo-Pareja, Félix; Del Ser, Teodoro; Benito-León, Julián

    2015-01-01

    The influence of education and oral word-reading ability on cognitive performance was examined in a sample of 1510 nondemented elders differing in socioeconomic status (SES) from three Spanish communities. All individuals were enrolled in the Neurological Disorders in Central Spain, a population-based epidemiological study in central Spain. They completed a detailed demographic survey and a short standardized neuropsychological battery assessing psychomotor speed, attention, language, and memory. The Word Accentuation Test (WAT) was used as measure of oral reading ability. The influence of education and oral reading on cognitive performance was determined by multiple linear regression models, first controlling for demographics (age and sex), and subsequently for the WAT score and education. The contribution of socioeconomic conditions was addressed by stratifying the sample into groups of high and low SES. The WAT showed a significant independent effect on cognitive scores, generally greater than that predicted by demographics. The higher predictive power of oral word reading on cognitive scores compared to education was consistent across the three communities. Although the variance explained by WAT was very similar in areas with diverse SES (low vs. high), WAT scores accounted for slightly more variance in naming and memory tasks in low SES areas. In contrast, the variance explained by WAT was higher for verbal fluency and the Trail-Making Test in areas with high SES. Oral word-reading ability predicts cognitive performance better than years of education across individuals with different SES. The influence of WAT may be modulated by SES and cognitive task properties.

  13. Hungry to learn: the prevalence and effects of food insecurity on health behaviors and outcomes over time among a diverse sample of university freshmen.

    Science.gov (United States)

    Bruening, Meg; van Woerden, Irene; Todd, Michael; Laska, Melissa N

    2018-01-18

    To examine longitudinal associations between food insecurity (FI) and health behaviors/outcomes among a diverse sample of university freshmen. Freshman students (n = 1138; 65% female; 49% non-white) participating in the Social impact of Physical Activity and nutRition in College study completed surveys on health behaviors and had height/weight measured up to 4 times (T1-T4) in Arizona during 2015-2016. Structural equation models were estimated to determine if, after adjusting for covariates, FI predicted concurrent behaviors/outcomes and subsequent behaviors/outcomes. Analyses reported here were conducted in 2017. The prevalence of FI was significantly higher at the end of each semester (35% and 36%, respectively) than at the start of the year (28%). Longitudinally, FI was not related to any health behaviors/outcomes at future time points. However, FI was significantly and inversely associated with concurrent breakfast consumption on most days of the week (OR = 0.67, 99% CI = 0.46, 0.99), daily evening meal consumption (OR = 0.55, 99% CI = 0.36, 0.86) healthy eating habits on campus (OR = 0.68, 99% CI = 0.46, 1.00), healthy physical activity habits on campus (OR = 0.66, 99% CI = 0.44, 1.00), and positively related to the likelihood of experiencing stress (OR = 1.69, 99% CI = 1.16, 2.46) and depressed mood (OR = 1.98, 99% CI = 1.34, 2.91). Compared with US prevalence rates, the sample FI prevalence was high. FI was related to poorer eating patterns, physical activity behaviors, and mental health, even after adjusting for prior levels of behavior.

  14. Active travel to non-school destinations but not to school is associated with higher physical activity levels in an ethnically diverse sample of inner-city schoolchildren

    Directory of Open Access Journals (Sweden)

    Lee Smith

    2017-01-01

    Full Text Available Abstract Background This study investigated the association of travel mode to school and non-school destinations with objectively assessed health markers and physical activity in an ethnically diverse sample of inner-city UK schoolchildren. Methods We used data from the Camden Active Spaces project (n = 450 children aged 9.1 yrs to examine associations of school travel mode and frequency of active travel to non-school destinations with daily and out-of-school physical activity, sedentary time and health markers; whilst controlling for appropriate covariates including objectively measured route length. Results High frequency of active travel to non-school destinations was associated with more time in moderate-to-vigorous physical activity during out-of-school periods (3.8, 0.8–6.9 min/d and greater out-of-school (738, 197.4–1278.6 steps/d and daily step counts (588.1, 51.6–1124.6 steps/d. No associations were observed between school travel mode, health outcomes and activity levels. Conclusion High frequency of active travel to non-school destinations is associated with higher levels of physical activity. These findings highlight the contribution of travel to non-school destinations to overall physical activity levels in schoolchildren.

  15. Breast Density Awareness and Knowledge, and Intentions for Breast Cancer Screening in a Diverse Sample of Women Age Eligible for Mammography.

    Science.gov (United States)

    Santiago-Rivas, Marimer; Benjamin, Shayna; Andrews, Janna Z; Jandorf, Lina

    2017-08-14

    The objectives of this study were to assess breast density knowledge and breast density awareness, and to identify information associated with intention to complete routine and supplemental screening for breast cancer in a diverse sample of women age eligible for mammography. We quantitatively (self-report) assessed breast density awareness and knowledge (N = 264) in black (47.7%), Latina (35.2%), and white (17%) women recruited online and in the community. Most participants reported having heard about breast density (69.2%); less than one third knew their own breast density status (30.4%). Knowing their own breast density, believing that women should be notified of their breast density in their mammogram report, and feeling informed if being provided this information are associated with likelihood of completing mammogram. Intending mammogram completion and knowledge regarding the impact of breast density on mammogram accuracy are associated with likelihood of completing supplemental ultrasound tests of the breast. These findings help inform practitioners and policy makers about information and communication factors that influence breast cancer screening concerns and decisions. Knowing this information should prepare practitioners to better identify women who may have not been exposed to breast density messages.

  16. Genetic diversity and connectivity in the East African giant mud crab Scylla serrata: Implications for fisheries management.

    Science.gov (United States)

    Rumisha, Cyrus; Huyghe, Filip; Rapanoel, Diary; Mascaux, Nemo; Kochzius, Marc

    2017-01-01

    The giant mud crab Scylla serrata provides an important source of income and food to coastal communities in East Africa. However, increasing demand and exploitation due to the growing coastal population, export trade, and tourism industry are threatening the sustainability of the wild stock of this species. Because effective management requires a clear understanding of the connectivity among populations, this study was conducted to assess the genetic diversity and connectivity in the East African mangrove crab S. serrata. A section of 535 base pairs of the cytochrome oxidase subunit I (COI) gene and eight microsatellite loci were analysed from 230 tissue samples of giant mud crabs collected from Kenya, Tanzania, Mozambique, Madagascar, and South Africa. Microsatellite genetic diversity (He) ranged between 0.56 and 0.6. The COI sequences showed 57 different haplotypes associated with low nucleotide diversity (current nucleotide diversity = 0.29%). In addition, the current nucleotide diversity was lower than the historical nucleotide diversity, indicating overexploitation or historical bottlenecks in the recent history of the studied population. Considering that the coastal population is growing rapidly, East African countries should promote sustainable fishing practices and sustainable use of mangrove resources to protect mud crabs and other marine fauna from the increasing pressure of exploitation. While microsatellite loci did not show significant genetic differentiation (p > 0.05), COI sequences revealed significant genetic divergence between sites on the East coast of Madagascar (ECM) and sites on the West coast of Madagascar, mainland East Africa, as well as the Seychelles. Since East African countries agreed to achieve the Convention on Biological Diversity (CBD) target to protect over 10% of their marine areas by 2020, the observed pattern of connectivity and the measured genetic diversity can serve to provide useful information for designing networks of

  17. Genetic diversity and connectivity in the East African giant mud crab Scylla serrata: Implications for fisheries management.

    Directory of Open Access Journals (Sweden)

    Cyrus Rumisha

    Full Text Available The giant mud crab Scylla serrata provides an important source of income and food to coastal communities in East Africa. However, increasing demand and exploitation due to the growing coastal population, export trade, and tourism industry are threatening the sustainability of the wild stock of this species. Because effective management requires a clear understanding of the connectivity among populations, this study was conducted to assess the genetic diversity and connectivity in the East African mangrove crab S. serrata. A section of 535 base pairs of the cytochrome oxidase subunit I (COI gene and eight microsatellite loci were analysed from 230 tissue samples of giant mud crabs collected from Kenya, Tanzania, Mozambique, Madagascar, and South Africa. Microsatellite genetic diversity (He ranged between 0.56 and 0.6. The COI sequences showed 57 different haplotypes associated with low nucleotide diversity (current nucleotide diversity = 0.29%. In addition, the current nucleotide diversity was lower than the historical nucleotide diversity, indicating overexploitation or historical bottlenecks in the recent history of the studied population. Considering that the coastal population is growing rapidly, East African countries should promote sustainable fishing practices and sustainable use of mangrove resources to protect mud crabs and other marine fauna from the increasing pressure of exploitation. While microsatellite loci did not show significant genetic differentiation (p > 0.05, COI sequences revealed significant genetic divergence between sites on the East coast of Madagascar (ECM and sites on the West coast of Madagascar, mainland East Africa, as well as the Seychelles. Since East African countries agreed to achieve the Convention on Biological Diversity (CBD target to protect over 10% of their marine areas by 2020, the observed pattern of connectivity and the measured genetic diversity can serve to provide useful information for designing

  18. [Cyclic nucleotide phosphodiesterases: role in the heart and therapeutic perspectives].

    Science.gov (United States)

    Bedioune, Ibrahim; Bobin, Pierre; Karam, Sarah; Lindner, Marta; Mika, Delphine; Lechêne, Patrick; Leroy, Jérôme; Fischmeister, Rodolphe; Vandecasteele, Grégoire

    2016-01-01

    Cyclic nucleotide phosphodiesterases (PDEs) degrade the second messengers cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP), thereby regulating multiple aspects of cardiac function. This highly diverse class of enzymes encoded by 21 genes encompasses 11 families that are not only responsible for the termination of cyclic nucleotide signalling, but are also involved in the generation of dynamic microdomains of cAMP and cGMP, controlling specific cell functions in response to various neurohormonal stimuli. In the myocardium, the PDE3 and PDE4 families predominate, degrading cAMP and thereby regulating cardiac excitation-contraction coupling. PDE3 inhibitors are positive inotropes and vasodilators in humans, but their use is limited to acute heart failure and intermittent claudication. PDE5 inhibitors, which are used with success to treat erectile dysfunction and pulmonary hypertension, do not seem efficient in heart failure with preserved ejection fraction. There is experimental evidence however that these PDE, as well as other PDE families including PDE1, PDE2 and PDE9, may play important roles in cardiac diseases, such as hypertrophy and heart failure (HF). After a brief presentation of the cyclic nucleotide pathways in cardiac myocytes and the major characteristics of the PDE superfamily, this review will focus on the potential use of PDE inhibitors in HF, and the recent research developments that could lead to a better exploitation of the therapeutic potential of these enzymes in the future. © Société de Biologie, 2016.

  19. Discovery of nucleotide polymorphisms in the Musa gene pool by Ecotilling.

    Science.gov (United States)

    Till, Bradley J; Jankowicz-Cieslak, Joanna; Sági, László; Huynh, Owen A; Utsushi, Hiroe; Swennen, Rony; Terauchi, Ryohei; Mba, Chikelu

    2010-11-01

    Musa (banana and plantain) is an important genus for the global export market and in local markets where it provides staple food for approximately 400 million people. Hybridization and polyploidization of several (sub)species, combined with vegetative propagation and human selection have produced a complex genetic history. We describe the application of the Ecotilling method for the discovery and characterization of nucleotide polymorphisms in diploid and polyploid accessions of Musa. We discovered over 800 novel alleles in 80 accessions. Sequencing and band evaluation shows Ecotilling to be a robust and accurate platform for the discovery of polymorphisms in homologous and homeologous gene targets. In the process of validating the method, we identified two single nucleotide polymorphisms that may be deleterious for the function of a gene putatively important for phototropism. Evaluation of heterozygous polymorphism and haplotype blocks revealed a high level of nucleotide diversity in Musa accessions. We further applied a strategy for the simultaneous discovery of heterozygous and homozygous polymorphisms in diploid accessions to rapidly evaluate nucleotide diversity in accessions of the same genome type. This strategy can be used to develop hypotheses for inheritance patterns of nucleotide polymorphisms within and between genome types. We conclude that Ecotilling is suitable for diversity studies in Musa, that it can be considered for functional genomics studies and as tool in selecting germplasm for traditional and mutation breeding approaches.

  20. Nucleotide Salvage Deficiencies, DNA Damage and Neurodegeneration

    Directory of Open Access Journals (Sweden)

    Michael Fasullo

    2015-04-01

    Full Text Available Nucleotide balance is critically important not only in replicating cells but also in quiescent cells. This is especially true in the nervous system, where there is a high demand for adenosine triphosphate (ATP produced from mitochondria. Mitochondria are particularly prone to oxidative stress-associated DNA damage because nucleotide imbalance can lead to mitochondrial depletion due to low replication fidelity. Failure to maintain nucleotide balance due to genetic defects can result in infantile death; however there is great variability in clinical presentation for particular diseases. This review compares genetic diseases that result from defects in specific nucleotide salvage enzymes and a signaling kinase that activates nucleotide salvage after DNA damage exposure. These diseases include Lesch-Nyhan syndrome, mitochondrial depletion syndromes, and ataxia telangiectasia. Although treatment options are available to palliate symptoms of these diseases, there is no cure. The conclusions drawn from this review include the critical role of guanine nucleotides in preventing neurodegeneration, the limitations of animals as disease models, and the need to further understand nucleotide imbalances in treatment regimens. Such knowledge will hopefully guide future studies into clinical therapies for genetic diseases.

  1. Complete nucleotide sequence of a monopartite Begomovirus and associated satellites infecting Carica papaya in Nepal.

    Science.gov (United States)

    Shahid, M S; Yoshida, S; Khatri-Chhetri, G B; Briddon, R W; Natsuaki, K T

    2013-06-01

    Carica papaya (papaya) is a fruit crop that is cultivated mostly in kitchen gardens throughout Nepal. Leaf samples of C. papaya plants with leaf curling, vein darkening, vein thickening, and a reduction in leaf size were collected from a garden in Darai village, Rampur, Nepal in 2010. Full-length clones of a monopartite Begomovirus, a betasatellite and an alphasatellite were isolated. The complete nucleotide sequence of the Begomovirus showed the arrangement of genes typical of Old World begomoviruses with the highest nucleotide sequence identity (>99 %) to an isolate of Ageratum yellow vein virus (AYVV), confirming it as an isolate of AYVV. The complete nucleotide sequence of betasatellite showed greater than 89 % nucleotide sequence identity to an isolate of Tomato leaf curl Java betasatellite originating from Indonesian. The sequence of the alphasatellite displayed 92 % nucleotide sequence identity to Sida yellow vein China alphasatellite. This is the first identification of these components in Nepal and the first time they have been identified in papaya.

  2. Teaching Diversity

    Directory of Open Access Journals (Sweden)

    Kay Young McChesney

    2015-10-01

    Full Text Available This article is targeted to faculty teaching race and ethnicity, racism, diversity, and multicultural courses. Many students equate race with skin color. The premise of this article is that to teach students about the social construction of race, teachers must first know enough science to teach students that race is not biological. This article examines the biology of race by showing how advances in DNA sequencing led to genetics research that supports arguments that race is not biological. DNA comparisons show that all human populations living today are one species that came from Africa. The article explains the migration of humans out of Africa about 60,000 years ago and how they populated Australia, then Asia, Europe, and the Americas. The article shows how recent research maps the timing of the migration and admixture of specific population groups into Europe and India. The article shows how a mutation in one nucleotide can result in a trait like blue eyes, or Hemoglobin S (which confers resistance to malaria, which can be subject to evolution through natural selection. DNA comparisons show how natural selection shaped the genetics of human skin color to adapt to less UV light in the northern latitudes of Europe and Asia. The article shows that there is no relation between skin color or other “racial” characteristics and complex traits like intelligence. The science in this article will help teachers explain that as race is not biological, race is socially constructed and culturally enacted.

  3. Chemical Diversity and Antimicrobial Activity of Volatile Compounds from Zanthoxylum zanthoxyloides Lam. according to Compound Classes, Plant Organs and Senegalese Sample Locations.

    Science.gov (United States)

    Tine, Yoro; Diop, Abdoulaye; Diatta, William; Desjobert, Jean-Marie; Boye, Cheikh Saad Bouh; Costa, Jean; Wélé, Alassane; Paolini, Julien

    2017-01-01

    The chemical diversity of Zanthoxylum zanthoxyloides growing wild in Senegal was studied according to volatile compound classes, plant organs and sample locations. The composition of fruit essential oil was investigated using an original targeted approach based on the combination of gas chromatography (GC) and liquid chromatography (LC) both coupled with mass spectrometry (MS). The volatile composition of Z. zanthoxyloides fruits exhibited relative high amounts of hydrocarbon monoterpenes (24.3 - 55.8%) and non-terpenic oxygenated compounds (34.5 - 63.1%). The main components were (E)-β-ocimene (12.1 - 39%), octyl acetate (11.6 - 21.8%) and decanol (9.7 - 15.4%). The GC and GC/MS profiling of fruit essential oils showed a chemical variability according to geographical locations of plant material. The LC/MS/MS analysis of fruit oils allowed the detection of seven coumarins in trace content. The chemical composition of fruit essential oils was compared with volatile fractions of leaves and barks (root and trunk) from the same plant station. Hexadecanoic acid, germacrene D and decanal were identified as the major constituents of leaves whereas the barks (root and trunk) were dominated by pellitorine (85.8% and 57%, respectively), an atypic linear compound with amide group. The fruit essential oil exhibited interesting antimicrobial activities against Staphylococcus aureus and Candida albicans, particularly the alcohol fraction of the oil. © 2017 Wiley-VHCA AG, Zurich, Switzerland.

  4. Evidence Against a Link Between Hyperemesis Gravidarum and Personality Characteristics from an Ethnically Diverse Sample of Pregnant Women: A Pilot Study

    Science.gov (United States)

    D'Orazio, Lina M.; Korst, Lisa M.; Romero, Roberto; Goodwin, Thomas M.

    2011-01-01

    Abstract Background Hyperemesis gravidarum (HG), a pregnancy-related condition marked by extreme nausea and vomiting, has been considered a psychosomatic illness associated with long-standing personality characteristics (e.g., hysteria). In this pilot study, we examined personality, somatic, and psychological variables with ethnically diverse samples of women with HG and women with typical levels of nausea and vomiting of pregnancy (NVP). Methods Personality (Minnesota Multiphasic Personality Index-2 [MMPI-2] and MMPI-2RF), somatic (MMPI-2RF), and psychological (Beck Depression Inventory-II [BDI-II] and NVP-related quality of life) variables collected during the first trimester of pregnancy were compared between 15 women with HG and 15 women with normal levels of NVP matched for age, education, marital status, insurance source, and race/ethnicity. A secondary analysis was performed comparing these variables among a group of 9 asymptomatic pregnant women to the HG and NVP groups. Results No significant differences were found between the HG and NVP groups on any personality, somatic, or psychological variables. Both groups had clinically significant elevations on the MMPI-2 hypochondriasis scale, which incorporates somatic symptoms. The NVP group had a clinically significant elevation on the MMPI-2RF gastrointestinal complaints scale. Both groups had significantly higher means on the MMPI-2 and MMPI-2RF scales than the asymptomatic group. Predominantly Spanish speakers appeared particularly vulnerable to psychological distress associated with somatic complaints. Conclusions The results of this pilot study suggest that research with HG patients is feasible and that psychological distress expressed by women with HG and NVP may reflect reactions to somatic symptoms. No evidence was found to support an association between HG and personality characteristics. Recommendations for future research are provided, such as examining the potential benefits of translation services

  5. Electronic Nicotine Delivery Systems (E-cigarette/Vape) use and Co-Occurring Health-Risk Behaviors Among an Ethnically Diverse Sample of Young Adults.

    Science.gov (United States)

    Lanza, H Isabella; Teeter, Heather

    2018-01-02

    Prevalence rates of electronic nicotine delivery systems (ENDS; i.e., e-cigarette/vape) use has grown exponentially in the past few years. College students present a particularly vulnerable group for ENDS use. The current study sought to expand the literature by examining the context in which college students use ENDS, co-occurring health risks beyond traditional tobacco use, and the role of ethnicity in ENDS use. Health-risk behavior survey data was collected from 452 undergraduates attending a large, public urban university during the 2015-2016 academic year. Ever ENDS users vs. non-ENDS users were compared across potential demographic, health-risk, and other health-related correlates. Almost 40% of participants reported lifetime use of ENDS. No ethnic or sex differences were found. The primary source for obtaining ENDS was friends and ENDS were most often used with friends vs. alone or with others not considered friends. Participants engaging in risky alcohol use and cigarette smoking had a higher likelihood of endorsing ENDS use. Conclusions/Importance: The current study indicated that a large proportion of college students have tried ENDS irrespective of ethnicity or sex. An increasingly normative social context may inform the popularity of ENDS use across ethnicity and sex, but additional research using ethnically diverse samples is warranted. Risky alcohol use appears to be a significant correlate of ENDS use, even after accounting for the robust relationship between ENDS use and cigarette smoking. The robust relationship between alcohol and tobacco use likely extends to ENDS use.

  6. Empirical validation of a short version of the Adolescent Sleep-Wake Scale using a sample of ethnically diverse adolescents from an economically disadvantage community.

    Science.gov (United States)

    Sufrinko, Alicia M; Valrie, Cecelia R; Lanzo, Lauren; Bond, Kayzandra E; Trout, Krystal L; Ladd, Rebecca E; Everhart, D Erik

    2015-10-01

    There is a need for brief, psychometrically sound instruments to assess adolescent sleep, particularly for ethnic minority and economically disadvantaged adolescents. A 10-item short version of the Adolescent Sleep-Wake Scale was recently proposed based upon exploratory factor analysis with primarily Caucasian healthy adolescents from middle- to high-income families. The aim of this study was to expand the utility of the short version of the Adolescent Sleep-Wake Scale by investigating the empirical and construct validity of the measure on an ethnically diverse sample of adolescents from an economically disadvantaged community. Participants included 467 adolescents (40% African American, 35.5% Caucasian, 16.5% Latino, and 7.9% multiethnic), aged 12-18 years (mean = 15.27 years, SD = 1.96 years), who completed the Adolescent Sleep-Wake Scale. A confirmatory factor analysis (CFA) was conducted with Mplus 7 based on the three-factor solution proposed by Essner et al. (2014). CFA indicated that the three-factor structure was a good fit for the data (χ(2) (29) = 52.053, p = 0.005, root mean square error of approximation (RMSEA) = 0.04, CFI = 0.98, TLI = 0.96, standardized root mean residuals (SRMR) = 0.03), and factor loadings for each item were >0.40. Cronbach's alphas by ethnicity indicated that the scale has acceptable reliability (0.70 ≤ α ≤ 0.90) for African American, Caucasian, and multiethnic adolescents, but not for Latino adolescents. Our results support the use of the Adolescent Sleep-Wake Scale short form for the majority of ethnic minority and economically disadvantaged adolescents. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. Adult Cigarette Smokers at Highest Risk for Concurrent Alternative Tobacco Product Use Among a Racially/Ethnically and Socioeconomically Diverse Sample.

    Science.gov (United States)

    Nollen, Nicole L; Ahluwalia, Jasjit S; Lei, Yang; Yu, Qing; Scheuermann, Taneisha S; Mayo, Matthew S

    2016-04-01

    Rates of alternative tobacco product use (ATPs; eg, cigars, cigarillos, pipes) among cigarette smokers are on the rise but little is known about the subgroups at highest risk. This study explored interactions between demographic, tobacco, and psychosocial factors to identify cigarette smokers at highest risk for ATP use from a racially/ethnically and socioeconomically diverse sample of adult smokers across the full smoking spectrum (nondaily, daily light, daily heavy). Two-thousand three-hundred seventy-six adult cigarette smokers participated in an online cross-sectional survey. Quotas ensured equal recruitment of African American (AA), white (W), Hispanic/Latino (H) as well as daily and nondaily smokers. Classification and Regression Tree modeling was used to identify subgroups of cigarette smokers at highest risk for ATP use. 51.3% were Cig+ATP smokers. Alcohol for men and age, race/ethnicity, and discrimination for women increased the probability of ATP use. Strikingly, 73.5% of men screening positive for moderate to heavy drinking and 62.2% of younger (≤45 years) African American/Hispanic/Latino women who experienced regular discrimination were Cig+ATP smokers. Screening for concurrent ATP use is necessary for the continued success of tobacco cessation efforts especially among male alcohol users and racial/ethnic minority women who are at greatest risk for ATP use. © The Author 2015. Published by Oxford University Press on behalf of the Society for Research on Nicotine and Tobacco. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  8. Towards a better understanding of the relationship between executive control and theory of mind: an intra-cultural comparison of three diverse samples.

    Science.gov (United States)

    Shahaeian, Ameneh; Henry, Julie D; Razmjoee, Maryam; Teymoori, Ali; Wang, Cen

    2015-09-01

    Previous research has consistently indicated that theory of mind (ToM) is associated with executive control in the preschool years. However, interpretation of this literature is limited by the fact that most studies have focused exclusively on urbanized Western cultural samples. Consequently, it is not clear whether the association between ToM and executive control reflects the specific features of this particular cohort or instead reflects a universal pattern. The present study provides the first empirical assessment of these two constructs in three diverse groups of Iranian children. Participants were 142 preschoolers (4-5 years old) from high-socioeconomic status (SES) urban (n = 33), low-SES urban (n = 37) and rural villages (n = 77). The results show that there is a robust association between ToM and executive control in all three groups, and that executive control contributes significant unique variance to ToM understanding, even after controlling for a range of variables that have been proposed as potential confounders of this relationship. However, although the three groups were equated in ToM, significant differences in executive control were evident. Moreover, cluster analysis identified three distinct clusters that were relatively homogeneous with respect to executive control and SES. One of these clusters was characterized by both low SES and low executive functioning, and showed little evidence of ToM understanding. Taken together, these findings provide possibly the clearest evidence to date that the association between ToM and executive control is not dependent on children's previous experiences on the tasks, or their family and cultural background. © 2014 John Wiley & Sons Ltd.

  9. Genetic equidistance at nucleotide level.

    Science.gov (United States)

    Yuan, Dejian; Huang, Shi

    2017-07-01

    The genetic equidistance phenomenon shows complex taxa to be all approximately equidistant to a less complex species in amino acid percentage identity. The overlooked mystery was re-interpreted by the maximum genetic diversity hypothesis (MGD). Here, we studied 14 proteomes and their coding DNA sequences (CDS) to see if the equidistance phenomenon also holds at the CDS level. We found that the outgroup taxon was equidistant to the two more complex taxa species. When two sister taxa were compared to human as the outgroup, the more complex taxon was closer to human, confirming species complexity to be the primary determinant of MGD. Finally, we found the fraction of overlap sites to be inversely correlated with CDS conservation, indicating saturation to be more common in less conserved DNAs. These results establish the genetic equidistance phenomenon to be universal at the DNA level and provide additional evidence for the MGD theory. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. Relationships between data from Rock-Eval pyrolysis and proximate, ultimate, petrographic, and physical analyses of 142 diverse U.S. coal samples

    Science.gov (United States)

    Bostick, N.H.; Daws, T.A.

    1994-01-01

    Basic research on coal and oil shale led to automated pyrolysis analysis of petroleum source rocks; most widely used is the Rock-Eval equipment. In order to interpret Rock-Eval analyses in relation to traditional coal data, we analyzed 142 commercial coals with diverse rank, age, maceral and sulfur contents, for most regions of the United States. We compared the Rock-Eval data with traditional industrial coal data, including volatile matter, calorific value, hydrogen and oxygen content, free swelling index, and vitrinite reflectance. We found: (1) there is a close relationship between Tmax and vitrinite reflectance in the ranges 420-590??C Tmax and 0.4-3%Romax of most coals. (2) A close relationship between Tmax and volatile matter (%VM) extends through the entire sample range, including low-rank samples with 35-70% VM, a range where %VM is not considered to be a useful rank parameter. (3) TOC of medium- and high-rank coals is seriously under-measured by Rock-Eval; TOC of low-rank coals (less than 0.8%Romax) is close to "dry basis" carbon from ultimate analysis. (4) The direct relationships between oxygen index (OI) and %O and between hydrogen index (HI) and %H are clear, though only broadly defined. However, there is virtually no band of concentrated data points on the HI versus OI pseudo-Van Krevelen diagram comparable to the "development line" on the H/C versus O/C diagram. (5) There are systematic relationships between Rock-Eval and industrial coal parameters such as calorific value and FSI, but much standardization would be needed before Rock-Eval could find a place in the coal industry. Tests with blends of coal and quartz sand and with various loads of coal alone showed that the amount of organic matter in the Rock-Eval load greatly influences results. Total load in the crucible, if largely inert, plays a small role, however. Increasing absolute or relative coal content causes under-evaluation of Rock-Eval TOC and over-rating of hydrogen. Blends of several

  11. Pyrosequencing of 16S rRNA genes in fecal samples reveals high diversity of hindgut microflora in horses and potential links to chronic laminitis

    Directory of Open Access Journals (Sweden)

    Steelman Samantha M

    2012-11-01

    Full Text Available Abstract Background The nutrition and health of horses is closely tied to their gastrointestinal microflora. Gut bacteria break down plant structural carbohydrates and produce volatile fatty acids, which are a major source of energy for horses. Bacterial communities are also essential for maintaining gut homeostasis and have been hypothesized to contribute to various diseases including laminitis. We performed pyrosequencing of 16S rRNA bacterial genes isolated from fecal material to characterize hindgut bacterial communities in healthy horses and those with chronic laminitis. Results Fecal samples were collected from 10 normal horses and 8 horses with chronic laminitis. Genomic DNA was extracted and the V4-V5 segment of the 16S rRNA gene was PCR amplified and sequenced on the 454 platform generating a mean of 2,425 reads per sample after quality trimming. The bacterial communities were dominated by Firmicutes (69.21% control, 56.72% laminitis and Verrucomicrobia (18.13% control, 27.63% laminitis, followed by Bacteroidetes, Proteobacteria, and Spirochaetes. We observed more OTUs per individual in the laminitis group than the control group (419.6 and 355.2, respectively, P = 0.019 along with a difference in the abundance of two unassigned Clostridiales genera (P = 0.03 and P = 0.01. The most abundant bacteria were Streptococcus spp., Clostridium spp., and Treponema spp.; along with unassigned genera from Subdivision 5 of Verrucomicrobia, Ruminococcaceae, and Clostridiaceae, which together constituted ~ 80% of all OTUs. There was a high level of individual variation across all taxonomic ranks. Conclusions Our exploration of the equine fecal microflora revealed higher bacterial diversity in horses with chronic laminitis and identification of two Clostridiales genera that differed in abundance from control horses. There was large individual variation in bacterial communities that was not explained in our study. The core hindgut microflora was

  12. Varietal identification of tea (Camellia sinensis) using nanofluidic array of single nucleotide polymorphism (SNP) markers.

    Science.gov (United States)

    Fang, Wan-Ping; Meinhardt, Lyndel W; Tan, Hua-Wei; Zhou, Lin; Mischke, Sue; Zhang, Dapeng

    2014-01-01

    Apart from water, tea is the world's most widely consumed beverage. Tea is produced in more than 50 countries with an annual production of approximately 4.7 million tons. The market segment for specialty tea has been expanding rapidly owing to increased demand, resulting in higher revenues and profits for tea growers and the industry. Accurate varietal identification is critically important to ensure traceability and authentication of premium tea products, which in turn contribute to on-farm conservation of tea genetic diversity. Using a set of single nucleotide polymorphism (SNP) markers developed from the expressed sequence tag (EST) database of Camilla senensis, we genotyped deoxyribonucleic acid (DNA) samples extracted from a diverse group of tea varieties, including both fresh and processed commercial loose-leaf teas. The validation led to the designation of 60 SNPs that unambiguously identified all 40 tested tea varieties with high statistical rigor (ptea varieties. This method provides a powerful tool for variety authentication and quality control for the tea industry. It is also highly useful for the management of tea genetic resources and breeding, where accurate and efficient genotype identification is essential.

  13. Structure and function of nucleotide sugar transporters: Current progress

    Directory of Open Access Journals (Sweden)

    Barbara Hadley

    2014-06-01

    Full Text Available The proteomes of eukaryotes, bacteria and archaea are highly diverse due, in part, to the complex post-translational modification of protein glycosylation. The diversity of glycosylation in eukaryotes is reliant on nucleotide sugar transporters to translocate specific nucleotide sugars that are synthesised in the cytosol and nucleus, into the endoplasmic reticulum and Golgi apparatus where glycosylation reactions occur. Thirty years of research utilising multidisciplinary approaches has contributed to our current understanding of NST function and structure. In this review, the structure and function, with reference to various disease states, of several NSTs including the UDP-galactose, UDP-N-acetylglucosamine, UDP-N-acetylgalactosamine, GDP-fucose, UDP-N-acetylglucosamine/UDP-glucose/GDP-mannose and CMP-sialic acid transporters will be described. Little is known regarding the exact structure of NSTs due to difficulties associated with crystallising membrane proteins. To date, no three-dimensional structure of any NST has been elucidated. What is known is based on computer predictions, mutagenesis experiments, epitope-tagging studies, in-vitro assays and phylogenetic analysis. In this regard the best-characterised NST to date is the CMP-sialic acid transporter (CST. Therefore in this review we will provide the current state-of-play with respect to the structure–function relationship of the (CST. In particular we have summarised work performed by a number groups detailing the affect of various mutations on CST transport activity, efficiency, and substrate specificity.

  14. A genomewide catalogue of single nucleotide polymorphisms in white-beaked and Atlantic white-sided dolphins

    DEFF Research Database (Denmark)

    Fernández, R.; Schubert, M.; Vargas-Velázquez, A. M.

    2015-01-01

    -beaked (Lagenorhynchus albirostris) and 43 Atlantic white-sided dolphins (L. acutus) gathered throughout their north-east Atlantic distribution range. Both species are at a high risk of being negatively affected by climate change. Here, we provide a resource of 38 240 RAD-tags and 52 981 nuclear SNPs shared between both...... species. We have estimated overall higher levels of nucleotide diversity in white-sided (π = 0.0492 ± 0.0006%) than in white-beaked dolphins (π = 0.0300 ± 0.0004%). White-sided dolphins sampled in the Faroe Islands, belonging to two pods (N = 7 and N = 11), showed similar levels of diversity (π = 0...... of genetic clusters among our sample set, we obtained an estimate of two to four clusters, corresponding to both species and possibly, two further clusters within each species. A higher diversity and lower population structuring was encountered in white-sided dolphins from the north-east Atlantic, in line...

  15. Development and characterization of 35 single nucleotide polymorphism markers for the brown alga Fucus vesiculosus

    NARCIS (Netherlands)

    Canovas, Fernando; Mota, Catarina; Ferreira-Costa, Joana; Serrao, Ester; Coyer, Jim; Olsen, Jeanine; Pearson, Gareth

    2011-01-01

    We characterized 35 single nucleotide polymorphism (SNP) markers for the brown alga Fucus vesiculosus. Based on existing Fucus Expressed Sequence Tag libraries for heat and desiccation-stressed tissue, SNPs were developed and confirmed by re-sequencing cDNA from a diverse panel of individuals. SNP

  16. Effects of nucleotides and nucleosides on coagulation

    DEFF Research Database (Denmark)

    Bune, Laurids; Thaning, Pia; Johansson, Pär I

    2010-01-01

    Nucleotides, including ADP, ATP and uridine triphosphate (UTP), are discharged profusely in the circulation during many pathological conditions including sepsis. Sepsis can cause hypotension and systemic activation of the coagulation and fibrinolytic systems in humans, which may cause disseminated...... intravascular coagulation. We investigated whether nucleotide-induced cardiovascular collapse as provoked by systemic infusion of adenosine, ADP, ATP, UTP and nitric oxide affected the haemostatic system as assessed by whole blood thromboelastography (TEG) analysis. Ten pigs received a randomized infusion...

  17. Effects of purine nucleotide administration on purine nucleotide metabolism in brains of heroin-dependent rats

    Directory of Open Access Journals (Sweden)

    Kun Li

    Full Text Available ABSTRACT Heroin is known to enhance catabolism and inhibit anabolism of purine nucleotides, leading to purine nucleotide deficiencies in rat brains. Here, we determined the effect of exogenous purine nucleotide administration on purine nucleotide metabolism in the brains of heroin-dependent rats. Heroin was administrated in increasing doses for 9 consecutive days to induce addiction, and the biochemical changes associated with heroin and purine nucleotide administration were compared among the treated groups. HPLC was performed to detect the absolute concentrations of purine nucleotides in the rat brain cortices. The enzymatic activities of adenosine deaminase (ADA and xanthine oxidase (XO in the treated rat cortices were analyzed, and qRT-PCR was performed to determine the relative expression of ADA, XO, adenine phosphoribosyl transferase (APRT, hypoxanthine-guaninephosphoribosyl transferase (HGPRT, and adenosine kinase (AK. Heroin increased the enzymatic activity of ADA and XO, and up-regulated the transcription of ADA and XO. Alternatively, heroin decreased the transcription of AK, APRT, and HGPRT in the rat cortices. Furthermore, purine nucleotide administration alleviated the effect of heroin on purine nucleotide content, activity of essential purine nucleotide metabolic enzymes, and transcript levels of these genes. Our findings therefore represent a novel, putative approach to the treatment of heroin addiction.

  18. SVOP is a nucleotide binding protein.

    Directory of Open Access Journals (Sweden)

    Jia Yao

    Full Text Available BACKGROUND: Synaptic Vesicle Protein 2 (SV2 and SV2-related protein (SVOP are transporter-like proteins that localize to neurotransmitter-containing vesicles. Both proteins share structural similarity with the major facilitator (MF family of small molecule transporters. We recently reported that SV2 binds nucleotides, a feature that has also been reported for another MF family member, the human glucose transporter 1 (Glut1. In the case of Glut1, nucleotide binding affects transport activity. In this study, we determined if SVOP also binds nucleotides and assessed its nucleotide binding properties. METHODOLOGY/PRINCIPAL FINDINGS: We performed in vitro photoaffinity labeling experiments with the photoreactive ATP analogue, 8-azido-ATP[gamma] biotin and purified recombinant SVOP-FLAG fusion protein. We found that SVOP is a nucleotide-binding protein, although both its substrate specificity and binding site differ from that of SV2. Within the nucleotides tested, ATP, GTP and NAD show same level of inhibition on SVOP-FLAG labeling. Dose dependent studies indicated that SVOP demonstrates the highest affinity for NAD, in contrast to SV2, which binds both NAD and ATP with equal affinity. Mapping of the binding site revealed a single region spanning transmembrane domains 9-12, which contrasts to the two binding sites in the large cytoplasmic domains in SV2A. CONCLUSIONS/SIGNIFICANCE: SVOP is the third MF family member to be found to bind nucleotides. Given that the binding sites are unique in SVOP, SV2 and Glut1, this feature appears to have arisen separately.

  19. RVD: a command-line program for ultrasensitive rare single nucleotide variant detection using targeted next-generation DNA resequencing.

    Science.gov (United States)

    Cushing, Anna; Flaherty, Patrick; Hopmans, Erik; Bell, John M; Ji, Hanlee P

    2013-05-23

    Rare single nucleotide variants play an important role in genetic diversity and heterogeneity of specific human disease. For example, an individual clinical sample can harbor rare mutations at minor frequencies. Genetic diversity within an individual clinical sample is oftentimes reflected in rare mutations. Therefore, detecting rare variants prior to treatment may prove to be a useful predictor for therapeutic response. Current rare variant detection algorithms using next generation DNA sequencing are limited by inherent sequencing error rate and platform availability. Here we describe an optimized implementation of a rare variant detection algorithm called RVD for use in targeted gene resequencing. RVD is available both as a command-line program and for use in MATLAB and estimates context-specific error using a beta-binomial model to call variants with minor allele frequency (MAF) as low as 0.1%. We show that RVD accepts standard BAM formatted sequence files. We tested RVD analysis on multiple Illumina sequencing platforms, among the most widely used DNA sequencing platforms. RVD meets a growing need for highly sensitive and specific tools for variant detection. To demonstrate the usefulness of RVD, we carried out a thorough analysis of the software's performance on synthetic and clinical virus samples sequenced on both an Illumina GAIIx and a MiSeq. We expect RVD can improve understanding the genetics and treatment of common viral diseases including influenza. RVD is available at the following URL:http://dna-discovery.stanford.edu/software/rvd/.

  20. Do pyrimidine nucleotides regulate translatability of globin mRNA as purine nucleotides do?

    Science.gov (United States)

    Rubin, H N; Almendarez, E; Halim, M N

    1988-01-01

    1. When rabbit globin mRNA was incubated with rabbit reticulocyte lysate in the presence of various concentrations of nucleotides, globin synthesis was inhibited or stimulated dependent on dose. 2. Pyrimidine nucleotides inhibited protein synthesis at 0.3 mM, whereas 2 mM of purine nucleotides were required to cause similar inhibition. 3. Adenosine mono- and diphosphate inhibited globin synthesis at a concentration of only 1 mM; however, the sequence is AMP greater than ADP greater than ATP. 4. Translation arrest by these nucleotides was instantaneous. 5. These results suggest that these nucleotides may provide a structural component for maintaining the integrity, the conformation of mRNA or of the messenger ribonucleoprotein (mRNP).

  1. Cyclic nucleotide phosphodiesterases in heart and vessels: A therapeutic perspective.

    Science.gov (United States)

    Bobin, Pierre; Belacel-Ouari, Milia; Bedioune, Ibrahim; Zhang, Liang; Leroy, Jérôme; Leblais, Véronique; Fischmeister, Rodolphe; Vandecasteele, Grégoire

    2016-01-01

    Cyclic nucleotide phosphodiesterases (PDEs) degrade the second messengers cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP), thereby regulating multiple aspects of cardiac and vascular muscle functions. This highly diverse class of enzymes encoded by 21 genes encompasses 11 families that are not only responsible for the termination of cyclic nucleotide signalling, but are also involved in the generation of dynamic microdomains of cAMP and cGMP, controlling specific cell functions in response to various neurohormonal stimuli. In the myocardium and vascular smooth muscle, the PDE3 and PDE4 families predominate, degrading cAMP and thereby regulating cardiac excitation-contraction coupling and smooth muscle contractile tone. PDE3 inhibitors are positive inotropes and vasodilators in humans, but their use is limited to acute heart failure and intermittent claudication. PDE5 is particularly important for the degradation of cGMP in vascular smooth muscle, and PDE5 inhibitors are used to treat erectile dysfunction and pulmonary hypertension. There is experimental evidence that these PDEs, as well as other PDE families, including PDE1, PDE2 and PDE9, may play important roles in cardiac diseases, such as hypertrophy and heart failure, as well as several vascular diseases. After a brief presentation of the cyclic nucleotide pathways in cardiac and vascular cells, and the major characteristics of the PDE superfamily, this review will focus on the current use of PDE inhibitors in cardiovascular diseases, and the recent research developments that could lead to better exploitation of the therapeutic potential of these enzymes in the future. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  2. Extracellular nucleotide derivatives protect cardiomyctes against hypoxic stress

    DEFF Research Database (Denmark)

    Golan, O; Issan, Y; Isak, A

    2011-01-01

    RATIONALE: Extracellular nucleotides have widespread effects and various cell responses. Whereas the effect of a purine nucleotide (ATP) and a pyrimidine nucleotide (UTP) on myocardial infarction has been examined, the role of different purine and pyrimidine nucleotides and nucleosides in cardiop...

  3. Development of a single nucleotide polymorphism barcode to genotype Plasmodium vivax infections.

    Directory of Open Access Journals (Sweden)

    Mary Lynn Baniecki

    2015-03-01

    Full Text Available Plasmodium vivax, one of the five species of Plasmodium parasites that cause human malaria, is responsible for 25-40% of malaria cases worldwide. Malaria global elimination efforts will benefit from accurate and effective genotyping tools that will provide insight into the population genetics and diversity of this parasite. The recent sequencing of P. vivax isolates from South America, Africa, and Asia presents a new opportunity by uncovering thousands of novel single nucleotide polymorphisms (SNPs. Genotyping a selection of these SNPs provides a robust, low-cost method of identifying parasite infections through their unique genetic signature or barcode. Based on our experience in generating a SNP barcode for P. falciparum using High Resolution Melting (HRM, we have developed a similar tool for P. vivax. We selected globally polymorphic SNPs from available P. vivax genome sequence data that were located in putatively selectively neutral sites (i.e., intergenic, intronic, or 4-fold degenerate coding. From these candidate SNPs we defined a barcode consisting of 42 SNPs. We analyzed the performance of the 42-SNP barcode on 87 P. vivax clinical samples from parasite populations in South America (Brazil, French Guiana, Africa (Ethiopia and Asia (Sri Lanka. We found that the P. vivax barcode is robust, as it requires only a small quantity of DNA (limit of detection 0.3 ng/μl to yield reproducible genotype calls, and detects polymorphic genotypes with high sensitivity. The markers are informative across all clinical samples evaluated (average minor allele frequency > 0.1. Population genetic and statistical analyses show the barcode captures high degrees of population diversity and differentiates geographically distinct populations. Our 42-SNP barcode provides a robust, informative, and standardized genetic marker set that accurately identifies a genomic signature for P. vivax infections.

  4. Development of a Single Nucleotide Polymorphism Barcode to Genotype Plasmodium vivax Infections

    Science.gov (United States)

    Baniecki, Mary Lynn; Faust, Aubrey L.; Schaffner, Stephen F.; Park, Daniel J.; Galinsky, Kevin; Daniels, Rachel F.; Hamilton, Elizabeth; Ferreira, Marcelo U.; Karunaweera, Nadira D.; Serre, David; Zimmerman, Peter A.; Sá, Juliana M.; Wellems, Thomas E.; Musset, Lise; Legrand, Eric; Melnikov, Alexandre; Neafsey, Daniel E.; Volkman, Sarah K.; Wirth, Dyann F.; Sabeti, Pardis C.

    2015-01-01

    Plasmodium vivax, one of the five species of Plasmodium parasites that cause human malaria, is responsible for 25–40% of malaria cases worldwide. Malaria global elimination efforts will benefit from accurate and effective genotyping tools that will provide insight into the population genetics and diversity of this parasite. The recent sequencing of P. vivax isolates from South America, Africa, and Asia presents a new opportunity by uncovering thousands of novel single nucleotide polymorphisms (SNPs). Genotyping a selection of these SNPs provides a robust, low-cost method of identifying parasite infections through their unique genetic signature or barcode. Based on our experience in generating a SNP barcode for P. falciparum using High Resolution Melting (HRM), we have developed a similar tool for P. vivax. We selected globally polymorphic SNPs from available P. vivax genome sequence data that were located in putatively selectively neutral sites (i.e., intergenic, intronic, or 4-fold degenerate coding). From these candidate SNPs we defined a barcode consisting of 42 SNPs. We analyzed the performance of the 42-SNP barcode on 87 P. vivax clinical samples from parasite populations in South America (Brazil, French Guiana), Africa (Ethiopia) and Asia (Sri Lanka). We found that the P. vivax barcode is robust, as it requires only a small quantity of DNA (limit of detection 0.3 ng/μl) to yield reproducible genotype calls, and detects polymorphic genotypes with high sensitivity. The markers are informative across all clinical samples evaluated (average minor allele frequency > 0.1). Population genetic and statistical analyses show the barcode captures high degrees of population diversity and differentiates geographically distinct populations. Our 42-SNP barcode provides a robust, informative, and standardized genetic marker set that accurately identifies a genomic signature for P. vivax infections. PMID:25781890

  5. Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis

    Energy Technology Data Exchange (ETDEWEB)

    Ansong, Charles; Ortega, Corrie; Payne, Samuel H.; Haft, Daniel H.; Chauvigne-Hines, Lacie M.; Lewis, Michael P.; Ollodart, Anja R.; Purvine, Samuel O.; Shukla, Anil K.; Fortuin, Suereta; Smith, Richard D.; Adkins, Joshua N.; Grundner, Christoph; Wright, Aaron T.

    2013-01-24

    The annotation of protein function is almost completely performed by in silico approaches. However, computational prediction of protein function is frequently incomplete and error prone. In Mycobacterium tuberculosis (Mtb), ~25% of all genes have no predicted function and are annotated as hypothetical proteins. This lack of functional information severely limits our understanding of Mtb pathogenicity. Current tools for experimental functional annotation are limited and often do not scale to entire protein families. Here, we report a generally applicable chemical biology platform to functionally annotate bacterial proteins by combining activity-based protein profiling (ABPP) and quantitative LC-MS-based proteomics. As an example of this approach for high-throughput protein functional validation and discovery, we experimentally annotate the families of ATP-binding proteins in Mtb. Our data experimentally validate prior in silico predictions of >250 ATPases and adenosine nucleotide-binding proteins, and reveal 73 hypothetical proteins as novel ATP-binding proteins. We identify adenosine cofactor interactions with many hypothetical proteins containing a diversity of unrelated sequences, providing a new and expanded view of adenosine nucleotide binding in Mtb. Furthermore, many of these hypothetical proteins are both unique to Mycobacteria and essential for infection, suggesting specialized functions in mycobacterial physiology and pathogenicity. Thus, we provide a generally applicable approach for high throughput protein function discovery and validation, and highlight several ways in which application of activity-based proteomics data can improve the quality of functional annotations to facilitate novel biological insights.

  6. Single-nucleotide polymorphism identification and genotyping in Camelina sativa.

    Science.gov (United States)

    Singh, Ravinder; Bollina, Venkatesh; Higgins, Erin E; Clarke, Wayne E; Eynck, Christina; Sidebottom, Christine; Gugel, Richard; Snowdon, Rod; Parkin, Isobel A P

    Camelina sativa, a largely relict crop, has recently returned to interest due to its potential as an industrial oilseed. Molecular markers are key tools that will allow C. sativa to benefit from modern breeding approaches. Two complementary methodologies, capture of 3' cDNA tags and genomic reduced-representation libraries, both of which exploited second generation sequencing platforms, were used to develop a low density (768) Illumina GoldenGate single nucleotide polymorphism (SNP) array. The array allowed 533 SNP loci to be genetically mapped in a recombinant inbred population of C. sativa. Alignment of the SNP loci to the C. sativa genome identified the underlying sequenced regions that would delimit potential candidate genes in any mapping project. In addition, the SNP array was used to assess genetic variation among a collection of 175 accessions of C. sativa, identifying two sub-populations, yet low overall gene diversity. The SNP loci will provide useful tools for future crop improvement of C. sativa.

  7. Retrieval and Representation of Nucleotide Sequence of ...

    African Journals Online (AJOL)

    Umar et al.: Retrieval and Representation of Nucleotide Sequence of Saccharomyces cerevisiae Cystathionine ............. 28. GenBank, information describing each sequence entry is given, including literature references, information about the function of the sequence, location of mRNA and coding regions, and position of ...

  8. Single-nucleotide polymorphisms in peroxisome proliferator ...

    Indian Academy of Sciences (India)

    We also investigated the correlation of these two single-nucleotide polymorphisms (SNPs) with plasma resistin levels. The C1431T SNP was associated with higher levels of plasma resistin ( = 0.017). Furthermore, C1431T was associated with resistin in different tertiles. Prevalence of the 'Pro-C' haplotype decreased with ...

  9. Expressed sequence tags (ESTs) and single nucleotide ...

    African Journals Online (AJOL)

    Expressed Sequence Tags (ESTs) and Single Nucleotide Polymorphisms (SNPs) are providing in depth knowledge in plant biology, breeding and biotechnology. The emergence of many novel molecular marker techniques are changing and accelerating the process of producing mutations in plant molecular biology ...

  10. Single-nucleotide polymorphisms in peroxisome proliferator ...

    Indian Academy of Sciences (India)

    Prakash

    the metabolic syndrome (MS) and type 2 diabetes. We also investigated the correlation of these two single-nucleotide polymorphisms (SNPs) with plasma resistin levels. The C1431T SNP was associated with higher levels of plasma resistin (P = 0.017). Furthermore, C1431T was associated with resistin in different tertiles.

  11. Estimation of Anadara tuberculosa genetic diversity in five mangroves from Tumaco, using Cytochrome oxidase I enzyme

    Directory of Open Access Journals (Sweden)

    Esmeralda Chamorro L

    2016-09-01

    Full Text Available Objective. To estimate the genetic diversity of the Anadara tuberculosa en five mangrove swams of Tumaco, Nariño, Colombia using as a mitocondrial molecular marker the cytochromo oxidase sub-unit I (COI. Materials and methods. A total of 50 individuals were collected from the San Jorge, La Tiburonera, El Pajal, La Playa y Bajito Vaquería mangrove swamps, randomly selecting 10 specimens of each zone. The tissue sample was worked with absolute alcohol at ambient temperature in microtubes. DNA was extracted, and the mitocondrial DNA was amplified using the PCR technique (polymerase chain reaction. The amplified and quantified products of PCR were sequenced on both sides (Macrogen. Each one of the obtained sequences was edited and aligned. Later, the parameters of genetic diversity (haplotypical and nucleotidical were measured, and the analysis of distribution between frequency pairs (Mistmach distribution was elaborated. Finally, the analysis of nucleotidic variation and population structure (AMOVA was completed. Results. The amplified product gene weighed 710 bp. The haplotypical diversity reported for all the populations was high (0.683±0.060 and the reported nucleotídical diversity was low for all the populations (0.040±0.020. The AMOVA results indicate that the variance amongst populations is low (4.20% and that the variance within populations is high (95.80%. Conclusions. The studied populations are not structured and although there is a decrease of natural banks, the genetic diversity is high.

  12. Assessing the genome level diversity of Listeria monocytogenes from contaminated ice cream and environmental samples linked to a listeriosis outbreak in the United States.

    Directory of Open Access Journals (Sweden)

    Yi Chen

    Full Text Available A listeriosis outbreak in the United States implicated contaminated ice cream produced by one company, which operated 3 facilities. We performed single nucleotide polymorphism (SNP-based whole genome sequencing (WGS analysis on Listeria monocytogenes from food, environmental and clinical sources, identifying two clusters and a single branch, belonging to PCR serogroup IIb and genetic lineage I. WGS Cluster I, representing one outbreak strain, contained 82 food and environmental isolates from Facility I and 4 clinical isolates. These isolates differed by up to 29 SNPs, exhibited 9 pulsed-field gel electrophoresis (PFGE profiles and multilocus sequence typing (MLST sequence type (ST 5 of clonal complex 5 (CC5. WGS Cluster II contained 51 food and environmental isolates from Facility II, 4 food isolates from Facility I and 5 clinical isolates. Among them the isolates from Facility II and clinical isolates formed a clade and represented another outbreak strain. Isolates in this clade differed by up to 29 SNPs, exhibited 3 PFGE profiles and ST5. The only isolate collected from Facility III belonged to singleton ST489, which was in a single branch separate from Clusters I and II, and was not associated with the outbreak. WGS analyses clustered together outbreak-associated isolates exhibiting multiple PFGE profiles, while differentiating them from epidemiologically unrelated isolates that exhibited outbreak PFGE profiles. The complete genome of a Cluster I isolate allowed the identification and analyses of putative prophages, revealing that Cluster I isolates differed by the gain or loss of three putative prophages, causing the banding pattern differences among all 3 AscI-PFGE profiles observed in Cluster I isolates. WGS data suggested that certain ice cream varieties and/or production lines might have contamination sources unique to them. The SNP-based analysis was able to distinguish CC5 as a group from non-CC5 isolates and differentiate among CC5

  13. Assessing the genome level diversity of Listeria monocytogenes from contaminated ice cream and environmental samples linked to a listeriosis outbreak in the United States.

    Science.gov (United States)

    Chen, Yi; Luo, Yan; Curry, Phillip; Timme, Ruth; Melka, David; Doyle, Matthew; Parish, Mickey; Hammack, Thomas S; Allard, Marc W; Brown, Eric W; Strain, Errol A

    2017-01-01

    A listeriosis outbreak in the United States implicated contaminated ice cream produced by one company, which operated 3 facilities. We performed single nucleotide polymorphism (SNP)-based whole genome sequencing (WGS) analysis on Listeria monocytogenes from food, environmental and clinical sources, identifying two clusters and a single branch, belonging to PCR serogroup IIb and genetic lineage I. WGS Cluster I, representing one outbreak strain, contained 82 food and environmental isolates from Facility I and 4 clinical isolates. These isolates differed by up to 29 SNPs, exhibited 9 pulsed-field gel electrophoresis (PFGE) profiles and multilocus sequence typing (MLST) sequence type (ST) 5 of clonal complex 5 (CC5). WGS Cluster II contained 51 food and environmental isolates from Facility II, 4 food isolates from Facility I and 5 clinical isolates. Among them the isolates from Facility II and clinical isolates formed a clade and represented another outbreak strain. Isolates in this clade differed by up to 29 SNPs, exhibited 3 PFGE profiles and ST5. The only isolate collected from Facility III belonged to singleton ST489, which was in a single branch separate from Clusters I and II, and was not associated with the outbreak. WGS analyses clustered together outbreak-associated isolates exhibiting multiple PFGE profiles, while differentiating them from epidemiologically unrelated isolates that exhibited outbreak PFGE profiles. The complete genome of a Cluster I isolate allowed the identification and analyses of putative prophages, revealing that Cluster I isolates differed by the gain or loss of three putative prophages, causing the banding pattern differences among all 3 AscI-PFGE profiles observed in Cluster I isolates. WGS data suggested that certain ice cream varieties and/or production lines might have contamination sources unique to them. The SNP-based analysis was able to distinguish CC5 as a group from non-CC5 isolates and differentiate among CC5 isolates from

  14. Single nucleotide polymorphisms minisequencing in hypervariable regions for screening of Thais.

    Science.gov (United States)

    Thongngam, Punlop; Leewattanapasuk, Worraanong; Bhoopat, Tanin; Sangthong, Padchanee

    2017-09-05

    Mitochondrial DNA (mtDNA) analysis has displayed an important role and been considered as a powerful tool in various fields of forensic science applications. Nowadays, single nucleotide polymorphisms (SNPs) on mtDNA have become additional DNA markers when conventional STR typing practically fails. mtDNA sequencing of polymerase chain reaction (PCR) products from the hypervariable region I (HVRI) and II (HVRII) is the standard method of mtDNA analysis. However, mtDNA sequencing is rather expensive, time consuming and technically complex. This study aims to develop the SNPs minisequencing for screening of Thai populations. For this purpose, sixteen SNPs that possess high discriminating power in hypervariable regions were selected. The DNA samples were obtained from 100 buccal swab samples of Thai healthy individuals. All DNA samples were extracted and were subsequently amplified by single duplex PCR technique. The duplex PCR products were genotyped by SNPs minisequencing. Based on 16 SNPs, a total of 63 haplotypes were observed of which 46 haplotypes were unique. The haplotype diversity, discriminating power and random match probability were calculated to be 0.9830, 0.9732 and 0.0268, respectively. The SNPs at 150, 199, 489, 16129, 16189, 16223, and 16304 were highly polymorphic in the studied population. Our results suggested that the SNPs minisequencing can be an alternative method of SNPs genotyping. This method can be used for an exclusion of a large number of mismatch samples and as a presumptive test prior to do confirmatory mtDNA sequencing. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Vaccination has minimal impact on the intrahost diversity of H3N2 influenza viruses.

    Directory of Open Access Journals (Sweden)

    Kari Debbink

    2017-01-01

    Full Text Available While influenza virus diversity and antigenic drift have been well characterized on a global scale, the factors that influence the virus' rapid evolution within and between human hosts are less clear. Given the modest effectiveness of seasonal vaccination, vaccine-induced antibody responses could serve as a potent selective pressure for novel influenza variants at the individual or community level. We used next generation sequencing of patient-derived viruses from a randomized, placebo-controlled trial of vaccine efficacy to characterize the diversity of influenza A virus and to define the impact of vaccine-induced immunity on within-host populations. Importantly, this study design allowed us to isolate the impact of vaccination while still studying natural infection. We used pre-season hemagglutination inhibition and neuraminidase inhibition titers to quantify vaccine-induced immunity directly and to assess its impact on intrahost populations. We identified 166 cases of H3N2 influenza over 3 seasons and 5119 person-years. We obtained whole genome sequence data for 119 samples and used a stringent and empirically validated analysis pipeline to identify intrahost single nucleotide variants at ≥1% frequency. Phylogenetic analysis of consensus hemagglutinin and neuraminidase sequences showed no stratification by pre-season HAI and NAI titer, respectively. In our study population, we found that the vast majority of intrahost single nucleotide variants were rare and that very few were found in more than one individual. Most samples had fewer than 15 single nucleotide variants across the entire genome, and the level of diversity did not significantly vary with day of sampling, vaccination status, or pre-season antibody titer. Contrary to what has been suggested in experimental systems, our data indicate that seasonal influenza vaccination has little impact on intrahost diversity in natural infection and that vaccine-induced immunity may be only a

  16. Serotype and genetic diversity of human rhinovirus strains that circulated in Kenya in 2008.

    Science.gov (United States)

    Milanoi, Sylvia; Ongus, Juliette R; Gachara, George; Coldren, Rodney; Bulimo, Wallace

    2016-05-01

    Human rhinoviruses (HRVs) are a well-established cause of the common cold and recent studies indicated that they may be associated with severe acute respiratory illnesses (SARIs) like pneumonia, asthma, and bronchiolitis. Despite global studies on the genetic diversity of the virus, the serotype diversity of these viruses across diverse geographic regions in Kenya has not been characterized. This study sought to characterize the serotype diversity of HRV strains that circulated in Kenya in 2008. A total of 517 archived nasopharyngeal samples collected in a previous respiratory virus surveillance program across Kenya in 2008 were selected. Participants enrolled were outpatients who presented with influenza-like (ILI) symptoms. Real-time RT-PCR was employed for preliminary HRV detection. HRV-positive samples were amplified using RT-PCR and thereafter the nucleotide sequences of the amplicons were determined followed by phylogenetic analysis. Twenty-five percent of the samples tested positive for HRV. Phylogenetic analysis revealed that the Kenyan HRVs clustered into three main species comprising HRV-A (54%), HRV-B (12%), and HRV-C (35%). Overall, 20 different serotypes were identified. Intrastrain sequence homology among the Kenyan strains ranged from 58% to 100% at the nucleotide level and 55% to 100% at the amino acid level. These results show that a wide range of HRV serotypes with different levels of nucleotide variation were present in Kenya. Furthermore, our data show that HRVs contributed substantially to influenza-like illness in Kenya in 2008. © 2016 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.

  17. Nucleotide sequence analyses of the MRP1 gene in four populations suggest negative selection on its coding region

    Directory of Open Access Journals (Sweden)

    Ryan Stephen

    2006-05-01

    Full Text Available Abstract Background The MRP1 gene encodes the 190 kDa multidrug resistance-associated protein 1 (MRP1/ABCC1 and effluxes diverse drugs and xenobiotics. Sequence variations within this gene might account for differences in drug response in different individuals. To facilitate association studies of this gene with diseases and/or drug response, exons and flanking introns of MRP1 were screened for polymorphisms in 142 DNA samples from four different populations. Results Seventy-one polymorphisms, including 60 biallelic single nucleotide polymorphisms (SNPs, ten insertions/deletions (indel and one short tandem repeat (STR were identified. Thirty-four of these polymorphisms have not been previously reported. Interestingly, the STR polymorphism at the 5' untranslated region (5'UTR occurs at high but different frequencies in the different populations. Frequencies of common polymorphisms in our populations were comparable to those of similar populations in HAPMAP or Perlegen. Nucleotide diversity indices indicated that the coding region of MRP1 may have undergone negative selection or recent population expansion. SNPs E10/1299 G>T (R433S and E16/2012 G>T (G671V which occur at low frequency in only one or two of four populations examined were predicted to be functionally deleterious and hence are likely to be under negative selection. Conclusion Through in silico approaches, we identified two rare SNPs that are potentially negatively selected. These SNPs may be useful for studies associating this gene with rare events including adverse drug reactions.

  18. Evaluation of cytochrome b mtDNA sequences in genetic diversity studies of Channa marulius (Channidae: Perciformes).

    Science.gov (United States)

    Habib, Maria; Lakra, W S; Mohindra, Vindhya; Khare, Praveen; Barman, A S; Singh, Akanksha; Lal, Kuldeep K; Punia, Peyush; Khan, Asif A

    2011-02-01

    Channa marulius (Hamilton, 1822) is a commercially important freshwater fish and a potential candidate species for aquaculture. The present study evaluated partial Cytochrome b gene sequence of mtDNA for determining the genetic variation in wild populations of C. marulius. Genomic DNA extracted from C. marulius samples (n = 23) belonging to 3 distant rivers; Mahanadi, Teesta and Yamuna was analyzed. Sequencing of 307 bp Cytochrome b mtDNA fragment revealed the presence of 5 haplotypes with haplotype diversity value of 0.763 and nucleotide diversity value of 0.0128. Single population specific haplotype was observed in Mahanadi and Yamuna samples and 3 haplotypes in Teesta samples. The analysis of data demonstrated the suitability of partial Cytochrome b sequence in determining the genetic diversity in C. marulius population.

  19. A genomewide catalogue of single nucleotide polymorphisms in white-beaked and Atlantic white-sided dolphins.

    Science.gov (United States)

    Fernández, R; Schubert, M; Vargas-Velázquez, A M; Brownlow, A; Víkingsson, G A; Siebert, U; Jensen, L F; Øien, N; Wall, D; Rogan, E; Mikkelsen, B; Dabin, W; Alfarhan, A H; Alquraishi, S A; Al-Rasheid, K A S; Guillot, G; Orlando, L

    2016-01-01

    The field of population genetics is rapidly moving into population genomics as the quantity of data generated by high-throughput sequencing platforms increases. In this study, we used restriction-site-associated DNA sequencing (RADSeq) to recover genomewide genotypes from 70 white-beaked (Lagenorhynchus albirostris) and 43 Atlantic white-sided dolphins (L. acutus) gathered throughout their north-east Atlantic distribution range. Both species are at a high risk of being negatively affected by climate change. Here, we provide a resource of 38,240 RAD-tags and 52,981 nuclear SNPs shared between both species. We have estimated overall higher levels of nucleotide diversity in white-sided (π = 0.0492 ± 0.0006%) than in white-beaked dolphins (π = 0.0300 ± 0.0004%). White-sided dolphins sampled in the Faroe Islands, belonging to two pods (N = 7 and N = 11), showed similar levels of diversity (π = 0.0317 ± 0.0007% and 0.0267 ± 0.0006%, respectively) compared to unrelated individuals of the same species sampled elsewhere (e.g. π = 0.0285 ± 0.0007% for 11 Scottish individuals). No evidence of higher levels of kinship within pods can be derived from our analyses. When identifying the most likely number of genetic clusters among our sample set, we obtained an estimate of two to four clusters, corresponding to both species and possibly, two further clusters within each species. A higher diversity and lower population structuring was encountered in white-sided dolphins from the north-east Atlantic, in line with their preference for pelagic waters, as opposed to white-beaked dolphins that have a more patchy distribution, mainly across continental shelves. © 2015 John Wiley & Sons Ltd.

  20. A modular method for the extraction of DNA and RNA, and the separation of DNA pools from diverse environmental sample types

    DEFF Research Database (Denmark)

    Lever, Mark; Torti, Andrea; Eickenbusch, Philip

    2015-01-01

    's oceans and the deepest borehole ever studied by scientific ocean drilling. Extraction yields of DNA and RNA are higher than with widely used commercial kits, indicating an advantage to optimizing extraction procedures to match specific sample characteristics. The ability to separate soluble extracellular......A method for the extraction of nucleic acids from a wide range of environmental samples was developed. This method consists of several modules, which can be individually modified to maximize yields in extractions of DNA and RNA or separations of DNA pools. Modules were designed based on elaborate...... tests, in which permutations of all nucleic acid extraction steps were compared. The final modular protocol is suitable for extractions from igneous rock, air, water, and sediments. Sediments range from high-biomass, organic rich coastal samples to samples from the most oligotrophic region of the world...

  1. Single-nucleotide polymorphisms in PtoCesA7 and their association with growth and wood properties in Populus tomentosa.

    Science.gov (United States)

    Tian, Jiaxing; Chang, Mengqi; Du, Qingzhang; Xu, Baohua; Zhang, Deqiang

    2014-06-01

    Cellulose synthase (CesA) genes encode the enzymes that synthesize cellulose; therefore, CesAs play central roles in plant development and affect the yield and quality of wood, essential properties for industrial applications of plant biomass. To effectively manipulate wood biosynthesis in trees and improve wood quality, we thus require a better understanding of the natural variation in CesAs. Association studies have emerged as a powerful tool for identification of variation associated with quantitative traits. Here, we used a candidate gene-based association mapping approach to identify PtoCesA7 allelic variants that associate with growth and wood quality traits in Populus tomentosa. We isolated a full-length PtoCesA7 cDNA and observed high PtoCesA7 expression in xylem, consistent with the xylem-specific expression of CesA7. Nucleotide diversity and linkage disequilibrium (LD) in PtoCesA7, sampled from the P. tomentosa natural distribution, revealed that PtoCesA7 harbors high nucleotide diversity (π(T) = 0.0091) and low LD (r(2) ≥ 0.1, within 800 bp). By association analysis, we identified seven single-nucleotide polymorphisms (SNPs) (false discovery rate Q wood properties, explaining 3.62-10.59 % of the phenotypic variance. We also validated 9 of the 10 significant marker-trait associations in at least one of three smaller subsets (climatic regions) or in a linkage-mapping population. Thus, our study identified functional PtoCesA7 allelic variants associated with growth and wood quality traits, giving new insights into genes affecting wood quality and quantity. From an applied perspective, the SNPs revealed in this study have potential applications in marker-assisted breeding.

  2. Single nucleotide polymorphism analysis of European archaeological M. leprae DNA.

    Directory of Open Access Journals (Sweden)

    Claire L Watson

    Full Text Available BACKGROUND: Leprosy was common in Europe eight to twelve centuries ago but molecular confirmation of this has been lacking. We have extracted M. leprae ancient DNA (aDNA from medieval bones and single nucleotide polymorphism (SNP typed the DNA, this provides insight into the pattern of leprosy transmission in Europe and may assist in the understanding of M. leprae evolution. METHODS AND FINDINGS: Skeletons have been exhumed from 3 European countries (the United Kingdom, Denmark and Croatia and are dated around the medieval period (476 to 1350 A.D.. we tested for the presence of 3 previously identified single nucleotide polymorphisms (SNPs in 10 aDNA extractions. M. leprae aDNA was extracted from 6 of the 10 bone samples. SNP analysis of these 6 extractions were compared to previously analysed European SNP data using the same PCR assays and were found to be the same. Testing for the presence of SNPs in M. leprae DNA extracted from ancient bone samples is a novel approach to analysing European M. leprae DNA and the findings concur with the previously published data that European M. leprae strains fall in to one group (SNP group 3. CONCLUSIONS: These findings support the suggestion that the M. leprae genome is extremely stable and show that archaeological M. leprae DNA can be analysed to gain detailed information about the genotypic make-up of European leprosy, which may assist in the understanding of leprosy transmission worldwide.

  3. A modular method for the extraction of DNA and RNA, and the separation of DNA pools from diverse environmental sample types

    Science.gov (United States)

    Lever, Mark A.; Torti, Andrea; Eickenbusch, Philip; Michaud, Alexander B.; Šantl-Temkiv, Tina; Jørgensen, Bo Barker

    2015-01-01

    A method for the extraction of nucleic acids from a wide range of environmental samples was developed. This method consists of several modules, which can be individually modified to maximize yields in extractions of DNA and RNA or separations of DNA pools. Modules were designed based on elaborate tests, in which permutations of all nucleic acid extraction steps were compared. The final modular protocol is suitable for extractions from igneous rock, air, water, and sediments. Sediments range from high-biomass, organic rich coastal samples to samples from the most oligotrophic region of the world's oceans and the deepest borehole ever studied by scientific ocean drilling. Extraction yields of DNA and RNA are higher than with widely used commercial kits, indicating an advantage to optimizing extraction procedures to match specific sample characteristics. The ability to separate soluble extracellular DNA pools without cell lysis from intracellular and particle-complexed DNA pools may enable new insights into the cycling and preservation of DNA in environmental samples in the future. A general protocol is outlined, along with recommendations for optimizing this general protocol for specific sample types and research goals. PMID:26042110

  4. Structural studies on MtRecA-nucleotide complexes: insights into DNA and nucleotide binding and the structural signature of NTP recognition.

    Science.gov (United States)

    Datta, S; Ganesh, N; Chandra, Nagasuma R; Muniyappa, K; Vijayan, M

    2003-02-15

    RecA protein plays a crucial role in homologous recombination and repair of DNA. Central to all activities of RecA is its binding to Mg(+2)-ATP. The active form of the protein is a helical nucleoprotein filament containing the nucleotide cofactor and single-stranded DNA. The stability and structure of the helical nucleoprotein filament formed by RecA are modulated by nucleotide cofactors. Here we report crystal structures of a MtRecA-ADP complex, complexes with ATPgammaS in the presence and absence of magnesium as well as a complex with dATP and Mg+2. Comparison with the recently solved crystal structures of the apo form as well as a complex with ADP-AlF4 confirms an expansion of the P-loop region in MtRecA, compared to its homologue in Escherichia coli, correlating with the reduced affinity of MtRecA for ATP. The ligand bound structures reveal subtle variations in nucleotide conformations among different nucleotides that serve in maintaining the network of interactions crucial for nucleotide binding. The nucleotide binding site itself, however, remains relatively unchanged. The analysis also reveals that ATPgammaS rather than ADP-AlF4 is structurally a better mimic of ATP. From among the complexed structures, a definition for the two DNA-binding loops L1 and L2 has clearly emerged for the first time and provides a basis to understand DNA binding by RecA. The structural information obtained from these complexes correlates well with the extensive biochemical data on mutants available in the literature, contributing to an understanding of the role of individual residues in the nucleotide binding pocket, at the molecular level. Modeling studies on the mutants again point to the relative rigidity of the nucleotide binding site. Comparison with other NTP binding proteins reveals many commonalties in modes of binding by diverse members in the structural family, contributing to our understanding of the structural signature of NTP recognition. Copyright 2003 Wiley

  5. Significance of overvaluation of shape and weight in an ethnically diverse sample of obese patients with binge-eating disorder in primary care settings.

    Science.gov (United States)

    Grilo, Carlos M; White, Marney A; Masheb, Robin M

    2012-05-01

    Undue influence of shape or weight on self-evaluation--referred to as overvaluation--is a core feature across eating disorders, but is not a diagnostic requirement for binge-eating disorder (BED). This study examined overvaluation of shape/weight in ethnically diverse obese patients with BED seeking treatment in primary care. Participants were a consecutive series of 142 (105 female and 37 male) participants with BED; 43% were Caucasian, 37% were African-American, 13% were Hispanic-American, and 7% were of "other" ethnicity. Participants categorized with overvaluation (N=97; 68%) versus without clinical overvaluation (N=45; 32%) did not differ significantly in ethnicity/race, age, gender, body mass index, or binge-eating frequency. The overvaluation group had significantly greater levels of eating disorder psychopathology, poorer psychological functioning (higher depression, lower self-esteem), and greater anxiety disorder co-morbidity than the group who did not overvalue their shape/weight. The greater eating disorder and psychological disturbance levels in the overvaluation group relative to the non-overvaluation group persisted after controlling for psychiatric co-morbidity. Our findings, based on an ethnically diverse series of patients seeking treatment in general primary care settings, are consistent with findings from specialist clinics and suggest that overvaluation does not simply reflect concerns commensurate with being obese or with frequency of binge-eating, but is strongly associated with heightened eating-related psychopathology and psychological distress. Overvaluation of shape/weight warrants consideration as a diagnostic specifier for BED as it provides important information about severity. Copyright © 2012 Elsevier Ltd. All rights reserved.

  6. Single-nucleotide polymorphism discovery by high-throughput sequencing in sorghum

    Directory of Open Access Journals (Sweden)

    White Frank F

    2011-07-01

    Full Text Available Abstract Background Eight diverse sorghum (Sorghum bicolor L. Moench accessions were subjected to short-read genome sequencing to characterize the distribution of single-nucleotide polymorphisms (SNPs. Two strategies were used for DNA library preparation. Missing SNP genotype data were imputed by local haplotype comparison. The effect of library type and genomic diversity on SNP discovery and imputation are evaluated. Results Alignment of eight genome equivalents (6 Gb to the public reference genome revealed 283,000 SNPs at ≥82% confirmation probability. Sequencing from libraries constructed to limit sequencing to start at defined restriction sites led to genotyping 10-fold more SNPs in all 8 accessions, and correctly imputing 11% more missing data, than from semirandom libraries. The SNP yield advantage of the reduced-representation method was less than expected, since up to one fifth of reads started at noncanonical restriction sites and up to one third of restriction sites predicted in silico to yield unique alignments were not sampled at near-saturation. For imputation accuracy, the availability of a genomically similar accession in the germplasm panel was more important than panel size or sequencing coverage. Conclusions A sequence quantity of 3 million 50-base reads per accession using a BsrFI library would conservatively provide satisfactory genotyping of 96,000 sorghum SNPs. For most reliable SNP-genotype imputation in shallowly sequenced genomes, germplasm panels should consist of pairs or groups of genomically similar entries. These results may help in designing strategies for economical genotyping-by-sequencing of large numbers of plant accessions.

  7. Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data

    Directory of Open Access Journals (Sweden)

    Niko eBeerenwinkel

    2012-09-01

    Full Text Available Many viruses, including the clinically relevant RNA viruses HIV and HCV, exist in large populations and display high genetic heterogeneity within and between infected hosts. Assessing intra-patient viral genetic diversity is essential for understanding the evolutionary dynamics of viruses, for designing effective vaccines, and for the success of antiviral therapy. Next-generation sequencing technologies allow the rapid and cost-effective acquisition of thousands to millions of short DNA sequences from a single sample. However, this approach entails several challenges in experimental design and computational data analysis. Here, we review the entire process of inferring viral diversity from sample collection to computing measures of genetic diversity. We discuss sample preparation, including reverse transcription and amplification, and the effect of experimental conditions on diversity estimates due to in vitro base substitutions, insertions, deletions, and recombination. The use of different next-generation sequencing platforms and their sequencing error profiles are compared in the context of various applications of diversity estimation, ranging from the detection of single nucleotide variants to the reconstruction of whole-genome haplotypes. We describe the statistical and computational challenges arising from these technical artifacts, and we review existing approaches, including available software, for their solution. Finally, we discuss open problems, and highlight successful biomedical applications and potential future clinical use of next-generation sequencing to estimate viral diversity.

  8. Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data.

    Science.gov (United States)

    Beerenwinkel, Niko; Günthard, Huldrych F; Roth, Volker; Metzner, Karin J

    2012-01-01

    Many viruses, including the clinically relevant RNA viruses HIV (human immunodeficiency virus) and HCV (hepatitis C virus), exist in large populations and display high genetic heterogeneity within and between infected hosts. Assessing intra-patient viral genetic diversity is essential for understanding the evolutionary dynamics of viruses, for designing effective vaccines, and for the success of antiviral therapy. Next-generation sequencing (NGS) technologies allow the rapid and cost-effective acquisition of thousands to millions of short DNA sequences from a single sample. However, this approach entails several challenges in experimental design and computational data analysis. Here, we review the entire process of inferring viral diversity from sample collection to computing measures of genetic diversity. We discuss sample preparation, including reverse transcription and amplification, and the effect of experimental conditions on diversity estimates due to in vitro base substitutions, insertions, deletions, and recombination. The use of different NGS platforms and their sequencing error profiles are compared in the context of various applications of diversity estimation, ranging from the detection of single nucleotide variants (SNVs) to the reconstruction of whole-genome haplotypes. We describe the statistical and computational challenges arising from these technical artifacts, and we review existing approaches, including available software, for their solution. Finally, we discuss open problems, and highlight successful biomedical applications and potential future clinical use of NGS to estimate viral diversity.

  9. Nucleotide Manipulatives to Illustrate the Central Dogma†

    OpenAIRE

    Yung, Sonja B.; Primm, Todd P.

    2015-01-01

    The central dogma is a core concept that is critical for introductory biology and microbiology students to master. However, students often struggle to conceptualize the processes involved, and fail to move beyond simply memorizing the basic facts. To encourage critical thinking, we have designed a set of magnetic nucleotide manipulatives that allow students to model DNA structure, along with the processes of replication, transcription, and translation.

  10. Nucleotide Manipulatives to Illustrate the Central Dogma

    Directory of Open Access Journals (Sweden)

    Sonja B. Yung

    2015-08-01

    Full Text Available The central dogma is a core concept that is critical for introductory biology and microbiology students to master. However, students often struggle to conceptualize the processes involved, and fail to move beyond simply memorizing the basic facts. To encourage critical thinking, we have designed a set of magnetic nucleotide manipulatives that allow students to model DNA structure, along with the processes of replication, transcription, and translation.

  11. Aggregation of rat neutrophils by nucleotide triphosphates.

    OpenAIRE

    Ford-Hutchinson, A. W.

    1982-01-01

    1 Adenosine 5'-triphosphate (ATP) and uridine 5'-triphosphate (UTP) at concentrations of 3 x 10(-7)M and greater cause a rapid partially reversible aggregation of rat polymorphonuclear leucocytes. 2 Other nucleotide phosphates are much less active at producing aggregation responses; the agonist potencies being UTP greater than ATP greater than guanosine 5'-triphosphate, cytidine 5'-triphosphate, thymidine 5'-triphosphate; ATP greater than adenosine 5'-diphosphate (ADP) greater than adenosine ...

  12. Genetic Diversity among Ancient Nordic Populations

    Science.gov (United States)

    Melchior, Linea; Lynnerup, Niels; Siegismund, Hans R.; Kivisild, Toomas; Dissing, Jørgen

    2010-01-01

    Using established criteria for work with fossil DNA we have analysed mitochondrial DNA from 92 individuals from 18 locations in Denmark ranging in time from the Mesolithic to the Medieval Age. Unequivocal assignment of mtDNA haplotypes was possible for 56 of the ancient individuals; however, the success rate varied substantially between sites; the highest rates were obtained with untouched, freshly excavated material, whereas heavy handling, archeological preservation and storage for many years influenced the ability to obtain authentic endogenic DNA. While the nucleotide diversity at two locations was similar to that among extant Danes, the diversity at four sites was considerably higher. This supports previous observations for ancient Britons. The overall occurrence of haplogroups did not deviate from extant Scandinavians, however, haplogroup I was significantly more frequent among the ancient Danes (average 13%) than among extant Danes and Scandinavians (∼2.5%) as well as among other ancient population samples reported. Haplogroup I could therefore have been an ancient Southern Scandinavian type “diluted” by later immigration events. Interestingly, the two Neolithic samples (4,200 YBP, Bell Beaker culture) that were typed were haplogroup U4 and U5a, respectively, and the single Bronze Age sample (3,300–3,500 YBP) was haplogroup U4. These two haplogroups have been associated with the Mesolithic populations of Central and Northern Europe. Therefore, at least for Southern Scandinavia, our findings do not support a possible replacement of a haplogroup U dominated hunter-gatherer population by a more haplogroup diverse Neolithic Culture. PMID:20689597

  13. Genetic diversity among ancient Nordic populations.

    Directory of Open Access Journals (Sweden)

    Linea Melchior

    Full Text Available Using established criteria for work with fossil DNA we have analysed mitochondrial DNA from 92 individuals from 18 locations in Denmark ranging in time from the Mesolithic to the Medieval Age. Unequivocal assignment of mtDNA haplotypes was possible for 56 of the ancient individuals; however, the success rate varied substantially between sites; the highest rates were obtained with untouched, freshly excavated material, whereas heavy handling, archeological preservation and storage for many years influenced the ability to obtain authentic endogenic DNA. While the nucleotide diversity at two locations was similar to that among extant Danes, the diversity at four sites was considerably higher. This supports previous observations for ancient Britons. The overall occurrence of haplogroups did not deviate from extant Scandinavians, however, haplogroup I was significantly more frequent among the ancient Danes (average 13% than among extant Danes and Scandinavians (approximately 2.5% as well as among other ancient population samples reported. Haplogroup I could therefore have been an ancient Southern Scandinavian type "diluted" by later immigration events. Interestingly, the two Neolithic samples (4,200 YBP, Bell Beaker culture that were typed were haplogroup U4 and U5a, respectively, and the single Bronze Age sample (3,300-3,500 YBP was haplogroup U4. These two haplogroups have been associated with the Mesolithic populations of Central and Northern Europe. Therefore, at least for Southern Scandinavia, our findings do not support a possible replacement of a haplogroup U dominated hunter-gatherer population by a more haplogroup diverse Neolithic Culture.

  14. Visualization of cyclic nucleotide dynamics in neurons

    Directory of Open Access Journals (Sweden)

    Kirill eGorshkov

    2014-12-01

    Full Text Available The second messengers cAMP and cGMP transduce many neuromodulatory signals from hormones and neurotransmitters into specific functional outputs. Their production, degradation and signaling are spatiotemporally regulated to achieve high specificity in signal transduction. The development of genetically encodable fluorescent biosensors has provided researchers with useful tools to study these versatile second messengers and their downstream effectors with unparalleled spatial and temporal resolution in cultured cells and living animals. In this review, we introduce the general design of these fluorescent biosensors and describe several of them in more detail. Then we discuss a few examples of using cyclic nucleotide fluorescent biosensors to study regulation of neuronal function and finish with a discussion of advances in the field. Although there has been significant progress made in understanding how the specific signaling of cyclic nucleotide second messengers is achieved, the mechanistic details in complex cell types like neurons are only just beginning to surface. Current and future fluorescent protein reporters will be essential to elucidate the role of cyclic nucleotide signaling dynamics in the functions of individual neurons and their networks.

  15. Single Nucleotide Polymorphism Identification, Characterization, and Linkage Mapping in Quinoa

    Directory of Open Access Journals (Sweden)

    P. J. Maughan

    2012-11-01

    Full Text Available Quinoa ( Willd. is an important seed crop throughout the Andean region of South America. It is important as a regional food security crop for millions of impoverished rural inhabitants of the Andean Altiplano (high plains. Efforts to improve the crop have led to an increased focus on genetic research. We report the identification of 14,178 putative single nucleotide polymorphisms (SNPs using a genomic reduction protocol as well as the development of 511 functional SNP assays. The SNP assays are based on KASPar genotyping chemistry and were detected using the Fluidigm dynamic array platform. A diversity screen of 113 quinoa accessions showed that the minor allele frequency (MAF of the SNPs ranged from 0.02 to 0.50, with an average MAF of 0.28. Structure analysis of the quinoa diversity panel uncovered the two major subgroups corresponding to the Andean and coastal quinoa ecotypes. Linkage mapping of the SNPs in two recombinant inbred line populations produced an integrated linkage map consisting of 29 linkage groups with 20 large linkage groups, spanning 1404 cM with a marker density of 3.1 cM per SNP marker. The SNPs identified here represent important genomic tools needed in emerging plant breeding programs for advanced genetic analysis of agronomic traits in quinoa.

  16. Towards a Better Understanding of the Relationship between Executive Control and Theory of Mind: An Intra-Cultural Comparison of Three Diverse Samples

    Science.gov (United States)

    Shahaeian, Ameneh; Henry, Julie D.; Razmjoee, Maryam; Teymoori, Ali; Wang, Cen

    2015-01-01

    Previous research has consistently indicated that theory of mind (ToM) is associated with executive control in the preschool years. However, interpretation of this literature is limited by the fact that most studies have focused exclusively on urbanized Western cultural samples. Consequently, it is not clear whether the association between ToM and…

  17. Prevalence and serogroup diversity of Salmonella for broiler neck skin, whole carcass rinse, and whole carcass enrichment sampling methodologies following air or immersion chilling

    Science.gov (United States)

    The purpose of this study was to evaluate neck skin (NS), whole carcass rinse (WCR), and whole carcass enrichment (WCE) sampling procedures for Salmonella isolation and serogroup from the same broiler carcass following either air or immersion chilling. Commercially processed and eviscerated broiler ...

  18. Nonsuicidal Self-Injury as a Time-Invariant Predictor of Adolescent Suicide Ideation and Attempts in a Diverse Community Sample

    Science.gov (United States)

    Guan, Karen; Fox, Kathryn R.; Prinstein, Mitchell J.

    2012-01-01

    Objective: Longitudinal data on adolescent self-injury are rare. Little is known regarding the associations between various forms of self-injurious thoughts and behaviors over time, particularly within community samples that are most relevant for prevention efforts. This study examined nonsuicidal self-injury (NSSI) as a time-invariant,…

  19. Nonsuicidal Self-Injury as a Time-Invariant Predictor of Adolescent Suicide Ideation and Attempts in a Diverse Community Sample

    NARCIS (Netherlands)

    Guan, K.; Fox, K.R.; Prinstein, M.J.

    2012-01-01

    Objective: Longitudinal data on adolescent self-injury are rare. Little is known regarding the associations between various forms of self-injurious thoughts and behaviors over time, particularly within community samples that are most relevant for prevention efforts. This study examined nonsuicidal

  20. Determination of a Screening Metric for High Diversity DNA Libraries.

    Directory of Open Access Journals (Sweden)

    Nicholas J Guido

    Full Text Available The fields of antibody engineering, enzyme optimization and pathway construction rely increasingly on screening complex variant DNA libraries. These highly diverse libraries allow researchers to sample a maximized sequence space; and therefore, more rapidly identify proteins with significantly improved activity. The current state of the art in synthetic biology allows for libraries with billions of variants, pushing the limits of researchers' ability to qualify libraries for screening by measuring the traditional quality metrics of fidelity and diversity of variants. Instead, when screening variant libraries, researchers typically use a generic, and often insufficient, oversampling rate based on a common rule-of-thumb. We have developed methods to calculate a library-specific oversampling metric, based on fidelity, diversity, and representation of variants, which informs researchers, prior to screening the library, of the amount of oversampling required to ensure that the desired fraction of variant molecules will be sampled. To derive this oversampling metric, we developed a novel alignment tool to efficiently measure frequency counts of individual nucleotide variant positions using next-generation sequencing data. Next, we apply a method based on the "coupon collector" probability theory to construct a curve of upper bound estimates of the sampling size required for any desired variant coverage. The calculated oversampling metric will guide researchers to maximize their efficiency in using highly variant libraries.

  1. Interrelationships between LGBT-Based Victimization, Suicide, and Substance Use Problems in a Diverse Sample of Sexual and Gender Minority Men and Women

    OpenAIRE

    Mereish, Ethan H.; O'Cleirigh, C; Bradford, Judith B.

    2013-01-01

    Research has documented significant relationships between sexual and gender minority stress and higher rates of suicidality (i.e., suicidal ideation and attempts) and substance use problems. We examined the potential mediating role of substance use problems on the relationship between sexual and gender minority stress (i.e., victimization based on lesbian, gay, bisexual, or transgender identity; LGBT) and suicidality. A non-probability sample of LGBT patients from a community health center (N...

  2. Fabrication of diverse pH-sensitive functional mesoporous silica for selective removal or depletion of highly abundant proteins from biological samples.

    Science.gov (United States)

    Wang, Jiaojiao; Lan, Jingfeng; Li, Huihui; Liu, Xiaoyan; Zhang, Haixia

    2017-01-01

    In proteomic studies, poor detection of low abundant proteins is a major problem due to the presence of highly abundant proteins. Therefore, the specific removal or depletion of highly abundant proteins prior to analysis is necessary. In response to this problem, a series of pH-sensitive functional mesoporous silica materials composed of 2-(diethylamino)ethyl methacrylate and methacrylic acid units were designed and synthesized via atom transfer radical polymerization. These functional mesoporous silica materials were characterized and their ability for adsorption and separation of proteins was evaluated. Possessing a pH-sensitive feature, the synthesized functional materials showed selective adsorption of some proteins in aqueous or buffer solutions at certain pH values. The specific removal of a particular protein from a mixed protein solution was subsequently studied. The analytical results confirmed that all the target proteins (bovine serum albumin, ovalbumin, and lysozyme) can be removed by the proposed materials from a five-protein mixture in a single operation. Finally, the practical application of this approach was also evaluated by the selective removal of certain proteins from real biological samples. The results revealed that the maximum removal efficiencies of ovalbumin and lysozyme from egg white sample were obtained as 99% and 92%, respectively, while the maximum removal efficiency of human serum albumin from human serum sample was about 80% by the proposed method. It suggested that this treatment process reduced the complexity of real biological samples and facilitated the identification of hidden proteins in chromatograms. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Nucleotide composition bias and codon usage trends of gene ...

    Indian Academy of Sciences (India)

    The GC and AT skews estimate nucleotide composition bias at different positions of nucleotide triplets and the protein consideration caused by the nucleotide composition bias at codon positions 1 and 2 largely take part in synonymous codon usage patterns of the two mycoplasmas. The correlation between the codon ...

  4. A Sensitive Cyclic Nucleotide Phosphodiesterase Assay for Transient Enzyme Kinetics

    NARCIS (Netherlands)

    Lookeren Campagne, Michiel M. van; Haastert, Peter J.M. van

    1983-01-01

    A new assay for cyclic nucleotide phosphodiesterase has been developed by using reverse-phase column chromatography for the separation of product and substrate of the enzymatic reaction. The polar 5'-nucleotides are not retarded by the column, while the more lipophilic cyclic nucleotides bind to the

  5. OCCURRENCE OF NUCLEOTIDES IN CULTURE FLUIDS OF MICROORGANISMS

    Science.gov (United States)

    Okabayashi, Tadashi; Yoshimoto, Akihiro; Ide, Misao

    1963-01-01

    Okabayashi, Tadashi (Shionogi & Co., Ltd., Fukushima-ku, Osaka, Japan), Akihiro Yoshimoto, and Misao Ide. Occurrence of nucleotides in culture fluids of microorganisms. V. Excretion of adenosine cyclic 3′,5′-phosphate by Brevibacterium liquefaciens sp. n. J. Bacteriol. 86:930–936. 1963.—Brevibacterium liquefaciens sp. n., when grown in a medium containing amino acids as the nitrogen source, excreted a considerable amount of an adenine ribonucleotide, which had not previously been noticed. The nucleotide was identified as adenosine cyclic 3′,5′-phosphate by analysis, ultraviolet-absorption spectra, infrared-absorption spectra, paper chromatography, paper electrophoresis, and by comparison of behavior in hydrolysis by HCl, NaOH, and Ba(OH)2; also, behavior in digestion with a crude enzyme preparation of adenosine cyclic 3′,5′-phosphate phosphodiesterase was compared with that of an authentic sample. Preliminary examination of culture conditions revealed that, at least superficially, the substitution of dl-alanine for Casamino Acids (as nitrogen source) is one of the causes of the excretion of adenosine cyclic 3′,5′-phosphate. PMID:14080803

  6. Effects of achievement differences for internal/external frame of reference model investigations: A test of robustness of findings over diverse student samples.

    Science.gov (United States)

    Schmidt, Isabelle; Brunner, Martin; Preckel, Franzis

    2017-11-12

    Achievement in math and achievement in verbal school subjects are more strongly correlated than the respective academic self-concepts. The internal/external frame of reference model (I/E model; Marsh, 1986, Am. Educ. Res. J., 23, 129) explains this finding by social and dimensional comparison processes. We investigated a key assumption of the model that dimensional comparisons mainly depend on the difference in achievement between subjects. We compared correlations between subject-specific self-concepts of groups of elementary and secondary school students with or without achievement differences in the respective subjects. The main goals were (1) to show that effects of dimensional comparisons depend to a large degree on the existence of achievement differences between subjects, (2) to demonstrate the generalizability of findings over different grade levels and self-concept scales, and (3) to test a rarely used correlation comparison approach (CCA) for the investigation of I/E model assumptions. We analysed eight German elementary and secondary school student samples (grades 3-8) from three independent studies (Ns 326-878). Correlations between math and German self-concepts of students with identical grades in the respective subjects were compared with the correlation of self-concepts of students having different grades using Fisher's Z test for independent samples. In all samples, correlations between math self-concept and German self-concept were higher for students having identical grades than for students having different grades. Differences in median correlations had small effect sizes for elementary school students and moderate effect sizes for secondary school students. Findings generalized over grades and indicated a developmental aspect in self-concept formation. The CCA complements investigations within I/E-research. © 2017 The British Psychological Society.

  7. La variedad, diversidad y características de la dieta en muestras de conveniencia de mujeres guatemaltecas Food variety, dietary diversity, and food characteristics among convenience samples of Guatemalan women

    Directory of Open Access Journals (Sweden)

    María José Soto-Méndez

    2011-08-01

    Full Text Available OBJETIVO: Comparar patrones y características de diversidad y variedad de la dieta de mujeres guatemaltecas. MATERIEL Y MÉTODOS: Se realizaron dos recordatorios de 24-horas en una muestra de conveniencia de 20 mujeres rurales y 20 estudiantes urbanas. Se calcularon puntajes de diversidad usando tres sistemas de grupos alimentarios. La variedad y diversidad, así como el origen y características de la dieta, se compararon entre ambos sitios. RESULTADOS: La variedad y diversidad en general fueron mayores en la muestra urbana en comparación con la muestra rural, dependiendo del número de días y del sistema de grupos de alimentos utilizados para la evaluación. La dieta rural fue predominantemente vegetal y compuesta de alimentos tradicionales no procesados. La dieta urbana estaba basada primordialmente en alimentos procesados. CONCLUSIÓN: Las consideraciones para crear estrategias de intervención para el mejoramiento de la dieta en el área rural dependen de la conservación de la selección de alimentos tradicionales.OBJECTIVE: To compare variety and diversity patterns and dietary characteristics in Guatemalan women. MATERIAL AND METHODS: Two non-consecutive 24-h recalls were conducted in convenience samples of 20 rural Mayan women and 20 urban students. Diversity scores were computed using three food-group systems.Variety and diversity scores and dietary origin and characteristics were compared between settings using independent t-test or Mann-Whitney-U-test. RESULTS: Dietary variety and diversity were generally greater in the urban sample when compared to the rural sample, depending on the number of days and food-group system used for evaluation.The diet was predominantly plant-based and composed of non-fortified food items in both areas.The rural diet was predominantly composed of traditional,non-processed foods. The urban diet was mostly based on non-traditional and processed items. CONCLUSION: Considerations of intervention strategies

  8. Nucleotide variation in ATHK1 region of Arabidopsis thaliana and its ...

    African Journals Online (AJOL)

    The ATHK1 gene in Arabidopsis encodes a putative histidine kinase that is transcriptionally upregulated in response to changes in external osmolarity. In this work, we investigated the nucleotide variability of the ATHK1 gene in a sample of 32 core Arabidopsis accessions originating from different ecoclimatic regions and ...

  9. Association of a single-nucleotide polymorphism (rs6180) in GHR ...

    Indian Academy of Sciences (India)

    Keywords. growth hormone receptor; single-nucleotide polymorphism; rs6180; physical traits; autopsied samples. Author Affiliations. Junko Fujihara1 Kaori Kimura-Kataoka1 Toshihiro Yasuda2 Rie Sano3 Yoshihiko Kominato3 Haruo Takeshita1. Faculty of Medicine, Department of Legal Medicine, Shimane University, ...

  10. Diversity Index

    Data.gov (United States)

    Town of Chapel Hill, North Carolina — This map service summarizes racial and ethnic diversity in the United States in 2012.The Diversity Index shows the likelihood that two persons chosen at random from...

  11. Does host plant richness explain diversity of ectomycorrhizal fungi? Re-evaluation of Gao et al. (2013) data sets reveals sampling effects.

    Science.gov (United States)

    Tedersoo, Leho; Bahram, Mohammad; Dickie, Ian A

    2014-03-01

    The generally positive relationship between biodiversity of groups of directly or indirectly interacting organisms is one of the most important ecological concepts (Gaston, 2000 Nature, 405, 220-227; Scherber C, Eisenhauer N, Weisser WW et al., 2010 Nature, 468, 553-556). In a recent issue of Molecular Ecology, Gao C, Shi N-N, Liu Y-X et al. (2013: 22, 3403-3414) reported that the richness of plants and ectomycorrhizal fungi is positively correlated both at local and at global scales. Here, we challenge these findings by re-analysis of data and ascribe the reported results to sampling effect and poor data compilation. © 2014 John Wiley & Sons Ltd.

  12. Assessment of PCR-DGGE for the identification of diverse Helicobacter species, and application to faecal samples from zoo animals to determine Helicobacter prevalence.

    Science.gov (United States)

    Al-Soud, Waleed Abu; Bennedsen, Mads; On, Stephen L W; Ouis, Ibn-Sina; Vandamme, Peter; Nilsson, Hans-Olof; Ljungh, Asa; Wadström, Torkel

    2003-09-01

    Helicobacter species are fastidious bacterial pathogens that are difficult to culture by standard methods. A PCR-denaturing gradient gel electrophoresis (PCR-DGGE) technique for detection and identification of different Helicobacter species was developed and evaluated. The method involves PCR detection of Helicobacter DNA by genus-specific primers that target 16S rDNA and subsequent differentiation of Helicobacter PCR products by use of DGGE. Strains are identified by comparing mobilities of unknown samples to those determined for reference strains; sequence analysis can also be performed on purified amplicons. Sixteen DGGE profiles were derived from 44 type and reference strains of 20 Helicobacter species, indicating the potential of this approach for resolving infection of a single host by multiple Helicobacter species. Some more highly related species were not differentiated whereas in highly heterogeneous species, sequence divergence was observed and more than one PCR-DGGE profile was obtained. Application of the PCR-DGGE method to DNA extracted from faeces of zoo animals revealed the presence of Helicobacter DNA in 13 of 16 samples; a correlation was seen between the mobility of PCR products in DGGE analysis and DNA sequencing. In combination, this indicated that zoo animals are colonized by a wide range of different Helicobacter species; seven animals appeared to be colonized by multiple Helicobacter species. By this approach, presumptive identifications were made of Helicobacter bilis and Helicobacter hepaticus in a Nile crocodile, Helicobacter cinaedi in a baboon and a red panda, and Helicobacter felis in a wolf and a Taiwan beauty snake. All of these PCR products ( approximately 400 bp) showed 100 % sequence similarity to 16S rDNA sequences of the mentioned species. These results demonstrate the potential of PCR-DGGE-based analysis for identification of Helicobacter species in complex ecosystems, such as the gastrointestinal tract, and could contribute to

  13. Diversity & Dartmouth.

    Science.gov (United States)

    Freedman, James O.

    1991-01-01

    The president of Dartmouth College (New Hampshire) discusses campus cultural pluralism, the need for diversity in higher education, overcoming resistance to change, techniques for supporting a diverse student population, monitoring diversity through institutional research, and the issue of "political correctness" in higher education…

  14. Embracing Diversity

    NARCIS (Netherlands)

    S. Puntoni (Stefano)

    2015-01-01

    markdownabstract__Abstract__ Societies are vastly more diverse today than they used to be and, in many industries, developing theories and approaches that recognize and capitalize on this greater consumer diversity is crucial. In business schools, diversity tends to be discussed only in relation

  15. Classifying Coding DNA with Nucleotide Statistics

    Directory of Open Access Journals (Sweden)

    Nicolas Carels

    2009-10-01

    Full Text Available In this report, we compared the success rate of classification of coding sequences (CDS vs. introns by Codon Structure Factor (CSF and by a method that we called Universal Feature Method (UFM. UFM is based on the scoring of purine bias (Rrr and stop codon frequency. We show that the success rate of CDS/intron classification by UFM is higher than by CSF. UFM classifies ORFs as coding or non-coding through a score based on (i the stop codon distribution, (ii the product of purine probabilities in the three positions of nucleotide triplets, (iii the product of Cytosine (C, Guanine (G, and Adenine (A probabilities in the 1st, 2nd, and 3rd positions of triplets, respectively, (iv the probabilities of G in 1st and 2nd position of triplets and (v the distance of their GC3 vs. GC2 levels to the regression line of the universal correlation. More than 80% of CDSs (true positives of Homo sapiens (>250 bp, Drosophila melanogaster (>250 bp and Arabidopsis thaliana (>200 bp are successfully classified with a false positive rate lower or equal to 5%. The method releases coding sequences in their coding strand and coding frame, which allows their automatic translation into protein sequences with 95% confidence. The method is a natural consequence of the compositional bias of nucleotides in coding sequences.

  16. Nucleotide variability and linkage disequilibrium patterns in the porcine MUC4 gene

    Directory of Open Access Journals (Sweden)

    Yang Ming

    2012-07-01

    Full Text Available Abstract Background MUC4 is a type of membrane anchored glycoprotein and serves as the major constituent of mucus that covers epithelial surfaces of many tissues such as trachea, colon and cervix. MUC4 plays important roles in the lubrication and protection of the surface epithelium, cell proliferation and differentiation, immune response, cell adhesion and cancer development. To gain insights into the evolution of the porcine MUC4 gene, we surveyed the nucleotide variability and linkage disequilibrium (LD within this gene in Chinese indigenous breeds and Western commercial breeds. Results A total of 53 SNPs covering the MUC4 gene were genotyped on 5 wild boars and 307 domestic pigs representing 11 Chinese breeds and 3 Western breeds. The nucleotide variability, haplotype phylogeny and LD extent of MUC4 were analyzed in these breeds. Both Chinese and Western breeds had considerable nucleotide diversity at the MUC4 locus. Western pig breeds like Duroc and Large White have comparable nucleotide diversity as many of Chinese breeds, thus artificial selection for lean pork production have not reduced the genetic variability of MUC4 in Western commercial breeds. Haplotype phylogeny analyses indicated that MUC4 had evolved divergently in Chinese and Western pigs. The dendrogram of genetic differentiation between breeds generally reflected demographic history and geographical distribution of these breeds. LD patterns were unexpectedly similar between Chinese and Western breeds, in which LD usually extended less than 20 kb. This is different from the presumed high LD extent (more than 100 kb in Western commercial breeds. The significant positive Tajima’D, and Fu and Li’s D statistics in a few Chinese and Western breeds implied that MUC4 might undergo balancing selection in domestic breeds. Nevertheless, we cautioned that the significant statistics could be upward biased by SNP ascertainment process. Conclusions Chinese and Western breeds have

  17. Genetic diversity in the desert warthog (Phacochoerus aethiopicus delameri) population of eastern Africa

    DEFF Research Database (Denmark)

    Muwanika, Vincent B.; Kock, Richard; Masembe, Charles

    2012-01-01

    in a population of the desert warthog (Phacochoerus aethiopicus) sampled from 12 localities in its natural range in eastern Africa. From the total sample (30 individuals), at the six microsatellite loci that were analysed, a total of 43 alleles was observed averaging seven alleles per locus. Expected...... heterozygosity (HE) per locus was high, ranging from 0.53 to 0.87. At the mitochondrial loci, nucleotide diversity was low (p = 0.12%) with two unique haplotypes observed from the 19 individuals that amplified successfully. The diversity indices observed in the desert warthog are comparable to those previously...... reported for the closely related but widespread species, the common warthog (Phacochoerus africanus). These results suggest that the desert warthog is not genetically depauperate despite the rinderpest epidemic of the 1880s that eliminated it from most of its natural range....

  18. Arachnid relationships based on mitochondrial genomes: asymmetric nucleotide and amino acid bias affects phylogenetic analyses.

    Science.gov (United States)

    Masta, Susan E; Longhorn, Stuart J; Boore, Jeffrey L

    2009-01-01

    Phylogenetic analyses based on mitochondrial DNA have yielded widely differing relationships among members of the arthropod lineage Arachnida, depending on the nucleotide coding schemes and models of evolution used. We enhanced taxonomic coverage within the Arachnida greatly by sequencing seven new arachnid mitochondrial genomes from five orders. We then used all 13 mitochondrial protein-coding genes from these genomes to evaluate patterns of nucleotide and amino acid biases. Our data show that two of the six orders of arachnids (spiders and scorpions) have experienced shifts in both nucleotide and amino acid usage in all their protein-coding genes, and that these biases mislead phylogeny reconstruction. These biases are most striking for the hydrophobic amino acids isoleucine and valine, which appear to have evolved asymmetrical exchanges in response to shifts in nucleotide composition. To improve phylogenetic accuracy based on amino acid differences, we tested two recoding methods: (1) removing all isoleucine and valine sites and (2) recoding amino acids based on their physiochemical properties. We find that these methods yield phylogenetic trees that are consistent in their support of ancient intraordinal divergences within the major arachnid lineages. Further refinement of amino acid recoding methods may help us better delineate interordinal relationships among these diverse organisms.

  19. Environmental heat stress, hyperammonemia and nucleotide metabolism during intermittent exercise

    DEFF Research Database (Denmark)

    Mohr, Magni; Rasmussen, Peter; Drust, Barry

    2006-01-01

    exercise with heat stress, the core and muscle temperatures peaked at 39.5±0.2 and 40.2±0.2°C to be ~ 1°C higher (P...Abstract  This study investigated the influence of environmental heat stress on ammonia (NH3) accumulation in relation to nucleotide metabolism and fatigue during intermittent exercise. Eight males performed 40 min of intermittent exercise (15 s at 306±22 W alternating with 15 s of unloaded cycling......) followed by five 15 s all-out sprints. Control trials were conducted in a 20°C environment while heat stress trials were performed at an ambient temperature of 40°C. Muscle biopsies and venous blood samples were obtained at rest, after 40 min of exercise and following the maximal sprints. Following...

  20. Pinched flow fractionation devices for detection of single nucleotide polymorphisms

    DEFF Research Database (Denmark)

    Larsen, A.V.; Poulsen, L.; Birgens, H.

    2008-01-01

    We demonstrate a new and flexible micro fluidic based method for genotyping single nucleotide polymorphisms ( SNPs). The method relies on size separation of selectively hybridized polystyrene microspheres in a micro fluidic pinched flow fractionation (PFF) device. The micro fluidic PFF devices...... and 5.6 mu m were functionalized with biotin-labeled oligonucleotides for the detection of a mutant (Mt) or wild-type (Wt) DNA sequence in the HBB gene, respectively. Hybridization to functionalized beads was performed with fluorescent targets comprising synthetic DNA oligonucleotides or amplified RNA......, synthesized using human DNA samples from individuals with point mutations in the HBB gene. Following a stringent wash, the beads were separated in a PFF device and the fluorescent signal from the beads was analyzed. Patients being wildtypes, heterozygotes or mutated respectively for the investigated mutation...

  1. Interrelationships between LGBT-Based Victimization, Suicide, and Substance Use Problems in a Diverse Sample of Sexual and Gender Minority Men and Women

    Science.gov (United States)

    Mereish, Ethan H.; O'Cleirigh, C; Bradford, Judith B.

    2013-01-01

    Research has documented significant relationships between sexual and gender minority stress and higher rates of suicidality (i.e., suicidal ideation and attempts) and substance use problems. We examined the potential mediating role of substance use problems on the relationship between sexual and gender minority stress (i.e., victimization based on lesbian, gay, bisexual, or transgender identity; LGBT) and suicidality. A non-probability sample of LGBT patients from a community health center (N = 1457) ranged in age 19 to 70 years. Participants reported history of lifetime suicidal ideation and attempts, and substance use problems, as well as experiences of LGBT-based verbal and physical attacks. Substance use problems were a significant partial mediator between LGBT-based victimization and suicidal ideation and between LGBT-based victimization and suicide attempts for sexual and gender minorities. Nuanced gender differences revealed that substance use problems did not significantly mediate the relationship between victimization and suicide attempts for sexual minority men. Substance use problems may be one insidious pathway that partially mediates the risk effects of sexual and gender minority stress on suicidality. Substances might be a temporary and deleterious coping resource in response to LGBT-based victimization, which have serious effects on suicidal ideation and behaviors. PMID:23535038

  2. Can the Theory of Planned Behavior Predict Dietary Intention and Future Dieting in an Ethnically Diverse Sample of Overweight and Obese Veterans Attending Medical Clinics?

    Science.gov (United States)

    Lash, Denise N.; Smith, Jane Ellen; Rinehart, Jenny K.

    2016-01-01

    Obesity has become a world-wide epidemic; in the United States (U.S.) approximately two-thirds of adults are classified as overweight or obese. Military veterans’ numbers are even higher, with 77% of retired or discharged U.S. veterans falling in these weight categories. One of the most common methods of changing one’s weight is through dieting, yet little is known regarding the factors that facilitate successful dieting behavior. The current investigation tested the Theory of Planned Behavior’s (TPB) ability to predict dietary intention and future dieting in a sample of 84 overweight and obese patients attending medical clinics at a Veterans Affairs Hospital in the southwestern part of the U.S. Participants primarily were male (92%) and ethnic/racial minorities (58%). Perceived need and anticipated regret were added to the standard TPB model. While the TPB predicted dietary intention, it did not significantly account for improved dietary behaviors. Anticipated regret significantly enhanced the basic TPB’s ability to predict intention to diet, while perceived need did not. These findings highlight the difficulty in predicting sustained change in a complex behavior such as dieting to lose weight. The need for more work with older, overweight/obese medical patients attending veterans’ facilities is stressed, as is the need for such work with male patients and ethnic minorities in particular. PMID:26792774

  3. Relational diversity.

    Science.gov (United States)

    Gregorius, Hans-Rolf

    2009-03-07

    In biology, the measurement of diversity traditionally focusses on reporting number of unambiguously distinguishable types, thus referring to qualitative (discontinuously varying) traits. Inclusion of frequencies or other weights has produced a large variety of diversity indices. Quantitative (continuously varying) traits do not readily fit into this perspective. In fact, in the context of quantitative traits, the concept of diversity is not always clearly distinguished from the (statistical) notion of dispersion. In many cases the ambiguity even extends to qualitative traits. This is at variance with the broad spectrum of diversity issues ranging, e.g., from ecological and genetic aspects of diversity to functional, structural, systematic, or evolutionary (including phylogenetic) aspects. In view of the urgent need for a more consistent perspective, it is called to attention that all of these aspects, whether of qualitative or quantitative nature, can be gathered under the common roof of binary relations (for qualitative traits two objects are related, for example, if they share the same trait state). A comprehensive concept of (relational) diversity can be developed in two steps: (1) determine the number of unrelated pairs of objects among all admissible pairs as a measure of implicit (relative) diversity, (2) invoke the concept of effective number to transform the implicit measure of diversity into an explicit (absolute) measure. The transformation operates by equating the observed implicit diversity to the implicit diversity obtained for the ideal model of an equivalence relation with classes of equal size. The number of these classes specifies the effective number as an explicit measure of diversity. The wealth of problems that can be treated from this unified perspective is briefly addressed by classifying and interpreting established diversity indices in the light of relational diversity. Desirable applications to the above-mentioned aspects are specified

  4. Cyclic nucleotides and production of prostanoids in human varicose veins.

    Science.gov (United States)

    Nemcova, S; Gloviczki, P; Rud, K S; Miller, V M

    1999-11-01

    Experiments were designed to determine the production of prostacyclin and thromboxane and the activation of cyclic nucleotides in human varicose and nonvaricose veins and to determine whether these second messenger pathways were differentially activated by the venotropic extract of Ruscus aculeatus. The experiments were designed to characterize the activity of cyclic nucleotides and the production of prostaglandins in human varicose and nonvaricose veins. Segments of the greater saphenous veins and the adjacent tributaries were obtained from patients who underwent vein stripping and excision of primary varicose veins. The saphenous veins from the patients who underwent peripheral arterial bypass grafting were used as controls. The segments of veins were incubated in Krebs-Ringer bicarbonate solution in the presence of venotropic extract of Ruscus aculeatus (10(-3) g/mL) or in water-miscible organic solvent (dimethyl sulfoxide, 10(-3) g/mL), for 1, 5, and 10 minutes at 37 degrees C. The nonspecific phosphodiesterase inhibitor (3-isobutyl-1-methylxanthine, 10(-4) g/mL) was used to block cyclic nucleotide degradation in some samples. Tissue and media samples were collected. Tissue concentrations of both cyclic adenosine monophosphate and cyclic guanosine monophosphate (cAMP and cGMP, respectively) and media concentrations of 6-ketoprostaglandin-F(1)(alpha) (the stable metabolite of prostacyclin) and thromboxane B(2) (the stable metabolite of thromboxane A(2)) were measured by means of radioimmunoassay. Cyclooxygenase 2 was measured with Western blot analysis. The varicose veins showed greater levels of cAMP but not of cGMP at all time points as compared with the control veins. Prostanoid production was not significantly altered in the varicose veins. Stimulation with Ruscus aculeatus increased the cAMP concentration in the varicose veins but did not affect the cGMP levels. The ratio between 6-ketoprostaglandin-F(1)(alpha) and thromboxane B(2) was two-fold greater in

  5. Analysis of plant nucleotide sugars by hydrophilic interaction liquid chromatography and tandem mass spectrometry.

    Science.gov (United States)

    Ito, Jun; Herter, Thomas; Baidoo, Edward E K; Lao, Jeemeng; Vega-Sánchez, Miguel E; Michelle Smith-Moritz, A; Adams, Paul D; Keasling, Jay D; Usadel, Björn; Petzold, Christopher J; Heazlewood, Joshua L

    2014-03-01

    Understanding the intricate metabolic processes involved in plant cell wall biosynthesis is limited by difficulties in performing sensitive quantification of many involved compounds. Hydrophilic interaction liquid chromatography is a useful technique for the analysis of hydrophilic metabolites from complex biological extracts and forms the basis of this method to quantify plant cell wall precursors. A zwitterionic silica-based stationary phase has been used to separate hydrophilic nucleotide sugars involved in cell wall biosynthesis from milligram amounts of leaf tissue. A tandem mass spectrometry operating in selected reaction monitoring mode was used to quantify nucleotide sugars. This method was highly repeatable and quantified 12 nucleotide sugars at low femtomole quantities, with linear responses up to four orders of magnitude to several 100pmol. The method was also successfully applied to the analysis of purified leaf extracts from two model plant species with variations in their cell wall sugar compositions and indicated significant differences in the levels of 6 out of 12 nucleotide sugars. The plant nucleotide sugar extraction procedure was demonstrated to have good recovery rates with minimal matrix effects. The approach results in a significant improvement in sensitivity when applied to plant samples over currently employed techniques. Copyright © 2013 Elsevier Inc. All rights reserved.

  6. Differences in Healthcare Access, Use, and Experiences Within a Community Sample of Racially Diverse Lesbian, Gay, Bisexual, Transgender, and Questioning Emerging Adults

    Science.gov (United States)

    Bhatia, Ramona; Greene, George J.

    2016-01-01

    Abstract Purpose: Health services research involving lesbian, gay, bisexual, transgender, queer, and questioning (LGBTQ) individuals has focused on differences in healthcare access, use, and experiences between cisgender, heterosexual adults and LGBTQ adults. Yet these factors may differ within the LGBTQ community and have not been well-studied among emerging adults (18–29 years), a group with unique barriers to healthcare. We sought to characterize healthcare challenges within a sample of LGBTQ emerging adults. Methods: From 2012 to 2013, 206 participants aged 18–27 (86% racial/ethnic minority, 10% transgender) completed questionnaires assessing healthcare access, use, and experiences during a longitudinal study. Descriptive statistics established patterns of healthcare access, use, and experiences, and nonparametric tests examined differences related to sociodemographic variables, HIV status, sexual orientation identity, and gender identity. Results: Overall, 68% of participants reported relatively easy access to care. White and bisexual participants reported higher rates of insurance than racial/ethnic minority (P = 0.01) and gay or lesbian participants (P = 0.005), respectively. Although most participants did not report having negative experiences in healthcare settings related to their LGBTQ identity, transgender participants were more likely to delay care (P queer or were questioning their sexual orientation identity reported negative healthcare experiences more frequently than LGB-identified participants (P = 0.001). Conclusions: Although LGBTQ emerging adults experienced fewer barriers to care than observed in previous studies on LGBTQ adults, the results suggest that queer, questioning, and transgender individuals may face additional healthcare challenges compared with their LGB and cisgender counterparts. PMID:27726496

  7. Psychosocial stressors contributing to emergency psychiatric service utilization in a sample of ethno-culturally diverse clients with psychosis in Toronto.

    Science.gov (United States)

    Rotenberg, Martin; Tuck, Andrew; McKenzie, Kwame

    2017-09-02

    Understanding the psychosocial stressors of people with psychoses from minority ethnic groups may help in the development of culturally appropriate services. This study aimed to compare psychosocial factors associated with attendance at an emergency department (ED) for six ethnic groups. Preventing crises or supporting people better in the community may decrease hospitalization and improve outcomes. A cohort was created by retrospective case note analysis of people of East-Asian, South-Asian, Black-African, Black-Caribbean, White-North American and White-European origin groups attending a specialized psychiatric ED in Toronto with a diagnosis of psychosis between 2009 and 2011. The psychological or social stressors which were linked to the presentation at the ED that were documented by the attending physicians were collected for this study. Logistic regression models were constructed to analyze the odds of presenting with specific stressors. Seven hundred sixty-five clients were included in this study. Forty-four percent of the sample did not have a psychiatrist, and 53% did not have a primary care provider. Social environmental stressors were the most frequent psychosocial stressor across all six groups, followed by issues in the primary support group, occupational and housing stressors. When compared to White-North American clients, East-Asian and White-European origin clients were less likely to present with a housing stressor, while Black-African clients had decreased odds of presenting with primary support group stressor. Having a primary care provider or psychiatrist were predominantly protective factors. In Toronto, moving people with chronic mental health conditions out of poverty, increasing the social safety net and improving access to primary care and community based mental health services may decrease many of the stressors which contribute to ED attendance.

  8. Alcohol and marijuana use trajectories in a diverse longitudinal sample of adolescents: examining use patterns from age 11 to 17 years.

    Science.gov (United States)

    D'Amico, Elizabeth J; Tucker, Joan S; Miles, Jeremy N V; Ewing, Brett A; Shih, Regina A; Pedersen, Eric R

    2016-10-01

    We tested race/ethnic differences in alcohol and marijuana (AM) trajectories (comprising an intercept term, reflecting overall probability of use, and a slope term, reflecting change in probability of use) during adolescence, whether AM use trajectories predicted high school outcomes, and whether outcomes differed by race/ethnicity after controlling for trajectory of AM use. This longitudinal study involved 6509 youth from 16 middle schools in Southern California surveyed from age 11.5 (2008) to age 17 (2015) years; all surveys assessed AM use, and the final survey also examined high school outcomes. Youth completed five surveys in middle school and two on-line surveys in high school. The sample was 50% male and 80% non-white. Intercept (at 2.75 years post-baseline) and slope of AM use were examined as outcomes for race/ethnic differences. AM use trajectories were examined as predictors of academic performance and unpreparedness, social functioning, mental and physical health and delinquency. We found differences in trajectories of use by race/ethnicity, with white youth reporting a higher overall intercept of alcohol use compared to all other groups (versus Asian P academic unpreparedness (P marijuana use reported greater academic unpreparedness (P academic performance (P = 0.032) and mental health (P = 0.002) in high school. At wave 7, compared to white youth, Hispanic and multi-ethnic youth reported poorer academic performance (P academic unpreparedness (P academics and health. © 2016 Society for the Study of Addiction.

  9. Identity, Diversity and Diversity Management

    DEFF Research Database (Denmark)

    Holck, Lotte; Muhr, Sara Louise; Villeseche, Florence

    2016-01-01

    The purpose of this paper is to examine the relationship between the identity and diversity literatures and discuss how a better understanding of the theoretical connections between the two informs both diversity research and diversity management practices. Design/methodology/approach – Literatur...

  10. Implication of Posttranslational Histone Modifications in Nucleotide Excision Repair

    Directory of Open Access Journals (Sweden)

    Shisheng Li

    2012-09-01

    Full Text Available Histones are highly alkaline proteins that package and order the DNA into chromatin in eukaryotic cells. Nucleotide excision repair (NER is a conserved multistep reaction that removes a wide range of generally bulky and/or helix-distorting DNA lesions. Although the core biochemical mechanism of NER is relatively well known, how cells detect and repair lesions in diverse chromatin environments is still under intensive research. As with all DNA-related processes, the NER machinery must deal with the presence of organized chromatin and the physical obstacles it presents. A huge catalogue of posttranslational histone modifications has been documented. Although a comprehensive understanding of most of these modifications is still lacking, they are believed to be important regulatory elements for many biological processes, including DNA replication and repair, transcription and cell cycle control. Some of these modifications, including acetylation, methylation, phosphorylation and ubiquitination on the four core histones (H2A, H2B, H3 and H4 or the histone H2A variant H2AX, have been found to be implicated in different stages of the NER process. This review will summarize our recent understanding in this area.

  11. Single nucleotide polymorphisms of myostatin gene in Chinese domestic horses.

    Science.gov (United States)

    Li, Ran; Liu, Dong-Hua; Cao, Chun-Na; Wang, Shao-Qiang; Dang, Rui-Hua; Lan, Xian-Yong; Chen, Hong; Zhang, Tao; Liu, Wu-Jun; Lei, Chu-Zhao

    2014-03-15

    The myostatin gene (MSTN) is a genetic determinant of skeletal muscle growth. Single nucleotide polymorphisms (SNP) in MSTN are of importance due to their strong associations with horse racing performances. In this study, we screened the SNPs in MSTN gene in 514 horses from 15 Chinese horse breeds. Six SNPs (g.26T>C, g.156T>C, g.587A>G, g.598C>T, g.1485C>T, g.2115A>G) in MSTN gene were detected by sequencing and genotyped using PCR-RFLP method. The g.587A>G and g.598C>T residing in the 5'UTR region were novel SNPs identified by this study. The g.2115A>G which have previously been associated with racing performances were present in Chinese horse breeds, providing valuable genetic information for evaluating the potential racing performances in Chinese domestic breeds. The six SNPs together defined thirteen haplotypes, demonstrating abundant haplotype diversities in Chinese horses. Most of the haplotypes were shared among different breeds with no haplotype restricted to a specific region or a single horse breed. AMOVA analysis indicated that most of the genetic variance was attributable to differences among individuals without any significant contribution by the four geographical groups. This study will provide fundamental and instrumental genetic information for evaluating the potential racing performances of Chinese horse breeds. Copyright © 2013 Elsevier B.V. All rights reserved.

  12. Classification of organisms using nucleotides frequencies

    OpenAIRE

    Kremličková, Lenka

    2014-01-01

    Tato bakalářská práce se zabývá klasifikací organismů na základě nukleotidové četnosti. Cílem práce je seznámit se s problematikou vyhodnocení příbuznosti organismů na základě podobnosti DNA sekvencí, navrhnout a realizovat v programovém prostředí Matlab algoritmus pro klasifikaci organismů na základě klasické fylogenetické metody, základních i pokročilých numerických metod a tyto metody mezi sebou porovnat. This thesis deals with the classification of organisms based on the nucleotide fre...

  13. Valuing Gender Diversity in Teams

    DEFF Research Database (Denmark)

    Lauring, Jakob; Villeseche, Florence

    Team gender diversity has been much debated in many different contexts – not least since the search for a main effect of diversity on performance was launched. However, results have so far been inconclusive, and a number of scholars suggest that more attention should be directed at contextual...... factors which could influence the effect of gender diversity on team performance. In this study, we explore the effect of positive diversity attitudes and assess the degree of gender diversity where such group attitudes have greater impact. This is done by using a sample of 1085 leaders of academic...... research teams. Findings show that positive diversity attitude in the form of group openness to diversity is strongly associated with team performance. We also find a moderating effect of gender diversity meaning that the effect of openness to diversity is stronger when gender groups are more balanced...

  14. GENETIC DIVERSITY OF KEJOBONG GOAT BASED ON MITOCHONDRIAL DNA D-LOOP SEQUENCE

    Directory of Open Access Journals (Sweden)

    M. F. Harlistyo

    2015-09-01

    Full Text Available This study was aimed to find out the diversity of mtDNA D-loop at Kejobong goat. The completemtDNA D-loop sequence of 12 goat blood samples were analyzed from 4 different location inPurbalingga Regency, Central Java province, sub-districts Kejobong, Pangadegan, Bukateja, andKaligondang. The mtDNA D-loop was extracted from blood sample. DNA obtained were amplified byPCR (Polymerase Chain Reaction method using primers (5’-tcactatcagcacccaaagc-3’ as forward and(5’-ggcattttcagtgccttgct-3’ as reverse and subsequently sequenced. After nucleotide sequencing analysisconducted, 548 bp along was obtained. Nucleotides were then aligned with Capra hircus (GenBankAccess No.: KF952601.1 and apparently there were 11 different sites on the segment of mtDNA Dloop.Five sites could be used as a specific marker to distinguish between the Capra hircus andKejobong goat, namely at the site of 317 (A-G, 403 (T-C, 434 (T-C, 537 (C-T, and 553 (A-G.Nucleotide sequence analysis also contained seven different haplotypes. It was concluded that thedistribution of the different sites showed different haplotype patterns in Kejobong goat.

  15. A genetic variation map for chicken with 2.8 million single nucleotide polymorphisms

    Energy Technology Data Exchange (ETDEWEB)

    Wong, G K; Hillier, L; Brandstrom, M; Croojmans, R; Ovcharenko, I; Gordon, L; Stubbs, L; Lucas, S; Glavina, T; Kaiser, P; Gunnarsson, U; Webber, C; Overton, I

    2005-02-20

    We describe a genetic variation map for the chicken genome containing 2.8 million single nucleotide polymorphisms (SNPs), based on a comparison of the sequences of 3 domestic chickens (broiler, layer, Silkie) to their wild ancestor Red Jungle Fowl (RJF). Subsequent experiments indicate that at least 90% are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about 5 SNP/kb for almost every possible comparison between RJF and domestic lines, between two different domestic lines, and within domestic lines--contrary to the idea that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated prior to domestication, and there is little to no evidence of selective sweeps for adaptive alleles on length scales of greater than 100 kb.

  16. Cultivation-independent assessment of the bathypelagic archaeal diversity of Tyrrhenian Sea: Comparative study of rDNA and rRNA-derived libraries and influence of sample decompression

    Science.gov (United States)

    La Cono, Violetta; Tamburini, Christian; Genovese, Lucrezia; Spada, Gina La; Denaro, Renata; Yakimov, Michail M.

    2009-05-01

    Two samples of the same bathypelagic bacterioplankton community (Tyrrhenian Sea at the depth of 3000 m) were collected during single cast by both traditional sampling with Niskin bottle and using a high pressure-maintaining HPSS sampler. Total RNA was isolated, reverse transcribed, amplified with Archaea-specific primers and cloned. Riboclones were sequenced, 117 riboclones from decompressed library and 104 rRNA-based riboclones retrieved from HPSS sampler. Both RNA libraries were additionally compared with 115 riboclones based on DNA obtained from the decompressed sample (16S rRNA genes). In terms of repetitive riboclones, obtained in all three libraries, the bathypelagic community was dominated by Crenarchaeota Marine Group I (52-64%). The combined analysis led to a characterization of sampling-specific phylotypes otherwise uncharacterized if only one type of library had been analyzed alone. Of the DNA riboclones, 22% were found only in this library and no close relatives of Euryarchaeota Marine Group II were detected in both RNA-based libraries, suggesting the dormant state of these organisms in deep-sea environment. For clones from the RNA libraries, one Crenarchaeota MG I phylotype did not indicate close relatives in the DNA library. In general, among 10 archaeal phylotypes recovered in total, 8, 7 and 6 of them were faced in DNA, RNA_HPSS and RNA decompressed libraries, respectively. Based on comparisons between all three libraries, our data indicate that (i) the short-term decompression of seawater samples during cast recovery and following treatments caused only slight changes in the total rRNA diversity and (ii) rRNA-based analysis is likely affected the characterization of phylotypes, present in deep-sea environment as the dormant cells, detected only on the DNA level.

  17. Genetic diversity of the merozoite surface protein-3 gene in Plasmodium falciparum populations in Thailand

    Directory of Open Access Journals (Sweden)

    Sittiporn Pattaradilokrat

    2016-10-01

    Full Text Available Abstract Background An effective malaria vaccine is an urgently needed tool to fight against human malaria, the most deadly parasitic disease of humans. One promising candidate is the merozoite surface protein-3 (MSP-3 of Plasmodium falciparum. This antigenic protein, encoded by the merozoite surface protein (msp-3 gene, is polymorphic and classified according to size into the two allelic types of K1 and 3D7. A recent study revealed that both the K1 and 3D7 alleles co-circulated within P. falciparum populations in Thailand, but the extent of the sequence diversity and variation within each allelic type remains largely unknown. Methods The msp-3 gene was sequenced from 59 P. falciparum samples collected from five endemic areas (Mae Hong Son, Kanchanaburi, Ranong, Trat and Ubon Ratchathani in Thailand and analysed for nucleotide sequence diversity, haplotype diversity and deduced amino acid sequence diversity. The gene was also subject to population genetic analysis (F st and neutrality tests (Tajima’s D, Fu and Li D* and Fu and Li’ F* tests to determine any signature of selection. Results The sequence analyses revealed eight unique DNA haplotypes and seven amino acid sequence variants, with a haplotype and nucleotide diversity of 0.828 and 0.049, respectively. Neutrality tests indicated that the polymorphism detected in the alanine heptad repeat region of MSP-3 was maintained by positive diversifying selection, suggesting its role as a potential target of protective immune responses and supporting its role as a vaccine candidate. Comparison of MSP-3 variants among parasite populations in Thailand, India and Nigeria also inferred a close genetic relationship between P. falciparum populations in Asia. Conclusion This study revealed the extent of the msp-3 gene diversity in P. falciparum in Thailand, providing the fundamental basis for the better design of future blood stage malaria vaccines against P. falciparum.

  18. Discovery and characterization of single nucleotide polymorphisms in Chinook salmon, Oncorhynchus tshawytscha.

    Science.gov (United States)

    Clemento, A J; Abadía-Cardoso, A; Starks, H A; Garza, J C

    2011-03-01

    Molecular population genetics of non-model organisms has been dominated by the use of microsatellite loci over the last two decades. The availability of extensive genomic resources for many species is contributing to a transition to the use of single nucleotide polymorphisms (SNPs) for the study of many natural populations. Here we describe the discovery of a large number of SNPs in Chinook salmon, one of the world's most important fishery species, through large-scale Sanger sequencing of expressed sequence tag (EST) regions. More than 3 Mb of sequence was collected in a survey of variation in almost 132 kb of unique genic regions, from 225 separate ESTs, in a diverse ascertainment panel of 24 salmon. This survey yielded 117 TaqMan (5' nuclease) assays, almost all from separate ESTs, which were validated in population samples from five major stocks of salmon from the three largest basins on the Pacific coast of the contiguous United States: the Sacramento, Klamath and Columbia Rivers. The proportion of these loci that was variable in each of these stocks ranged from 86.3% to 90.6% and the mean minor allele frequency ranged from 0.194 to 0.236. There was substantial differentiation between populations with these markers, with a mean F(ST) estimate of 0.107, and values for individual loci ranging from 0 to 0.592. This substantial polymorphism and population-specific differentiation indicates that these markers will be broadly useful, including for both pedigree reconstruction and genetic stock identification applications. © 2011 Blackwell Publishing Ltd.

  19. Genetic Diversity and Phylogenetic Evolution of Tibetan Sheep Based on mtDNA D-Loop Sequences.

    Directory of Open Access Journals (Sweden)

    Jianbin Liu

    Full Text Available The molecular and population genetic evidence of the phylogenetic status of the Tibetan sheep (Ovis aries is not well understood, and little is known about this species' genetic diversity. This knowledge gap is partly due to the difficulty of sample collection. This is the first work to address this question. Here, the genetic diversity and phylogenetic relationship of 636 individual Tibetan sheep from fifteen populations were assessed using 642 complete sequences of the mitochondrial DNA D-loop. Samples were collected from the Qinghai-Tibetan Plateau area in China, and reference data were obtained from the six reference breed sequences available in GenBank. The length of the sequences varied considerably, between 1031 and 1259 bp. The haplotype diversity and nucleotide diversity were 0.992±0.010 and 0.019±0.001, respectively. The average number of nucleotide differences was 19.635. The mean nucleotide composition of the 350 haplotypes was 32.961% A, 29.708% T, 22.892% C, 14.439% G, 62.669% A+T, and 37.331% G+C. Phylogenetic analysis showed that all four previously defined haplogroups (A, B, C, and D were found in the 636 individuals of the fifteen Tibetan sheep populations but that only the D haplogroup was found in Linzhou sheep. Further, the clustering analysis divided the fifteen Tibetan sheep populations into at least two clusters. The estimation of the demographic parameters from the mismatch analyses showed that haplogroups A, B, and C had at least one demographic expansion in Tibetan sheep. These results contribute to the knowledge of Tibetan sheep populations and will help inform future conservation programs about the Tibetan sheep native to the Qinghai-Tibetan Plateau.

  20. ENGINES: exploring single nucleotide variation in entire human genomes

    Directory of Open Access Journals (Sweden)

    Salas Antonio

    2011-04-01

    Full Text Available Abstract Background Next generation ultra-sequencing technologies are starting to produce extensive quantities of data from entire human genome or exome sequences, and therefore new software is needed to present and analyse this vast amount of information. The 1000 Genomes project has recently released raw data for 629 complete genomes representing several human populations through their Phase I interim analysis and, although there are certain public tools available that allow exploration of these genomes, to date there is no tool that permits comprehensive population analysis of the variation catalogued by such data. Description We have developed a genetic variant site explorer able to retrieve data for Single Nucleotide Variation (SNVs, population by population, from entire genomes without compromising future scalability and agility. ENGINES (ENtire Genome INterface for Exploring SNVs uses data from the 1000 Genomes Phase I to demonstrate its capacity to handle large amounts of genetic variation (>7.3 billion genotypes and 28 million SNVs, as well as deriving summary statistics of interest for medical and population genetics applications. The whole dataset is pre-processed and summarized into a data mart accessible through a web interface. The query system allows the combination and comparison of each available population sample, while searching by rs-number list, chromosome region, or genes of interest. Frequency and FST filters are available to further refine queries, while results can be visually compared with other large-scale Single Nucleotide Polymorphism (SNP repositories such as HapMap or Perlegen. Conclusions ENGINES is capable of accessing large-scale variation data repositories in a fast and comprehensive manner. It allows quick browsing of whole genome variation, while providing statistical information for each variant site such as allele frequency, heterozygosity or FST values for genetic differentiation. Access to the data mart

  1. Short Communication Single nucleotide polymorphisms in five ...

    African Journals Online (AJOL)

    Genetic diversity in candidate genes for fitness and production traits was explored in three populations of dairy cattle. The study focused on adipokines, including leptin (LEP), tumor necrosis factor alpha (TNF), interleukin-8 (IL8) and interleukin-10 (IL10) as candidate genes. The three populations of interest included young ...

  2. RNA editing generates cellular subsets with diverse sequence within populations.

    Science.gov (United States)

    Harjanto, Dewi; Papamarkou, Theodore; Oates, Chris J; Rayon-Estrada, Violeta; Papavasiliou, F Nina; Papavasiliou, Anastasia

    2016-07-15

    RNA editing is a mutational mechanism that specifically alters the nucleotide content in transcribed RNA. However, editing rates vary widely, and could result from equivalent editing amongst individual cells, or represent an average of variable editing within a population. Here we present a hierarchical Bayesian model that quantifies the variance of editing rates at specific sites using RNA-seq data from both single cells, and a cognate bulk sample to distinguish between these two possibilities. The model predicts high variance for specific edited sites in murine macrophages and dendritic cells, findings that we validated experimentally by using targeted amplification of specific editable transcripts from single cells. The model also predicts changes in variance in editing rates for specific sites in dendritic cells during the course of LPS stimulation. Our data demonstrate substantial variance in editing signatures amongst single cells, supporting the notion that RNA editing generates diversity within cellular populations.

  3. Bacterial diversity characterization in petroleum samples from Brazilian reservoirs Caracterização da diversidade bacteriana em amostras de petróleo provenientes de reservatórios brasileiros

    Directory of Open Access Journals (Sweden)

    Valéria Maia de Oliveira

    2008-09-01

    Full Text Available This study aimed at evaluating potential differences among the bacterial communities from formation water and oil samples originated from biodegraded and non-biodegraded Brazilian petroleum reservoirs by using a PCR-DGGE based approach. Environmental DNA was isolated and used in PCR reactions with bacterial primers, followed by separation of 16S rDNA fragments in the DGGE. PCR products were also cloned and sequenced, aiming at the taxonomic affiliation of the community members. The fingerprints obtained allowed the direct comparison among the bacterial communities from oil samples presenting distinct degrees of biodegradation, as well as between the communities of formation water and oil sample from the non-biodegraded reservoir. Very similar DGGE band profiles were observed for all samples, and the diversity of the predominant bacterial phylotypes was shown to be low. Cloning and sequencing results revealed major differences between formation water and oil samples from the non-biodegraded reservoir. Bacillus sp. and Halanaerobium sp. were shown to be the predominant components of the bacterial community from the formation water sample, whereas the oil sample also included Alicyclobacillus acidoterrestris, Rhodococcus sp., Streptomyces sp. and Acidithiobacillus ferrooxidans. The PCR-DGGE technique, combined with cloning and sequencing of PCR products, revealed the presence of taxonomic groups not found previously in these samples when using cultivation-based methods and 16S rRNA gene library assembly, confirming the need of a polyphasic study in order to improve the knowledge of the extent of microbial diversity in such extreme environments.Este estudo teve como objetivo comparar as comunidades bacterianas de amostras de água de formação e de óleo de reservatórios de petróleo brasileiros com diferentes graus de biodegradação usando a técnica de PCR-DGGE. O DNA ambiental foi isolado e empregado em reações de PCR com primers bacterianos

  4. Identity, Diversity and Diversity Management

    DEFF Research Database (Denmark)

    Holck, Lotte; Muhr, Sara Louise; Villeseche, Florence

    2016-01-01

    The purpose of this paper is to examine the relationship between the identity and diversity literatures and discuss how a better understanding of the theoretical connections between the two informs both diversity research and diversity management practices. Design/methodology/approach – Literature...... review followed by a discussion of the theoretical and practical consequences of connecting the identity and diversity literatures. Findings – The authors inform future research in three ways. First, by showing how definitions of identity influence diversity theorizing in specific ways. Second...... and limitations – is crucial for successful diversity management research and practice. Research limitations/implications – The authors argue for a better understanding of differences, overlaps and limits of different identity perspectives, and for a stronger engagement with practice. Practical implications...

  5. Cyclic nucleotide specific phosphodiesterases of Leishmania major

    Directory of Open Access Journals (Sweden)

    Linder Markus

    2006-03-01

    Full Text Available Abstract Background Leishmania represent a complex of important human pathogens that belong to the systematic order of the kinetoplastida. They are transmitted between their human and mammalian hosts by different bloodsucking sandfly vectors. In their hosts, the Leishmania undergo several differentiation steps, and their coordination and optimization crucially depend on numerous interactions between the parasites and the physiological environment presented by the fly and human hosts. Little is still known about the signalling networks involved in these functions. In an attempt to better understand the role of cyclic nucleotide signalling in Leishmania differentiation and host-parasite interaction, we here present an initial study on the cyclic nucleotide-specific phosphodiesterases of Leishmania major. Results This paper presents the identification of three class I cyclic-nucleotide-specific phosphodiesterases (PDEs from L. major, PDEs whose catalytic domains exhibit considerable sequence conservation with, among other, all eleven human PDE families. In contrast to other protozoa such as Dictyostelium, or fungi such as Saccharomyces cerevisiae, Candida ssp or Neurospora, no genes for class II PDEs were found in the Leishmania genomes. LmjPDEA contains a class I catalytic domain at the C-terminus of the polypeptide, with no other discernible functional domains elsewhere. LmjPDEB1 and LmjPDEB2 are coded for by closely related, tandemly linked genes on chromosome 15. Both PDEs contain two GAF domains in their N-terminal region, and their almost identical catalytic domains are located at the C-terminus of the polypeptide. LmjPDEA, LmjPDEB1 and LmjPDEB2 were further characterized by functional complementation in a PDE-deficient S. cerevisiae strain. All three enzymes conferred complementation, demonstrating that all three can hydrolyze cAMP. Recombinant LmjPDEB1 and LmjPDEB2 were shown to be cAMP-specific, with Km values in the low micromolar range

  6. Maternal genealogical patterns of chicken breeds sampled in Europe.

    Science.gov (United States)

    Lyimo, C M; Weigend, A; Msoffe, P L; Hocking, P M; Simianer, H; Weigend, S

    2015-08-01

    The aim of this study was to investigate the maternal genealogical pattern of chicken breeds sampled in Europe. Sequence polymorphisms of 1256 chickens of the hypervariable region (D-loop) of mitochondrial DNA (mtDNA) were used. Median-joining networks were constructed to establish evolutionary relationships among mtDNA haplotypes of chickens, which included a wide range of breeds with different origin and history. Chicken breeds which have had their roots in Europe for more than 3000 years were categorized by their founding regions, encompassing Mediterranean type, East European type and Northwest European type. Breeds which were introduced to Europe from Asia since the mid-19th century were classified as Asian type, and breeds based on crossbreeding between Asian breeds and European breeds were classified as Intermediate type. The last group, Game birds, included fighting birds from Asia. The classification of mtDNA haplotypes was based on Liu et al.'s (2006) nomenclature. Haplogroup E was the predominant clade among the European chicken breeds. The results showed, on average, the highest number of haplotypes, highest haplotype diversity, and highest nucleotide diversity for Asian type breeds, followed by Intermediate type chickens. East European and Northwest European breeds had lower haplotype and nucleotide diversity compared to Mediterranean, Intermediate, Game and Asian type breeds. Results of our study support earlier findings that chicken breeds sampled in Europe have their roots in the Indian subcontinent and East Asia. This is consistent with historical and archaeological evidence of chicken migration routes to Europe. © 2015 Stichting International Foundation for Animal Genetics.

  7. Diversity Management

    DEFF Research Database (Denmark)

    Ravazzani, Silvia

    2018-01-01

    This entry provides an overview of diversity management which, in the context of organizations, consists in the strategic process of harnessing the potential of all employees to create an inclusive environment and, at the same time, contribute to meeting organizational goals. The entry first...... describes the complex construct of diversity that has been variously conceptualized in the literature, embracing multiple social and informational diversity dimensions such as gender, age, culture, values, and workstyle. This is followed by illustration of the historical development of diversity-management...... discourse and practice, and possible overarching approaches guiding organizations. It goes on to elucidate elements linked to the implementation of diversity management: positive and negative outcomes, most spread practices including communication, and contingency factors shaping the understanding...

  8. Nucleotide Excision Repair in Caenorhabditis elegans

    Directory of Open Access Journals (Sweden)

    Hannes Lans

    2011-01-01

    Full Text Available Nucleotide excision repair (NER plays an essential role in many organisms across life domains to preserve and faithfully transmit DNA to the next generation. In humans, NER is essential to prevent DNA damage-induced mutation accumulation and cell death leading to cancer and aging. NER is a versatile DNA repair pathway that repairs many types of DNA damage which distort the DNA helix, such as those induced by solar UV light. A detailed molecular model of the NER pathway has emerged from in vitro and live cell experiments, particularly using model systems such as bacteria, yeast, and mammalian cell cultures. In recent years, the versatility of the nematode C. elegans to study DNA damage response (DDR mechanisms including NER has become increasingly clear. In particular, C. elegans seems to be a convenient tool to study NER during the UV response in vivo, to analyze this process in the context of a developing and multicellular organism, and to perform genetic screening. Here, we will discuss current knowledge gained from the use of C. elegans to study NER and the response to UV-induced DNA damage.

  9. Cyclic Nucleotide Signalling in Kidney Fibrosis

    Directory of Open Access Journals (Sweden)

    Elisabeth Schinner

    2015-01-01

    Full Text Available Kidney fibrosis is an important factor for the progression of kidney diseases, e.g., diabetes mellitus induced kidney failure, glomerulosclerosis and nephritis resulting in chronic kidney disease or end-stage renal disease. Cyclic adenosine monophosphate (cAMP and cyclic guanosine monophosphate (cGMP were implicated to suppress several of the above mentioned renal diseases. In this review article, identified effects and mechanisms of cGMP and cAMP regarding renal fibrosis are summarized. These mechanisms include several signalling pathways of nitric oxide/ANP/guanylyl cyclases/cGMP-dependent protein kinase and cAMP/Epac/adenylyl cyclases/cAMP-dependent protein kinase. Furthermore, diverse possible drugs activating these pathways are discussed. From these diverse mechanisms it is expected that new pharmacological treatments will evolve for the therapy or even prevention of kidney failure.

  10. Genome-wide diversity and differentiation in New World populations of the human malaria parasite Plasmodium vivax.

    Directory of Open Access Journals (Sweden)

    Thais C de Oliveira

    2017-07-01

    Full Text Available The Americas were the last continent colonized by humans carrying malaria parasites. Plasmodium falciparum from the New World shows very little genetic diversity and greater linkage disequilibrium, compared with its African counterparts, and is clearly subdivided into local, highly divergent populations. However, limited available data have revealed extensive genetic diversity in American populations of another major human malaria parasite, P. vivax.We used an improved sample preparation strategy and next-generation sequencing to characterize 9 high-quality P. vivax genome sequences from northwestern Brazil. These new data were compared with publicly available sequences from recently sampled clinical P. vivax isolates from Brazil (BRA, total n = 11 sequences, Peru (PER, n = 23, Colombia (COL, n = 31, and Mexico (MEX, n = 19.We found that New World populations of P. vivax are as diverse (nucleotide diversity π between 5.2 × 10-4 and 6.2 × 10-4 as P. vivax populations from Southeast Asia, where malaria transmission is substantially more intense. They display several non-synonymous nucleotide substitutions (some of them previously undescribed in genes known or suspected to be involved in antimalarial drug resistance, such as dhfr, dhps, mdr1, mrp1, and mrp-2, but not in the chloroquine resistance transporter ortholog (crt-o gene. Moreover, P. vivax in the Americas is much less geographically substructured than local P. falciparum populations, with relatively little between-population genome-wide differentiation (pairwise FST values ranging between 0.025 and 0.092. Finally, P. vivax populations show a rapid decline in linkage disequilibrium with increasing distance between pairs of polymorphic sites, consistent with very frequent outcrossing. We hypothesize that the high diversity of present-day P. vivax lineages in the Americas originated from successive migratory waves and subsequent admixture between parasite lineages from geographically

  11. Prebiotic nucleotide synthesis demonstration of a geologically plausible pathway

    NARCIS (Netherlands)

    Schwartz, A.W.; Veen, van der M.; Bisseling, T.; Chittenden, G.J.

    1975-01-01

    Mineral phosphate (apatite) is activated for the synthesis of nucleotides when dilute solutions containing nucleoside and ammonium oxalate are evaporated in its presence. A natural, igneous fluorapatite was found to be even more effective in nucleotide synthesis than the more soluble

  12. Supplementary Material for: The arabidopsis cyclic nucleotide interactome

    KAUST Repository

    Donaldson, Lara

    2016-01-01

    Abstract Background Cyclic nucleotides have been shown to play important signaling roles in many physiological processes in plants including photosynthesis and defence. Despite this, little is known about cyclic nucleotide-dependent signaling mechanisms in plants since the downstream target proteins remain unknown. This is largely due to the fact that bioinformatics searches fail to identify plant homologs of protein kinases and phosphodiesterases that are the main targets of cyclic nucleotides in animals. Methods An affinity purification technique was used to identify cyclic nucleotide binding proteins in Arabidopsis thaliana. The identified proteins were subjected to a computational analysis that included a sequence, transcriptional co-expression and functional annotation analysis in order to assess their potential role in plant cyclic nucleotide signaling. Results A total of twelve cyclic nucleotide binding proteins were identified experimentally including key enzymes in the Calvin cycle and photorespiration pathway. Importantly, eight of the twelve proteins were shown to contain putative cyclic nucleotide binding domains. Moreover, the identified proteins are post-translationally modified by nitric oxide, transcriptionally co-expressed and annotated to function in hydrogen peroxide signaling and the defence response. The activity of one of these proteins, GLYGOLATE OXIDASE 1, a photorespiratory enzyme that produces hydrogen peroxide in response to Pseudomonas, was shown to be repressed by a combination of cGMP and nitric oxide treatment. Conclusions We propose that the identified proteins function together as points of cross-talk between cyclic nucleotide, nitric oxide and reactive oxygen species signaling during the defence response.

  13. In-silico single nucleotide polymorphisms (SNP) mining of Sorghum ...

    African Journals Online (AJOL)

    Single nucleotide polymorphisms (SNPs) may be considered the ultimate genetic markers as they represent the finest resolution of a DNA sequence (a single nucleotide), and are generally abundant in populations with a low mutation rate. SNPs are important tools in studying complex genetic traits and genome evolution.

  14. Condensing the information in DNA with double-headed nucleotides

    DEFF Research Database (Denmark)

    Hornum, Mick; Sharma, Pawan K; Reslow-Jacobsen, Charlotte

    2017-01-01

    A normal duplex holds as many Watson-Crick base pairs as the number of nucleotides in its constituent strands. Here we establish that single nucleotides can be designed to functionally imitate dinucleotides without compromising binding affinity. This effectively allows sequence information...

  15. Single nucleotide polymorphism genotyping and its application on ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-03-20

    Mar 20, 2009 ... wide trait analysis. Single-nucleotide polymorphisms (SNP) are the most common sequence variation and a significant amount of effort has been invested in re-sequencing alleles to discover .... logical markers and are usually visually characterized .... regard two-nucleotide changes and small indels up to a.

  16. Genetic diversity and recombination analysis of sweepoviruses from Brazil

    Directory of Open Access Journals (Sweden)

    Albuquerque Leonardo C

    2012-10-01

    Full Text Available Abstract Background Monopartite begomoviruses (genus Begomovirus, family Geminiviridae that infect sweet potato (Ipomoea batatas around the world are known as sweepoviruses. Because sweet potato plants are vegetatively propagated, the accumulation of viruses can become a major constraint for root production. Mixed infections of sweepovirus species and strains can lead to recombination, which may contribute to the generation of new recombinant sweepoviruses. Results This study reports the full genome sequence of 34 sweepoviruses sampled from a sweet potato germplasm bank and commercial fields in Brazil. These sequences were compared with others from public nucleotide sequence databases to provide a comprehensive overview of the genetic diversity and patterns of genetic exchange in sweepoviruses isolated from Brazil, as well as to review the classification and nomenclature of sweepoviruses in accordance with the current guidelines proposed by the Geminiviridae Study Group of the International Committee on Taxonomy of Viruses (ICTV. Co-infections and extensive recombination events were identified in Brazilian sweepoviruses. Analysis of the recombination breakpoints detected within the sweepovirus dataset revealed that most recombination events occurred in the intergenic region (IR and in the middle of the C1 open reading frame (ORF. Conclusions The genetic diversity of sweepoviruses was considerably greater than previously described in Brazil. Moreover, recombination analysis revealed that a genomic exchange is responsible for the emergence of sweepovirus species and strains and provided valuable new information for understanding the diversity and evolution of sweepoviruses.

  17. Limited genetic diversity preceded extinction of the Tasmanian tiger.

    Directory of Open Access Journals (Sweden)

    Brandon R Menzies

    Full Text Available The Tasmanian tiger or thylacine was the largest carnivorous marsupial when Europeans first reached Australia. Sadly, the last known thylacine died in captivity in 1936. A recent analysis of the genome of the closely related and extant Tasmanian devil demonstrated limited genetic diversity between individuals. While a similar lack of diversity has been reported for the thylacine, this analysis was based on just two individuals. Here we report the sequencing of an additional 12 museum-archived specimens collected between 102 and 159 years ago. We examined a portion of the mitochondrial DNA hyper-variable control region and determined that all sequences were on average 99.5% identical at the nucleotide level. As a measure of accuracy we also sequenced mitochondrial DNA from a mother and two offspring. As expected, these samples were found to be 100% identical, validating our methods. We also used 454 sequencing to reconstruct 2.1 kilobases of the mitochondrial genome, which shared 99.91% identity with the two complete thylacine mitochondrial genomes published previously. Our thylacine genomic data also contained three highly divergent putative nuclear mitochondrial sequences, which grouped phylogenetically with the published thylacine mitochondrial homologs but contained 100-fold more polymorphisms than the conserved fragments. Together, our data suggest that the thylacine population in Tasmania had limited genetic diversity prior to its extinction, possibly as a result of their geographic isolation from mainland Australia approximately 10,000 years ago.

  18. Limited genetic diversity preceded extinction of the Tasmanian tiger.

    Science.gov (United States)

    Menzies, Brandon R; Renfree, Marilyn B; Heider, Thomas; Mayer, Frieder; Hildebrandt, Thomas B; Pask, Andrew J

    2012-01-01

    The Tasmanian tiger or thylacine was the largest carnivorous marsupial when Europeans first reached Australia. Sadly, the last known thylacine died in captivity in 1936. A recent analysis of the genome of the closely related and extant Tasmanian devil demonstrated limited genetic diversity between individuals. While a similar lack of diversity has been reported for the thylacine, this analysis was based on just two individuals. Here we report the sequencing of an additional 12 museum-archived specimens collected between 102 and 159 years ago. We examined a portion of the mitochondrial DNA hyper-variable control region and determined that all sequences were on average 99.5% identical at the nucleotide level. As a measure of accuracy we also sequenced mitochondrial DNA from a mother and two offspring. As expected, these samples were found to be 100% identical, validating our methods. We also used 454 sequencing to reconstruct 2.1 kilobases of the mitochondrial genome, which shared 99.91% identity with the two complete thylacine mitochondrial genomes published previously. Our thylacine genomic data also contained three highly divergent putative nuclear mitochondrial sequences, which grouped phylogenetically with the published thylacine mitochondrial homologs but contained 100-fold more polymorphisms than the conserved fragments. Together, our data suggest that the thylacine population in Tasmania had limited genetic diversity prior to its extinction, possibly as a result of their geographic isolation from mainland Australia approximately 10,000 years ago.

  19. Limited Genetic Diversity Preceded Extinction of the Tasmanian Tiger

    Science.gov (United States)

    Menzies, Brandon R.; Renfree, Marilyn B.; Heider, Thomas; Mayer, Frieder; Hildebrandt, Thomas B.; Pask, Andrew J.

    2012-01-01

    The Tasmanian tiger or thylacine was the largest carnivorous marsupial when Europeans first reached Australia. Sadly, the last known thylacine died in captivity in 1936. A recent analysis of the genome of the closely related and extant Tasmanian devil demonstrated limited genetic diversity between individuals. While a similar lack of diversity has been reported for the thylacine, this analysis was based on just two individuals. Here we report the sequencing of an additional 12 museum-archived specimens collected between 102 and 159 years ago. We examined a portion of the mitochondrial DNA hyper-variable control region and determined that all sequences were on average 99.5% identical at the nucleotide level. As a measure of accuracy we also sequenced mitochondrial DNA from a mother and two offspring. As expected, these samples were found to be 100% identical, validating our methods. We also used 454 sequencing to reconstruct 2.1 kilobases of the mitochondrial genome, which shared 99.91% identity with the two complete thylacine mitochondrial genomes published previously. Our thylacine genomic data also contained three highly divergent putative nuclear mitochondrial sequences, which grouped phylogenetically with the published thylacine mitochondrial homologs but contained 100-fold more polymorphisms than the conserved fragments. Together, our data suggest that the thylacine population in Tasmania had limited genetic diversity prior to its extinction, possibly as a result of their geographic isolation from mainland Australia approximately 10,000 years ago. PMID:22530022

  20. Gender Diversities

    DEFF Research Database (Denmark)

    Agustin, Lise Rolandsen; Siim, Birte

    2014-01-01

    The article analyses the European Year for Combating Poverty and Social Exclusion (2010) (EY 2010) with the aim of identifying the nature of gender diversities in EU policies. We argue that the EU handles issues related to gender and diversity in particular ways; this approach is characterized...... by non-citizen/citizen and redistribution/recognition divisions. Employing intersectionality as the methodological approach to gender diversities, the article shows how gender and ethnicity are articulated in the policy-making process which led to the adoption of EY 201, the activities undertaken during...... the EY 2010, and the evaluation of EY 2010. The case study is suitable for developing a dynamic multi-level model for analysing gendered diversities at the transnationmal level: It illustrates how the EU policy frame interacts with particular national contexts in promoting or hundering the advancement...

  1. Ecological diversity

    National Research Council Canada - National Science Library

    Pielou E. C

    1975-01-01

    The richness and variety-in a word, the diversity-of natural ecological communities have never been more highly valued than they are now, as they become increasingly threatened by the environmental crisis...

  2. Understanding Diversity

    NARCIS (Netherlands)

    D.L. van Knippenberg (Daan)

    2007-01-01

    textabstractDaan van Knippenberg is Professor of Organizational Behavior at RSM Erasmus University, Erasmus University Rotterdam, The Netherlands. His research interests include work group performance, especially work group diversity and group decision making, leadership, in particular the roles of

  3. Nucleotide-time alignment for molecular recorders.

    Directory of Open Access Journals (Sweden)

    Thaddeus R Cybulski

    2017-05-01

    Full Text Available Using a DNA polymerase to record intracellular calcium levels has been proposed as a novel neural recording technique, promising massive-scale, single-cell resolution monitoring of large portions of the brain. This technique relies on local storage of neural activity in strands of DNA, followed by offline analysis of that DNA. In simple implementations of this scheme, the time when each nucleotide was written cannot be determined directly by post-hoc DNA sequencing; the timing data must be estimated instead. Here, we use a Dynamic Time Warping-based algorithm to perform this estimation, exploiting correlations between neural activity and observed experimental variables to translate DNA-based signals to an estimate of neural activity over time. This algorithm improves the parallelizability of traditional Dynamic Time Warping, allowing several-fold increases in computation speed. The algorithm also provides a solution to several critical problems with the molecular recording paradigm: determining recording start times and coping with DNA polymerase pausing. The algorithm can generally locate DNA-based records to within <10% of a recording window, allowing for the estimation of unobserved incorporation times and latent neural tunings. We apply our technique to an in silico motor control neuroscience experiment, using the algorithm to estimate both timings of DNA-based data and the directional tuning of motor cortical cells during a center-out reaching task. We also use this algorithm to explore the impact of polymerase characteristics on system performance, determining the precision of a molecular recorder as a function of its kinetic and error-generating properties. We find useful ranges of properties for DNA polymerase-based recorders, providing guidance for future protein engineering attempts. This work demonstrates a useful general extension to dynamic alignment algorithms, as well as direct applications of that extension toward the development

  4. Building the library of RNA 3D nucleotide conformations using the clustering approach

    Directory of Open Access Journals (Sweden)

    Zok Tomasz

    2015-09-01

    Full Text Available An increasing number of known RNA 3D structures contributes to the recognition of various RNA families and identification of their features. These tasks are based on an analysis of RNA conformations conducted at different levels of detail. On the other hand, the knowledge of native nucleotide conformations is crucial for structure prediction and understanding of RNA folding. However, this knowledge is stored in structural databases in a rather distributed form. Therefore, only automated methods for sampling the space of RNA structures can reveal plausible conformational representatives useful for further analysis. Here, we present a machine learning-based approach to inspect the dataset of RNA three-dimensional structures and to create a library of nucleotide conformers. A median neural gas algorithm is applied to cluster nucleotide structures upon their trigonometric description. The clustering procedure is two-stage: (i backbone- and (ii ribose-driven. We show the resulting library that contains RNA nucleotide representatives over the entire data, and we evaluate its quality by computing normal distribution measures and average RMSD between data points as well as the prototype within each cluster.

  5. A new single nucleotide polymorphism in the ryanodine gene of chicken skeletal muscle.

    Science.gov (United States)

    Droval, A A; Binneck, E; Marin, S R R; Paião, F G; Oba, A; Nepomuceno, A L; Shimokomaki, M

    2012-04-03

    Some genes affect meat quality in chickens. We looked for polymorphisms in the Gallus gallus α-RyR gene (homologous to RyR 1) that could be associated with PSE (pale, soft and exudative) meat. Because RyR genes are over 100,000 bp long and code for proteins with about 5000 amino acids, primers were designed to amplify a fragment of hotspot region 2, a region with a high density of mutations in other species. Total blood DNA was extracted from 50 birds, 25 that had PSE meat and 25 normal chickens. The DNA samples were amplified by PCR, cloned, sequenced, and used to identify single nucleotide polymorphisms (SNPs). The amplified fragment of α-RyR was 604 nucleotides in length; 181 nucleotides were similar to two exons from a hypothetical turkey cDNA sequence for α-RyR. A non-synonymous nucleotide substitution (G/A) was identified in at least one of the three sequenced clones obtained from nine animals, six PSE (HAL+) birds and three normal (HAL-) birds; they were heterozygous for this mutation. This SNP causes a change from Val to Met in the α-RYR protein. Since the frequencies of this SNP were not significantly different in the PSE versus normal chickens, it appears that this mutation (in heterozygosity) does not alter the structure or function of the muscle protein, making it an inappropriate candidate as a genetic marker for PSE meat.

  6. Clusters of nucleotide substitutions and insertion/deletion mutations are associated with repeat sequences.

    Directory of Open Access Journals (Sweden)

    Michael J McDonald

    2011-06-01

    Full Text Available The genome-sequencing gold rush has facilitated the use of comparative genomics to uncover patterns of genome evolution, although their causal mechanisms remain elusive. One such trend, ubiquitous to prokarya and eukarya, is the association of insertion/deletion mutations (indels with increases in the nucleotide substitution rate extending over hundreds of base pairs. The prevailing hypothesis is that indels are themselves mutagenic agents. Here, we employ population genomics data from Escherichia coli, Saccharomyces paradoxus, and Drosophila to provide evidence suggesting that it is not the indels per se but the sequence in which indels occur that causes the accumulation of nucleotide substitutions. We found that about two-thirds of indels are closely associated with repeat sequences and that repeat sequence abundance could be used to identify regions of elevated sequence diversity, independently of indels. Moreover, the mutational signature of indel-proximal nucleotide substitutions matches that of error-prone DNA polymerases. We propose that repeat sequences promote an increased probability of replication fork arrest, causing the persistent recruitment of error-prone DNA polymerases to specific sequence regions over evolutionary time scales. Experimental measures of the mutation rates of engineered DNA sequences and analyses of experimentally obtained collections of spontaneous mutations provide molecular evidence supporting our hypothesis. This study uncovers a new role for repeat sequences in genome evolution and provides an explanation of how fine-scale sequence contextual effects influence mutation rates and thereby evolution.

  7. Diversity Evaluation of Xylella fastidiosa from Infected Olive Trees in Apulia (Southern Italy

    Directory of Open Access Journals (Sweden)

    Stefania M. Mang

    2016-04-01

    Full Text Available Olive culture is very important in the Mediterranean Basin. A severe outbreak of Olive Quick Decline Syndrome (OQDS caused by Xylella fastidiosa infection was first noticed in 2013 on olive trees in the southern part of Apulia region (Lecce province, southern Italy. Studies were carried out for detection and diversity evaluation of the Apulian strain of Xylella fastidiosa. The presence of the pathogen in olive samples was detected by PCR amplifying the 16S rDNA, gyrase B subunit (gyrB and HL hypothetical protein genes and single nucleotide polymorphisms (SNPs assessment was performed to genotype X. fastidiosa. Twelve SNPs were recorded over gyrB and six SNPs were found for HL gene. Less variations were detected on 16S rDNA gene. Only gyrB and HL provided sufficient information for dividing the Apulian X. fastidiosa olive strains into subspecies. Using HL nucleotide sequences was possible to separate X. fastidiosa into subspecies pauca and fastidiosa. Whereas, nucleotide variation present on gyrB gene allowed separation of X. fastidiosa subsp. pauca from the other subspecies multiplex and fastidiosa. The X. fastidiosa strain from Apulia region was included into the subspecies pauca based on three genes phylogenetic analyses.

  8. Single nucleotide polymorphism discovery in elite north american potato germplasm

    Directory of Open Access Journals (Sweden)

    De Jong Walter S

    2011-06-01

    Full Text Available Abstract Background Current breeding approaches in potato rely almost entirely on phenotypic evaluations; molecular markers, with the exception of a few linked to disease resistance traits, are not widely used. Large-scale sequence datasets generated primarily through Sanger Expressed Sequence Tag projects are available from a limited number of potato cultivars and access to next generation sequencing technologies permits rapid generation of sequence data for additional cultivars. When coupled with the advent of high throughput genotyping methods, an opportunity now exists for potato breeders to incorporate considerably more genotypic data into their decision-making. Results To identify a large number of Single Nucleotide Polymorphisms (SNPs in elite potato germplasm, we sequenced normalized cDNA prepared from three commercial potato cultivars: 'Atlantic', 'Premier Russet' and 'Snowden'. For each cultivar, we generated 2 Gb of sequence which was assembled into a representative transcriptome of ~28-29 Mb for each cultivar. Using the Maq SNP filter that filters read depth, density, and quality, 575,340 SNPs were identified within these three cultivars. In parallel, 2,358 SNPs were identified within existing Sanger sequences for three additional cultivars, 'Bintje', 'Kennebec', and 'Shepody'. Using a stringent set of filters in conjunction with the potato reference genome, we identified 69,011 high confidence SNPs from these six cultivars for use in genotyping with the Infinium platform. Ninety-six of these SNPs were used with a BeadXpress assay to assess allelic diversity in a germplasm panel of 248 lines; 82 of the SNPs proved sufficiently informative for subsequent analyses. Within diverse North American germplasm, the chip processing market class was most distinct, clearly separated from all other market classes. The round white and russet market classes both include fresh market and processing cultivars. Nevertheless, the russet and round

  9. Diversity and molecular phylogeny of mitochondrial DNA of rhesus macaques (Macaca mulatta) in Bangladesh.

    Science.gov (United States)

    Hasan, M Kamrul; Feeroz, M Mostafa; Jones-Engel, Lisa; Engel, Gregory A; Kanthaswamy, Sree; Smith, David Glenn

    2014-11-01

    While studies of rhesus macaques (Macaca mulatta) in the eastern (e.g., China) and western (e.g., India) parts of their geographic range have revealed major genetic differences that warrant the recognition of two different subspecies, little is known about genetic characteristics of rhesus macaques in the transitional zone extending from eastern India and Bangladesh through the northern part of Indo-China, the probable original homeland of the species. We analyzed genetic variation of 762 base pairs of mitochondrial DNA from 86 fecal swab samples and 19 blood samples from 25 local populations of rhesus macaque in Bangladesh collected from January 2010 to August 2012. These sequences were compared with those of rhesus macaques from India, China, and Myanmar. Forty-six haplotypes defined by 200 (26%) polymorphic nucleotide sites were detected. Estimates of gene diversity, expected heterozygosity, and nucleotide diversity for the total population were 0.9599 ± 0.0097, 0.0193 ± 0.0582, and 0.0196 ± 0.0098, respectively. A mismatch distribution of paired nucleotide differences yielded a statistically significantly negative value of Tajima's D, reflecting a population that rapidly expanded after the terminal Pleistocene. Most haplotypes throughout regions of Bangladesh, including an isolated region in the southwestern area (Sundarbans), clustered with haplotypes assigned to the minor haplogroup Ind-2 from India reflecting an east to west dispersal of rhesus macaques to India. Haplotypes from the southeast region of Bangladesh formed a cluster with those from Myanmar, and represent the oldest rhesus macaque haplotypes of Bangladesh. These results are consistent with the hypothesis that rhesus macaques first entered Bangladesh from the southeast, probably from Indo-China, then dispersed westward throughout eastern and central India. © 2014 Wiley Periodicals, Inc.

  10. Approach to analysis of single nucleotide polymorphisms by automated constant denaturant capillary electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Bjoerheim, Jens; Abrahamsen, Torveig Weum; Kristensen, Annette Torgunrud; Gaudernack, Gustav; Ekstroem, Per O

    2003-05-15

    Melting gel techniques have proven to be amenable and powerful tools in point mutation and single nucleotide polymorphism (SNP) analysis. With the introduction of commercially available capillary electrophoresis instruments, a partly automated platform for denaturant capillary electrophoresis with potential for routine screening of selected target sequences has been established. The aim of this article is to demonstrate the use of automated constant denaturant capillary electrophoresis (ACDCE) in single nucleotide polymorphism analysis of various target sequences. Optimal analysis conditions for different single nucleotide polymorphisms on ACDCE are evaluated with the Poland algorithm. Laboratory procedures include only PCR and electrophoresis. For direct genotyping of individual SNPs, the samples are analyzed with an internal standard and the alleles are identified by co-migration of sample and standard peaks. In conclusion, SNPs suitable for melting gel analysis based on theoretical thermodynamics were separated by ACDCE under appropriate conditions. With this instrumentation (ABI 310 Genetic Analyzer), 48 samples could be analyzed without any intervention. Several institutions have capillary instrumentation in-house, thus making this SNP analysis method accessible to large groups of researchers without any need for instrument modification.

  11. Nucleotide Excision Repair in Cellular Chromatin: Studies with Yeast from Nucleotide to Gene to Genome

    Directory of Open Access Journals (Sweden)

    Simon Reed

    2012-09-01

    Full Text Available Here we review our development of, and results with, high resolution studies on global genome nucleotide excision repair (GGNER in Saccharomyces cerevisiae. We have focused on how GGNER relates to histone acetylation for its functioning and we have identified the histone acetyl tranferase Gcn5 and acetylation at lysines 9/14 of histone H3 as a major factor in enabling efficient repair. We consider results employing primarily MFA2 as a model gene, but also those with URA3 located at subtelomeric sequences. In the latter case we also see a role for acetylation at histone H4. We then go on to outline the development of a high resolution genome-wide approach that enables one to examine correlations between histone modifications and the nucleotide excision repair (NER of UV-induced cyclobutane pyrimidine dimers throughout entire genomes. This is an approach that will enable rapid advances in understanding the complexities of how compacted chromatin in chromosomes is processed to access DNA damage and then returned to its pre-damaged status to maintain epigenetic codes.

  12. DEAD-box Helicases as Integrators of RNA, Nucleotide and Protein Binding

    Science.gov (United States)

    Putnam, Andrea A.

    2013-01-01

    DEAD-box helicases perform diverse cellular functions in virtually all steps of RNA metabolism from Bacteria to Humans. Although DEAD-box helicases share a highly conserved core domain, the enzymes catalyze a wide range of biochemical reactions. In addition to the well established RNA unwinding and corresponding ATPase activities, DEAD-box helicases promote duplex formation and displace proteins from RNA. They can also function as assembly platforms for larger ribonucleoprotein complexes, and as metabolite sensors. This review aims to provide a perspective on the diverse biochemical features of DEAD-box helicases and connections to structural information. We discuss these data in the context of a model that views the enzymes as integrators of RNA, nucleotide, and protein binding. PMID:23416748

  13. Environmental heat stress, hyperammonemia and nucleotide metabolism during intermittent exercise.

    Science.gov (United States)

    Mohr, Magni; Rasmussen, Peter; Drust, Barry; Nielsen, Bodil; Nybo, Lars

    2006-05-01

    This study investigated the influence of environmental heat stress on ammonia (NH3) accumulation in relation to nucleotide metabolism and fatigue during intermittent exercise. Eight males performed 40 min of intermittent exercise (15 s at 306+/-22 W alternating with 15 s of unloaded cycling) followed by five 15 s all-out sprints. Control trials were conducted in a 20 degrees C environment while heat stress trials were performed at an ambient temperature of 40 degrees C. Muscle biopsies and venous blood samples were obtained at rest, after 40 min of exercise and following the maximal sprints. Following exercise with heat stress, the core and muscle temperatures peaked at 39.5+/-0.2 and 40.2+/-0.2 degrees C to be approximately 1 degrees C higher (Pheat stress trial (PNH3 increased from 31+/-2 microM at rest to 93+/-6 at 40 min and 151+/-15 microM after the maximal sprints to be 34% higher than control (Pheat stress compared to control, while muscle glycogen, CP, ATP and IMP levels were similar across trials. In conclusion, altered levels of "classical peripheral fatiguing agents" does apparently not explain the reduced capacity for performing repeated sprints following intermittent exercise in the heat, whereas the augmented systemic NH3 response may be a factor influencing fatigue during exercise with superimposed heat stress.

  14. Genetic diversity and variation of mitochondrial DNA in native and introduced bighead carp

    Science.gov (United States)

    Li, Si-Fa; Yang, Qin-Ling; Xu, Jia-Wei; Wang, Cheng-Hui; Chapman, Duane C.; Lu, Guoping

    2010-01-01

    The bighead carp Hypophthalmichthys nobilis is native to China but has been introduced to over 70 countries and is established in many large river systems. Genetic diversity and variation in introduced bighead carp have not previously been evaluated, and a systematic comparison among fish from different river systems was unavailable. In this study, 190 bighead carp specimens were sampled from five river systems in three countries (Yangtze, Pearl, and Amur rivers, China; Danube River, Hungary; Mississippi River basin, USA) and their mitochondrial 16S ribosomal RNA gene and D-loop region were sequenced (around 1,345 base pairs). Moderate genetic diversity was found in bighead carp, ranging from 0.0014 to 0.0043 for nucleotide diversity and from 0.6879 to 0.9333 for haplotype diversity. Haplotype analysis provided evidence that (1) multiple haplotype groups might be present among bighead carp, (2) bighead carp probably originated from the Yangtze River, and (3) bighead carp in the Mississippi River basin may have some genetic ancestry in the Danube River. The analysis of molecular variance showed significant genetic differentiation among these five populations but also revealed limited differentiation between the Yangtze and Amur River bighead carp. This large-scale study of bighead carp genetic diversity and variation provides the first global perspective of bighead carp in the context of biodiversity conservation as well as invasive species control and management.

  15. Reading biological processes from nucleotide sequences

    Science.gov (United States)

    Murugan, Anand

    Cellular processes have traditionally been investigated by techniques of imaging and biochemical analysis of the molecules involved. The recent rapid progress in our ability to manipulate and read nucleic acid sequences gives us direct access to the genetic information that directs and constrains biological processes. While sequence data is being used widely to investigate genotype-phenotype relationships and population structure, here we use sequencing to understand biophysical mechanisms. We present work on two different systems. First, in chapter 2, we characterize the stochastic genetic editing mechanism that produces diverse T-cell receptors in the human immune system. We do this by inferring statistical distributions of the underlying biochemical events that generate T-cell receptor coding sequences from the statistics of the observed sequences. This inferred model quantitatively describes the potential repertoire of T-cell receptors that can be produced by an individual, providing insight into its potential diversity and the probability of generation of any specific T-cell receptor. Then in chapter 3, we present work on understanding the functioning of regulatory DNA sequences in both prokaryotes and eukaryotes. Here we use experiments that measure the transcriptional activity of large libraries of mutagenized promoters and enhancers and infer models of the sequence-function relationship from this data. For the bacterial promoter, we infer a physically motivated 'thermodynamic' model of the interaction of DNA-binding proteins and RNA polymerase determining the transcription rate of the downstream gene. For the eukaryotic enhancers, we infer heuristic models of the sequence-function relationship and use these models to find synthetic enhancer sequences that optimize inducibility of expression. Both projects demonstrate the utility of sequence information in conjunction with sophisticated statistical inference techniques for dissecting underlying biophysical

  16. Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide-protein complexes.

    Science.gov (United States)

    Kondo, Jiro; Westhof, Eric

    2011-10-01

    Nucleotide bases are recognized by amino acid residues in a variety of DNA/RNA binding and nucleotide binding proteins. In this study, a total of 446 crystal structures of nucleotide-protein complexes are analyzed manually and pseudo pairs together with single and bifurcated hydrogen bonds observed between bases and amino acids are classified and annotated. Only 5 of the 20 usual amino acid residues, Asn, Gln, Asp, Glu and Arg, are able to orient in a coplanar fashion in order to form pseudo pairs with nucleotide bases through two hydrogen bonds. The peptide backbone can also form pseudo pairs with nucleotide bases and presents a strong bias for binding to the adenine base. The Watson-Crick side of the nucleotide bases is the major interaction edge participating in such pseudo pairs. Pseudo pairs between the Watson-Crick edge of guanine and Asp are frequently observed. The Hoogsteen edge of the purine bases is a good discriminatory element in recognition of nucleotide bases by protein side chains through the pseudo pairing: the Hoogsteen edge of adenine is recognized by various amino acids while the Hoogsteen edge of guanine is only recognized by Arg. The sugar edge is rarely recognized by either the side-chain or peptide backbone of amino acid residues.

  17. A novel method to discover fluoroquinolone antibiotic resistance (qnr) genes in fragmented nucleotide sequences.

    Science.gov (United States)

    Boulund, Fredrik; Johnning, Anna; Pereira, Mariana Buongermino; Larsson, D G Joakim; Kristiansson, Erik

    2012-12-11

    Broad-spectrum fluoroquinolone antibiotics are central in modern health care and are used to treat and prevent a wide range of bacterial infections. The recently discovered qnr genes provide a mechanism of resistance with the potential to rapidly spread between bacteria using horizontal gene transfer. As for many antibiotic resistance genes present in pathogens today, qnr genes are hypothesized to originate from environmental bacteria. The vast amount of data generated by shotgun metagenomics can therefore be used to explore the diversity of qnr genes in more detail. In this paper we describe a new method to identify qnr genes in nucleotide sequence data. We show, using cross-validation, that the method has a high statistical power of correctly classifying sequences from novel classes of qnr genes, even for fragments as short as 100 nucleotides. Based on sequences from public repositories, the method was able to identify all previously reported plasmid-mediated qnr genes. In addition, several fragments from novel putative qnr genes were identified in metagenomes. The method was also able to annotate 39 chromosomal variants of which 11 have previously not been reported in literature. The method described in this paper significantly improves the sensitivity and specificity of identification and annotation of qnr genes in nucleotide sequence data. The predicted novel putative qnr genes in the metagenomic data support the hypothesis of a large and uncharacterized diversity within this family of resistance genes in environmental bacterial communities. An implementation of the method is freely available at http://bioinformatics.math.chalmers.se/qnr/.

  18. A novel method to discover fluoroquinolone antibiotic resistance (qnr genes in fragmented nucleotide sequences

    Directory of Open Access Journals (Sweden)

    Boulund Fredrik

    2012-12-01

    Full Text Available Abstract Background Broad-spectrum fluoroquinolone antibiotics are central in modern health care and are used to treat and prevent a wide range of bacterial infections. The recently discovered qnr genes provide a mechanism of resistance with the potential to rapidly spread between bacteria using horizontal gene transfer. As for many antibiotic resistance genes present in pathogens today, qnr genes are hypothesized to originate from environmental bacteria. The vast amount of data generated by shotgun metagenomics can therefore be used to explore the diversity of qnr genes in more detail. Results In this paper we describe a new method to identify qnr genes in nucleotide sequence data. We show, using cross-validation, that the method has a high statistical power of correctly classifying sequences from novel classes of qnr genes, even for fragments as short as 100 nucleotides. Based on sequences from public repositories, the method was able to identify all previously reported plasmid-mediated qnr genes. In addition, several fragments from novel putative qnr genes were identified in metagenomes. The method was also able to annotate 39 chromosomal variants of which 11 have previously not been reported in literature. Conclusions The method described in this paper significantly improves the sensitivity and specificity of identification and annotation of qnr genes in nucleotide sequence data. The predicted novel putative qnr genes in the metagenomic data support the hypothesis of a large and uncharacterized diversity within this family of resistance genes in environmental bacterial communities. An implementation of the method is freely available at http://bioinformatics.math.chalmers.se/qnr/.

  19. Assessment of the geographic origins of pinewood nematode isolates via single nucleotide polymorphism in effector genes.

    Directory of Open Access Journals (Sweden)

    Joana Figueiredo

    Full Text Available The pinewood nematode, Bursaphelenchus xylophilus, is native to North America but it only causes damaging pine wilt disease in those regions of the world where it has been introduced. The accurate detection of the species and its dispersal routes are thus essential to define effective control measures. The main goals of this study were to analyse the genetic diversity among B. xylophilus isolates from different geographic locations and identify single nucleotide polymorphism (SNPs markers for geographic origin, through a comparative transcriptomic approach. The transcriptomes of seven B. xylophilus isolates, from Continental Portugal (4, China (1, Japan (1 and USA (1, were sequenced in the next generation platform Roche 454. Analysis of effector gene transcripts revealed inter-isolate nucleotide diversity that was validated by Sanger sequencing in the genomic DNA of the seven isolates and eight additional isolates from different geographic locations: Madeira Island (2, China (1, USA (1, Japan (2 and South Korea (2. The analysis identified 136 polymorphic positions in 10 effector transcripts. Pairwise comparison of the 136 SNPs through Neighbor-Joining and the Maximum Likelihood methods and 5-mer frequency analysis with the alignment-independent bilinear multivariate modelling approach correlated the SNPs with the isolates geographic origin. Furthermore, the SNP analysis indicated a closer proximity of the Portuguese isolates to the Korean and Chinese isolates than to the Japanese or American isolates. Each geographic cluster carried exclusive alleles that can be used as SNP markers for B. xylophilus isolate identification.

  20. Y-CHROMOSOMAL STR HAPLOTYPE DIVERSITY IN A SAMPLE FROM THE METROPOLITAN AREA OF BUENOS AIRES (ARGENTINA/Diversidad de Haplotipos del cromosoma Y en una muestra del área metropolitana de Buenos Aires (Argentina

    Directory of Open Access Journals (Sweden)

    Maria Laura Parolin

    2012-11-01

    Full Text Available El objetivo de este trabajo fue analizar el origen de los haplotipos del cromosoma Y en una muestra poblacional del Área Metropolitana de Buenos Aires (AMBA, y comparar estos resultados con los obtenidos previamente a nivel mitocondrial. Se determinaron 17 marcadores Y-STRs en 85 donantes no emparentados. Un total de 85 haplotipos únicos fueron observados. La diversidad haplotípica  fue de 1,000+/-0.0018, y la diversidad genética media de 0,680+/-0,095. Los linajes paternos evidenciaron una homogeneidad genética de raíces Europeas (93%, procedentes principalmente de Italia y España. La contribución amerindia paterna asociada al sub-haplogrupo Q1a3a fue relativamente baja (6%. La menor proporción de haplotipos amerindios y el elevado número de linajes maternos (44% de ese origen, revela que ha habido un aporte diferencial por género en la historia de mestizaje de esa población. Se observó un único perfil E1b1a, el cual es predominante en  África subsahariana. Estos datos, conjuntamente con la información histórica y demográfica, nos permite afirmar que el bajo aporte amerindio y subsahariano observado en  la muestra del AMBA, sería el resultado de las migraciones recientes, iniciadas a mediados del siglo XX, principalmente desde el norte de Argentina y de países limítrofes de elevada composición nativa y, en menor medida, africana. Abstract The aim of this work was to analyze the origin of Y-chromosome haplotypes in a sample from Buenos Aires Metropolitan Area (BAMA, and compare these results with those obtained at a mitochondrial level. In order to reach this objective, 17 Y-STRs were determined from 85 unrelated blood donors. A total of 85 unique haplotypes were observed. The haplotype diversity was 1.000+/-0.0018, and the average genetic diversity 0.680+/-0.095. Paternal lineages showed a genetic homogeneity of European roots (93%, mainly from Italy and Spain. Amerindian paternal contribution associated to sub

  1. Nucleotide Metabolism and its Control in Lactic Acid Bacteria

    DEFF Research Database (Denmark)

    Kilstrup, Mogens; Hammer, Karin; Jensen, Peter Ruhdal

    2005-01-01

    Most metabolic reactions are connected through either their utilization of nucleotides or their utilization of nucleotides or their regulation by these metabolites. In this review the biosynthetic pathways for pyrimidine and purine metabolism in lactic acid bacteria are described including...... the interconversion pathways, the formation of deoxyribonucleotides and the salvage pathways for use of exogenous precursors. The data for the enzymatic and the genetic regulation of these pathways are reviewed, as well as the gene organizations in different lactic acid bacteria. Mutant phenotypes and methods...... for manipulation of nucleotide pools are also discussed. Our aim is to provide an overview of the physiology and genetics of nucleotide metabolism and its regulation that will facilitate the interpretation of data arising from genetics, metabolomics, proteomics, and transcriptomics in lactic acid bacteria....

  2. Association study of nonsynonymous single nucleotide polymorphisms in schizophrenia

    DEFF Research Database (Denmark)

    Carrera, Noa; Arrojo, Manuel; Sanjuán, Julio

    2012-01-01

    Genome-wide association studies using several hundred thousand anonymous markers present limited statistical power. Alternatively, association studies restricted to common nonsynonymous single nucleotide polymorphisms (nsSNPs) have the advantage of strongly reducing the multiple testing problem, ...

  3. Enzymatic Incorporation of Modified Purine Nucleotides in DNA.

    Science.gov (United States)

    Abu El Asrar, Rania; Margamuljana, Lia; Abramov, Mikhail; Bande, Omprakash; Agnello, Stefano; Jang, Miyeon; Herdewijn, Piet

    2017-12-14

    A series of nucleotide analogues, with a hypoxanthine base moiety (8-aminohypoxanthine, 1-methyl-8-aminohypoxanthine, and 8-oxohypoxanthine), together with 5-methylisocytosine were tested as potential pairing partners of N 8 -glycosylated nucleotides with an 8-azaguanine or 8-aza-9-deazaguanine base moiety by using DNA polymerases (incorporation studies). The best results were obtained with the 5-methylisocytosine nucleotide followed by the 1-methyl-8-aminohypoxanthine nucleotide. The experiments demonstrated that small differences in the structure (8-azaguanine versus 8-aza-9-deazaguanine) might lead to significant differences in recognition efficiency and selectivity, base pairing by Hoogsteen recognition at the polymerase level is possible, 8-aza-9-deazaguanine represents a self-complementary base pair, and a correlation exists between in vitro incorporation studies and in vivo recognition by natural bases in Escherichia coli, but this recognition is not absolute (exceptions were observed). © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Microsporidia: Why Make Nucleotides if You Can Steal Them?

    Directory of Open Access Journals (Sweden)

    Paul Dean

    2016-11-01

    Full Text Available Microsporidia are strict obligate intracellular parasites that infect a wide range of eukaryotes including humans and economically important fish and insects. Surviving and flourishing inside another eukaryotic cell is a very specialised lifestyle that requires evolutionary innovation. Genome sequence analyses show that microsporidia have lost most of the genes needed for making primary metabolites, such as amino acids and nucleotides, and also that they have only a limited capacity for making adenosine triphosphate (ATP. Since microsporidia cannot grow and replicate without the enormous amounts of energy and nucleotide building blocks needed for protein, DNA, and RNA biosynthesis, they must have evolved ways of stealing these substrates from the infected host cell. Providing they can do this, genome analyses suggest that microsporidia have the enzyme repertoire needed to use and regenerate the imported nucleotides efficiently. Recent functional studies suggest that a critical innovation for adapting to intracellular life was the acquisition by lateral gene transfer of nucleotide transport (NTT proteins that are now present in multiple copies in all microsporidian genomes. These proteins are expressed on the parasite surface and allow microsporidia to steal ATP and other purine nucleotides for energy and biosynthesis from their host. However, it remains unclear how other essential metabolites, such as pyrimidine nucleotides, are acquired. Transcriptomic and experimental studies suggest that microsporidia might manipulate host cell metabolism and cell biological processes to promote nucleotide synthesis and to maximise the potential for ATP and nucleotide import. In this review, we summarise recent genomic and functional data relating to how microsporidia exploit their hosts for energy and building blocks needed for growth and nucleic acid metabolism and we identify some remaining outstanding questions.

  5. Diverse Multilateralism

    DEFF Research Database (Denmark)

    Wuthnow, Joel; Li, Xin; Qi, Lingling

    2012-01-01

    in both the economic and security domains, the article argues that China’s multilateralism is diverse, and that it cannot be un-problematically characterized as either status-quo or revisionist in nature. However, the general trend appears to be towards engagement, but with an assertive tact as China...

  6. Generational diversity.

    Science.gov (United States)

    Kramer, Linda W

    2010-01-01

    Generational diversity has proven challenges for nurse leaders, and generational values may influence ideas about work and career planning. This article discusses generational gaps, influencing factors and support, and the various generational groups present in today's workplace as well as the consequences of need addressing these issues. The article ends with a discussion of possible solutions.

  7. Discovering Diversity.

    Science.gov (United States)

    Manner, Barbara M.; Hattler, Jean Anne

    2000-01-01

    Introduces a preservice teacher field trip to the rain forests and coastal areas. This experience develops an awareness for different cultures among preservice teachers by experiencing biological and cultural diversity in Costa Rica. Presents students' own ideas on this experience. (YDS)

  8. Representative Diversity.

    Science.gov (United States)

    Jacklin, Phil

    1978-01-01

    Presents eight propositions for different kinds of diversity, in order of importance, based on relevance to democracy; specifically, relevance to openness in the marketplace of ideas, and to creation of the system of communications which is least restrictive of freedom of speech and of the press. (JMF)

  9. Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history.

    Directory of Open Access Journals (Sweden)

    Jeffrey L Peters

    Full Text Available Inferring aspects of the population histories of species using coalescent analyses of non-coding nuclear DNA has grown in popularity. These inferences, such as divergence, gene flow, and changes in population size, assume that genetic data reflect simple population histories and neutral evolutionary processes. However, violating model assumptions can result in a poor fit between empirical data and the models. We sampled 22 nuclear intron sequences from at least 19 different chromosomes (a genomic transect to test for deviations from selective neutrality in the gadwall (Anas strepera, a Holarctic duck. Nucleotide diversity among these loci varied by nearly two orders of magnitude (from 0.0004 to 0.029, and this heterogeneity could not be explained by differences in substitution rates alone. Using two different coalescent methods to infer models of population history and then simulating neutral genetic diversity under these models, we found that the observed among-locus heterogeneity in nucleotide diversity was significantly higher than expected for these simple models. Defining more complex models of population history demonstrated that a pre-divergence bottleneck was also unlikely to explain this heterogeneity. However, both selection and interspecific hybridization could account for the heterogeneity observed among loci. Regardless of the cause of the deviation, our results illustrate that violating key assumptions of coalescent models can mislead inferences of population history.

  10. Survey of methanotrophic diversity in various ecosystems by degenerate methane monooxygenase gene primers.

    Science.gov (United States)

    Ghashghavi, Mohammad; Jetten, Mike S M; Lüke, Claudia

    2017-08-23

    Methane is the second most important greenhouse gas contributing to about 20% of global warming. Its mitigation is conducted by methane oxidizing bacteria that act as a biofilter using methane as their energy and carbon source. Since their first discovery in 1906, methanotrophs have been studied using a complementary array of methods. One of the most used molecular methods involves PCR amplification of the functional gene marker for the diagnostic of copper and iron containing particulate methane monooxygenase. To investigate the diversity of methanotrophs and to extend their possible molecular detection, we designed a new set of degenerate methane monooxygenase primers to target an 850 nucleotide long sequence stretch from pmoC to pmoA. The primers were based on all available full genomic pmoCAB operons. The newly designed primers were tested on various pure cultures, enrichment cultures and environmental samples using PCR. The results demonstrated that this primer set has the ability to correctly amplify the about 850 nucleotide long pmoCA product from Alphaproteobacteria, Gammaproteobacteria, Verrucomicrobia and the NC10 phyla methanotrophs. The new primer set will thus be a valuable tool to screen ecosystems and can be applied in conjunction with previously used pmoA primers to extend the diversity of currently known methane-oxidizing bacteria.

  11. Nucleotide-sugar transporters: structure, function and roles in vivo

    Directory of Open Access Journals (Sweden)

    Handford M.

    2006-01-01

    Full Text Available The glycosylation of glycoconjugates and the biosynthesis of polysaccharides depend on nucleotide-sugars which are the substrates for glycosyltransferases. A large proportion of these enzymes are located within the lumen of the Golgi apparatus as well as the endoplasmic reticulum, while many of the nucleotide-sugars are synthesized in the cytosol. Thus, nucleotide-sugars are translocated from the cytosol to the lumen of the Golgi apparatus and endoplasmic reticulum by multiple spanning domain proteins known as nucleotide-sugar transporters (NSTs. These proteins were first identified biochemically and some of them were cloned by complementation of mutants. Genome and expressed sequence tag sequencing allowed the identification of a number of sequences that may encode for NSTs in different organisms. The functional characterization of some of these genes has shown that some of them can be highly specific in their substrate specificity while others can utilize up to three different nucleotide-sugars containing the same nucleotide. Mutations in genes encoding for NSTs can lead to changes in development in Drosophila melanogaster or Caenorhabditis elegans, as well as alterations in the infectivity of Leishmania donovani. In humans, the mutation of a GDP-fucose transporter is responsible for an impaired immune response as well as retarded growth. These results suggest that, even though there appear to be a fair number of genes encoding for NSTs, they are not functionally redundant and seem to play specific roles in glycosylation.

  12. Using molecular beacons to detect single-nucleotide polymorphisms with real-time PCR.

    Science.gov (United States)

    Mhlanga, M M; Malmberg, L

    2001-12-01

    Detection of single-nucleotide polymorphisms (SNPs) in high-throughput studies promises to be an expanding field of molecular medicine in the near future. Highly specific, simple, and accessible methods are needed to meet the rigorous requirements of single-nucleotide detection needed in pharmacogenomic studies, linkage analysis, and the detection of pathogens. Molecular beacons present such a solution for the high-throughput screening of SNPs in homogeneous assays using the polymerase chain reaction (PCR). Molecular beacons are probes that fluoresce on hybridization to their perfectly complementary targets. In recent years they have emerged as a leading genetic analysis tool in a wide range of contexts from quantification of RNA transcripts, to probes on microarrays, to single-nucleotide polymorphism detection. The majority of these methods use PCR to obtain sufficient amounts of sample to analyze. The use of molecular beacons with other amplification schemes has been reliably demonstrated, though PCR remains the method of choice. Here we discuss and present how to design and use molecular beacons to achieve reliable SNP genotyping and allele discrimination in real-time PCR. In addition, we provide a new means of analyzing data outputs from such real-time PCR assays that compensates for differences between sample condition, assay conditions, variations in fluorescent signal, and amplification efficiency. The mechanisms by which molecular beacons are able to have extraordinary specificity are also presented. Copyright 2001 Elsevier Science (USA).

  13. Purine and pyrimidine nucleotide metabolism in Mollicutes

    Directory of Open Access Journals (Sweden)

    Cristiano Valim Bizarro

    2007-01-01

    Full Text Available Several mollicute genome projects are underway, offering unique opportunities to study genes and metabolic pathways on a genome-wide scale. Here, we have analyzed the conservation and diversity of purine and pyrimidine metabolism in mycoplasmas. An evaluation of discrepancies between genomic analysis and enzymatic data revealed interesting aspects about these organisms. We found important examples in which enzyme activity was reported without the annotation of a corresponding gene. An interesting example concerns phosphopentomutase. In Mollicutes, we have identified CDSs orthologous to sequences recently identified as new phosphopentomutases in archaeobacteria that are structurally related to phosphomannomutases. It is suggested that these sequences could replace the function of phosphopentomutases in mollicutes lacking the canonical phosphopentomutase gene (deoB. Also, the activity of 5'-nucleotidase was reported in mollicutes that do not possess any CDS related to ushA. Hypothetical proteins exhibiting domains similar to newly characterized 5' nucleotidases in Escherichia coli are proposed as possible CDSs related to this enzymatic activity in Mollicutes. Based on our analysis, the reductive genome evolution of Mollicutes does not appear to result in a minimum set of genes nor a minimum set of metabolic functions shared by all mollicute species.

  14. An algorithm and program for finding sequence specific oligo-nucleotide probes for species identification

    Directory of Open Access Journals (Sweden)

    Tautz Diethard

    2002-03-01

    Full Text Available Abstract Background The identification of species or species groups with specific oligo-nucleotides as molecular signatures is becoming increasingly popular for bacterial samples. However, it shows also great promise for other small organisms that are taxonomically difficult to tract. Results We have devised here an algorithm that aims to find the optimal probes for any given set of sequences. The program requires only a crude alignment of these sequences as input and is optimized for performance to deal also with very large datasets. The algorithm is designed such that the position of mismatches in the probes influences the selection and makes provision of single nucleotide outloops. Program implementations are available for Linux and Windows.

  15. Mitochondrial DNA diversity of present-day Aboriginal Australians and implications for human evolution in Oceania.

    Science.gov (United States)

    Nagle, Nano; Ballantyne, Kaye N; van Oven, Mannis; Tyler-Smith, Chris; Xue, Yali; Wilcox, Stephen; Wilcox, Leah; Turkalov, Rust; van Oorschot, Roland A H; van Holst Pellekaan, Sheila; Schurr, Theodore G; McAllister, Peter; Williams, Lesley; Kayser, Manfred; Mitchell, R John

    2017-03-01

    Aboriginal Australians are one of the more poorly studied populations from the standpoint of human evolution and genetic diversity. Thus, to investigate their genetic diversity, the possible date of their ancestors' arrival and their relationships with neighboring populations, we analyzed mitochondrial DNA (mtDNA) diversity in a large sample of Aboriginal Australians. Selected mtDNA single-nucleotide polymorphisms and the hypervariable segment haplotypes were analyzed in 594 Aboriginal Australians drawn from locations across the continent, chiefly from regions not previously sampled. Most (~78%) samples could be assigned to mtDNA haplogroups indigenous to Australia. The indigenous haplogroups were all ancient (with estimated ages >40 000 years) and geographically widespread across the continent. The most common haplogroup was P (44%) followed by S (23%) and M42a (9%). There was some geographic structure at the haplotype level. The estimated ages of the indigenous haplogroups range from 39 000 to 55 000 years, dates that fit well with the estimated date of colonization of Australia based on archeological evidence (~47 000 years ago). The distribution of mtDNA haplogroups in Australia and New Guinea supports the hypothesis that the ancestors of Aboriginal Australians entered Sahul through at least two entry points. The mtDNA data give no support to the hypothesis of secondary gene flow into Australia during the Holocene, but instead suggest long-term isolation of the continent.

  16. Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs.

    Science.gov (United States)

    Esteve-Codina, Anna; Paudel, Yogesh; Ferretti, Luca; Raineri, Emanuele; Megens, Hendrik-Jan; Silió, Luis; Rodríguez, María C; Groenen, Martein A M; Ramos-Onsins, Sebastian E; Pérez-Enciso, Miguel

    2013-03-05

    In contrast to international pig breeds, the Iberian breed has not been admixed with Asian germplasm. This makes it an important model to study both domestication and relevance of Asian genes in the pig. Besides, Iberian pigs exhibit high meat quality as well as appetite and propensity to obesity. Here we provide a genome wide analysis of nucleotide and structural diversity in a reduced representation library from a pool (n=9 sows) and shotgun genomic sequence from a single sow of the highly inbred Guadyerbas strain. In the pool, we applied newly developed tools to account for the peculiarities of these data. A total of 254,106 SNPs in the pool (79.6 Mb covered) and 643,783 in the Guadyerbas sow (1.47 Gb covered) were called. The nucleotide diversity (1.31x10-3 per bp in autosomes) is very similar to that reported in wild boar. A much lower than expected diversity in the X chromosome was confirmed (1.79x10-4 per bp in the individual and 5.83x10-4 per bp in the pool). A strong (0.70) correlation between recombination and variability was observed, but not with gene density or GC content. Multicopy regions affected about 4% of annotated pig genes in their entirety, and 2% of the genes partially. Genes within the lowest variability windows comprised interferon genes and, in chromosome X, genes involved in behavior like HTR2C or MCEP2. A modified Hudson-Kreitman-Aguadé test for pools also indicated an accelerated evolution in genes involved in behavior, as well as in spermatogenesis and in lipid metabolism. This work illustrates the strength of current sequencing technologies to picture a comprehensive landscape of variability in livestock species, and to pinpoint regions containing genes potentially under selection. Among those genes, we report genes involved in behavior, including feeding behavior, and lipid metabolism. The pig X chromosome is an outlier in terms of nucleotide diversity, which suggests selective constraints. Our data further confirm the importance of

  17. Patterns of nucleotide diversity in Meisa1 and G3pdh in wild and ...

    African Journals Online (AJOL)

    G3pdh is under diversifying selection in both populations. This may indicate the importance for isoamylase1 in starch quality traits in cassava, a trait that is likely to have been the target for artificial selection by farmers and breeders, in addition to natural selection. This study also suggests that G3pdh may be a good marker ...

  18. The Tomato Nucleotide-binding Leucine-rich Repeat (NLR) Immune Receptor I-2 Couples DNA-Binding to Nucleotide-Binding Domain Nucleotide Exchange

    NARCIS (Netherlands)

    Fenyk, S.; Dixon, C.H.; Gittens, W.H.; Townsend, P.D.; Sharples, G.J.; Pålsson, L.O.; Takken, F.L.W.; Cann, M.J.

    2016-01-01

    Plant nucleotide-binding leucine-rich repeat (NLR) proteins enable plants to recognise and respond to pathogen attack. Previously, we demonstrated that the Rx1 NLR of potato is able to bind and bend DNA in vitro. DNA binding in situ requires its genuine activation following pathogen perception.

  19. [Natural nucleotide polymorphism of the Srlk gene that determines salt stress tolerance in alfalfa (Medicago sativa L)].

    Science.gov (United States)

    Vishnevskaia, M S; Pavlov, A V; Dziubenko, E A; Dziubenko, N I; Potokina, E K

    2014-04-01

    Based on legume genome syntheny, the nucleotide sequence of Srlk gene, key role of which in response to salt stress was demonstrated for the model species Medicago truncatula, was identified in the major forage and siderate crop alfalfa (Medicago sativa). In twelve alfalfa samples originating from regions with contrasting growing conditions, 19 SNPs were revealed in the Srlk gene. For two nonsynonymous SNPs, molecular markers were designed that could be further used to analyze the association between Srlk gene nucleotide polymorphism and the variability in salt stress tolerance among alfalfa cultivars.

  20. Troubling Diversity?

    DEFF Research Database (Denmark)

    Jæger, Kirsten; Jensen, Annie Aarup

    2009-01-01

    are related to recent contributions to diversity management theory and intercultural communication theory, calling for a strengthened focus on the historical, political, and social dimensions of intercultural contact. In continuation of these trends, an alternative, theoretical framework......Focussing on the cultural encounter between nurses and ethnic minority patients in Danish hospitals, this paper presents the results of a comprehensive analysis of nursing discourses on cultural difference and intercultural contact. Articles from the Danish professional journal ‘The Nurse......', published in the period from 2000 to 2008, pertaining to cultural contact and intercultural understanding have been analyzed in order to uncover nurses' experience of ethnic and cultural diversity and the ways, in which these experiences challenge their cultural and professional expertise. Results...

  1. Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide

    Science.gov (United States)

    Freudenthal, Bret D.; Beard, William A.; Perera, Lalith; Shock, David D.; Kim, Taejin; Schlick, Tamar; Wilson, Samuel H.

    2015-01-01

    Oxidative stress promotes genomic instability and human diseases. A common oxidized nucleoside is 8-oxo-7,8-dihydro-2'-deoxyguanosine, which is found both in DNA (8-oxo-G) and as a free nucleotide (8-oxo-dGTP). Nucleotide pools are especially vulnerable to oxidative damage. Therefore cells encode an enzyme (MutT/MTH1) that removes free oxidized nucleotides. This cleansing function is required for cancer cell survival and to modulate Escherichia coli antibiotic sensitivity in a DNA polymerase (pol)-dependent manner. How polymerases discriminate between damaged and non-damaged nucleotides is not well understood. This analysis is essential given the role of oxidized nucleotides in mutagenesis, cancer therapeutics, and bacterial antibiotics. Even with cellular sanitizing activities, nucleotide pools contain enough 8-oxo-dGTP to promote mutagenesis. This arises from the dual coding potential where 8-oxo-dGTP(anti) base pairs with cytosine and 8-oxo-dGTP(syn) uses its Hoogsteen edge to base pair with adenine. Here we use time-lapse crystallography to follow 8-oxo-dGTP insertion opposite adenine or cytosine with human pol β, to reveal that insertion is accommodated in either the syn- or anti-conformation, respectively. For 8-oxo-dGTP(anti) insertion, a novel divalent metal relieves repulsive interactions between the adducted guanine base and the triphosphate of the oxidized nucleotide. With either templating base, hydrogen-bonding interactions between the bases are lost as the enzyme reopens after catalysis, leading to a cytotoxic nicked DNA repair intermediate. Combining structural snapshots with kinetic and computational analysis reveals how 8-oxo-dGTP uses charge modulation during insertion that can lead to a blocked DNA repair intermediate.

  2. Evolution of Nucleotide Punctuation Marks: From Structural to Linear Signals

    Science.gov (United States)

    El Houmami, Nawal; Seligmann, Hervé

    2017-01-01

    We present an evolutionary hypothesis assuming that signals marking nucleotide synthesis (DNA replication and RNA transcription) evolved from multi- to unidimensional structures, and were carried over from transcription to translation. This evolutionary scenario presumes that signals combining secondary and primary nucleotide structures are evolutionary transitions. Mitochondrial replication initiation fits this scenario. Some observations reported in the literature corroborate that several signals for nucleotide synthesis function in translation, and vice versa. (a) Polymerase-induced frameshift mutations occur preferentially at translational termination signals (nucleotide deletion is interpreted as termination of nucleotide polymerization, paralleling the role of stop codons in translation). (b) Stem-loop hairpin presence/absence modulates codon-amino acid assignments, showing that translational signals sometimes combine primary and secondary nucleotide structures (here codon and stem-loop). (c) Homopolymer nucleotide triplets (AAA, CCC, GGG, TTT) cause transcriptional and ribosomal frameshifts. Here we find in recently described human mitochondrial RNAs that systematically lack mono-, dinucleotides after each trinucleotide (delRNAs) that delRNA triplets include 2x more homopolymers than mitogenome regions not covered by delRNA. Further analyses of delRNAs show that the natural circular code X (a little-known group of 20 translational signals enabling ribosomal frame retrieval consisting of 20 codons {AAC, AAT, ACC, ATC, ATT, CAG, CTC, CTG, GAA, GAC, GAG, GAT, GCC, GGC, GGT, GTA, GTC, GTT, TAC, TTC} universally overrepresented in coding versus other frames of gene sequences), regulates frameshift in transcription and translation. This dual transcription and translation role confirms for X the hypothesis that translational signals were carried over from transcriptional signals. PMID:28396681

  3. Landscape genetics, adaptive diversity and population structure in Phaseolus vulgaris.

    Science.gov (United States)

    Rodriguez, Monica; Rau, Domenico; Bitocchi, Elena; Bellucci, Elisa; Biagetti, Eleonora; Carboni, Andrea; Gepts, Paul; Nanni, Laura; Papa, Roberto; Attene, Giovanna

    2016-03-01

    Here we studied the organization of genetic variation of the common bean (Phaseolus vulgaris) in its centres of domestication. We used 131 single nucleotide polymorphisms to investigate 417 wild common bean accessions and a representative sample of 160 domesticated genotypes, including Mesoamerican and Andean genotypes, for a total of 577 accessions. By analysing the genetic spatial patterns of the wild common bean, we documented the existence of several genetic groups and the occurrence of variable degrees of diversity in Mesoamerica and the Andes. Moreover, using a landscape genetics approach, we demonstrated that both demographic processes and selection for adaptation were responsible for the observed genetic structure. We showed that the study of correlations between markers and ecological variables at a continental scale can help in identifying local adaptation genes. We also located putative areas of common bean domestication in Mesoamerica, in the Oaxaca Valley, and the Andes, in southern Bolivia-northern Argentina. These observations are of paramount importance for the conservation and exploitation of the genetic diversity preserved within this species and other plant genetic resources. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  4. AANT: the Amino Acid-Nucleotide Interaction Database.

    Science.gov (United States)

    Hoffman, Michael M; Khrapov, Maksim A; Cox, J Colin; Yao, Jianchao; Tong, Lingnan; Ellington, Andrew D

    2004-01-01

    We have created an Amino Acid-Nucleotide Interaction Database (AANT; http://aant.icmb.utexas. edu/) that categorizes all amino acid-nucleotide interactions from experimentally determined protein-nucleic acid structures, and provides users with a graphic interface for visualizing these interactions in aggregate. AANT accomplishes this by extracting individual amino acid-nucleotide interactions from structures in the Protein Data Bank, combining and superimposing these interactions into multiple structure files (e.g. 20 amino acids x 5 nucleotides) and grouping structurally similar interactions into more readily identifiable clusters. Using the Chime web browser plug-in, users can view 3D representations of the superimpositions and clusters. The unique collection and representation of data on amino acid-nucleotide interactions facilitates understanding the specificity of protein-nucleic acid interactions at a more fundamental level, and allows comparison of otherwise extremely disparate sets of structures. Moreover, by modularly representing the fundamental interactions that govern binding specificity it may prove possible to better engineer nucleic acid binding proteins.

  5. The regulation of nucleotide metabolism of immune cells: papaverine induced nucleotide breakdown.

    Science.gov (United States)

    Sheppard, H; Sass, S; Tsien, W H

    1980-06-01

    During a period of prelabeling of mouse thymus cells with any nucleoside at 4 degrees C, nucleoside phosphates accumulated, but no nucleic acid synthesis occurred. Elevating the temperature to 37 degrees C then led to incorporation into the respective nucleic acid reaching a maximum in 5--15 min. Papaverine inhibited this incorporation (IC50:50 muM) and caused an efflux of label into the medium as a nonphosphorylated product. The responses of the different nucleotide phosphate pools showed more dependency on the base then the sugar moeity. The effect of papaverine could not be altered or mimicked by deprivation of oxygen, glucose, or calcium. Mouse spleen cells responded like thymocytes to papaverine, but rat GH3 pituitary cell DNA syntesis was only transiently inhibited with no concomitant efflux of 3H into the medium. As expected, thymus cellular adenosine triphosphate (ATP), determined by the luciferin-luciferase reaction, decreased in the presence of papaverine; suprisingly, extracellular ATP fell as well. The results suggest that decreases in cellular ATP of mouse thymus cells leads to reductions of all nucleoside phosphates and the efflux of the resultant nucleosides. Papaverine may effect a decrease in the ATP levels by activating a phosphohydrolase rather than, or in addition to, the previously suggested inhibition of mitochondrial electron transport.

  6. Genetic Diversity and Structure among Isolated Populations of the Endangered Gees Golden Langur in Assam, India.

    Directory of Open Access Journals (Sweden)

    Muthuvarmadam S Ram

    Full Text Available Gee's golden langur (Trachypithecus geei is an endangered colobine primate, endemic to the semi-evergreen and mixed-deciduous forests of Indo-Bhutan border. During the last few decades, extensive fragmentation has caused severe population decline and local extinction of golden langur from several fragments. However, no studies are available on the impact of habitat fragmentation and the genetic diversity of golden langur in the fragmented habitats. The present study aimed to estimate the genetic diversity in the Indian population of golden langur. We sequenced and analyzed around 500 bases of the mitochondrial DNA (mtDNA hypervariable region-I from 59 fecal samples of wild langur collected from nine forest fragments. Overall, genetic diversity was high (h = 0.934, π = 0.0244 and comparable with other colobines. Populations in smaller fragments showed lower nucleotide diversity compared to the larger forest fragments. The median-joining network of haplotypes revealed a genetic structure that corresponded with the geographical distribution. The Aie and Champabati Rivers were found to be a barrier to gene flow between golden langur populations. In addition, it also established that T. geei is monophyletic but revealed possible hybridization with capped langur, T. pileatus, in the wild. It is hoped that these findings would result in a more scientific approach towards managing the fragmented populations of this enigmatic species.

  7. Understanding in-line probing experiments by modeling cleavage of nonreactive RNA nucleotides.

    Science.gov (United States)

    Mlýnský, Vojtěch; Bussi, Giovanni

    2017-05-01

    Ribonucleic acid (RNA) is involved in many regulatory and catalytic processes in the cell. The function of any RNA molecule is intimately related with its structure. In-line probing experiments provide valuable structural data sets for a variety of RNAs and are used to characterize conformational changes in riboswitches. However, the structural determinants that lead to differential reactivities in unpaired nucleotides have not been investigated yet. In this work, we used a combination of theoretical approaches, i.e., classical molecular dynamics simulations, multiscale quantum mechanical/molecular mechanical calculations, and enhanced sampling techniques in order to compute and interpret the differential reactivity of individual residues in several RNA motifs, including members of the most important GNRA and UNCG tetraloop families. Simulations on the multinanosecond timescale are required to converge the related free-energy landscapes. The results for uGAAAg and cUUCGg tetraloops and double helices are compared with available data from in-line probing experiments and show that the introduced technique is able to distinguish between nucleotides of the uGAAAg tetraloop based on their structural predispositions toward phosphodiester backbone cleavage. For the cUUCGg tetraloop, more advanced ab initio calculations would be required. This study is the first attempt to computationally classify chemical probing experiments and paves the way for an identification of tertiary structures based on the measured reactivity of nonreactive nucleotides. © 2017 Mlýnský and Bussi; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  8. Doing Diversity

    DEFF Research Database (Denmark)

    Just, Sine Nørholm; Christiansen, Tanja Juul

    2012-01-01

    Questions of agency in text–audience relations are less studied than other aspects of rhetorical agency. We suggest conceptualizing and analyzing the relationship between texts and audiences from the perspective of performativity, as it has been developed by Judith Butler. Thus, we argue that texts...... invite audiences to take up subject positions, understood as combinations of identity and agency. Danish diversity management rhetoric functions as an illustrative example; in analyzing this type of rhetoric we show how subjects are called into restrained positions of similarity/difference and thereby...

  9. Complete nucleotide sequence and genome organization of butterbur mosaic virus.

    Science.gov (United States)

    Hashimoto, Masayoshi; Komatsu, Ken; Maejima, Kensaku; Yamaji, Yasuyuki; Okano, Yukari; Shiraishi, Takuya; Takahashi, Shuichiro; Kagiwada, Satoshi; Namba, Shigetou

    2009-01-01

    Butterbur mosaic virus (ButMV), a member of the genus Carlavirus, was isolated from Japanese butterbur. Here we report the complete nucleotide sequence and genome organization of ButMV. The genome of ButMV consists of 8,662 nucleotides in length and is predicted to contain six ORFs. The ButMV replicase and CP genes share 46.4-54.9 and 43.2-62.1% nucleotide and 38.6-46.6 and 31.3-65.0% amino acid sequence identities, respectively, with those of other carlaviruses. Based on phylogenetic analysis, we suggested that ButMV replicase and CP is most closely related to coleus vein necrosis virus and carnation latent virus, respectively. Together, our results demonstrate that ButMV was a distinct species of the genus Carlavirus.

  10. Effect of nucleotides on broiler performance and carcass yield

    Directory of Open Access Journals (Sweden)

    VC Pelícia

    2010-03-01

    Full Text Available This study aimed at evaluating the effect of nucleotides on the performance and carcass yield of broilers fed diets with no antibiotic growth promoters (AGP, anticoccidials, or animal feedstuffs. In the trial, 600 Ross 308 male broilers were distributed in a completely randomized experimental design into six treatments with four replicates of 25 birds each. Treatments consisted of a control diet (CD, CD + AGP, CD + 0.04%, CD + 0.05%, CD + 0.06%, and CD + 0.07% nucleotides. The experimental diets did not contain anticoccidials, and birds were vaccinated against coccidiosis at three days of age. No significant differences were detected among broilers submitted to the different treatments in none of the studied parameters. Under the conditions of this experiment, diets supplemented with nucleotides did not influence broiler performance or carcass yield at 42 days of age, and were not different from the feeds not containing any additive or with AGP.

  11. Palladium-Catalyzed Modification of Unprotected Nucleosides, Nucleotides, and Oligonucleotides

    Directory of Open Access Journals (Sweden)

    Kevin H. Shaughnessy

    2015-05-01

    Full Text Available Synthetic modification of nucleoside structures provides access to molecules of interest as pharmaceuticals, biochemical probes, and models to study diseases. Covalent modification of the purine and pyrimidine bases is an important strategy for the synthesis of these adducts. Palladium-catalyzed cross-coupling is a powerful method to attach groups to the base heterocycles through the formation of new carbon-carbon and carbon-heteroatom bonds. In this review, approaches to palladium-catalyzed modification of unprotected nucleosides, nucleotides, and oligonucleotides are reviewed. Polar reaction media, such as water or polar aprotic solvents, allow reactions to be performed directly on the hydrophilic nucleosides and nucleotides without the need to use protecting groups. Homogeneous aqueous-phase coupling reactions catalyzed by palladium complexes of water-soluble ligands provide a general approach to the synthesis of modified nucleosides, nucleotides, and oligonucleotides.

  12. Compositions and methods for detecting single nucleotide polymorphisms

    Energy Technology Data Exchange (ETDEWEB)

    Yeh, Hsin-Chih; Werner, James; Martinez, Jennifer S.

    2016-11-22

    Described herein are nucleic acid based probes and methods for discriminating and detecting single nucleotide variants in nucleic acid molecules (e.g., DNA). The methods include use of a pair of probes can be used to detect and identify polymorphisms, for example single nucleotide polymorphism in DNA. The pair of probes emit a different fluorescent wavelength of light depending on the association and alignment of the probes when hybridized to a target nucleic acid molecule. Each pair of probes is capable of discriminating at least two different nucleic acid molecules that differ by at least a single nucleotide difference. The methods can probes can be used, for example, for detection of DNA polymorphisms that are indicative of a particular disease or condition.

  13. Non-thiolate ligation of nickel by nucleotide-free UreG of Klebsiella aerogenes

    Energy Technology Data Exchange (ETDEWEB)

    Martin-Diaconescu, Vlad; Joseph, Crisjoe A.; Boer, Jodi L.; Mulrooney, Scott B.; Hausinger, Robert P.; Maroney, Michael J.

    2016-12-21

    Nickel-dependent ureases are activated by a multiprotein complex that includes the GTPase UreG. Prior studies showed that nucleotide-free UreG from Klebsiella aerogenes is monomeric and binds one nickel or zinc ion with near-equivalent affinity using an undefined binding site, whereas nucleotide-free UreG from Helicobacter pylori selectively binds one zinc ion per dimer via a universally conserved Cys-Pro-His motif in each protomer. Iodoacetamide-treated K. aerogenes UreG was nearly unaffected in nickel binding compared to non-treated sample, suggesting the absence of thiolate ligands to the metal. X-ray absorption spectroscopy of nickel-bound UreG showed the metal possessed four-coordinate geometry with all O/N donor ligands including one imidazole, thus confirming the absence of thiolate ligation. The nickel site in Strep-tag II-modified protein possessed six-coordinate geometry, again with all O/N donor ligands, but now including two or three imidazoles. An identical site was noted for the Strep-tag II-modified H74A variant, substituted in the Cys-Pro-His motif, ruling out coordination by this His residue. These results are consistent with metal binding to both His6 and a His residue of the fusion peptide in Strep-tagged K. aerogenes UreG. We conclude that the nickel- and zinc-binding site in nucleotide-free K. aerogenes UreG is distinct from that of nucleotide-free H. pylori UreG and does not involve the Cys-Pro-His motif. Further, we show the Strep-tag II can perturb metal coordination of this protein.

  14. Pyrimidine Salvage Enzymes Are Essential for De Novo Biosynthesis of Deoxypyrimidine Nucleotides in Trypanosoma brucei.

    Directory of Open Access Journals (Sweden)

    Christopher Leija

    2016-11-01

    Full Text Available The human pathogenic parasite Trypanosoma brucei possess both de novo and salvage routes for the biosynthesis of pyrimidine nucleotides. Consequently, they do not require salvageable pyrimidines for growth. Thymidine kinase (TK catalyzes the formation of dTMP and dUMP and is one of several salvage enzymes that appear redundant to the de novo pathway. Surprisingly, we show through analysis of TK conditional null and RNAi cells that TK is essential for growth and for infectivity in a mouse model, and that a catalytically active enzyme is required for its function. Unlike humans, T. brucei and all other kinetoplastids lack dCMP deaminase (DCTD, which provides an alternative route to dUMP formation. Ectopic expression of human DCTD resulted in full rescue of the RNAi growth phenotype and allowed for selection of viable TK null cells. Metabolite profiling by LC-MS/MS revealed a buildup of deoxypyrimidine nucleosides in TK depleted cells. Knockout of cytidine deaminase (CDA, which converts deoxycytidine to deoxyuridine led to thymidine/deoxyuridine auxotrophy. These unexpected results suggested that T. brucei encodes an unidentified 5'-nucleotidase that converts deoxypyrimidine nucleotides to their corresponding nucleosides, leading to their dead-end buildup in TK depleted cells at the expense of dTTP pools. Bioinformatics analysis identified several potential candidate genes that could encode 5'-nucleotidase activity including an HD-domain protein that we show catalyzes dephosphorylation of deoxyribonucleotide 5'-monophosphates. We conclude that TK is essential for synthesis of thymine nucleotides regardless of whether the nucleoside precursors originate from the de novo pathway or through salvage. Reliance on TK in the absence of DCTD may be a shared vulnerability among trypanosomatids and may provide a unique opportunity to selectively target a diverse group of pathogenic single-celled eukaryotes with a single drug.

  15. Nucleotide-induced conformational dynamics in ABC transporters from structure-based coarse grained modelling.

    Science.gov (United States)

    Flechsig, Holger

    2016-02-01

    ATP-binding cassette (ABC) transporters are integral membrane proteins which mediate the exchange of diverse substrates across membranes powered by ATP molecules. Our understanding of their activity is still hampered since the conformational dynamics underlying the operation of such proteins cannot yet be resolved in detailed molecular dynamics studies. Here a coarse grained model which allows to mimic binding of nucleotides and follow subsequent conformational motions of full-length transporter structures in computer simulations is proposed and implemented. To justify its explanatory quality, the model is first applied to the maltose transporter system for which multiple conformations are known and we find that the model predictions agree remarkably well with the experimental data. For the MalK subunit the switching from open to the closed dimer configuration upon ATP binding is reproduced and, moreover, for the full-length maltose transporter, progression from inward-facing to the outward-facing state is correctly obtained. For the heme transporter HmuUV, for which only the free structure could yet be determined, the model was then applied to predict nucleotide-induced conformational motions. Upon binding of ATP-mimicking ligands the structure changed from a conformation in which the nucleotide-binding domains formed an open shape, to a conformation in which they were found in tight contact, while, at the same time, a pronounced rotation of the transmembrane domains was observed. This finding is supported by normal mode analysis, and, comparison with structural data of the homologous vitamin B12 transporter BtuCD suggests that the observed rotation mechanism may contribute a common functional aspect for this class of ABC transporters. Although in HmuuV noticeable rearrangement of essential transmembrane helices was detected, there are no indications from our simulations that ATP binding alone may facilitate propagation of substrate molecules in this transporter

  16. Nucleotide compositional asymmetry between the leading and lagging strands of eubacterial genomes

    KAUST Repository

    Qu, Hongzhu

    2010-12-01

    Nucleotide compositional asymmetry (NCA) between leading and lagging strands (LeS and LaS) is dynamic and diverse among eubacterial genomes due to different mutation and selection forces. A thorough investigation is needed in order to study the relationship between nucleotide composition dynamics and gene distribution biases. Based on a collection of 364 eubacterial genomes that were grouped according to a DnaE-based scheme (DnaE1-DnaE1, DnaE2-DnaE1, and DnaE3-PolC), we investigated NCA and nucleotide composition gradients at three codon positions and found that there was universal G-enrichment on LeS among all groups. This was due to a strong selection for G-heading (codon position1 or cp1) codons and mutation pressure that led to more G-ending (cp3) codons. Moreover, a slight T-enrichment of LeS due to the mutation of cytosine deamination at cp3 was universal among DnaE1-DnaE1 and DnaE2-DnaE1 genomes, but was not clearly seen among DnaE3-PolC genomes, in which A-enrichment of LeS was proposed to be the effect of selections unique to polC and a mutation bias toward A-richness at cp1 that may be a result of transcription-coupled DNA repair mechanisms. Furthermore, strand-biased gene distribution enhances the purine-richness of LeS for DnaE3-PolC genomes and T-richness of LeS for DnaE1-DnaE1 and DnaE2-dnaE1 genomes. © 2010 Institut Pasteur.

  17. Recombinant synthesis, purification, and nucleotide binding characteristics of the first nucleotide binding domain of the cystic fibrosis gene product.

    Science.gov (United States)

    Hartman, J; Huang, Z; Rado, T A; Peng, S; Jilling, T; Muccio, D D; Sorscher, E J

    1992-04-05

    The majority of mutations which lead to clinical cystic fibrosis are located within the two predicted nucleotide binding domains of the cystic fibrosis gene product. We have used a prokaryotic expression system to synthesize and purify the first nucleotide binding domain (NBD-1, amino acids 426-588) with and without the most common mutation associated with the disease (the deletion of phenylalanine at position 508, delta F508). Both wild type and delta F508 NBD-1 bind ATP-agarose in a quantitatively comparable manner; this binding was inhibited by excess Na2ATP, trinitrophenol-ATP, or 8-azido-ATP. Irreversible NBD-1 labeling by an ATP analog was demonstrated using [32P]8-azido-ATP. This covalent labeling was inhibited by preincubation with Na2ATP, with half-maximal inhibition for Na2ATP occurring at approximately 5 mM for both the wild type and delta F508 nucleotide binding domain. These experiments are among the first to confirm the expectation that the cystic fibrosis transmembrane conductance regulator NBD-1 binds nucleotide. Since, under the conditions used in our study, NBD-1 without phenylalanine 508 displays very similar nucleotide binding characteristics to the wild type protein, our results support previous structural models which predict that the delta F508 mutation should not cause an alteration in ATP binding.

  18. Investigating intra-host and intra-herd sequence diversity of foot-and-mouth disease virus.

    Science.gov (United States)

    King, David J; Freimanis, Graham L; Orton, Richard J; Waters, Ryan A; Haydon, Daniel T; King, Donald P

    2016-10-01

    Due to the poor-fidelity of the enzymes involved in RNA genome replication, foot-and-mouth disease (FMD) virus samples comprise of unique polymorphic populations. In this study, deep sequencing was utilised to characterise the diversity of FMD virus (FMDV) populations in 6 infected cattle present on a single farm during the series of outbreaks in the UK in 2007. A novel RT-PCR method was developed to amplify a 7.6kb nucleotide fragment encompassing the polyprotein coding region of the FMDV genome. Illumina sequencing of each sample identified the fine polymorphic structures at each nucleotide position, from consensus level changes to variants present at a 0.24% frequency. These data were used to investigate population dynamics of FMDV at both herd and host levels, evaluate the impact of host on the viral swarm structure and to identify transmission links with viruses recovered from other farms in the same series of outbreaks. In 7 samples, from 6 different animals, a total of 5 consensus level variants were identified, in addition to 104 sub-consensus variants of which 22 were shared between 2 or more animals. Further analysis revealed differences in swarm structures from samples derived from the same animal suggesting the presence of distinct viral populations evolving independently at different lesion sites within the same infected animal. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  19. Genetic diversity and structure in semiwild and domesticated chiles (Capsicum annuum; Solanaceae) from Mexico.

    Science.gov (United States)

    Aguilar-Meléndez, Araceli; Morrell, Peter L; Roose, Mikeal L; Kim, Seung-Chul

    2009-06-01

    The chile of Mesoamerica, Capsicum annuum, is one of five domesticated chiles in the Americas. Among the chiles, it varies the most in size, form, and color of its fruits. Together with maize, C. annuum is one of the principal elements of the neotropical diets of Mesoamerican civilizations. Despite the great economic and cultural importance of C. annuum both worldwide and in Mexico, however, very little is known about its geographic origin and number of domestications. Here we sampled a total of 80 accessions from Mexico (58 semiwild and 22 domesticated) and examined nucleotide sequence diversity at three single- or low-copy nuclear loci, Dhn, G3pdh, and Waxy. Across the three loci, we found an average reduction of ca. 10% in the diversity of domesticates relative to semiwild chiles and geographic structure within Mexican populations. The Yucatan Peninsula contained a large number of haplotypes, many of which were unique, suggesting an important region of chile domestication and center of diversity. The present sampling of loci did not conclusively resolve the number and location of domestications, but several lines of evidence suggest multiple independent domestications from widely distributed progenitor populations.

  20. Genetic structure and diversity in Juniperus communis populations in Saxony, Germany

    Directory of Open Access Journals (Sweden)

    Reim Stefanie

    2016-06-01

    Full Text Available In recent years, land use changes led to a rapid decline and fragmentation of J. communis populations in Germany. Population isolation may lead to a restricted gene flow and, further, to negative effects on genetic variation. In this study, genetic diversity and population structure in seven fragmented J. communis populations in Saxony, Germany, were investigated using nuclear microsatellites (nSSR and chloroplast single nucleotide polymorphism (cpSNP. In all Saxony J. communis populations, a high genetic diversity was determined but no population differentiation could be detected whatever method was applied (Bayesian cluster analysis, F-statistics, AMOVA. The same was true for three J. communis out-group samples originating from Italy, Slovakia and Norway, which also showed high genetic diversity and low genetic differences regarding other J. communis populations. Low genetic differentiation among the J. communis populations ascertained with nuclear and chloroplast markers indicated high levels of gene flow by pollen and also by seeds between the sampled locations. Low genetic differentiation may also provide an indicator of Juniper survival during the last glacial maximum (LGM in Europe. The results of this study serve as a basis for the implementation of appropriate conservation measures in Saxony.

  1. First regional evaluation of nuclear genetic diversity and population structure in northeastern coyotes ( Canis latrans)

    Science.gov (United States)

    Monzón, Javier

    2014-01-01

    Previous genetic studies of eastern coyotes ( Canis latrans) are based on one of two strategies: sampling many individuals using one or very few molecular markers, or sampling very few individuals using many genomic markers. Thus, a regional analysis of genetic diversity and population structure in eastern coyotes using many samples and several molecular markers is lacking. I evaluated genetic diversity and population structure in 385 northeastern coyotes using 16 common single nucleotide polymorphisms (SNPs). A region-wide analysis of population structure revealed three primary genetic populations, but these do not correspond to the same three subdivisions inferred in a previous analysis of mitochondrial DNA sequences. More focused geographic analyses of population structure indicated that ample genetic structure occurs in coyotes from an intermediate contact zone where two range expansion fronts meet. These results demonstrate that genotyping several highly heterozygous SNPs in a large, geographically dense sample is an effective way to detect cryptic population genetic structure. The importance of SNPs in studies of population and wildlife genomics is rapidly increasing; this study adds to the growing body of recent literature that demonstrates the utility of SNPs ascertained from a model organism for evolutionary inference in closely related species. PMID:25075291

  2. First regional evaluation of nuclear genetic diversity and population structure in northeastern coyotes ( Canis latrans).

    Science.gov (United States)

    Monzón, Javier

    2014-01-01

    Previous genetic studies of eastern coyotes ( Canis latrans) are based on one of two strategies: sampling many individuals using one or very few molecular markers, or sampling very few individuals using many genomic markers. Thus, a regional analysis of genetic diversity and population structure in eastern coyotes using many samples and several molecular markers is lacking. I evaluated genetic diversity and population structure in 385 northeastern coyotes using 16 common single nucleotide polymorphisms (SNPs). A region-wide analysis of population structure revealed three primary genetic populations, but these do not correspond to the same three subdivisions inferred in a previous analysis of mitochondrial DNA sequences. More focused geographic analyses of population structure indicated that ample genetic structure occurs in coyotes from an intermediate contact zone where two range expansion fronts meet. These results demonstrate that genotyping several highly heterozygous SNPs in a large, geographically dense sample is an effective way to detect cryptic population genetic structure. The importance of SNPs in studies of population and wildlife genomics is rapidly increasing; this study adds to the growing body of recent literature that demonstrates the utility of SNPs ascertained from a model organism for evolutionary inference in closely related species.

  3. Nucleotide bias of DCL and AGO in plant anti-virus gene silencing.

    Science.gov (United States)

    Ho, Thien; Wang, Liang; Huang, Linfeng; Li, Zhigang; Pallett, Denise W; Dalmay, Tamas; Ohshima, Kazusato; Walsh, John A; Wang, Hui

    2010-09-01

    Plant Dicer-like (DCL) and Argonaute (AGO) are the key enzymes involved in anti-virus post-transcriptional gene silencing (AV-PTGS). Here we show that AV-PTGS exhibited nucleotide preference by calculating a relative AV-PTGS efficiency on processing viral RNA substrates. In comparison with genome sequences of dicot-infecting Turnip mosaic virus (TuMV) and monocot-infecting Cocksfoot streak virus (CSV), viral-derived small interfering RNAs (vsiRNAs) displayed positive correlations between AV-PTGS efficiency and G+C content (GC%). Further investigations on nucleotide contents revealed that the vsiRNA populations had G-biases. This finding was further supported by our analyses of previously reported vsiRNA populations in diverse plant-virus associations, and AGO associated Arabidopsis endogenous siRNA populations, indicating that plant AGOs operated with G-preference. We further propose a hypothesis that AV-PTGS imposes selection pressure(s) on the evolution of plant viruses. This hypothesis was supported when potyvirus genomes were analysed for evidence of GC elimination, suggesting that plant virus evolution to have low GC% genomes would have a unique function, which is to reduce the host AV-PTGS attack during infections.

  4. Evolutionary and structural perspectives of plant cyclic nucleotide-gated cation channels

    KAUST Repository

    Zelman, Alice K.

    2012-05-29

    Ligand-gated cation channels are a frequent component of signaling cascades in eukaryotes. Eukaryotes contain numerous diverse gene families encoding ion channels, some of which are shared and some of which are unique to particular kingdoms. Among the many different types are cyclic nucleotide-gated channels (CNGCs). CNGCs are cation channels with varying degrees of ion conduction selectivity. They are implicated in numerous signaling pathways and permit diffusion of divalent and monovalent cations, including Ca2+ and K+. CNGCs are present in both plant and animal cells, typically in the plasma membrane; recent studies have also documented their presence in prokaryotes. All eukaryote CNGC polypeptides have a cyclic nucleotide-binding domain and a calmodulin binding domain as well as a six transmembrane/one pore tertiary structure. This review summarizes existing knowledge about the functional domains present in these cation-conducting channels, and considers the evidence indicating that plant and animal CNGCs evolved separately. Additionally, an amino acid motif that is only found in the phosphate binding cassette and hinge regions of plant CNGCs, and is present in all experimentally confirmed CNGCs but no other channels was identified. This CNGC-specific amino acid motif provides an additional diagnostic tool to identify plant CNGCs, and can increase confidence in the annotation of open reading frames in newly sequenced genomes as putative CNGCs. Conversely, the absence of the motif in some plant sequences currently identified as probable CNGCs may suggest that they are misannotated or protein fragments. 2012 Zelman, Dawe, Gehring and Berkowitz.

  5. High diversity of genogroup I picobirnaviruses in mammals

    Directory of Open Access Journals (Sweden)

    Patrick CY Woo

    2016-11-01

    Full Text Available In a molecular epidemiology study using 791 fecal samples collected from different terrestrial and marine mammals in Hong Kong, genogroup I picobirnaviruses (PBVs were positive by RT-PCR targeting the partial RdRp gene in specimens from 5 cattle, 6 monkeys, 17 horses, 9 pigs, 1 rabbit, 1 dog and 12 California sea lions, with 11, 9, 23, 17, 1, 1 and 15 sequence types in the positive specimens from the corresponding animals, respectively. Phylogenetic analysis showed that the PBV sequences from each kind of animal were widely distributed in the whole tree with high diversity, sharing 47.4 to 89.0% nucleotide identities with other genogroup I PBV strains based on the partial RdRp gene. Nine complete segments 1 (viral loads 1.7×104 to 5.9×106/ml and 15 segments 2 (viral loads 4.1×103 to 1.3×106/ml of otarine PBVs from fecal samples serially collected from California sea lions were sequenced. In the two phylogenetic trees constructed using ORF2 and ORF3 of segment 1, the nine segment 1 sequences were clustered into four distinct clades (C1 to C4. In the tree constructed using RdRp gene of segment 2, the 15 segment 2 sequences were clustered into nine distinct clades (R1 to R9. In four sea lions, PBVs were detected in two different years, with the same segment 1 clade (C3 present in two consecutive years from one sea lion and different clades present in different years from three sea lions. A high diversity of PBVs was observed in a variety of terrestrial and marine mammals. Multiple sequence types with significant differences, representing multiple strains of PBV, were present in the majority of PBV-positive samples from different kinds of animals.

  6. High diversity at PRDM9 in chimpanzees and bonobos.